---
_id: '8465'
abstract:
- lang: eng
text: We demonstrate that conformational exchange processes in proteins on microsecond-to-millisecond
time scales can be detected and quantified by solid-state NMR spectroscopy. We
show two independent approaches that measure the effect of conformational exchange
on transverse relaxation parameters, namely Carr–Purcell–Meiboom–Gill relaxation-dispersion
experiments and measurement of differential multiple-quantum coherence decay.
Long coherence lifetimes, as required for these experiments, are achieved by the
use of highly deuterated samples and fast magic-angle spinning. The usefulness
of the approaches is demonstrated by application to microcrystalline ubiquitin.
We detect a conformational exchange process in a region of the protein for which
dynamics have also been observed in solution. Interestingly, quantitative analysis
of the data reveals that the exchange process is more than 1 order of magnitude
slower than in solution, and this points to the impact of the crystalline environment
on free energy barriers.
article_processing_charge: No
article_type: original
author:
- first_name: Martin
full_name: Tollinger, Martin
last_name: Tollinger
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. Site-resolved measurement
of microsecond-to-millisecond conformational-exchange processes in proteins by
solid-state NMR spectroscopy. Journal of the American Chemical Society.
2012;134(36):14800-14807. doi:10.1021/ja303591y
apa: Tollinger, M., Sivertsen, A. C., Meier, B. H., Ernst, M., & Schanda, P.
(2012). Site-resolved measurement of microsecond-to-millisecond conformational-exchange
processes in proteins by solid-state NMR spectroscopy. Journal of the American
Chemical Society. American Chemical Society. https://doi.org/10.1021/ja303591y
chicago: Tollinger, Martin, Astrid C. Sivertsen, Beat H. Meier, Matthias Ernst,
and Paul Schanda. “Site-Resolved Measurement of Microsecond-to-Millisecond Conformational-Exchange
Processes in Proteins by Solid-State NMR Spectroscopy.” Journal of the American
Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja303591y.
ieee: M. Tollinger, A. C. Sivertsen, B. H. Meier, M. Ernst, and P. Schanda, “Site-resolved
measurement of microsecond-to-millisecond conformational-exchange processes in
proteins by solid-state NMR spectroscopy,” Journal of the American Chemical
Society, vol. 134, no. 36. American Chemical Society, pp. 14800–14807, 2012.
ista: Tollinger M, Sivertsen AC, Meier BH, Ernst M, Schanda P. 2012. Site-resolved
measurement of microsecond-to-millisecond conformational-exchange processes in
proteins by solid-state NMR spectroscopy. Journal of the American Chemical Society.
134(36), 14800–14807.
mla: Tollinger, Martin, et al. “Site-Resolved Measurement of Microsecond-to-Millisecond
Conformational-Exchange Processes in Proteins by Solid-State NMR Spectroscopy.”
Journal of the American Chemical Society, vol. 134, no. 36, American Chemical
Society, 2012, pp. 14800–07, doi:10.1021/ja303591y.
short: M. Tollinger, A.C. Sivertsen, B.H. Meier, M. Ernst, P. Schanda, Journal of
the American Chemical Society 134 (2012) 14800–14807.
date_created: 2020-09-18T10:10:20Z
date_published: 2012-08-21T00:00:00Z
date_updated: 2021-01-12T08:19:27Z
day: '21'
doi: 10.1021/ja303591y
extern: '1'
intvolume: ' 134'
issue: '36'
language:
- iso: eng
month: '08'
oa_version: None
page: 14800-14807
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Site-resolved measurement of microsecond-to-millisecond conformational-exchange
processes in proteins by solid-state NMR spectroscopy
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 134
year: '2012'
...
---
_id: '8466'
abstract:
- lang: eng
text: Recent advances in NMR spectroscopy and the availability of high magnetic
field strengths now offer the possibility to record real-time 3D NMR spectra of
short-lived protein states, e.g., states that become transiently populated during
protein folding. Here we present a strategy for obtaining sequential NMR assignments
as well as atom-resolved information on structural and dynamic features within
a folding intermediate of the amyloidogenic protein β2-microglobulin that has
a half-lifetime of only 20 min.
article_processing_charge: No
article_type: original
author:
- first_name: Enrico
full_name: Rennella, Enrico
last_name: Rennella
- first_name: Thomas
full_name: Cutuil, Thomas
last_name: Cutuil
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Isabel
full_name: Ayala, Isabel
last_name: Ayala
- first_name: Vincent
full_name: Forge, Vincent
last_name: Forge
- first_name: Bernhard
full_name: Brutscher, Bernhard
last_name: Brutscher
citation:
ama: Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. Real-time NMR
characterization of structure and dynamics in a transiently populated protein
folding intermediate. Journal of the American Chemical Society. 2012;134(19):8066-8069.
doi:10.1021/ja302598j
apa: Rennella, E., Cutuil, T., Schanda, P., Ayala, I., Forge, V., & Brutscher,
B. (2012). Real-time NMR characterization of structure and dynamics in a transiently
populated protein folding intermediate. Journal of the American Chemical Society.
American Chemical Society. https://doi.org/10.1021/ja302598j
chicago: Rennella, Enrico, Thomas Cutuil, Paul Schanda, Isabel Ayala, Vincent Forge,
and Bernhard Brutscher. “Real-Time NMR Characterization of Structure and Dynamics
in a Transiently Populated Protein Folding Intermediate.” Journal of the American
Chemical Society. American Chemical Society, 2012. https://doi.org/10.1021/ja302598j.
ieee: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, and B. Brutscher,
“Real-time NMR characterization of structure and dynamics in a transiently populated
protein folding intermediate,” Journal of the American Chemical Society,
vol. 134, no. 19. American Chemical Society, pp. 8066–8069, 2012.
ista: Rennella E, Cutuil T, Schanda P, Ayala I, Forge V, Brutscher B. 2012. Real-time
NMR characterization of structure and dynamics in a transiently populated protein
folding intermediate. Journal of the American Chemical Society. 134(19), 8066–8069.
mla: Rennella, Enrico, et al. “Real-Time NMR Characterization of Structure and Dynamics
in a Transiently Populated Protein Folding Intermediate.” Journal of the American
Chemical Society, vol. 134, no. 19, American Chemical Society, 2012, pp. 8066–69,
doi:10.1021/ja302598j.
short: E. Rennella, T. Cutuil, P. Schanda, I. Ayala, V. Forge, B. Brutscher, Journal
of the American Chemical Society 134 (2012) 8066–8069.
date_created: 2020-09-18T10:10:28Z
date_published: 2012-05-03T00:00:00Z
date_updated: 2021-01-12T08:19:28Z
day: '03'
doi: 10.1021/ja302598j
extern: '1'
intvolume: ' 134'
issue: '19'
language:
- iso: eng
month: '05'
oa_version: None
page: 8066-8069
publication: Journal of the American Chemical Society
publication_identifier:
issn:
- 0002-7863
- 1520-5126
publication_status: published
publisher: American Chemical Society
quality_controlled: '1'
status: public
title: Real-time NMR characterization of structure and dynamics in a transiently populated
protein folding intermediate
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 134
year: '2012'
...
---
_id: '8467'
abstract:
- lang: eng
text: Partial deuteration is a powerful tool to increase coherence life times and
spectral resolution in proton solid-state NMR. The J coupling to deuterium needs,
however, to be decoupled to maintain the good resolution in the (usually indirect)
13C dimension(s). We present a simple and reversible way to expand a commercial
1.3 mm HCN MAS probe with a 2H channel with sufficient field strength for J-decoupling
of deuterium, namely 2–3 kHz. The coil is placed at the outside of the stator
and requires no significant modifications to the probe. The performance and the
realizable gains in sensitivity and resolution are demonstrated using perdeuterated
ubiquitin, with selectively CHD2-labeled methyl groups.
article_processing_charge: No
article_type: original
author:
- first_name: Matthias
full_name: Huber, Matthias
last_name: Huber
- first_name: Oliver
full_name: With, Oliver
last_name: With
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: René
full_name: Verel, René
last_name: Verel
- first_name: Matthias
full_name: Ernst, Matthias
last_name: Ernst
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
citation:
ama: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. A supplementary coil
for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance.
2012;214:76-80. doi:10.1016/j.jmr.2011.10.010
apa: Huber, M., With, O., Schanda, P., Verel, R., Ernst, M., & Meier, B. H.
(2012). A supplementary coil for 2H decoupling with commercial HCN MAS probes.
Journal of Magnetic Resonance. Elsevier. https://doi.org/10.1016/j.jmr.2011.10.010
chicago: Huber, Matthias, Oliver With, Paul Schanda, René Verel, Matthias Ernst,
and Beat H. Meier. “A Supplementary Coil for 2H Decoupling with Commercial HCN
MAS Probes.” Journal of Magnetic Resonance. Elsevier, 2012. https://doi.org/10.1016/j.jmr.2011.10.010.
ieee: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, and B. H. Meier, “A supplementary
coil for 2H decoupling with commercial HCN MAS probes,” Journal of Magnetic
Resonance, vol. 214. Elsevier, pp. 76–80, 2012.
ista: Huber M, With O, Schanda P, Verel R, Ernst M, Meier BH. 2012. A supplementary
coil for 2H decoupling with commercial HCN MAS probes. Journal of Magnetic Resonance.
