[{"date_created":"2020-08-15T11:04:07Z","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"day":"27","type":"journal_article","oa":1,"author":[{"last_name":"Shelyakin","full_name":"Shelyakin, Pavel V.","first_name":"Pavel V.","orcid":"0000-0003-0120-9319"},{"orcid":"0000-0003-1006-6639","id":"C4558D3C-6102-11E9-A62E-F418E6697425","full_name":"Bochkareva, Olga","last_name":"Bochkareva","first_name":"Olga"},{"full_name":"Karan, Anna A.","last_name":"Karan","first_name":"Anna A."},{"last_name":"Gelfand","full_name":"Gelfand, Mikhail S.","first_name":"Mikhail S."}],"publisher":"Springer Nature","doi":"10.1186/s12862-019-1403-6","publication":"BMC Evolutionary Biology","publication_status":"published","article_type":"original","publication_identifier":{"issn":["1471-2148"]},"title":"Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow","citation":{"apa":"Shelyakin, P. V., Bochkareva, O., Karan, A. A., & Gelfand, M. S. (2019). Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. Springer Nature. https://doi.org/10.1186/s12862-019-1403-6","ieee":"P. V. Shelyakin, O. Bochkareva, A. A. Karan, and M. S. Gelfand, “Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow,” BMC Evolutionary Biology, vol. 19. Springer Nature, 2019.","chicago":"Shelyakin, Pavel V., Olga Bochkareva, Anna A. Karan, and Mikhail S. Gelfand. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology. Springer Nature, 2019. https://doi.org/10.1186/s12862-019-1403-6.","ista":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. 2019. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 19, 83.","short":"P.V. Shelyakin, O. Bochkareva, A.A. Karan, M.S. Gelfand, BMC Evolutionary Biology 19 (2019).","mla":"Shelyakin, Pavel V., et al. “Micro-Evolution of Three Streptococcus Species: Selection, Antigenic Variation, and Horizontal Gene Inflow.” BMC Evolutionary Biology, vol. 19, 83, Springer Nature, 2019, doi:10.1186/s12862-019-1403-6.","ama":"Shelyakin PV, Bochkareva O, Karan AA, Gelfand MS. Micro-evolution of three Streptococcus species: Selection, antigenic variation, and horizontal gene inflow. BMC Evolutionary Biology. 2019;19. doi:10.1186/s12862-019-1403-6"},"month":"03","status":"public","intvolume":" 19","_id":"8263","article_processing_charge":"No","date_published":"2019-03-27T00:00:00Z","year":"2019","article_number":"83","extern":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1186/s12862-019-1403-6"}],"date_updated":"2023-02-23T13:28:54Z","abstract":[{"lang":"eng","text":"Background: The genus Streptococcus comprises pathogens that strongly influence the health of humans and animals. Genome sequencing of multiple Streptococcus strains demonstrated high variability in gene content and order even in closely related strains of the same species and created a newly emerged object for genomic analysis, the pan-genome. Here we analysed the genome evolution of 25 strains of Streptococcus suis, 50 strains of Streptococcus pyogenes and 28 strains of Streptococcus pneumoniae.\r\n\r\nResults: Fractions of the pan-genome, unique, periphery, and universal genes differ in size, functional composition, the level of nucleotide substitutions, and predisposition to horizontal gene transfer and genomic rearrangements. The density of substitutions in intergenic regions appears to be correlated with selection acting on adjacent genes, implying that more conserved genes tend to have more conserved regulatory regions.\r\nThe total pan-genome of the genus is open, but only due to strain-specific genes, whereas other pan-genome fractions reach saturation. We have identified the set of genes with phylogenies inconsistent with species and non-conserved location in the chromosome; these genes are rare in at least one species and have likely experienced recent horizontal transfer between species. The strain-specific fraction is enriched with mobile elements and hypothetical proteins, but also contains a number of candidate virulence-related genes, so it may have a strong impact on adaptability and pathogenicity.\r\nMapping the rearrangements to the phylogenetic tree revealed large parallel inversions in all species. A parallel inversion of length 15 kB with breakpoints formed by genes encoding surface antigen proteins PhtD and PhtB in S. pneumoniae leads to replacement of gene fragments that likely indicates the action of an antigen variation mechanism.\r\n\r\nConclusions: Members of genus Streptococcus have a highly dynamic, open pan-genome, that potentially confers them with the ability to adapt to changing environmental conditions, i.e. antibiotic resistance or transmission between different hosts. Hence, integrated analysis of all aspects of genome evolution is important for the identification of potential pathogens and design of drugs and vaccines."}],"oa_version":"Published Version","volume":19},{"type":"book_chapter","day":"29","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Mathematical models in population genetics","publication":"Handbook of statistical genomics","doi":"10.1002/9781119487845.ch4","publisher":"Wiley","isi":1,"year":"2019","date_published":"2019-07-29T00:00:00Z","_id":"8281","status":"public","ddc":["576"],"oa_version":"None","date_updated":"2023-09-08T11:24:15Z","page":"115-144","external_id":{"isi":["000261343000003"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2020-08-21T04:25:39Z","publication_identifier":{"isbn":["9781119429142"]},"publication_status":"published","author":[{"first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"},{"first_name":"Alison","full_name":"Etheridge, Alison","last_name":"Etheridge"}],"article_processing_charge":"No","month":"07","citation":{"ieee":"N. H. Barton and A. Etheridge, “Mathematical models in population genetics,” in Handbook of statistical genomics, 4th ed., D. Balding, I. Moltke, and J. Marioni, Eds. Wiley, 2019, pp. 115–144.","apa":"Barton, N. H., & Etheridge, A. (2019). Mathematical models in population genetics. In D. Balding, I. Moltke, & J. Marioni (Eds.), Handbook of statistical genomics (4th ed., pp. 115–144). Wiley. https://doi.org/10.1002/9781119487845.ch4","chicago":"Barton, Nicholas H, and Alison Etheridge. “Mathematical Models in Population Genetics.” In Handbook of Statistical Genomics, edited by David Balding, Ida Moltke, and John Marioni, 4th ed., 115–44. Wiley, 2019. https://doi.org/10.1002/9781119487845.ch4.","ista":"Barton NH, Etheridge A. 2019.Mathematical models in population genetics. In: Handbook of statistical genomics. , 115–144.","ama":"Barton NH, Etheridge A. Mathematical models in population genetics. In: Balding D, Moltke I, Marioni J, eds. Handbook of Statistical Genomics. 4th ed. Wiley; 2019:115-144. doi:10.1002/9781119487845.ch4","mla":"Barton, Nicholas H., and Alison Etheridge. “Mathematical Models in Population Genetics.” Handbook of Statistical Genomics, edited by David Balding et al., 4th ed., Wiley, 2019, pp. 115–44, doi:10.1002/9781119487845.ch4.","short":"N.H. Barton, A. Etheridge, in:, D. Balding, I. Moltke, J. Marioni (Eds.), Handbook of Statistical Genomics, 4th ed., Wiley, 2019, pp. 115–144."},"department":[{"_id":"NiBa"}],"editor":[{"first_name":"David","full_name":"Balding, David","last_name":"Balding"},{"full_name":"Moltke, Ida","last_name":"Moltke","first_name":"Ida"},{"first_name":"John","full_name":"Marioni, John","last_name":"Marioni"}],"abstract":[{"lang":"eng","text":"We review the history of population genetics, starting with its origins a century ago from the synthesis between Mendel and Darwin's ideas, through to the recent development of sophisticated schemes of inference from sequence data, based on the coalescent. We explain the close relation between the coalescent and a diffusion process, which we illustrate by their application to understand spatial structure. We summarise the powerful methods available for analysis of multiple loci, when linkage equilibrium can be assumed, and then discuss approaches to the more challenging case, where associations between alleles require that we follow genotype, rather than allele, frequencies. Though we can hardly cover the whole of population genetics, we give an overview of the current state of the subject, and future challenges to it."