---
_id: '846'
abstract:
- lang: eng
text: Whether or not evolutionary change is inherently irreversible remains a controversial
topic. Some examples of evolutionary irreversibility are known; however, this
question has not been comprehensively addressed at the molecular level. Here,
we use data from 221 human genes with known pathogenic mutations to estimate the
rate of irreversibility in protein evolution. For these genes, we reconstruct
ancestral amino acid sequences along the mammalian phylogeny and identify ancestral
amino acid states that match known pathogenic mutations. Such cases represent
inherent evolutionary irreversibility because, at the present moment, reversals
to these ancestral amino acid states are impossible for the human lineage. We
estimate that approximately 10% of all amino acid substitutions along the mammalian
phylogeny are irreversible, such that a return to the ancestral amino acid state
would lead to a pathogenic phenotype. For a subset of 51 genes with high rates
of irreversibility, as much as 40% of all amino acid evolution was estimated to
be irreversible. Because pathogenic phenotypes do not resemble ancestral phenotypes,
the molecular nature of the high rate of irreversibility in proteins is best explained
by evolution with a high prevalence of compensatory, epistatic interactions between
amino acid sites. Under such mode of protein evolution, once an amino acid substitution
is fixed, the probability of its reversal declines as the protein sequence accumulates
changes that affect the phenotypic manifestation of the ancestral state. The prevalence
of epistasis in evolution indicates that the observed high rate of irreversibility
in protein evolution is an inherent property of protein structure and function.
acknowledgement: This work was supported by Plan Nacional grant BFU2009-09271 from
the Spanish Ministry of Science and Innovation and by FPU (Formación del Profesorado
Universitario) program grant AP2008-01888 from the Spanish Ministry of Education
to O.S. F.A.K. is a European Molecular Biology Organization Young Investigator and
Howard Hughes Medical Institute International Early Career Scientist.
author:
- first_name: Onuralp
full_name: Soylemez, Onuralp
last_name: Soylemez
- first_name: Fyodor
full_name: Fyodor Kondrashov
id: 44FDEF62-F248-11E8-B48F-1D18A9856A87
last_name: Kondrashov
orcid: 0000-0001-8243-4694
citation:
ama: Soylemez O, Kondrashov F. Estimating the rate of irreversibility in protein
evolution. Genome Biology and Evolution. 2012;4(12):1213-1222. doi:10.1093/gbe/evs096
apa: Soylemez, O., & Kondrashov, F. (2012). Estimating the rate of irreversibility
in protein evolution. Genome Biology and Evolution. Oxford University Press.
https://doi.org/10.1093/gbe/evs096
chicago: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility
in Protein Evolution.” Genome Biology and Evolution. Oxford University
Press, 2012. https://doi.org/10.1093/gbe/evs096.
ieee: O. Soylemez and F. Kondrashov, “Estimating the rate of irreversibility in
protein evolution,” Genome Biology and Evolution, vol. 4, no. 12. Oxford
University Press, pp. 1213–1222, 2012.
ista: Soylemez O, Kondrashov F. 2012. Estimating the rate of irreversibility in
protein evolution. Genome Biology and Evolution. 4(12), 1213–1222.
mla: Soylemez, Onuralp, and Fyodor Kondrashov. “Estimating the Rate of Irreversibility
in Protein Evolution.” Genome Biology and Evolution, vol. 4, no. 12, Oxford
University Press, 2012, pp. 1213–22, doi:10.1093/gbe/evs096.
short: O. Soylemez, F. Kondrashov, Genome Biology and Evolution 4 (2012) 1213–1222.
date_created: 2018-12-11T11:48:49Z
date_published: 2012-01-01T00:00:00Z
date_updated: 2021-01-12T08:19:25Z
day: '01'
doi: 10.1093/gbe/evs096
extern: 1
intvolume: ' 4'
issue: '12'
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
page: 1213 - 1222
publication: Genome Biology and Evolution
publication_status: published
publisher: Oxford University Press
publist_id: '6802'
quality_controlled: 0
status: public
title: Estimating the rate of irreversibility in protein evolution
tmp:
image: /images/cc_by_nc.png
legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
short: CC BY-NC (4.0)
type: journal_article
volume: 4
year: '2012'
...
---
_id: '8463'
abstract:
- lang: eng
text: The 1H dipolar network, which is the major obstacle for applying proton detection
in the solid-state, can be reduced by deuteration, employing the RAP (Reduced
Adjoining Protonation) labeling scheme, which yields random protonation at non-exchangeable
sites. We present here a systematic study on the optimal degree of random sidechain
protonation in RAP samples as a function of the MAS (magic angle spinning) frequency.