214, 76–80.
mla: Huber, Matthias, et al. “A Supplementary Coil for 2H Decoupling with Commercial
HCN MAS Probes.” Journal of Magnetic Resonance, vol. 214, Elsevier, 2012,
pp. 76–80, doi:10.1016/j.jmr.2011.10.010.
short: M. Huber, O. With, P. Schanda, R. Verel, M. Ernst, B.H. Meier, Journal of
Magnetic Resonance 214 (2012) 76–80.
date_created: 2020-09-18T10:10:36Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:28Z
day: '01'
doi: 10.1016/j.jmr.2011.10.010
extern: '1'
intvolume: ' 214'
language:
- iso: eng
month: '01'
oa_version: None
page: 76-80
publication: Journal of Magnetic Resonance
publication_identifier:
issn:
- 1090-7807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: A supplementary coil for 2H decoupling with commercial HCN MAS probes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 214
year: '2012'
...
---
_id: '8502'
abstract:
- lang: eng
text: 'The famous ergodic hypothesis suggests that for a typical Hamiltonian on
a typical energy surface nearly all trajectories are dense. KAM theory disproves
it. Ehrenfest (The Conceptual Foundations of the Statistical Approach in Mechanics.
Ithaca, NY: Cornell University Press, 1959) and Birkhoff (Collected Math Papers.
Vol 2, New York: Dover, pp 462–465, 1968) stated the quasi-ergodic hypothesis
claiming that a typical Hamiltonian on a typical energy surface has a dense orbit.
This question is wide open. Herman (Proceedings of the International Congress
of Mathematicians, Vol II (Berlin, 1998). Doc Math 1998, Extra Vol II, Berlin:
Int Math Union, pp 797–808, 1998) proposed to look for an example of a Hamiltonian
near H0(I)=⟨I,I⟩2 with a dense orbit on the unit energy surface. In this paper
we construct a Hamiltonian H0(I)+εH1(θ,I,ε) which has an orbit dense in a set
of maximal Hausdorff dimension equal to 5 on the unit energy surface.'
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: Maria
full_name: Saprykina, Maria
last_name: Saprykina
citation:
ama: Kaloshin V, Saprykina M. An example of a nearly integrable Hamiltonian system
with a trajectory dense in a set of maximal Hausdorff dimension. Communications
in Mathematical Physics. 2012;315(3):643-697. doi:10.1007/s00220-012-1532-x
apa: Kaloshin, V., & Saprykina, M. (2012). An example of a nearly integrable
Hamiltonian system with a trajectory dense in a set of maximal Hausdorff dimension.
Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-012-1532-x
chicago: Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable
Hamiltonian System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.”
Communications in Mathematical Physics. Springer Nature, 2012. https://doi.org/10.1007/s00220-012-1532-x.
ieee: V. Kaloshin and M. Saprykina, “An example of a nearly integrable Hamiltonian
system with a trajectory dense in a set of maximal Hausdorff dimension,” Communications
in Mathematical Physics, vol. 315, no. 3. Springer Nature, pp. 643–697, 2012.
ista: Kaloshin V, Saprykina M. 2012. An example of a nearly integrable Hamiltonian
system with a trajectory dense in a set of maximal Hausdorff dimension. Communications
in Mathematical Physics. 315(3), 643–697.
mla: Kaloshin, Vadim, and Maria Saprykina. “An Example of a Nearly Integrable Hamiltonian
System with a Trajectory Dense in a Set of Maximal Hausdorff Dimension.” Communications
in Mathematical Physics, vol. 315, no. 3, Springer Nature, 2012, pp. 643–97,
doi:10.1007/s00220-012-1532-x.
short: V. Kaloshin, M. Saprykina, Communications in Mathematical Physics 315 (2012)
643–697.
date_created: 2020-09-18T10:47:16Z
date_published: 2012-11-01T00:00:00Z
date_updated: 2021-01-12T08:19:44Z
day: '01'
doi: 10.1007/s00220-012-1532-x
extern: '1'
intvolume: ' 315'
issue: '3'
keyword:
- Mathematical Physics
- Statistical and Nonlinear Physics
language:
- iso: eng
month: '11'
oa_version: None
page: 643-697
publication: Communications in Mathematical Physics
publication_identifier:
issn:
- 0010-3616
- 1432-0916
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: An example of a nearly integrable Hamiltonian system with a trajectory dense
in a set of maximal Hausdorff dimension
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 315
year: '2012'
...
---
_id: '8503'
abstract:
- lang: eng
text: We prove there are finitely many isometry classes of planar central configurations
(also called relative equilibria) in the Newtonian 5-body problem, except perhaps
if the 5-tuple of positive masses belongs to a given codimension 2 subvariety
of the mass space.
article_processing_charge: No
article_type: original
author:
- first_name: Alain
full_name: Albouy, Alain
last_name: Albouy
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
citation:
ama: Albouy A, Kaloshin V. Finiteness of central configurations of five bodies in
the plane. Annals of Mathematics. 2012;176(1):535-588. doi:10.4007/annals.2012.176.1.10
apa: Albouy, A., & Kaloshin, V. (2012). Finiteness of central configurations
of five bodies in the plane. Annals of Mathematics. Princeton University
Press. https://doi.org/10.4007/annals.2012.176.1.10
chicago: Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations
of Five Bodies in the Plane.” Annals of Mathematics. Princeton University
Press, 2012. https://doi.org/10.4007/annals.2012.176.1.10.
ieee: A. Albouy and V. Kaloshin, “Finiteness of central configurations of five bodies
in the plane,” Annals of Mathematics, vol. 176, no. 1. Princeton University
Press, pp. 535–588, 2012.
ista: Albouy A, Kaloshin V. 2012. Finiteness of central configurations of five bodies
in the plane. Annals of Mathematics. 176(1), 535–588.
mla: Albouy, Alain, and Vadim Kaloshin. “Finiteness of Central Configurations of
Five Bodies in the Plane.” Annals of Mathematics, vol. 176, no. 1, Princeton
University Press, 2012, pp. 535–88, doi:10.4007/annals.2012.176.1.10.
short: A. Albouy, V. Kaloshin, Annals of Mathematics 176 (2012) 535–588.
date_created: 2020-09-18T10:47:24Z
date_published: 2012-07-01T00:00:00Z
date_updated: 2021-01-12T08:19:44Z
day: '01'
doi: 10.4007/annals.2012.176.1.10
extern: '1'
intvolume: ' 176'
issue: '1'
language:
- iso: eng
month: '07'
oa_version: None
page: 535-588
publication: Annals of Mathematics
publication_identifier:
issn:
- 0003-486X
publication_status: published
publisher: Princeton University Press
quality_controlled: '1'
status: public
title: Finiteness of central configurations of five bodies in the plane
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 176
year: '2012'
...
---
_id: '8504'
abstract:
- lang: eng
text: In this paper we present a surprising example of a Cr unimodal map of an interval
f:I→I whose number of periodic points Pn(f)=∣{x∈I:fnx=x}∣ grows faster than any
ahead given sequence along a subsequence nk=3k. This example also shows that ‘non-flatness’
of critical points is necessary for the Martens–de Melo–van Strien theorem [M.
Martens, W. de Melo and S. van Strien. Julia–Fatou–Sullivan theory for real one-dimensional
dynamics. Acta Math.168(3–4) (1992), 273–318] to hold.
article_processing_charge: No
article_type: original
author:
- first_name: Vadim
full_name: Kaloshin, Vadim
id: FE553552-CDE8-11E9-B324-C0EBE5697425
last_name: Kaloshin
orcid: 0000-0002-6051-2628
- first_name: O. S.
full_name: KOZLOVSKI, O. S.
last_name: KOZLOVSKI
citation:
ama: Kaloshin V, KOZLOVSKI OS. A Cr unimodal map with an arbitrary fast growth of
the number of periodic points. Ergodic Theory and Dynamical Systems. 2012;32(1):159-165.
doi:10.1017/s0143385710000817
apa: Kaloshin, V., & KOZLOVSKI, O. S. (2012). A Cr unimodal map with an arbitrary
fast growth of the number of periodic points. Ergodic Theory and Dynamical
Systems. Cambridge University Press. https://doi.org/10.1017/s0143385710000817
chicago: Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary
Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical
Systems. Cambridge University Press, 2012. https://doi.org/10.1017/s0143385710000817.
ieee: V. Kaloshin and O. S. KOZLOVSKI, “A Cr unimodal map with an arbitrary fast
growth of the number of periodic points,” Ergodic Theory and Dynamical Systems,
vol. 32, no. 1. Cambridge University Press, pp. 159–165, 2012.
ista: Kaloshin V, KOZLOVSKI OS. 2012. A Cr unimodal map with an arbitrary fast growth
of the number of periodic points. Ergodic Theory and Dynamical Systems. 32(1),
159–165.
mla: Kaloshin, Vadim, and O. S. KOZLOVSKI. “A Cr Unimodal Map with an Arbitrary
Fast Growth of the Number of Periodic Points.” Ergodic Theory and Dynamical
Systems, vol. 32, no. 1, Cambridge University Press, 2012, pp. 159–65, doi:10.1017/s0143385710000817.
short: V. Kaloshin, O.S. KOZLOVSKI, Ergodic Theory and Dynamical Systems 32 (2012)
159–165.
date_created: 2020-09-18T10:47:33Z
date_published: 2012-02-01T00:00:00Z
date_updated: 2021-01-12T08:19:44Z
day: '01'
doi: 10.1017/s0143385710000817
extern: '1'
intvolume: ' 32'
issue: '1'
keyword:
- Applied Mathematics
- General Mathematics
language:
- iso: eng
month: '02'
oa_version: None
page: 159-165
publication: Ergodic Theory and Dynamical Systems
publication_identifier:
issn:
- 0143-3857
- 1469-4417
publication_status: published
publisher: Cambridge University Press
quality_controlled: '1'
status: public
title: A Cr unimodal map with an arbitrary fast growth of the number of periodic points
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 32
year: '2012'
...