}],"edition":"4"},{"_id":"8296","citation":{"apa":"Alp, E. C., Kokoris Kogias, E., Fragkouli, G., & Ford, B. (2019). Rethinking general-purpose decentralized computing. In Proceedings of the Workshop on Hot Topics in Operating Systems (pp. 105–112). Bertinoro, Italy: ACM. https://doi.org/10.1145/3317550.3321448","ieee":"E. C. Alp, E. Kokoris Kogias, G. Fragkouli, and B. Ford, “Rethinking general-purpose decentralized computing,” in Proceedings of the Workshop on Hot Topics in Operating Systems, Bertinoro, Italy, 2019, pp. 105–112.","chicago":"Alp, Enis Ceyhun, Eleftherios Kokoris Kogias, Georgia Fragkouli, and Bryan Ford. “Rethinking General-Purpose Decentralized Computing.” In Proceedings of the Workshop on Hot Topics in Operating Systems, 105–12. ACM, 2019. https://doi.org/10.1145/3317550.3321448.","ama":"Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. Rethinking general-purpose decentralized computing. In: Proceedings of the Workshop on Hot Topics in Operating Systems. ACM; 2019:105-112. doi:10.1145/3317550.3321448","short":"E.C. Alp, E. Kokoris Kogias, G. Fragkouli, B. Ford, in:, Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–112.","mla":"Alp, Enis Ceyhun, et al. “Rethinking General-Purpose Decentralized Computing.” Proceedings of the Workshop on Hot Topics in Operating Systems, ACM, 2019, pp. 105–12, doi:10.1145/3317550.3321448.","ista":"Alp EC, Kokoris Kogias E, Fragkouli G, Ford B. 2019. Rethinking general-purpose decentralized computing. Proceedings of the Workshop on Hot Topics in Operating Systems. HotOS: Workshop on Hot Topics in Operating Systems, 105–112."},"status":"public","month":"05","year":"2019","date_published":"2019-05-01T00:00:00Z","article_processing_charge":"No","extern":"1","scopus_import":"1","oa_version":"None","date_updated":"2021-01-12T08:17:56Z","abstract":[{"lang":"eng","text":"While showing great promise, smart contracts are difficult to program correctly, as they need a deep understanding of cryptography and distributed algorithms, and offer limited functionality, as they have to be deterministic and cannot operate on secret data. In this paper we present Protean, a general-purpose decentralized computing platform that addresses these limitations by moving from a monolithic execution model, where all participating nodes store all the state and execute every computation, to a modular execution-model. Protean employs secure specialized modules, called functional units, for building decentralized applications that are currently insecure or impossible to implement with smart contracts. Each functional unit is a distributed system that provides a special-purpose functionality by exposing atomic transactions to the smart-contract developer. Combining these transactions into arbitrarily-defined workflows, developers can build a larger class of decentralized applications, such as provably-secure and fair lotteries or e-voting."}],"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-26T11:45:45Z","type":"conference","page":"105-112","day":"01","language":[{"iso":"eng"}],"conference":{"start_date":"2019-05-13","location":"Bertinoro, Italy","name":"HotOS: Workshop on Hot Topics in Operating Systems","end_date":"2019-05-15"},"publication_status":"published","publication":"Proceedings of the Workshop on Hot Topics in Operating Systems","publisher":"ACM","doi":"10.1145/3317550.3321448","author":[{"full_name":"Alp, Enis Ceyhun","last_name":"Alp","first_name":"Enis Ceyhun"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias"},{"first_name":"Georgia","last_name":"Fragkouli","full_name":"Fragkouli, Georgia"},{"first_name":"Bryan","last_name":"Ford","full_name":"Ford, Bryan"}],"title":"Rethinking general-purpose decentralized computing","publication_identifier":{"isbn":["9781450367271"]}},{"title":"Robust and scalable consensus for sharded distributed ledgers","publication":"Cryptology ePrint Archive","publication_status":"submitted","author":[{"last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios"}],"oa":1,"type":"preprint","day":"06","language":[{"iso":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2020-08-26T12:13:56Z","oa_version":"Preprint","abstract":[{"lang":"eng","text":"ByzCoin, a promising alternative of Bitcoin, is a scalable consensus protocol used as a building block of many research and enterprise-level decentralized systems. In this paper, we show that ByzCoin is unsuitable for deployment in an anopen, adversarial network and instead introduceMOTOR. MOTORis designed as a secure, robust, and scalable consensus suitable for permissionless sharded blockchains. MOTORachieves these properties by making four key design choices: (a) it prioritizes robustness in adversarial environments while maintaining adequate scalability, (b) it employees provably correct cryptography that resists DoS attacks from individual nodes, (c) it deploys unpredictable rotating leaders to defend against mildly-adaptive adversaries and prevents censorship, and (d) it creates an incentive compatible reward mechanism. These choices are materialized as (a) a “rotating subleader” communication pattern that balances the scalability needs with the robustness requirements under failures, (b) deployment of provable secure BLS multi-signatures, (c) use of deterministic thresh-old signatures as a source of randomness and (d) careful design of the reward allocation mechanism. We have implemented MOTORand compare it withByzCoin. We show that MOTORcan scale similar to ByzCoin with an at most2xoverhead whereas it maintains good performance even under high-percentage of faults, unlike ByzCoin."}],"date_updated":"2021-09-24T12:07:11Z","main_file_link":[{"url":"https://eprint.iacr.org/2019/676","open_access":"1"}],"extern":"1","article_number":"2019/676","year":"2019","date_published":"2019-06-06T00:00:00Z","article_processing_charge":"No","_id":"8303","status":"public","citation":{"ista":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive, 2019/676.","mla":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, 2019/676.","ama":"Kokoris Kogias E. Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive.","short":"E. Kokoris Kogias, Cryptology EPrint Archive (n.d.).","chicago":"Kokoris Kogias, Eleftherios. “Robust and Scalable Consensus for Sharded Distributed Ledgers.” Cryptology EPrint Archive, n.d.","apa":"Kokoris Kogias, E. (n.d.). Robust and scalable consensus for sharded distributed ledgers. Cryptology ePrint Archive.","ieee":"E. Kokoris Kogias, “Robust and scalable consensus for sharded distributed ledgers,” Cryptology ePrint Archive. ."},"month":"06"},{"_id":"8304","month":"10","status":"public","citation":{"short":"A. Zamyatin, M. Al-Bassam, D. Zindros, E. Kokoris Kogias, P. Moreno-Sanchez, A. Kiayias, W.J. Knottenbelt, Cryptology EPrint Archive (n.d.).","ama":"Zamyatin A, Al-Bassam M, Zindros D, et al. SoK: Communication across distributed ledgers. Cryptology ePrint Archive.","ista":"Zamyatin A, Al-Bassam M, Zindros D, Kokoris Kogias E, Moreno-Sanchez P, Kiayias A, Knottenbelt WJ. SoK: Communication across distributed ledgers. Cryptology ePrint Archive, 2019/1128.","mla":"Zamyatin, Alexei, et al. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, 2019/1128.","chicago":"Zamyatin, Alexei, Mustafa Al-Bassam, Dionysis Zindros, Eleftherios Kokoris Kogias, Pedro Moreno-Sanchez, Aggelos Kiayias, and William J. Knottenbelt. “SoK: Communication across Distributed Ledgers.” Cryptology EPrint Archive, n.d.","ieee":"A. Zamyatin et al., “SoK: Communication across distributed ledgers,” Cryptology ePrint Archive. .","apa":"Zamyatin, A., Al-Bassam, M., Zindros, D., Kokoris Kogias, E., Moreno-Sanchez, P., Kiayias, A., & Knottenbelt, W. J. (n.d.). SoK: Communication across distributed ledgers. Cryptology ePrint Archive."