In particular, we compare 1H sensitivity and linewidth of a microcrystalline protein,
the SH3 domain of chicken α-spectrin, for samples, prepared with 5–25 % H2O in
the E. coli growth medium, in the MAS frequency range of 20–60 kHz. At an external
field of 19.96 T (850 MHz), we find that using a proton concentration between
15 and 25 % in the M9 medium yields the best compromise in terms of sensitivity
and resolution, with an achievable average 1H linewidth on the order of 40–50
Hz. Comparing sensitivities at a MAS frequency of 60 versus 20 kHz, a gain in
sensitivity by a factor of 4–4.5 is observed in INEPT-based 1H detected 1D 1H,13C
correlation experiments. In total, we find that spectra recorded with a 1.3 mm
rotor at 60 kHz have almost the same sensitivity as spectra recorded with a fully
packed 3.2 mm rotor at 20 kHz, even though ~20× less material is employed. The
improved sensitivity is attributed to 1H line narrowing due to fast MAS and to
the increased efficiency of the 1.3 mm coil.
article_processing_charge: No
article_type: original
author:
- first_name: Sam
full_name: Asami, Sam
last_name: Asami
- first_name: Kathrin
full_name: Szekely, Kathrin
last_name: Szekely
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Beat H.
full_name: Meier, Beat H.
last_name: Meier
- first_name: Bernd
full_name: Reif, Bernd
last_name: Reif
citation:
ama: Asami S, Szekely K, Schanda P, Meier BH, Reif B. Optimal degree of protonation
for 1H detection of aliphatic sites in randomly deuterated proteins as a function
of the MAS frequency. Journal of Biomolecular NMR. 2012;54(2):155-168.
doi:10.1007/s10858-012-9659-9
apa: Asami, S., Szekely, K., Schanda, P., Meier, B. H., & Reif, B. (2012). Optimal
degree of protonation for 1H detection of aliphatic sites in randomly deuterated
proteins as a function of the MAS frequency. Journal of Biomolecular NMR.
Springer Nature. https://doi.org/10.1007/s10858-012-9659-9
chicago: Asami, Sam, Kathrin Szekely, Paul Schanda, Beat H. Meier, and Bernd Reif.
“Optimal Degree of Protonation for 1H Detection of Aliphatic Sites in Randomly
Deuterated Proteins as a Function of the MAS Frequency.” Journal of Biomolecular
NMR. Springer Nature, 2012. https://doi.org/10.1007/s10858-012-9659-9.
ieee: S. Asami, K. Szekely, P. Schanda, B. H. Meier, and B. Reif, “Optimal degree
of protonation for 1H detection of aliphatic sites in randomly deuterated proteins
as a function of the MAS frequency,” Journal of Biomolecular NMR, vol.
54, no. 2. Springer Nature, pp. 155–168, 2012.
ista: Asami S, Szekely K, Schanda P, Meier BH, Reif B. 2012. Optimal degree of protonation
for 1H detection of aliphatic sites in randomly deuterated proteins as a function
of the MAS frequency. Journal of Biomolecular NMR. 54(2), 155–168.
mla: Asami, Sam, et al. “Optimal Degree of Protonation for 1H Detection of Aliphatic
Sites in Randomly Deuterated Proteins as a Function of the MAS Frequency.” Journal
of Biomolecular NMR, vol. 54, no. 2, Springer Nature, 2012, pp. 155–68, doi:10.1007/s10858-012-9659-9.
short: S. Asami, K. Szekely, P. Schanda, B.H. Meier, B. Reif, Journal of Biomolecular
NMR 54 (2012) 155–168.
date_created: 2020-09-18T10:09:18Z
date_published: 2012-08-23T00:00:00Z
date_updated: 2021-01-12T08:19:27Z
day: '23'
doi: 10.1007/s10858-012-9659-9
extern: '1'
intvolume: ' 54'
issue: '2'
language:
- iso: eng
month: '08'
oa_version: None
page: 155-168
publication: Journal of Biomolecular NMR
publication_identifier:
issn:
- 0925-2738
- 1573-5001
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Optimal degree of protonation for 1H detection of aliphatic sites in randomly
deuterated proteins as a function of the MAS frequency
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 54
year: '2012'
...
---
_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'
...