---
_id: '858'
abstract:
- lang: eng
text: 'ackground: The evolution and genomic stop codon frequencies have not been
rigorously studied with the exception of coding of non-canonical amino acids.
Here we study the rate of evolution and frequency distribution of stop codons
in bacterial genomes.Results: We show that in bacteria stop codons evolve slower
than synonymous sites, suggesting the action of weak negative selection. However,
the frequency of stop codons relative to genomic nucleotide content indicated
that this selection regime is not straightforward. The frequency of TAA and TGA
stop codons is GC-content dependent, with TAA decreasing and TGA increasing with
GC-content, while TAG frequency is independent of GC-content. Applying a formal,
analytical model to these data we found that the relationship between stop codon
frequencies and nucleotide content cannot be explained by mutational biases or
selection on nucleotide content. However, with weak nucleotide content-dependent
selection on TAG, -0.5 < Nes < 1.5, the model fits all of the data and recapitulates
the relationship between TAG and nucleotide content. For biologically plausible
rates of mutations we show that, in bacteria, TAG stop codon is universally associated
with lower fitness, with TAA being the optimal for G-content < 16% while for G-content
> 16% TGA has a higher fitness than TAG.Conclusions: Our data indicate that TAG
codon is universally suboptimal in the bacterial lineage, such that TAA is likely
to be the preferred stop codon for low GC content while the TGA is the preferred
stop codon for high GC content. The optimization of stop codon usage may therefore
be useful in genome engineering or gene expression optimization applications.Reviewers:
This article was reviewed by Michail Gelfand, Arcady Mushegian and Shamil Sunyaev.
For the full reviews, please go to the Reviewers'' Comments section.'
acknowledgement: |
We thank Elena Alkalaeva and Peter Kolosov for insightful discussion and Brian Charlesworth for a critical reading of our manuscript. The work has been supported by a Plan Nacional grant from the Spanish Ministry of Science and Innovation, EMBO Young Investigator and Howard Hughes Medical Institute International Early Career Scientist awards.
author:
- first_name: Inna
full_name: Povolotskaya, Inna
last_name: Povolotskaya
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
- first_name: Alice
full_name: Ledda, Alice
last_name: Ledda
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
citation:
ama: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. Stop codons in bacteria are
not selectively equivalent. Biology Direct. 2012;7. doi:10.1186/1745-6150-7-30
apa: Povolotskaya, I., Kondrashov, F., Ledda, A., & Vlasov, P. (2012). Stop
codons in bacteria are not selectively equivalent. Biology Direct. BioMed
Central. https://doi.org/10.1186/1745-6150-7-30
chicago: Povolotskaya, Inna, Fyodor Kondrashov, Alice Ledda, and Peter Vlasov. “Stop
Codons in Bacteria Are Not Selectively Equivalent.” Biology Direct. BioMed
Central, 2012. https://doi.org/10.1186/1745-6150-7-30.
ieee: I. Povolotskaya, F. Kondrashov, A. Ledda, and P. Vlasov, “Stop codons in bacteria
are not selectively equivalent,” Biology Direct, vol. 7. BioMed Central,
2012.
ista: Povolotskaya I, Kondrashov F, Ledda A, Vlasov P. 2012. Stop codons in bacteria
are not selectively equivalent. Biology Direct. 7.
mla: Povolotskaya, Inna, et al. “Stop Codons in Bacteria Are Not Selectively Equivalent.”
Biology Direct, vol. 7, BioMed Central, 2012, doi:10.1186/1745-6150-7-30.
short: I. Povolotskaya, F. Kondrashov, A. Ledda, P. Vlasov, Biology Direct 7 (2012).
date_created: 2018-12-11T11:48:52Z
date_published: 2012-09-01T00:00:00Z
date_updated: 2021-01-12T08:20:08Z
day: '01'
doi: 10.1186/1745-6150-7-30
extern: 1
intvolume: ' 7'
month: '09'
publication: Biology Direct
publication_status: published
publisher: BioMed Central
publist_id: '6792'
quality_controlled: 0
status: public
title: Stop codons in bacteria are not selectively equivalent
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 7
year: '2012'
...
---
_id: '887'
abstract:
- lang: eng
text: A subject of extensive study in evolutionary theory has been the issue of
how neutral, redundant copies can be maintained in the genome for long periods
of time. Concurrently, examples of adaptive gene duplications to various environmental
conditions in different species have been described. At this point, it is too
early to tell whether or not a substantial fraction of gene copies have initially
achieved fixation by positive selection for increased dosage. Nevertheless, enough
examples have accumulated in the literature that such a possibility should be
considered. Here, I review the recent examples of adaptive gene duplications and
make an attempt to draw generalizations on what types of genes may be particularly
prone to be selected for under certain environmental conditions. The identification
of copy-number variation in ecological field studies of species adapting to stressful
or novel environmental conditions may improve our understanding of gene duplications
as a mechanism of adaptation and its relevance to the long-term persistence of
gene duplications.
acknowledgement: The work was supported by a Plan Nacional grant no. BFU2009-09271
from the Spanish Ministry of Science and Innovation. The author is a European Molecular
Biology Organization Young Investigator and Howard Hughes Medical Institute International
Early Career Scientist.
author:
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Kondrashov F. Gene duplication as a mechanism of genomic adaptation to a changing
environment. Proceedings of the Royal Society of London Series B Biological
Sciences. 2012;279(1749):5048-5057. doi:10.1098/rspb.2012.1108
apa: Kondrashov, F. (2012). Gene duplication as a mechanism of genomic adaptation
to a changing environment. Proceedings of the Royal Society of London Series
B Biological Sciences. Royal Society, The. https://doi.org/10.1098/rspb.2012.1108
chicago: Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation
to a Changing Environment.” Proceedings of the Royal Society of London Series
B Biological Sciences. Royal Society, The, 2012. https://doi.org/10.1098/rspb.2012.1108.
ieee: F. Kondrashov, “Gene duplication as a mechanism of genomic adaptation to a
changing environment,” Proceedings of the Royal Society of London Series B
Biological Sciences, vol. 279, no. 1749. Royal Society, The, pp. 5048–5057,
2012.
ista: Kondrashov F. 2012. Gene duplication as a mechanism of genomic adaptation
to a changing environment. Proceedings of the Royal Society of London Series B
Biological Sciences. 279(1749), 5048–5057.
mla: Kondrashov, Fyodor. “Gene Duplication as a Mechanism of Genomic Adaptation
to a Changing Environment.” Proceedings of the Royal Society of London Series
B Biological Sciences, vol. 279, no. 1749, Royal Society, The, 2012, pp. 5048–57,
doi:10.1098/rspb.2012.1108.
short: F. Kondrashov, Proceedings of the Royal Society of London Series B Biological
Sciences 279 (2012) 5048–5057.
date_created: 2018-12-11T11:49:01Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:21:16Z
day: '01'
doi: 10.1098/rspb.2012.1108
extern: 1
intvolume: ' 279'
issue: '1749'
month: '01'
page: 5048 - 5057
publication: Proceedings of the Royal Society of London Series B Biological Sciences
publication_status: published
publisher: Royal Society, The
publist_id: '6765'
quality_controlled: 0
status: public
title: Gene duplication as a mechanism of genomic adaptation to a changing environment
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
volume: 279
year: '2012'
...