},"article_number":"2019/1128","year":"2019","date_published":"2019-10-01T00:00:00Z","article_processing_charge":"No","extern":"1","oa_version":"Preprint","abstract":[{"lang":"eng","text":"Enabling secure communication across distributed systems is usually studied under the assumption of trust between the different systems and an external adversary trying to compromise the messages. With the appearance of distributed ledgers or blockchains, numerous protocols have emerged, which attempt to achieve trustless communication between distrusting ledgers and participants. Cross-chain communication (CCC) thereby plays a fundamental role in cryptocurrency exchanges, sharding, bootstrapping of new and feature-extension of existing distributed ledgers. Unfortunately, existing proposals are designed ad-hoc for specific use-cases, making it hard to gain confidence on their correctness and composability.\r\nWe provide the first systematic exposition of protocols for CCC. First, we formalize the underlying research problem and show that CCC is impossible without a trusted third party, contrary to common beliefs in the blockchain community. We then develop a framework to evaluate existing and to design new cross-chain protocols. The framework is based on the use case, the trust model, and the security assumptions of interlinked blockchains. Finally, we identify security and privacy challenges faced by protocols in the cross-chain setting.\r\nThis Systematization of Knowledge (SoK) offers a comprehensive guide for designing protocols bridging the numerous distributed ledgers available today. It aims to facilitate clearer communication between academia and industry in the field."}],"date_updated":"2021-09-24T12:08:14Z","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2019/1128 "}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2020-08-26T12:16:38Z","oa":1,"type":"preprint","day":"01","language":[{"iso":"eng"}],"publication":"Cryptology ePrint Archive","publication_status":"submitted","author":[{"full_name":"Zamyatin, Alexei","last_name":"Zamyatin","first_name":"Alexei"},{"full_name":"Al-Bassam, Mustafa","last_name":"Al-Bassam","first_name":"Mustafa"},{"full_name":"Zindros, Dionysis","last_name":"Zindros","first_name":"Dionysis"},{"last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"last_name":"Moreno-Sanchez","full_name":"Moreno-Sanchez, Pedro","first_name":"Pedro"},{"full_name":"Kiayias, Aggelos","last_name":"Kiayias","first_name":"Aggelos"},{"full_name":"Knottenbelt, William J.","last_name":"Knottenbelt","first_name":"William J."}],"title":"SoK: Communication across distributed ledgers"},{"type":"preprint","oa":1,"day":"10","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-08-26T12:18:00Z","title":"Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation","publication_status":"submitted","publication":"Cryptology ePrint Archive","author":[{"last_name":"KOKORIS KOGIAS","full_name":"KOKORIS KOGIAS, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"},{"first_name":"Alexander","last_name":"Spiegelman","full_name":"Spiegelman, Alexander"},{"last_name":"Malkhi","full_name":"Malkhi, Dahlia","first_name":"Dahlia"},{"first_name":"Ittai","last_name":"Abraham","full_name":"Abraham, Ittai"}],"article_number":"2019/1015","year":"2019","date_published":"2019-09-10T00:00:00Z","article_processing_charge":"No","_id":"8305","month":"09","status":"public","citation":{"chicago":"Kokoris Kogias, Eleftherios, Alexander Spiegelman, Dahlia Malkhi, and Ittai Abraham. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive, n.d.","apa":"Kokoris Kogias, E., Spiegelman, A., Malkhi, D., & Abraham, I. (n.d.). Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive.","ieee":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, and I. Abraham, “Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation,” Cryptology ePrint Archive. .","ama":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive.","short":"E. Kokoris Kogias, A. Spiegelman, D. Malkhi, I. Abraham, Cryptology EPrint Archive (n.d.).","ista":"Kokoris Kogias E, Spiegelman A, Malkhi D, Abraham I. Bootstrapping consensus without trusted setup: fully asynchronous distributed key generation. Cryptology ePrint Archive, 2019/1015.","mla":"Kokoris Kogias, Eleftherios, et al. “Bootstrapping Consensus without Trusted Setup: Fully Asynchronous Distributed Key Generation.” Cryptology EPrint Archive, 2019/1015."},"oa_version":"Preprint","abstract":[{"lang":"eng","text":"In this paper, we present the first fully asynchronous distributed key generation (ADKG) algorithm as well as the first distributed key generation algorithm that can create keys with a dual (f,2f+1)−threshold that are necessary for scalable consensus (which so far needs a trusted dealer assumption). In order to create a DKG with a dual (f,2f+1)− threshold we first answer in the affirmative the open question posed by Cachin et al. how to create an AVSS protocol with recovery thresholds f+1Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne. https://doi.org/10.5075/epfl-thesis-7101","ieee":"E. Kokoris Kogias, “Secure, confidential blockchains providing high throughput and low latency,” École Polytechnique Fédérale de Lausanne, 2019.","chicago":"Kokoris Kogias, Eleftherios. “Secure, Confidential Blockchains Providing High Throughput and Low Latency.” École Polytechnique Fédérale de Lausanne, 2019. https://doi.org/10.5075/epfl-thesis-7101.","ama":"Kokoris Kogias E. Secure, confidential blockchains providing high throughput and low latency. 2019. doi:10.5075/epfl-thesis-7101","mla":"Kokoris Kogias, Eleftherios. Secure, Confidential Blockchains Providing High Throughput and Low Latency. École Polytechnique Fédérale de Lausanne, 2019, doi:10.5075/epfl-thesis-7101.","short":"E. Kokoris Kogias, Secure, Confidential Blockchains Providing High Throughput and Low Latency, École Polytechnique Fédérale de Lausanne, 2019.","ista":"Kokoris Kogias E. 2019. Secure, confidential blockchains providing high throughput and low latency. École Polytechnique Fédérale de Lausanne."},"_id":"8311","abstract":[{"lang":"eng","text":"One of the core promises of blockchain technology is that of enabling trustworthy data dissemination in a trustless environment. What current blockchain systems deliver, however, is slow dissemination of public data, rendering blockchain technology unusable in settings where latency, transaction capacity, or data confidentiality are important. In this thesis we focus on providing solutions on two of the most pressing problems blockchain technology currently faces: scalability and data confidentiality. To address the scalability issue, we present OMNILEDGER, a novel scale-out distributed ledger that preserves long-term security under permissionless operation. It ensures security and correctness by using a bias-resistant public-randomness protocol for choosing large, statistically representative shards that process transactions, and by introducing an efficient cross-shard commit protocol that atomically handles transactions affecting multiple shards. To enable secure sharing of confidential data we present CALYPSO, the first fully decentralized, auditable access-control framework for secure blockchain-based data sharing which builds upon two abstractions. First, on-chain secrets enable collective management of (verifiably shared) secrets under a Byzantine adversary where an access-control blockchain enforces user-specific access rules and a secret-management cothority administers encrypted data. Second, skipchain-based identity and access management enables efficient administration of dynamic, sovereign identities and access policies and, in particular, permits clients to maintain long-term relationships with respect to evolving user identities thanks to the trust-delegating forward links of skipchains. In order to build OMNILEDGER and CALYPSO, we first build a set of tools for efficient decentralization, which are presented in Part II of this dissertation. These tools can be used in decentralized and distributed systems to achieve (1) scalable consensus (BYZCOIN), (2) bias- resistant distributed randomness creations (RANDHOUND), and (3) relationship-keeping between independently updating communication endpoints (SKIPCHAINIAC). Although we use this tools in the scope off this thesis, they can be (and already have been) used in a far wider scope."