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Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins.

作者信息

Voortman-Sheetz Keila, Wrabl James O, Hilser Vincent J

机构信息

Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA.

Chemical Biology Interface Graduate Program, Johns Hopkins University, Baltimore, Maryland, USA.

出版信息

Protein Sci. 2025 Mar;34(3):e70015. doi: 10.1002/pro.70015.


DOI:10.1002/pro.70015
PMID:39969063
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11837041/
Abstract

The number of distinct structural environments in the proteome (as observed in the Protein Data Bank) may belie an organizing framework, whereby evolution conserves the relative stability of different sequence segments, regardless of the specific structural details present in the final fold. If true, the question arises as to whether the energetic consequences of amino acid substitutions, and thus the frequencies of amino acids within each of these so-called thermodynamic environments, could depend less on what local structure that sequence segment may adopt in the final fold, and more on the local stability of that final structure relative to the unfolded state. To address this question, a previously described ensemble-based approach (the COREX algorithm) was used to define proteins in terms of thermodynamic environments, and the naturally occurring frequencies of amino acids within these environments were used to generate statistical energies (a type of knowledge-based potential). By comparing compatibility scores from the statistical energies with energies calculated using the Rosetta all-atom energy function, we assessed the information overlap between the two approaches. Results revealed a substantial correlation between the statistical scores and those obtained using Rosetta, directly demonstrating that a small number of thermodynamic environments are sufficient to capture the perceived multiplicity of different structural environments in proteins. More importantly, the agreement suggests that regional amino acid distributions within each protein in any proteome have been substantially driven by the evolutionary conservation of the regional differences in stabilities within protein families.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/d3a122e7c2de/PRO-34-e70015-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/10904df59a2c/PRO-34-e70015-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/3ccee4c07903/PRO-34-e70015-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/bca2186fe3b0/PRO-34-e70015-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/91f95dc546d8/PRO-34-e70015-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/480c1fe772ce/PRO-34-e70015-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/683e1bae8ed1/PRO-34-e70015-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/d3a122e7c2de/PRO-34-e70015-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/10904df59a2c/PRO-34-e70015-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/3ccee4c07903/PRO-34-e70015-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/bca2186fe3b0/PRO-34-e70015-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/91f95dc546d8/PRO-34-e70015-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/480c1fe772ce/PRO-34-e70015-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/683e1bae8ed1/PRO-34-e70015-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5382/11837041/d3a122e7c2de/PRO-34-e70015-g006.jpg

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Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins.

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[2]
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[7]
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引用本文的文献

[1]
The Ensemble Basis of Allostery and Function: Insights from Models of Local Unfolding.

J Mol Biol. 2025-6-9

本文引用的文献

[1]
Deep generative models of protein structure uncover distant relationships across a continuous fold space.

Nat Commun. 2024-9-16

[2]
Accurate structure prediction of biomolecular interactions with AlphaFold 3.

Nature. 2024-6

[3]
Predicting multiple conformations via sequence clustering and AlphaFold2.

Nature. 2024-1

[4]
Similar protein segments shared between domains of different evolutionary lineages.

Protein Sci. 2022-9

[5]
On the reliability and the limits of inference of amino acid sequence alignments.

Bioinformatics. 2022-6-24

[6]
AlphaFold2 fails to predict protein fold switching.

Protein Sci. 2022-6

[7]
Where to From Here?

Front Mol Biosci. 2022-3-25

[8]
A Thermodynamic Atlas of Proteomes Reveals Energetic Innovation across the Tree of Life.

Mol Biol Evol. 2022-3-2

[9]
Critical assessment of methods of protein structure prediction (CASP)-Round XIV.

Proteins. 2021-12

[10]
Highly accurate protein structure prediction with AlphaFold.

Nature. 2021-8

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