---
_id: '900'
abstract:
- lang: eng
text: 'The main forces directing long-term molecular evolution remain obscure. A
sizable fraction of amino-acid substitutions seem to be fixed by positive selection,
but it is unclear to what degree long-term protein evolution is constrained by
epistasis, that is, instances when substitutions that are accepted in one genotype
are deleterious in another. Here we obtain a quantitative estimate of the prevalence
of epistasis in long-term protein evolution by relating data on amino-acid usage
in 14 organelle proteins and 2 nuclear-encoded proteins to their rates of short-term
evolution. We studied multiple alignments of at least 1,000 orthologues for each
of these 16 proteins from species from a diverse phylogenetic background and found
that an average site contained approximately eight different amino acids. Thus,
without epistasis an average site should accept two-fifths of all possible amino
acids, and the average rate of amino-acid substitutions should therefore be about
three-fifths lower than the rate of neutral evolution. However, we found that
the measured rate of amino-acid substitution in recent evolution is 20 times lower
than the rate of neutral evolution and an order of magnitude lower than that expected
in the absence of epistasis. These data indicate that epistasis is pervasive throughout
protein evolution: about 90 per cent of all amino-acid substitutions have a neutral
or beneficial impact only in the genetic backgrounds in which they occur, and
must therefore be deleterious in a different background of other species. Our
findings show that most amino-acid substitutions have different fitness effects
in different species and that epistasis provides the primary conceptual framework
to describe the tempo and mode of long-term protein evolution.'
acknowledgement: |
The work was supported by Plan Nacional grants from the Spanish Ministry of Science and Innovation, to F.A.K. and C.N. C.K. was supported by the European Union FP7 project Quantomics (KBBE2A222664). F.A.K. is a European Molecular Biology Organization Young Investigator and Howard Hughes Medical Institute International Early Career Scientist. We thank B. Lehner and T. Warnecke for input and a critical reading of the manuscript.
author:
- first_name: Michael
full_name: Breen, Michael S
last_name: Breen
- first_name: Carsten
full_name: Kemena, Carsten
last_name: Kemena
- first_name: Peter
full_name: Vlasov, Peter K
last_name: Vlasov
- first_name: Cédric
full_name: Notredame, Cédric
last_name: Notredame
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. Epistasis as the primary
factor in molecular evolution. Nature. 2012;490(7421):535-538. doi:10.1038/nature11510
apa: Breen, M., Kemena, C., Vlasov, P., Notredame, C., & Kondrashov, F. (2012).
Epistasis as the primary factor in molecular evolution. Nature. Nature
Publishing Group. https://doi.org/10.1038/nature11510
chicago: Breen, Michael, Carsten Kemena, Peter Vlasov, Cédric Notredame, and Fyodor
Kondrashov. “Epistasis as the Primary Factor in Molecular Evolution.” Nature.
Nature Publishing Group, 2012. https://doi.org/10.1038/nature11510.
ieee: M. Breen, C. Kemena, P. Vlasov, C. Notredame, and F. Kondrashov, “Epistasis
as the primary factor in molecular evolution,” Nature, vol. 490, no. 7421.
Nature Publishing Group, pp. 535–538, 2012.
ista: Breen M, Kemena C, Vlasov P, Notredame C, Kondrashov F. 2012. Epistasis as
the primary factor in molecular evolution. Nature. 490(7421), 535–538.
mla: Breen, Michael, et al. “Epistasis as the Primary Factor in Molecular Evolution.”
Nature, vol. 490, no. 7421, Nature Publishing Group, 2012, pp. 535–38,
doi:10.1038/nature11510.
short: M. Breen, C. Kemena, P. Vlasov, C. Notredame, F. Kondrashov, Nature 490 (2012)
535–538.
date_created: 2018-12-11T11:49:06Z
date_published: 2012-10-25T00:00:00Z
date_updated: 2021-01-12T08:21:45Z
day: '25'
doi: 10.1038/nature11510
extern: 1
intvolume: ' 490'
issue: '7421'
month: '10'
page: 535 - 538
publication: Nature
publication_status: published
publisher: Nature Publishing Group
publist_id: '6748'
quality_controlled: 0
status: public
title: Epistasis as the primary factor in molecular evolution
type: journal_article
volume: 490
year: '2012'
...
---
_id: '171'
abstract:
- lang: eng
text: For given non-zero integers a, b, q we investigate the density of solutions
(x, y) ∈ ℤ2 to the binary cubic congruence ax2 + by3 ≡ 0 mod q, and use it to
establish the Manin conjecture for a singular del Pezzo surface of degree 2 defined
over ℚ.
author:
- first_name: Timothy D
full_name: Timothy Browning
id: 35827D50-F248-11E8-B48F-1D18A9856A87
last_name: Browning
orcid: 0000-0002-8314-0177
- first_name: Stephan
full_name: Baier, Stephan
last_name: Baier
citation:
ama: Browning TD, Baier S. Inhomogeneous cubic congruences and rational points on
del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2012;2013(680):1-65.
doi:https://doi.org/10.1515/crelle.2012.039
apa: Browning, T. D., & Baier, S. (2012). Inhomogeneous cubic congruences and
rational points on del Pezzo surfaces. Journal Fur Die Reine Und Angewandte
Mathematik. Walter de Gruyter. https://doi.org/10.1515/crelle.2012.039
chicago: Browning, Timothy D, and Stephan Baier. “Inhomogeneous Cubic Congruences
and Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte
Mathematik. Walter de Gruyter, 2012. https://doi.org/10.1515/crelle.2012.039.
ieee: T. D. Browning and S. Baier, “Inhomogeneous cubic congruences and rational
points on del Pezzo surfaces,” Journal fur die Reine und Angewandte Mathematik,
vol. 2013, no. 680. Walter de Gruyter, pp. 1–65, 2012.
ista: Browning TD, Baier S. 2012. Inhomogeneous cubic congruences and rational points
on del Pezzo surfaces. Journal fur die Reine und Angewandte Mathematik. 2013(680),
1–65.
mla: Browning, Timothy D., and Stephan Baier. “Inhomogeneous Cubic Congruences and
Rational Points on Del Pezzo Surfaces.” Journal Fur Die Reine Und Angewandte
Mathematik, vol. 2013, no. 680, Walter de Gruyter, 2012, pp. 1–65, doi:https://doi.org/10.1515/crelle.2012.039.
short: T.D. Browning, S. Baier, Journal Fur Die Reine Und Angewandte Mathematik
2013 (2012) 1–65.
date_created: 2018-12-11T11:45:00Z
date_published: 2012-04-03T00:00:00Z
date_updated: 2021-01-12T06:52:41Z
day: '03'
doi: https://doi.org/10.1515/crelle.2012.039
extern: 1
intvolume: ' 2013'
issue: '680'
main_file_link:
- open_access: '1'
url: https://arxiv.org/abs/1011.3434
month: '04'
oa: 1
page: 1 - 65
publication: Journal fur die Reine und Angewandte Mathematik
publication_status: published
publisher: Walter de Gruyter
publist_id: '7750'
quality_controlled: 0
status: public
title: Inhomogeneous cubic congruences and rational points on del Pezzo surfaces
type: journal_article
volume: 2013
year: '2012'
...
---
_id: '1725'
abstract:
- lang: eng
text: The spatial organization of cell fates during development involves the interpretation
of morphogen gradients by cellular signaling cascades and transcriptional networks.
Recent studies use biophysical models, genetics, and quantitative imaging to unravel
how tissue-level morphogen behavior arises from subcellular events. Moreover,
data from several systems show that morphogen gradients, downstream signaling,
and the activity of cell-intrinsic transcriptional networks change dynamically
during pattern formation. Studies from Drosophila and now also vertebrates suggest
that transcriptional network dynamics are central to the generation of gene expression
patterns. Together, this leads to the view that pattern formation is an emergent
behavior that results from the coordination of events occurring across molecular,
cellular, and tissue scales. The development of novel approaches to study this
complex process remains a challenge.
acknowledgement: 'Funding provided by the Medical Research Council (UK). '
author:
- first_name: Anna
full_name: Anna Kicheva
id: 3959A2A0-F248-11E8-B48F-1D18A9856A87
last_name: Kicheva
orcid: 0000-0003-4509-4998
- first_name: Michael
full_name: Cohen, Michael H
last_name: Cohen
- first_name: James
full_name: Briscoe, James
last_name: Briscoe
citation:
ama: 'Kicheva A, Cohen M, Briscoe J. Developmental pattern formation: Insights from
physics and biology. Science. 2012;338(6104):210-212. doi:10.1126/science.1225182'
apa: 'Kicheva, A., Cohen, M., & Briscoe, J. (2012). Developmental pattern formation:
Insights from physics and biology. Science. American Association for the
Advancement of Science. https://doi.org/10.1126/science.1225182'
chicago: 'Kicheva, Anna, Michael Cohen, and James Briscoe. “Developmental Pattern
Formation: Insights from Physics and Biology.” Science. American Association
for the Advancement of Science, 2012. https://doi.org/10.1126/science.1225182.'
ieee: 'A. Kicheva, M. Cohen, and J. Briscoe, “Developmental pattern formation: Insights
from physics and biology,” Science, vol. 338, no. 6104. American Association
for the Advancement of Science, pp. 210–212, 2012.'
ista: 'Kicheva A, Cohen M, Briscoe J. 2012. Developmental pattern formation: Insights
from physics and biology. Science. 338(6104), 210–212.'
mla: 'Kicheva, Anna, et al. “Developmental Pattern Formation: Insights from Physics
and Biology.” Science, vol. 338, no. 6104, American Association for the
Advancement of Science, 2012, pp. 210–12, doi:10.1126/science.1225182.'
short: A. Kicheva, M. Cohen, J. Briscoe, Science 338 (2012) 210–212.
date_created: 2018-12-11T11:53:40Z
date_published: 2012-10-12T00:00:00Z
date_updated: 2021-01-12T06:52:47Z
day: '12'
doi: 10.1126/science.1225182
extern: 1
intvolume: ' 338'
issue: '6104'
month: '10'
page: 210 - 212
publication: Science
publication_status: published
publisher: American Association for the Advancement of Science
publist_id: '5404'
quality_controlled: 0
status: public
title: 'Developmental pattern formation: Insights from physics and biology'
type: journal_article
volume: 338
year: '2012'
...