}],"date_updated":"2021-12-20T15:30:47Z","main_file_link":[{"open_access":"1","url":"https://www.doi.org/10.5075/epfl-thesis-7101"}],"oa_version":"Published Version","extern":"1","language":[{"iso":"eng"}],"type":"dissertation","oa":1,"degree_awarded":"PhD","page":"244","day":"27","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2020-08-27T11:22:24Z","title":"Secure, confidential blockchains providing high throughput and low latency","supervisor":[{"last_name":"Ford","full_name":"Ford, Bryan Alexander","first_name":"Bryan Alexander"}],"publisher":"École Polytechnique Fédérale de Lausanne","doi":"10.5075/epfl-thesis-7101","author":[{"last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","first_name":"Eleftherios"}],"publication_status":"published"},{"day":"22","oa":1,"type":"patent","date_created":"2020-08-27T11:24:44Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","title":"Methods and systems for secure data exchange","ipc":"G06F21/62 ; H04L9/08 ; H04L9/32","ipn":"WO2019158209 (A1)","author":[{"first_name":"Bryan","full_name":"Ford, Bryan","last_name":"Ford"},{"first_name":"Linus","full_name":"Gasser, Linus","last_name":"Gasser"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"full_name":"Janovic, Philipp","last_name":"Janovic","first_name":"Philipp"}],"applicant":["École Polytechnique Fédérale De Lausanne "],"year":"2019","article_processing_charge":"No","date_published":"2019-08-22T00:00:00Z","_id":"8313","publication_date":"2019-08-22","citation":{"ieee":"B. Ford, L. Gasser, E. Kokoris Kogias, and P. Janovic, “Methods and systems for secure data exchange.” 2019.","apa":"Ford, B., Gasser, L., Kokoris Kogias, E., & Janovic, P. (2019). Methods and systems for secure data exchange.","chicago":"Ford, Bryan, Linus Gasser, Eleftherios Kokoris Kogias, and Philipp Janovic. “Methods and Systems for Secure Data Exchange,” 2019.","ama":"Ford B, Gasser L, Kokoris Kogias E, Janovic P. Methods and systems for secure data exchange. 2019.","short":"B. Ford, L. Gasser, E. Kokoris Kogias, P. Janovic, (2019).","ista":"Ford B, Gasser L, Kokoris Kogias E, Janovic P. 2019. Methods and systems for secure data exchange.","mla":"Ford, Bryan, et al. Methods and Systems for Secure Data Exchange. 2019."},"month":"08","status":"public","oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://patents.google.com/patent/WO2019158209A1"}],"abstract":[{"lang":"eng","text":"The present invention concerns a computer-implemented method for secure data exchange between a sender (A) and a recipient (B), wherein the method is performed by the sender (A) and comprises encrypting data using a symmetric key k, creating a write transaction T W , wherein the write transaction T W comprises information usable to derive the symmetric key k and an access policy identifying the recipient (B) as being allowed to decrypt the encrypted data, providing the recipient (B) access to the encrypted data, and sending the write transaction T W to a first group of servers (AC) for being stored in a blockchain data structure maintained by the first group of servers (AC)."}],"date_updated":"2022-01-05T14:00:32Z","extern":"1"},{"day":"27","type":"preprint","oa":1,"language":[{"iso":"eng"}],"external_id":{"arxiv":["1905.11360"]},"date_created":"2020-08-27T11:36:54Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"title":"Brick: Asynchronous payment channels","publication":"arXiv","publication_status":"submitted","author":[{"last_name":"Avarikioti","full_name":"Avarikioti, Georgia","first_name":"Georgia"},{"id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","first_name":"Eleftherios"},{"first_name":"Roger","last_name":"Wattenhofer","full_name":"Wattenhofer, Roger"},{"first_name":"Dionysis","full_name":"Zindros, Dionysis","last_name":"Zindros"}],"year":"2019","article_number":"1905.11360","article_processing_charge":"No","date_published":"2019-05-27T00:00:00Z","_id":"8314","month":"05","status":"public","citation":{"mla":"Avarikioti, Georgia, et al. “Brick: Asynchronous Payment Channels.” ArXiv, 1905.11360.","short":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, D. Zindros, ArXiv (n.d.).","ista":"Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv, 1905.11360.","ama":"Avarikioti G, Kokoris Kogias E, Wattenhofer R, Zindros D. Brick: Asynchronous payment channels. arXiv.","chicago":"Avarikioti, Georgia, Eleftherios Kokoris Kogias, Roger Wattenhofer, and Dionysis Zindros. “Brick: Asynchronous Payment Channels.” ArXiv, n.d.","apa":"Avarikioti, G., Kokoris Kogias, E., Wattenhofer, R., & Zindros, D. (n.d.). Brick: Asynchronous payment channels. arXiv.","ieee":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, and D. Zindros, “Brick: Asynchronous payment channels,” arXiv. ."},"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1905.11360","open_access":"1"}],"abstract":[{"lang":"eng","text":"Off-chain protocols (channels) are a promising solution to the scalability and privacy challenges of blockchain payments. Current proposals, however, require synchrony assumptions to preserve the safety of a channel, leaking to an adversary the exact amount of time needed to control the network for a successful attack. In this paper, we introduce Brick, the first payment channel that remains secure under network asynchrony and concurrently provides correct incentives. The core idea is to incorporate the conflict resolution process within the channel by introducing a rational committee of external parties, called Wardens. Hence, if a party wants to close a channel unilaterally, it can only get the committee's approval for the last valid state. Brick provides sub-second latency because it does not employ heavy-weight consensus. Instead,\r\nBrick uses consistent broadcast to announce updates and close the channel, a light-weight abstraction that is powerful enough to preserve safety and liveness to any rational parties. Furthermore, we consider permissioned blockchains, where the additional property of auditability might be desired for regulatory purposes. We introduce Brick+, an off-chain construction that provides auditability on top of Brick without conflicting with its privacy guarantees. We formally define the properties our payment channel construction should fulfill, and prove that both Brick and Brick+ satisfy them. We also design incentives for Brick such that honest and rational behavior aligns. Finally, we provide a reference implementation of the smart contracts in Solidity."}],"date_updated":"2021-01-12T08:18:04Z","extern":"1"},{"date_created":"2020-08-27T11:37:43Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"23","type":"preprint","oa":1,"external_id":{"arxiv":["1910.10434"]},"language":[{"iso":"eng"}],"publication_status":"submitted","publication":"arXiv","author":[{"last_name":"Avarikioti","full_name":"Avarikioti, Georgia","first_name":"Georgia"},{"first_name":"Eleftherios","full_name":"Kokoris Kogias, Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias"},{"last_name":"Wattenhofer","full_name":"Wattenhofer, Roger","first_name":"Roger"}],"title":"Divide and scale: Formalization of distributed ledger sharding protocols","arxiv":1,"_id":"8315","citation":{"ista":"Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv, 1910.10434.","short":"G. Avarikioti, E. Kokoris Kogias, R. Wattenhofer, ArXiv (n.d.).","mla":"Avarikioti, Georgia, et al. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv, 1910.10434.","ama":"Avarikioti G, Kokoris Kogias E, Wattenhofer R. Divide and scale: Formalization of distributed ledger sharding protocols. arXiv.","apa":"Avarikioti, G., Kokoris Kogias, E., & Wattenhofer, R. (n.d.). Divide and scale: Formalization of distributed ledger sharding protocols. arXiv.","ieee":"G. Avarikioti, E. Kokoris Kogias, and R. Wattenhofer, “Divide and scale: Formalization of distributed ledger sharding protocols,” arXiv. .","chicago":"Avarikioti, Georgia, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide and Scale: Formalization of Distributed Ledger Sharding Protocols.” ArXiv, n.d."},"month":"10","status":"public","year":"2019","article_number":"1910.10434","article_processing_charge":"No","date_published":"2019-10-23T00:00:00Z","extern":"1","oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1910.10434"}],"date_updated":"2021-01-12T08:18:05Z","abstract":[{"lang":"eng","text":"Sharding distributed ledgers is the most promising on-chain solution for scaling blockchain technology. In this work, we define and analyze the properties a sharded distributed ledger should fulfill. More specifically, we show that a sharded blockchain cannot be scalable under a fully adaptive adversary, but it can scale up to $O(n/\\log n)$ under an epoch-adaptive adversary. This is possible only if the distributed ledger creates succinct proofs of the valid state updates at the end of each epoch. Our model builds upon and extends the Bitcoin backbone protocol by defining consistency and\r\nscalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system. In\r\norder to show the power of our framework, we analyze the most prominent sharded blockchains and either prove their correctness (OmniLedger, RapidChain) under our model or pinpoint where they fail to balance the consistency and\r\nscalability requirements (Elastico, Monoxide). "}]},{"extern":"1","volume":10,"oa_version":"Published Version","date_updated":"2021-01-12T08:19:03Z","intvolume":" 10","_id":"8405","status":"public","year":"2019","date_published":"2019-06-19T00:00:00Z","publication":"Nature Communications","publisher":"Springer Nature","doi":"10.1038/s41467-019-10490-9","pmid":1,"title":"Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex","quality_controlled":"1","day":"19","oa":1,"type":"journal_article","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1038/s41467-019-10490-9","open_access":"1"}],"abstract":[{"text":"Atomic-resolution structure determination is crucial for understanding protein function. Cryo-EM and NMR spectroscopy both provide structural information, but currently cryo-EM does not routinely give access to atomic-level structural data, and, generally, NMR structure determination is restricted to small (<30 kDa) proteins. We introduce an integrated structure determination approach that simultaneously uses NMR and EM data to overcome the limits of each of these methods. The approach enables structure determination of the 468 kDa large dodecameric aminopeptidase TET2 to a precision and accuracy below 1 Å by combining secondary-structure information obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large subunits, distance restraints from backbone amides and ILV methyl groups, and a 4.1 Å resolution EM map. The resulting structure exceeds current standards of NMR and EM structure determination in terms of molecular weight and precision. Importantly, the approach is successful even in cases where only medium-resolution cryo-EM data are available.","lang":"eng"}],"citation":{"short":"D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier, A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A. Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019).","mla":"Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications, vol. 10, 2697, Springer Nature, 2019, doi:10.1038/s41467-019-10490-9.","ista":"Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 10, 2697.","ama":"Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 2019;10. doi:10.1038/s41467-019-10490-9","chicago":"Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin, Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.” Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-10490-9.","apa":"Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier, R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-019-10490-9","ieee":"D. F. Gauto et al., “Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex,” Nature Communications, vol. 10. Springer Nature, 2019."},"month":"06","article_number":"2697","article_processing_charge":"No","publication_status":"published","author":[{"first_name":"Diego F.","last_name":"Gauto","full_name":"Gauto, Diego F."},{"last_name":"Estrozi","full_name":"Estrozi, Leandro F.","first_name":"Leandro F."},{"first_name":"Charles D.","last_name":"Schwieters","full_name":"Schwieters, Charles D."},{"first_name":"Gregory","last_name":"Effantin","full_name":"Effantin, Gregory"},{"last_name":"Macek","full_name":"Macek, Pavel","first_name":"Pavel"},{"first_name":"Remy","full_name":"Sounier, Remy","last_name":"Sounier"},{"first_name":"Astrid C.","full_name":"Sivertsen, Astrid C.","last_name":"Sivertsen"},{"full_name":"Schmidt, Elena","last_name":"Schmidt","first_name":"Elena"},{"full_name":"Kerfah, Rime","last_name":"Kerfah","first_name":"Rime"},{"first_name":"Guillaume","full_name":"Mas, Guillaume","last_name":"Mas"},{"first_name":"Jacques-Philippe","full_name":"Colletier, Jacques-Philippe","last_name":"Colletier"},{"last_name":"Güntert","full_name":"Güntert, Peter","first_name":"Peter"},{"first_name":"Adrien","full_name":"Favier, Adrien","last_name":"Favier"},{"first_name":"Guy","last_name":"Schoehn","full_name":"Schoehn, Guy"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda"},{"last_name":"Boisbouvier","full_name":"Boisbouvier, Jerome","first_name":"Jerome"}],"publication_identifier":{"issn":["2041-1723"]},"article_type":"original","date_created":"2020-09-17T10:28:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["31217444"]},"keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"]},{"title":"Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors","doi":"10.1126/sciadv.aaw3818","publisher":"American Association for the Advancement of Science","publication":"Science Advances","language":[{"iso":"eng"}],"day":"04","oa":1,"type":"journal_article","quality_controlled":"1","date_updated":"2021-01-12T08:19:03Z","volume":5,"oa_version":"Published Version","extern":"1","date_published":"2019-09-04T00:00:00Z","year":"2019","status":"public","_id":"8406","intvolume":" 5","article_type":"original","publication_identifier":{"issn":["2375-2548"]},"author":[{"last_name":"Felix","full_name":"Felix, Jan","first_name":"Jan"},{"full_name":"Weinhäupl, Katharina","last_name":"Weinhäupl","first_name":"Katharina"},{"first_name":"Christophe","full_name":"Chipot, Christophe","last_name":"Chipot"},{"last_name":"Dehez","full_name":"Dehez, François","first_name":"François"},{"last_name":"Hessel","full_name":"Hessel, Audrey","first_name":"Audrey"},{"last_name":"Gauto","full_name":"Gauto, Diego F.","first_name":"Diego F."},{"first_name":"Cecile","full_name":"Morlot, Cecile","last_name":"Morlot"},{"first_name":"Olga","last_name":"Abian","full_name":"Abian, Olga"},{"first_name":"Irina","last_name":"Gutsche","full_name":"Gutsche, Irina"},{"first_name":"Adrian","full_name":"Velazquez-Campoy, Adrian","last_name":"Velazquez-Campoy"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425"},{"full_name":"Fraga, Hugo","last_name":"Fraga","first_name":"Hugo"}],"publication_status":"published","issue":"9","date_created":"2020-09-17T10:28:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":" https://doi.org/10.1126/sciadv.aaw3818"}],"abstract":[{"lang":"eng","text":"Coordinated conformational transitions in oligomeric enzymatic complexes modulate function in response to substrates and play a crucial role in enzyme inhibition and activation. Caseinolytic protease (ClpP) is a tetradecameric complex, which has emerged as a drug target against multiple pathogenic bacteria. Activation of different ClpPs by inhibitors has been independently reported from drug development efforts, but no rationale for inhibitor-induced activation has been hitherto proposed. Using an integrated approach that includes x-ray crystallography, solid- and solution-state nuclear magnetic resonance, molecular dynamics simulations, and isothermal titration calorimetry, we show that the proteasome inhibitor bortezomib binds to the ClpP active-site serine, mimicking a peptide substrate, and induces a concerted allosteric activation of the complex. The bortezomib-activated conformation also exhibits a higher affinity for its cognate unfoldase ClpX. We propose a universal allosteric mechanism, where substrate binding to a single subunit locks ClpP into an active conformation optimized for chaperone association and protein processive degradation."