---
_id: '1756'
abstract:
- lang: eng
text: We report on the electronic transport properties of multiple-gate devices
fabricated from undoped silicon nanowires. Understanding and control of the relevant
transport mechanisms was achieved by means of local electrostatic gating and temperature-dependent
measurements. The roles of the source/drain contacts and of the silicon channel
could be independently evaluated and tuned. Wrap gates surrounding the silicide-silicon
contact interfaces were proved to be effective in inducing a full suppression
of the contact Schottky barriers, thereby enabling carrier injection down to liquid
helium temperature. By independently tuning the effective Schottky barrier heights,
a variety of reconfigurable device functionalities could be obtained. In particular,
the same nanowire device could be configured to work as a Schottky barrier transistor,
a Schottky diode, or a p-n diode with tunable polarities. This versatility was
eventually exploited to realize a NAND logic gate with gain well above one.
acknowledgement: This work was supported by the Agence Nationale de la Recherche (ANR)
through the ACCESS and COHESION projects and by the European Commission through
the Chemtronics program MEST-CT-2005-020513
author:
- first_name: Massimo
full_name: Mongillo, Massimo
last_name: Mongillo
- first_name: Panayotis
full_name: Spathis, Panayotis N
last_name: Spathis
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Pascal
full_name: Gentile, Pascal
last_name: Gentile
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
citation:
ama: Mongillo M, Spathis P, Katsaros G, Gentile P, De Franceschi S. Multifunctional
devices and logic gates with undoped silicon nanowires. Nano Letters. 2012;12(6):3074-3079.
doi:10.1021/nl300930m
apa: Mongillo, M., Spathis, P., Katsaros, G., Gentile, P., & De Franceschi,
S. (2012). Multifunctional devices and logic gates with undoped silicon nanowires.
Nano Letters. American Chemical Society. https://doi.org/10.1021/nl300930m
chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Pascal Gentile,
and Silvano De Franceschi. “Multifunctional Devices and Logic Gates with Undoped
Silicon Nanowires.” Nano Letters. American Chemical Society, 2012. https://doi.org/10.1021/nl300930m.
ieee: M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, and S. De Franceschi, “Multifunctional
devices and logic gates with undoped silicon nanowires,” Nano Letters,
vol. 12, no. 6. American Chemical Society, pp. 3074–3079, 2012.
ista: Mongillo M, Spathis P, Katsaros G, Gentile P, De Franceschi S. 2012. Multifunctional
devices and logic gates with undoped silicon nanowires. Nano Letters. 12(6), 3074–3079.
mla: Mongillo, Massimo, et al. “Multifunctional Devices and Logic Gates with Undoped
Silicon Nanowires.” Nano Letters, vol. 12, no. 6, American Chemical Society,
2012, pp. 3074–79, doi:10.1021/nl300930m.
short: M. Mongillo, P. Spathis, G. Katsaros, P. Gentile, S. De Franceschi, Nano
Letters 12 (2012) 3074–3079.
date_created: 2018-12-11T11:53:50Z
date_published: 2012-06-13T00:00:00Z
date_updated: 2021-01-12T06:53:00Z
day: '13'
doi: 10.1021/nl300930m
extern: 1
intvolume: ' 12'
issue: '6'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1208.1465
month: '06'
oa: 1
page: 3074 - 3079
publication: Nano Letters
publication_status: published
publisher: American Chemical Society
publist_id: '5368'
quality_controlled: 0
status: public
title: Multifunctional devices and logic gates with undoped silicon nanowires
type: journal_article
volume: 12
year: '2012'
...
---
_id: '1757'
abstract:
- lang: eng
text: Self-assembled Ge wires with a height of only 3 unit cells and a length of
up to 2 micrometers were grown on Si(001) by means of a catalyst-free method based
on molecular beam epitaxy. The wires grow horizontally along either the [100]
or the [010] direction. On atomically flat surfaces, they exhibit a highly uniform,
triangular cross section. A simple thermodynamic model accounts for the existence
of a preferential base width for longitudinal expansion, in quantitative agreement
with the experimental findings. Despite the absence of intentional doping, the
first transistor-type devices made from single wires show low-resistive electrical
contacts and single-hole transport at sub-Kelvin temperatures. In view of their
exceptionally small and self-defined cross section, these Ge wires hold promise
for the realization of hole systems with exotic properties and provide a new development
route for silicon-based nanoelectronics.
acknowledgement: We acknowledge the financial support by the DFG SPP1386, P. Chen
and D. J. Thurmer for MBE assistance, R. Wacquez for providing the ultrathin SOI
wafers, and G. Bauer, Y. Hu, X. Jehl, S. Kiravittaya, C. Klöffel, E. J. H. Lee,
F. Liu, D. Loss, and S. Mahapatra for helpful discussions. G. K. acknowledges support
from the European commission via a Marie Curie Carrer Integration Grant. S. D. F.
acknowledges support from the European Research Council through the starting grant
program
author:
- first_name: Jianjun
full_name: Zhang, Jianjun
last_name: Zhang
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Francesco
full_name: Montalenti, Francesco
last_name: Montalenti
- first_name: Daniele
full_name: Scopece, Daniele
last_name: Scopece
- first_name: Roman
full_name: Rezaev, Roman O
last_name: Rezaev
- first_name: Christine
full_name: Mickel, Christine H
last_name: Mickel
- first_name: Bernd
full_name: Rellinghaus, Bernd
last_name: Rellinghaus
- first_name: Leo
full_name: Miglio, Leo P
last_name: Miglio
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
- first_name: Armando
full_name: Rastelli, Armando
last_name: Rastelli
- first_name: Oliver
full_name: Schmidt, Oliver G
last_name: Schmidt
citation:
ama: Zhang J, Katsaros G, Montalenti F, et al. Monolithic growth of ultrathin Ge
nanowires on Si(001) . Physical Review Letters. 2012;109(8). doi:10.1103/PhysRevLett.109.085502
apa: Zhang, J., Katsaros, G., Montalenti, F., Scopece, D., Rezaev, R., Mickel, C.,
… Schmidt, O. (2012). Monolithic growth of ultrathin Ge nanowires on Si(001) .
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.085502
chicago: Zhang, Jianjun, Georgios Katsaros, Francesco Montalenti, Daniele Scopece,
Roman Rezaev, Christine Mickel, Bernd Rellinghaus, et al. “Monolithic Growth of
Ultrathin Ge Nanowires on Si(001) .” Physical Review Letters. American
Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.085502.
ieee: J. Zhang et al., “Monolithic growth of ultrathin Ge nanowires on Si(001)
,” Physical Review Letters, vol. 109, no. 8. American Physical Society,
2012.
ista: Zhang J, Katsaros G, Montalenti F, Scopece D, Rezaev R, Mickel C, Rellinghaus
B, Miglio L, De Franceschi S, Rastelli A, Schmidt O. 2012. Monolithic growth of
ultrathin Ge nanowires on Si(001) . Physical Review Letters. 109(8).
mla: Zhang, Jianjun, et al. “Monolithic Growth of Ultrathin Ge Nanowires on Si(001)
.” Physical Review Letters, vol. 109, no. 8, American Physical Society,
2012, doi:10.1103/PhysRevLett.109.085502.
short: J. Zhang, G. Katsaros, F. Montalenti, D. Scopece, R. Rezaev, C. Mickel, B.
Rellinghaus, L. Miglio, S. De Franceschi, A. Rastelli, O. Schmidt, Physical Review
Letters 109 (2012).
date_created: 2018-12-11T11:53:51Z
date_published: 2012-08-23T00:00:00Z
date_updated: 2021-01-12T06:53:00Z
day: '23'
doi: 10.1103/PhysRevLett.109.085502
extern: 1
intvolume: ' 109'
issue: '8'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1208.0666
month: '08'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5367'
quality_controlled: 0
status: public
title: 'Monolithic growth of ultrathin Ge nanowires on Si(001) '
type: journal_article
volume: 109
year: '2012'
...
---
_id: '1758'
abstract:
- lang: eng
text: We studied the low-energy states of spin-1/2 quantum dots defined in InAs/InP
nanowires and coupled to aluminum superconducting leads. By varying the superconducting
gap Δ with a magnetic field B we investigated the transition from strong coupling
Δ≪T K to weak-coupling Δ≫T K, where T K is the Kondo temperature. Below the critical
field, we observe a persisting zero-bias Kondo resonance that vanishes only for
low B or higher temperatures, leaving the room to more robust subgap structures
at bias voltages between Δ and 2Δ. For strong and approximately symmetric tunnel
couplings, a Josephson supercurrent is observed in addition to the Kondo peak.
We ascribe the coexistence of a Kondo resonance and a superconducting gap to a
significant density of intragap quasiparticle states, and the finite-bias subgap
structures to tunneling through Shiba states. Our results, supported by numerical
calculations, own relevance also in relation to tunnel-spectroscopy experiments
aiming at the observation of Majorana fermions in hybrid nanostructures.
acknowledgement: This work was supported by the EU Marie Curie program and by the
Agence Nationale de la Recherche. R. A. acknowledges support from the Spanish Ministry
of Science and Innovation through Grant No. FIS2009-08744
author:
- first_name: Eduardo
full_name: Lee, Eduardo J
last_name: Lee
- first_name: Xiaocheng
full_name: Jiang, Xiaocheng
last_name: Jiang
- first_name: Ramón
full_name: Aguado, Ramón
last_name: Aguado
- first_name: Georgios
full_name: Georgios Katsaros
id: 38DB5788-F248-11E8-B48F-1D18A9856A87
last_name: Katsaros
- first_name: Charles
full_name: Lieber, Charles M
last_name: Lieber
- first_name: Silvano
full_name: De Franceschi, Silvano
last_name: De Franceschi
citation:
ama: Lee E, Jiang X, Aguado R, Katsaros G, Lieber C, De Franceschi S. Zero-bias
anomaly in a nanowire quantum dot coupled to superconductors. Physical Review
Letters. 2012;109(18). doi:10.1103/PhysRevLett.109.186802
apa: Lee, E., Jiang, X., Aguado, R., Katsaros, G., Lieber, C., & De Franceschi,
S. (2012). Zero-bias anomaly in a nanowire quantum dot coupled to superconductors.
Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.109.186802
chicago: Lee, Eduardo, Xiaocheng Jiang, Ramón Aguado, Georgios Katsaros, Charles
Lieber, and Silvano De Franceschi. “Zero-Bias Anomaly in a Nanowire Quantum Dot
Coupled to Superconductors.” Physical Review Letters. American Physical
Society, 2012. https://doi.org/10.1103/PhysRevLett.109.186802.
ieee: E. Lee, X. Jiang, R. Aguado, G. Katsaros, C. Lieber, and S. De Franceschi,
“Zero-bias anomaly in a nanowire quantum dot coupled to superconductors,” Physical
Review Letters, vol. 109, no. 18. American Physical Society, 2012.
ista: Lee E, Jiang X, Aguado R, Katsaros G, Lieber C, De Franceschi S. 2012. Zero-bias
anomaly in a nanowire quantum dot coupled to superconductors. Physical Review
Letters. 109(18).
mla: Lee, Eduardo, et al. “Zero-Bias Anomaly in a Nanowire Quantum Dot Coupled to
Superconductors.” Physical Review Letters, vol. 109, no. 18, American Physical
Society, 2012, doi:10.1103/PhysRevLett.109.186802.
short: E. Lee, X. Jiang, R. Aguado, G. Katsaros, C. Lieber, S. De Franceschi, Physical
Review Letters 109 (2012).
date_created: 2018-12-11T11:53:51Z
date_published: 2012-10-31T00:00:00Z
date_updated: 2021-01-12T06:53:01Z
day: '31'
doi: 10.1103/PhysRevLett.109.186802
extern: 1
intvolume: ' 109'
issue: '18'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1207.1259
month: '10'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5366'
quality_controlled: 0
status: public
title: Zero-bias anomaly in a nanowire quantum dot coupled to superconductors
type: journal_article
volume: 109
year: '2012'
...
---
_id: '1782'
abstract:
- lang: eng
text: Steering a quantum harmonic oscillator state along cyclic trajectories leads
to a path-dependent geometric phase. Here we describe its experimental observation
in an electronic harmonic oscillator. We use a superconducting qubit as a nonlinear
probe of the phase, which is otherwise unobservable due to the linearity of the
oscillator. We show that the geometric phase is, for a variety of cyclic paths,
proportional to the area enclosed in the quadrature plane. At the transition to
the nonadiabatic regime, we study corrections to the phase and dephasing of the
qubit caused by qubit-resonator entanglement. In particular, we identify parameters
for which this dephasing mechanism is negligible even in the nonadiabatic regime.
The demonstrated controllability makes our system a versatile tool to study geometric
phases in open quantum systems and to investigate their potential for quantum
information processing.
acknowledgement: This work is supported by the EU project GEOMDISS, the Austrian Science
Foundation (S. F.), and the Swiss National Science Foundation (SNSF)
author:
- first_name: M
full_name: Pechal, M
last_name: Pechal
- first_name: Stefan
full_name: Berger, Stefan T
last_name: Berger
- first_name: Abdufarrukh
full_name: Abdumalikov, Abdufarrukh A
last_name: Abdumalikov
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: Jonas
full_name: Mlynek, Jonas A
last_name: Mlynek
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
citation:
ama: Pechal M, Berger S, Abdumalikov A, et al. Geometric phase and nonadiabatic
effects in an electronic harmonic oscillator. Physical Review Letters.
2012;108(17). doi:10.1103/PhysRevLett.108.170401
apa: Pechal, M., Berger, S., Abdumalikov, A., Fink, J. M., Mlynek, J., Steffen,
L., … Filipp, S. (2012). Geometric phase and nonadiabatic effects in an electronic
harmonic oscillator. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.108.170401
chicago: Pechal, M, Stefan Berger, Abdufarrukh Abdumalikov, Johannes M Fink, Jonas
Mlynek, L. Steffen, Andreas Wallraff, and Stefan Filipp. “Geometric Phase and
Nonadiabatic Effects in an Electronic Harmonic Oscillator.” Physical Review
Letters. American Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.108.170401.
ieee: M. Pechal et al., “Geometric phase and nonadiabatic effects in an electronic
harmonic oscillator,” Physical Review Letters, vol. 108, no. 17. American
Physical Society, 2012.
ista: Pechal M, Berger S, Abdumalikov A, Fink JM, Mlynek J, Steffen L, Wallraff
A, Filipp S. 2012. Geometric phase and nonadiabatic effects in an electronic harmonic
oscillator. Physical Review Letters. 108(17).
mla: Pechal, M., et al. “Geometric Phase and Nonadiabatic Effects in an Electronic
Harmonic Oscillator.” Physical Review Letters, vol. 108, no. 17, American
Physical Society, 2012, doi:10.1103/PhysRevLett.108.170401.
short: M. Pechal, S. Berger, A. Abdumalikov, J.M. Fink, J. Mlynek, L. Steffen, A.
Wallraff, S. Filipp, Physical Review Letters 108 (2012).
date_created: 2018-12-11T11:53:59Z
date_published: 2012-04-23T00:00:00Z
date_updated: 2021-01-12T06:53:10Z
day: '23'
doi: 10.1103/PhysRevLett.108.170401
extern: 1
intvolume: ' 108'
issue: '17'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1109.1157
month: '04'
oa: 1
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5333'
quality_controlled: 0
status: public
title: Geometric phase and nonadiabatic effects in an electronic harmonic oscillator
type: journal_article
volume: 108
year: '2012'
...
---
_id: '1783'
abstract:
- lang: eng
text: Nonlinearity and entanglement are two important properties by which physical
systems can be identified as nonclassical. We study the dynamics of the resonant
interaction of up to N=3 two-level systems and a single mode of the electromagnetic
field sharing a single excitation dynamically. We observe coherent vacuum Rabi
oscillations and their nonlinear √N speedup by tracking the populations of all
qubits and the resonator in time. We use quantum state tomography to show explicitly
that the dynamics generates maximally entangled states of the W class in a time
limited only by the collective interaction rate. We use an entanglement witness
and the 3-tangle to characterize the state whose fidelity F=78% is limited in
our experiments by crosstalk arising during the simultaneous qubit manipulations
which is absent in a sequential approach with F=91%.
acknowledgement: This work was supported by the Swiss National Science Foundation
(SNF) and the EU IP SOLID
author:
- first_name: Jonas
full_name: Mlynek, Jonas A
last_name: Mlynek
- first_name: Abdufarrukh
full_name: Abdumalikov, Abdufarrukh A
last_name: Abdumalikov
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: L.