}],"article_processing_charge":"No","article_number":"eaaw3818","citation":{"chicago":"Felix, Jan, Katharina Weinhäupl, Christophe Chipot, François Dehez, Audrey Hessel, Diego F. Gauto, Cecile Morlot, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances. American Association for the Advancement of Science, 2019. https://doi.org/10.1126/sciadv.aaw3818.","ieee":"J. Felix et al., “Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors,” Science Advances, vol. 5, no. 9. American Association for the Advancement of Science, 2019.","apa":"Felix, J., Weinhäupl, K., Chipot, C., Dehez, F., Hessel, A., Gauto, D. F., … Fraga, H. (2019). Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.aaw3818","mla":"Felix, Jan, et al. “Mechanism of the Allosteric Activation of the ClpP Protease Machinery by Substrates and Active-Site Inhibitors.” Science Advances, vol. 5, no. 9, eaaw3818, American Association for the Advancement of Science, 2019, doi:10.1126/sciadv.aaw3818.","short":"J. Felix, K. Weinhäupl, C. Chipot, F. Dehez, A. Hessel, D.F. Gauto, C. Morlot, O. Abian, I. Gutsche, A. Velazquez-Campoy, P. Schanda, H. Fraga, Science Advances 5 (2019).","ista":"Felix J, Weinhäupl K, Chipot C, Dehez F, Hessel A, Gauto DF, Morlot C, Abian O, Gutsche I, Velazquez-Campoy A, Schanda P, Fraga H. 2019. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 5(9), eaaw3818.","ama":"Felix J, Weinhäupl K, Chipot C, et al. Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors. Science Advances. 2019;5(9). doi:10.1126/sciadv.aaw3818"},"month":"09"},{"date_updated":"2021-01-12T08:19:04Z","oa_version":"Submitted Version","volume":306,"extern":"1","date_published":"2019-09-01T00:00:00Z","article_processing_charge":"No","year":"2019","citation":{"chicago":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance. Elsevier, 2019. https://doi.org/10.1016/j.jmr.2019.07.025.","ieee":"P. Schanda, “Relaxing with liquids and solids – A perspective on biomolecular dynamics,” Journal of Magnetic Resonance, vol. 306. Elsevier, pp. 180–186, 2019.","apa":"Schanda, P. (2019). Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2019.07.025","mla":"Schanda, Paul. “Relaxing with Liquids and Solids – A Perspective on Biomolecular Dynamics.” Journal of Magnetic Resonance, vol. 306, Elsevier, 2019, pp. 180–86, doi:10.1016/j.jmr.2019.07.025.","short":"P. Schanda, Journal of Magnetic Resonance 306 (2019) 180–186.","ama":"Schanda P. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 2019;306:180-186. doi:10.1016/j.jmr.2019.07.025","ista":"Schanda P. 2019. Relaxing with liquids and solids – A perspective on biomolecular dynamics. Journal of Magnetic Resonance. 306, 180–186."},"month":"09","status":"public","intvolume":" 306","_id":"8407","article_type":"original","pmid":1,"publication_identifier":{"issn":["1090-7807"]},"title":"Relaxing with liquids and solids – A perspective on biomolecular dynamics","publisher":"Elsevier","author":[{"first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"}],"doi":"10.1016/j.jmr.2019.07.025","publication":"Journal of Magnetic Resonance","publication_status":"published","keyword":["Nuclear and High Energy Physics","Biophysics","Biochemistry","Condensed Matter Physics"],"language":[{"iso":"eng"}],"external_id":{"pmid":["31350165"]},"type":"journal_article","day":"01","page":"180-186","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","date_created":"2020-09-17T10:28:47Z"},{"extern":"1","volume":141,"oa_version":"Submitted Version","date_updated":"2021-01-12T08:19:04Z","intvolume":" 141","_id":"8408","status":"public","year":"2019","date_published":"2019-06-14T00:00:00Z","publication":"Journal of the American Chemical Society","publisher":"American Chemical Society","doi":"10.1021/jacs.9b04219","pmid":1,"title":"Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR","quality_controlled":"1","day":"14","type":"journal_article","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artefact-free dynamics measurements, and allows probing motions effectively without molecular-weight limitations. The application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (ps-ms). We quantitatively probe ring flip motions, and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples."}],"month":"06","citation":{"short":"D.F. Gauto, P. Macek, A. Barducci, H. Fraga, A. Hessel, T. Terauchi, D. Gajan, Y. Miyanoiri, J. Boisbouvier, R. Lichtenecker, M. Kainosho, P. Schanda, Journal of the American Chemical Society 141 (2019) 11183–11195.","mla":"Gauto, Diego F., et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society, vol. 141, no. 28, American Chemical Society, 2019, pp. 11183–95, doi:10.1021/jacs.9b04219.","ista":"Gauto DF, Macek P, Barducci A, Fraga H, Hessel A, Terauchi T, Gajan D, Miyanoiri Y, Boisbouvier J, Lichtenecker R, Kainosho M, Schanda P. 2019. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 141(28), 11183–11195.","ama":"Gauto DF, Macek P, Barducci A, et al. Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. 2019;141(28):11183-11195. doi:10.1021/jacs.9b04219","apa":"Gauto, D. F., Macek, P., Barducci, A., Fraga, H., Hessel, A., Terauchi, T., … Schanda, P. (2019). Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b04219","ieee":"D. F. Gauto et al., “Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR,” Journal of the American Chemical Society, vol. 141, no. 28. American Chemical Society, pp. 11183–11195, 2019.","chicago":"Gauto, Diego F., Pavel Macek, Alessandro Barducci, Hugo Fraga, Audrey Hessel, Tsutomu Terauchi, David Gajan, et al. “Aromatic Ring Dynamics, Thermal Activation, and Transient Conformations of a 468 KDa Enzyme by Specific 1H–13C Labeling and Fast Magic-Angle Spinning NMR.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b04219."},"article_processing_charge":"No","publication_status":"published","author":[{"full_name":"Gauto, Diego F.","last_name":"Gauto","first_name":"Diego F."},{"first_name":"Pavel","last_name":"Macek","full_name":"Macek, Pavel"},{"last_name":"Barducci","full_name":"Barducci, Alessandro","first_name":"Alessandro"},{"full_name":"Fraga, Hugo","last_name":"Fraga","first_name":"Hugo"},{"first_name":"Audrey","last_name":"Hessel","full_name":"Hessel, Audrey"},{"last_name":"Terauchi","full_name":"Terauchi, Tsutomu","first_name":"Tsutomu"},{"full_name":"Gajan, David","last_name":"Gajan","first_name":"David"},{"full_name":"Miyanoiri, Yohei","last_name":"Miyanoiri","first_name":"Yohei"},{"last_name":"Boisbouvier","full_name":"Boisbouvier, Jerome","first_name":"Jerome"},{"full_name":"Lichtenecker, Roman","last_name":"Lichtenecker","first_name":"Roman"},{"last_name":"Kainosho","full_name":"Kainosho, Masatsune","first_name":"Masatsune"},{"first_name":"Paul","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606"}],"publication_identifier":{"issn":["0002-7863","1520-5126"]},"article_type":"original","issue":"28","date_created":"2020-09-17T10:29:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"11183-11195","external_id":{"pmid":["31199882"]},"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"]},{"title":"Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency","pmid":1,"publication":"Journal of Structural Biology","doi":"10.1016/j.jsb.2018.07.009","publisher":"Elsevier","type":"journal_article","day":"01","language":[{"iso":"eng"}],"quality_controlled":"1","volume":206,"oa_version":"Submitted Version","date_updated":"2021-01-12T08:19:05Z","extern":"1","year":"2019","date_published":"2019-04-01T00:00:00Z","_id":"8409","intvolume":" 206","status":"public","publication_identifier":{"issn":["1047-8477"]},"article_type":"original","publication_status":"published","author":[{"full_name":"Bougault, Catherine","last_name":"Bougault","first_name":"Catherine"},{"full_name":"Ayala, Isabel","last_name":"Ayala","first_name":"Isabel"},{"first_name":"Waldemar","last_name":"Vollmer","full_name":"Vollmer, Waldemar"},{"full_name":"Simorre, Jean-Pierre","last_name":"Simorre","first_name":"Jean-Pierre"},{"first_name":"Paul","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","last_name":"Schanda","orcid":"0000-0002-9350-7606"}],"page":"66-72","keyword":["Structural Biology"],"external_id":{"pmid":["30031884"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"1","date_created":"2020-09-17T10:29:10Z","abstract":[{"lang":"eng","text":"The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling."}],"article_processing_charge":"No","month":"04","citation":{"chicago":"Bougault, Catherine, Isabel Ayala, Waldemar Vollmer, Jean-Pierre Simorre, and Paul Schanda. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology. Elsevier, 2019. https://doi.org/10.1016/j.jsb.2018.07.009.","ieee":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, and P. Schanda, “Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency,” Journal of Structural Biology, vol. 206, no. 1. Elsevier, pp. 66–72, 2019.","apa":"Bougault, C., Ayala, I., Vollmer, W., Simorre, J.-P., & Schanda, P. (2019). Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. Elsevier. https://doi.org/10.1016/j.jsb.2018.07.009","ista":"Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. 2019. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 206(1), 66–72.","ama":"Bougault C, Ayala I, Vollmer W, Simorre J-P, Schanda P. Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency. Journal of Structural Biology. 2019;206(1):66-72. doi:10.1016/j.jsb.2018.07.009","short":"C. Bougault, I. Ayala, W. Vollmer, J.-P. Simorre, P. Schanda, Journal of Structural Biology 206 (2019) 66–72.","mla":"Bougault, Catherine, et al. “Studying Intact Bacterial Peptidoglycan by Proton-Detected NMR Spectroscopy at 100 kHz MAS Frequency.” Journal of Structural Biology, vol. 206, no. 1, Elsevier, 2019, pp. 66–72, doi:10.1016/j.jsb.2018.07.009."}},{"date_updated":"2021-01-12T08:19:05Z","oa_version":"Published Version","volume":20,"extern":"1","date_published":"2019-01-21T00:00:00Z","year":"2019","status":"public","intvolume":" 20","_id":"8410","pmid":1,"title":"NMR for Biological Systems","publisher":"Wiley","doi":"10.1002/cphc.201801100","publication":"ChemPhysChem","language":[{"iso":"eng"}],"oa":1,"type":"journal_article","day":"21","quality_controlled":"1","main_file_link":[{"url":"https://doi.org/10.1002/cphc.201801100","open_access":"1"}],"article_processing_charge":"No","month":"01","citation":{"ieee":"P. Schanda and E. Y. Chekmenev, “NMR for Biological Systems,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 177–177, 2019.","apa":"Schanda, P., & Chekmenev, E. Y. (2019). NMR for Biological Systems. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201801100","chicago":"Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201801100.","ama":"Schanda P, Chekmenev EY. NMR for Biological Systems. ChemPhysChem. 2019;20(2):177-177. doi:10.1002/cphc.201801100","mla":"Schanda, Paul, and Eduard Y. Chekmenev. “NMR for Biological Systems.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 177–177, doi:10.1002/cphc.201801100.","ista":"Schanda P, Chekmenev EY. 2019. NMR for Biological Systems. ChemPhysChem. 20(2), 177–177.","short":"P. Schanda, E.Y. Chekmenev, ChemPhysChem 20 (2019) 177–177."},"article_type":"letter_note","publication_identifier":{"issn":["1439-4235"]},"author":[{"first_name":"Paul","last_name":"Schanda","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","orcid":"0000-0002-9350-7606"},{"last_name":"Chekmenev","full_name":"Chekmenev, Eduard Y.","first_name":"Eduard Y."}],"publication_status":"published","external_id":{"pmid":["30556633"]},"page":"177-177","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-17T10:29:26Z","issue":"2"},{"page":"276-284","external_id":{"pmid":["30444575"]},"keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"date_created":"2020-09-17T10:29:36Z","issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1439-4235"]},"article_type":"original","publication_status":"published","author":[{"first_name":"Dominique","full_name":"Marion, Dominique","last_name":"Marion"},{"last_name":"Gauto","full_name":"Gauto, Diego F.","first_name":"Diego F."},{"first_name":"Isabel","last_name":"Ayala","full_name":"Ayala, Isabel"},{"last_name":"Giandoreggio-Barranco","full_name":"Giandoreggio-Barranco, Karine","first_name":"Karine"},{"orcid":"0000-0002-9350-7606","last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul"}],"article_processing_charge":"No","month":"01","citation":{"apa":"Marion, D., Gauto, D. F., Ayala, I., Giandoreggio-Barranco, K., & Schanda, P. (2019). Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800935","ieee":"D. Marion, D. F. Gauto, I. Ayala, K. Giandoreggio-Barranco, and P. Schanda, “Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 276–284, 2019.","chicago":"Marion, Dominique, Diego F. Gauto, Isabel Ayala, Karine Giandoreggio-Barranco, and Paul Schanda. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800935.","ama":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 2019;20(2):276-284. doi:10.1002/cphc.201800935","mla":"Marion, Dominique, et al. “Microsecond Protein Dynamics from Combined Bloch-McConnell and Near-Rotary-Resonance R1p Relaxation-Dispersion MAS NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 276–84, doi:10.1002/cphc.201800935.","ista":"Marion D, Gauto DF, Ayala I, Giandoreggio-Barranco K, Schanda P. 2019. Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR. ChemPhysChem. 20(2), 276–284.","short":"D. Marion, D.F. Gauto, I. Ayala, K. Giandoreggio-Barranco, P. Schanda, ChemPhysChem 20 (2019) 276–284."},"abstract":[{"text":"Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales can provide important insight into protein function. In magic‐angle‐spinning (MAS) NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion experiments in different regimes of radio‐frequency field strengths: at low RF field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.","lang":"eng"}],"day":"21","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR","pmid":1,"publication":"ChemPhysChem","publisher":"Wiley","doi":"10.1002/cphc.201800935","year":"2019","date_published":"2019-01-21T00:00:00Z","intvolume":" 20","_id":"8411","status":"public","volume":20,"oa_version":"Submitted Version","date_updated":"2021-01-12T08:19:06Z","extern":"1"},{"date_updated":"2021-01-12T08:19:06Z","volume":20,"oa_version":"Submitted Version","extern":"1","date_published":"2019-01-21T00:00:00Z","year":"2019","status":"public","intvolume":" 20","_id":"8412","title":"Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR","pmid":1,"publisher":"Wiley","doi":"10.1002/cphc.201800779","publication":"ChemPhysChem","language":[{"iso":"eng"}],"type":"journal_article","day":"21","quality_controlled":"1","abstract":[{"lang":"eng","text":"Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two‐state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited‐state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited‐state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid."}],"article_processing_charge":"No","citation":{"mla":"Shannon, Matthew D., et al. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem, vol. 20, no. 2, Wiley, 2019, pp. 311–17, doi:10.1002/cphc.201800779.","ista":"Shannon MD, Theint T, Mukhopadhyay D, Surewicz K, Surewicz WK, Marion D, Schanda P, Jaroniec CP. 2019. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 20(2), 311–317.","short":"M.D. Shannon, T. Theint, D. Mukhopadhyay, K. Surewicz, W.K. Surewicz, D. Marion, P. Schanda, C.P. Jaroniec, ChemPhysChem 20 (2019) 311–317.","ama":"Shannon MD, Theint T, Mukhopadhyay D, et al. Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. 2019;20(2):311-317. doi:10.1002/cphc.201800779","apa":"Shannon, M. D., Theint, T., Mukhopadhyay, D., Surewicz, K., Surewicz, W. K., Marion, D., … Jaroniec, C. P. (2019). Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR. ChemPhysChem. Wiley. https://doi.org/10.1002/cphc.201800779","ieee":"M. D. Shannon et al., “Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR,” ChemPhysChem, vol. 20, no. 2. Wiley, pp. 311–317, 2019.","chicago":"Shannon, Matthew D., Theint Theint, Dwaipayan Mukhopadhyay, Krystyna Surewicz, Witold K. Surewicz, Dominique Marion, Paul Schanda, and Christopher P. Jaroniec. “Conformational Dynamics in the Core of Human Y145Stop Prion Protein Amyloid Probed by Relaxation Dispersion NMR.” ChemPhysChem. Wiley, 2019. https://doi.org/10.1002/cphc.201800779."},"month":"01","article_type":"original","publication_identifier":{"issn":["1439-4235"]},"author":[{"first_name":"Matthew D.","last_name":"Shannon","full_name":"Shannon, Matthew D."},{"first_name":"Theint","full_name":"Theint, Theint","last_name":"Theint"},{"first_name":"Dwaipayan","last_name":"Mukhopadhyay","full_name":"Mukhopadhyay, Dwaipayan"},{"first_name":"Krystyna","last_name":"Surewicz","full_name":"Surewicz, Krystyna"},{"first_name":"Witold K.","last_name":"Surewicz","full_name":"Surewicz, Witold K."},{"first_name":"Dominique","full_name":"Marion, Dominique","last_name":"Marion"},{"last_name":"Schanda","full_name":"Schanda, Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","first_name":"Paul","orcid":"0000-0002-9350-7606"},{"first_name":"Christopher P.","full_name":"Jaroniec, Christopher P.","last_name":"Jaroniec"}],"publication_status":"published","keyword":["Physical and Theoretical Chemistry","Atomic and Molecular Physics","and Optics"],"external_id":{"pmid":["30276945"]},"page":"311-317","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"2","date_created":"2020-09-17T10:29:43Z"},{"date_published":"2019-01-08T00:00:00Z","year":"2019","status":"public","_id":"8413","intvolume":" 141","date_updated":"2021-01-12T08:19:07Z","volume":141,"oa_version":"Submitted Version","extern":"1","language":[{"iso":"eng"}],"type":"journal_article","day":"08","quality_controlled":"1","pmid":1,"title":"Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques","publisher":"American Chemical Society","doi":"10.1021/jacs.8b09258","publication":"Journal of the American Chemical Society","article_processing_charge":"No","citation":{"ama":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 2019;141(2):858-869. doi:10.1021/jacs.8b09258","short":"P. Rovó, C.A. Smith, D. Gauto, B.L. de Groot, P. Schanda, R. Linser, Journal of the American Chemical Society 141 (2019) 858–869.","mla":"Rovó, Petra, et al. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society, vol. 141, no. 2, American Chemical Society, 2019, pp. 858–69, doi:10.1021/jacs.8b09258.","ista":"Rovó P, Smith CA, Gauto D, de Groot BL, Schanda P, Linser R. 2019. Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. 141(2), 858–869.","ieee":"P. Rovó, C. A. Smith, D. Gauto, B. L. de Groot, P. Schanda, and R. Linser, “Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques,” Journal of the American Chemical Society, vol. 141, no. 2. American Chemical Society, pp. 858–869, 2019.","apa":"Rovó, P., Smith, C. A., Gauto, D., de Groot, B. L., Schanda, P., & Linser, R. (2019). Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.8b09258","chicago":"Rovó, Petra, Colin A. Smith, Diego Gauto, Bert L. de Groot, Paul Schanda, and Rasmus Linser. “Mechanistic Insights into Microsecond Time-Scale Motion of Solid Proteins Using Complementary 15N and 1H Relaxation Dispersion Techniques.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.8b09258."},"month":"01","abstract":[{"lang":"eng","text":"NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains."}],"keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"external_id":{"pmid":["30620186"]},"page":"858-869","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-09-17T10:29:50Z","issue":"2","article_type":"original","publication_identifier":{"issn":["0002-7863","1520-5126"]},"author":[{"first_name":"Petra","last_name":"Rovó","full_name":"Rovó, Petra"},{"first_name":"Colin A.","full_name":"Smith, Colin A.","last_name":"Smith"},{"first_name":"Diego","full_name":"Gauto, Diego","last_name":"Gauto"},{"first_name":"Bert L.","full_name":"de Groot, Bert L.","last_name":"de Groot"},{"orcid":"0000-0002-9350-7606","first_name":"Paul","id":"7B541462-FAF6-11E9-A490-E8DFE5697425","full_name":"Schanda, Paul","last_name":"Schanda"},{"last_name":"Linser","full_name":"Linser, Rasmus","first_name":"Rasmus"}],"publication_status":"published"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","date_created":"2020-09-17T10:41:27Z","page":"1531-1575","keyword":["Mathematical Physics","Statistical and Nonlinear Physics"],"external_id":{"arxiv":["1809.08947"]},"publication_status":"published","author":[{"full_name":"Bálint, Péter","last_name":"Bálint","first_name":"Péter"},{"full_name":"De Simoi, Jacopo","last_name":"De Simoi","first_name":"Jacopo"},{"last_name":"Kaloshin","id":"FE553552-CDE8-11E9-B324-C0EBE5697425","full_name":"Kaloshin, Vadim","first_name":"Vadim","orcid":"0000-0002-6051-2628"},{"first_name":"Martin","full_name":"Leguil, Martin","last_name":"Leguil"}],"publication_identifier":{"issn":["0010-3616","1432-0916"]},"article_type":"original","citation":{"chicago":"Bálint, Péter, Jacopo De Simoi, Vadim Kaloshin, and Martin Leguil. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03448-x.","apa":"Bálint, P., De Simoi, J., Kaloshin, V., & Leguil, M. (2019). Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03448-x","ieee":"P. Bálint, J. De Simoi, V. Kaloshin, and M. Leguil, “Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards,” Communications in Mathematical Physics, vol. 374, no. 3. Springer Nature, pp. 1531–1575, 2019.","ista":"Bálint P, De Simoi J, Kaloshin V, Leguil M. 2019. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 374(3), 1531–1575.","ama":"Bálint P, De Simoi J, Kaloshin V, Leguil M. Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards. Communications in Mathematical Physics. 2019;374(3):1531-1575. doi:10.1007/s00220-019-03448-x","mla":"Bálint, Péter, et al. “Marked Length Spectrum, Homoclinic Orbits and the Geometry of Open Dispersing Billiards.” Communications in Mathematical Physics, vol. 374, no. 3, Springer Nature, 2019, pp. 1531–75, doi:10.1007/s00220-019-03448-x.","short":"P. Bálint, J. De Simoi, V. Kaloshin, M. Leguil, Communications in Mathematical Physics 374 (2019) 1531–1575."},"month":"05","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We consider billiards obtained by removing three strictly convex obstacles satisfying the non-eclipse condition on the plane. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift on three symbols that provides a natural labeling of all periodic orbits. We study the following inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of periodic orbits together with their labeling), determine the geometry of the billiard table? We show that from the Marked Length Spectrum it is possible to recover the curvature at periodic points of period two, as well as the Lyapunov exponent of each periodic orbit."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.08947"}],"quality_controlled":"1","type":"journal_article","oa":1,"day":"09","language":[{"iso":"eng"}],"publication":"Communications in Mathematical Physics","publisher":"Springer Nature","doi":"10.1007/s00220-019-03448-x","arxiv":1,"title":"Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards","intvolume":" 374","_id":"8415","status":"public","year":"2019","date_published":"2019-05-09T00:00:00Z","extern":"1","volume":374,"oa_version":"Preprint","date_updated":"2021-01-12T08:19:08Z"}]