full_name: Steffen, L. Kraig
last_name: Steffen
- first_name: Matthias
full_name: Baur, Matthias P
last_name: Baur
- first_name: C
full_name: Lang, C
last_name: Lang
- first_name: Arjan
full_name: Van Loo, Arjan F
last_name: Van Loo
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Mlynek J, Abdumalikov A, Fink JM, et al. Demonstrating W-type entanglement
of Dicke states in resonant cavity quantum electrodynamics. Physical Review
A - Atomic, Molecular, and Optical Physics. 2012;86(5). doi:10.1103/PhysRevA.86.053838
apa: Mlynek, J., Abdumalikov, A., Fink, J. M., Steffen, L., Baur, M., Lang, C.,
… Wallraff, A. (2012). Demonstrating W-type entanglement of Dicke states in resonant
cavity quantum electrodynamics. Physical Review A - Atomic, Molecular, and
Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.86.053838
chicago: Mlynek, Jonas, Abdufarrukh Abdumalikov, Johannes M Fink, L. Steffen, Matthias
Baur, C Lang, Arjan Van Loo, and Andreas Wallraff. “Demonstrating W-Type Entanglement
of Dicke States in Resonant Cavity Quantum Electrodynamics.” Physical Review
A - Atomic, Molecular, and Optical Physics. American Physical Society, 2012.
https://doi.org/10.1103/PhysRevA.86.053838.
ieee: J. Mlynek et al., “Demonstrating W-type entanglement of Dicke states
in resonant cavity quantum electrodynamics,” Physical Review A - Atomic, Molecular,
and Optical Physics, vol. 86, no. 5. American Physical Society, 2012.
ista: Mlynek J, Abdumalikov A, Fink JM, Steffen L, Baur M, Lang C, Van Loo A, Wallraff
A. 2012. Demonstrating W-type entanglement of Dicke states in resonant cavity
quantum electrodynamics. Physical Review A - Atomic, Molecular, and Optical Physics.
86(5).
mla: Mlynek, Jonas, et al. “Demonstrating W-Type Entanglement of Dicke States in
Resonant Cavity Quantum Electrodynamics.” Physical Review A - Atomic, Molecular,
and Optical Physics, vol. 86, no. 5, American Physical Society, 2012, doi:10.1103/PhysRevA.86.053838.
short: J. Mlynek, A. Abdumalikov, J.M. Fink, L. Steffen, M. Baur, C. Lang, A. Van
Loo, A. Wallraff, Physical Review A - Atomic, Molecular, and Optical Physics 86
(2012).
date_created: 2018-12-11T11:53:59Z
date_published: 2012-11-30T00:00:00Z
date_updated: 2021-01-12T06:53:10Z
day: '30'
doi: 10.1103/PhysRevA.86.053838
extern: 1
intvolume: ' 86'
issue: '5'
main_file_link:
- open_access: '1'
url: http://arxiv.org/abs/1202.5191
month: '11'
oa: 1
publication: Physical Review A - Atomic, Molecular, and Optical Physics
publication_status: published
publisher: American Physical Society
publist_id: '5332'
quality_controlled: 0
status: public
title: Demonstrating W-type entanglement of Dicke states in resonant cavity quantum
electrodynamics
type: journal_article
volume: 86
year: '2012'
...
---
_id: '1784'
abstract:
- lang: eng
text: A localized qubit entangled with a propagating quantum field is well suited
to study nonlocal aspects of quantum mechanics and may also provide a channel
to communicate between spatially separated nodes in a quantum network. Here, we
report the on-demand generation and characterization of Bell-type entangled states
between a superconducting qubit and propagating microwave fields composed of zero-,
one-, and two-photon Fock states. Using low noise linear amplification and efficient
data acquisition we extract all relevant correlations between the qubit and the
photon states and demonstrate entanglement with high fidelity.
acknowledgement: This work was supported by the European Research Council (ERC) through
a Starting Grant and by ETHZ
author:
- first_name: Christopher
full_name: Eichler, Christopher
last_name: Eichler
- first_name: C
full_name: Lang, C
last_name: Lang
- first_name: Johannes M
full_name: Johannes Fink
id: 4B591CBA-F248-11E8-B48F-1D18A9856A87
last_name: Fink
orcid: 0000-0001-8112-028X
- first_name: J
full_name: Govenius, J
last_name: Govenius
- first_name: Stefan
full_name: Filipp, Stefan
last_name: Filipp
- first_name: Andreas
full_name: Wallraff, Andreas
last_name: Wallraff
citation:
ama: Eichler C, Lang C, Fink JM, Govenius J, Filipp S, Wallraff A. Observation of
entanglement between itinerant microwave photons and a superconducting qubit.
Physical Review Letters. 2012;109(24). doi:10.1103/PhysRevLett.109.240501
apa: Eichler, C., Lang, C., Fink, J. M., Govenius, J., Filipp, S., & Wallraff,
A. (2012). Observation of entanglement between itinerant microwave photons and
a superconducting qubit. Physical Review Letters. American Physical Society.
https://doi.org/10.1103/PhysRevLett.109.240501
chicago: Eichler, Christopher, C Lang, Johannes M Fink, J Govenius, Stefan Filipp,
and Andreas Wallraff. “Observation of Entanglement between Itinerant Microwave
Photons and a Superconducting Qubit.” Physical Review Letters. American
Physical Society, 2012. https://doi.org/10.1103/PhysRevLett.109.240501.
ieee: C. Eichler, C. Lang, J. M. Fink, J. Govenius, S. Filipp, and A. Wallraff,
“Observation of entanglement between itinerant microwave photons and a superconducting
qubit,” Physical Review Letters, vol. 109, no. 24. American Physical Society,
2012.
ista: Eichler C, Lang C, Fink JM, Govenius J, Filipp S, Wallraff A. 2012. Observation
of entanglement between itinerant microwave photons and a superconducting qubit.
Physical Review Letters. 109(24).
mla: Eichler, Christopher, et al. “Observation of Entanglement between Itinerant
Microwave Photons and a Superconducting Qubit.” Physical Review Letters,
vol. 109, no. 24, American Physical Society, 2012, doi:10.1103/PhysRevLett.109.240501.
short: C. Eichler, C. Lang, J.M. Fink, J. Govenius, S. Filipp, A. Wallraff, Physical
Review Letters 109 (2012).
date_created: 2018-12-11T11:53:59Z
date_published: 2012-12-10T00:00:00Z
date_updated: 2021-01-12T06:53:10Z
day: '10'
doi: 10.1103/PhysRevLett.109.240501
extern: 1
intvolume: ' 109'
issue: '24'
main_file_link:
- open_access: '0'
url: http://arxiv.org/abs/1209.0441
month: '12'
publication: Physical Review Letters
publication_status: published
publisher: American Physical Society
publist_id: '5330'
quality_controlled: 0
status: public
title: Observation of entanglement between itinerant microwave photons and a superconducting
qubit
type: journal_article
volume: 109
year: '2012'
...
---
_id: '1801'
abstract:
- lang: eng
text: Brain circuits are assembled from a large variety of morphologically and functionally
diverse cell types. It is not known how the intermingled cell types of an individual
adult brain region differ in their expressed genomes. Here we describe an atlas
of cell type transcriptomes in one brain region, the mouse retina. We found that
each adult cell type expressed a specific set of genes, including a unique set
of transcription factors, forming a 'barcode' for cell identity. Cell type transcriptomes
carried enough information to categorize cells into morphological classes and
types. Several genes that were specifically expressed in particular retinal circuit
elements, such as inhibitory neuron types, are associated with eye diseases. The
resource described here allows gene expression to be compared across adult retinal
cell types, experimenting with specific transcription factors to differentiate
stem or somatic cells to retinal cell types, and predicting cellular targets of
newly discovered disease-associated genes.
acknowledgement: The study was supported by Friedrich Miescher Institute funds, Alcon
award, a National Center of Competence in Research Genetics grant, a European Research
Council grant, a Swiss-Hungarian grant, and RETICIRC, TREATRUSH, SEEBETTER and OPTONEURO
grants from the European Union to B.R.
author:
- first_name: Sandra
full_name: Sandra Siegert
id: 36ACD32E-F248-11E8-B48F-1D18A9856A87
last_name: Siegert
orcid: 0000-0001-8635-0877
- first_name: Erik
full_name: Cabuy, Erik
last_name: Cabuy
- first_name: Brigitte
full_name: Scherf, Brigitte G
last_name: Scherf
- first_name: Hubertus
full_name: Kohler, Hubertus
last_name: Kohler
- first_name: Satchidananda
full_name: Panda, Satchidananda
last_name: Panda
- first_name: Yunzheng
full_name: Le, Yunzheng
last_name: Le
- first_name: Hans
full_name: Fehling, Hans J
last_name: Fehling
- first_name: Dimos
full_name: Gaidatzis, Dimos
last_name: Gaidatzis
- first_name: Michael
full_name: Stadler, Michael B
last_name: Stadler
- first_name: Botond
full_name: Roska, Botond M
last_name: Roska
citation:
ama: Siegert S, Cabuy E, Scherf B, et al. Transcriptional code and disease map for
adult retinal cell types. Nature Neuroscience. 2012;15(3):487-495. doi:10.1038/nn.3032
apa: Siegert, S., Cabuy, E., Scherf, B., Kohler, H., Panda, S., Le, Y., … Roska,
B. (2012). Transcriptional code and disease map for adult retinal cell types.
Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.3032
chicago: Siegert, Sandra, Erik Cabuy, Brigitte Scherf, Hubertus Kohler, Satchidananda
Panda, Yunzheng Le, Hans Fehling, Dimos Gaidatzis, Michael Stadler, and Botond
Roska. “Transcriptional Code and Disease Map for Adult Retinal Cell Types.” Nature
Neuroscience. Nature Publishing Group, 2012. https://doi.org/10.1038/nn.3032.
ieee: S. Siegert et al., “Transcriptional code and disease map for adult
retinal cell types,” Nature Neuroscience, vol. 15, no. 3. Nature Publishing
Group, pp. 487–495, 2012.
ista: Siegert S, Cabuy E, Scherf B, Kohler H, Panda S, Le Y, Fehling H, Gaidatzis
D, Stadler M, Roska B. 2012. Transcriptional code and disease map for adult retinal
cell types. Nature Neuroscience. 15(3), 487–495.
mla: Siegert, Sandra, et al. “Transcriptional Code and Disease Map for Adult Retinal
Cell Types.” Nature Neuroscience, vol. 15, no. 3, Nature Publishing Group,
2012, pp. 487–95, doi:10.1038/nn.3032.
short: S. Siegert, E. Cabuy, B. Scherf, H. Kohler, S. Panda, Y. Le, H. Fehling,
D. Gaidatzis, M. Stadler, B. Roska, Nature Neuroscience 15 (2012) 487–495.
date_created: 2018-12-11T11:54:05Z
date_published: 2012-03-01T00:00:00Z
date_updated: 2021-01-12T06:53:17Z
day: '01'
doi: 10.1038/nn.3032
extern: 1
intvolume: ' 15'
issue: '3'
month: '03'
page: 487 - 495
publication: Nature Neuroscience
publication_status: published
publisher: Nature Publishing Group
publist_id: '5309'
quality_controlled: 0
status: public
title: Transcriptional code and disease map for adult retinal cell types
type: journal_article
volume: 15
year: '2012'
...
---
_id: '1972'
abstract:
- lang: eng
text: Outer membrane protein F, a major component of the Escherichia coli outer
membrane, was crystallized for the first time in lipidic mesophase of monoolein
in novel space groups, P1 and H32. Due to ease of its purification and crystallization
OmpF can be used as a benchmark protein for establishing membrane protein crystallization
in meso, as a "membrane lyzozyme" The packing of porin trimers in the
crystals of space group H32 is similar to natural outer membranes, providing the
first high-resolution insight into the close to native packing of OmpF. Surprisingly,
interaction between trimers is mediated exclusively by lipids, without direct
protein-protein contacts. Multiple ordered lipids are observed and many of them
occupy identical positions independently of the space group, identifying preferential
interaction sites of lipid acyl chains. Presence of ordered aliphatic chains close
to a positively charged area on the porin surface suggests a position for a lipopolysaccharide
binding site on the surface of the major E. coli porins.
acknowledgement: This work was funded by the Medical Research Council.
author:
- first_name: Rouslan
full_name: Efremov, Rouslan G
last_name: Efremov
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Efremov R, Sazanov LA. Structure of Escherichia coli OmpF porin from lipidic
mesophase. Journal of Structural Biology. 2012;178(3):311-318. doi:10.1016/j.jsb.2012.03.005
apa: Efremov, R., & Sazanov, L. A. (2012). Structure of Escherichia coli OmpF
porin from lipidic mesophase. Journal of Structural Biology. Academic Press.
https://doi.org/10.1016/j.jsb.2012.03.005
chicago: Efremov, Rouslan, and Leonid A Sazanov. “Structure of Escherichia Coli
OmpF Porin from Lipidic Mesophase.” Journal of Structural Biology. Academic
Press, 2012. https://doi.org/10.1016/j.jsb.2012.03.005.
ieee: R. Efremov and L. A. Sazanov, “Structure of Escherichia coli OmpF porin from
lipidic mesophase,” Journal of Structural Biology, vol. 178, no. 3. Academic
Press, pp. 311–318, 2012.
ista: Efremov R, Sazanov LA. 2012. Structure of Escherichia coli OmpF porin from
lipidic mesophase. Journal of Structural Biology. 178(3), 311–318.
mla: Efremov, Rouslan, and Leonid A. Sazanov. “Structure of Escherichia Coli OmpF
Porin from Lipidic Mesophase.” Journal of Structural Biology, vol. 178,
no. 3, Academic Press, 2012, pp. 311–18, doi:10.1016/j.jsb.2012.03.005.
short: R. Efremov, L.A. Sazanov, Journal of Structural Biology 178 (2012) 311–318.
date_created: 2018-12-11T11:54:59Z
date_published: 2012-06-01T00:00:00Z
date_updated: 2021-01-12T06:54:26Z
day: '01'
doi: 10.1016/j.jsb.2012.03.005
extern: 1
intvolume: ' 178'
issue: '3'
month: '06'
page: 311 - 318
publication: Journal of Structural Biology
publication_status: published
publisher: Academic Press
publist_id: '5109'
quality_controlled: 0
status: public
title: Structure of Escherichia coli OmpF porin from lipidic mesophase
type: journal_article
volume: 178
year: '2012'
...
---
_id: '1976'
abstract:
- lang: eng
text: 'Complex I is a key enzyme of the respiratory chain in many organisms. This
multi-protein complex with an intricate evolutionary history originated from the
unification of prebuilt modules of hydrogenases and transporters. Using recently
determined crystallographic structures of complex I we reanalyzed evolutionarily
related complexes that couple oxidoreduction to trans-membrane ion translocation.
Our analysis points to the previously unnoticed structural homology of the electron
input module of formate dehydrogenlyases and subunit NuoG of complex I. We also
show that all related to complex I hydrogenases likely operate via a conformation
driven mechanism with structural changes generated in the conserved coupling site
located at the interface of subunits NuoB/D/H. The coupling apparently originated
once in evolutionary history, together with subunit NuoH joining hydrogenase and
transport modules. Analysis of quinone oxidoreduction properties and the structure
of complex I allows us to suggest a fully reversible coupling mechanism. Our model
predicts that: 1) proton access to the ketone groups of the bound quinone is rigorously
controlled by the protein, 2) the negative electric charge of the anionic ubiquinol
head group is a major driving force for conformational changes.'
acknowledgement: The work in authors' laboratory was funded by the Medical Research
Council.
author:
- first_name: Rouslan
full_name: Efremov, Rouslan G
last_name: Efremov
- first_name: Leonid A
full_name: Leonid Sazanov
id: 338D39FE-F248-11E8-B48F-1D18A9856A87
last_name: Sazanov
orcid: 0000-0002-0977-7989
citation:
ama: Efremov R, Sazanov LA. The coupling mechanism of respiratory complex i - A
structural and evolutionary perspective. Biochimica et Biophysica Acta - Bioenergetics.
2012;1817(10):1785-1795. doi:10.1016/j.bbabio.2012.02.015
apa: Efremov, R., & Sazanov, L. A. (2012). The coupling mechanism of respiratory
complex i - A structural and evolutionary perspective. Biochimica et Biophysica
Acta - Bioenergetics. Elsevier. https://doi.org/10.1016/j.bbabio.2012.02.015
chicago: Efremov, Rouslan, and Leonid A Sazanov. “The Coupling Mechanism of Respiratory
Complex i - A Structural and Evolutionary Perspective.” Biochimica et Biophysica
Acta - Bioenergetics. Elsevier, 2012. https://doi.org/10.1016/j.bbabio.2012.02.015.
ieee: R. Efremov and L. A. Sazanov, “The coupling mechanism of respiratory complex
i - A structural and evolutionary perspective,” Biochimica et Biophysica Acta
- Bioenergetics, vol. 1817, no. 10. Elsevier, pp. 1785–1795, 2012.
ista: Efremov R, Sazanov LA. 2012. The coupling mechanism of respiratory complex
i - A structural and evolutionary perspective. Biochimica et Biophysica Acta -
Bioenergetics. 1817(10), 1785–1795.
mla: Efremov, Rouslan, and Leonid A. Sazanov. “The Coupling Mechanism of Respiratory
Complex i - A Structural and Evolutionary Perspective.” Biochimica et Biophysica
Acta - Bioenergetics, vol. 1817, no. 10, Elsevier, 2012, pp. 1785–95, doi:10.1016/j.bbabio.2012.02.015.
short: R. Efremov, L.A. Sazanov, Biochimica et Biophysica Acta - Bioenergetics 1817
(2012) 1785–1795.
date_created: 2018-12-11T11:55:00Z
date_published: 2012-10-01T00:00:00Z
date_updated: 2019-04-26T07:22:06Z
day: '01'
doi: 10.1016/j.bbabio.2012.02.015
extern: 1
intvolume: ' 1817'
issue: '10'
month: '10'
page: 1785 - 1795
publication: Biochimica et Biophysica Acta - Bioenergetics
publication_status: published
publisher: Elsevier
publist_id: '5108'
quality_controlled: 0
status: public
title: The coupling mechanism of respiratory complex i - A structural and evolutionary
perspective
type: review
volume: 1817
year: '2012'
...