Interplay between Conformational Strain and Intramolecular Interaction in Protein Structures: Which of Them Is Evolutionarily Conserved?

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F20%3A00524184" target="_blank" >RIV/61388963:_____/20:00524184 - isvavai.cz</a>

Result on the web

<a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.9b11784" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jpcb.9b11784</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jpcb.9b11784" target="_blank" >10.1021/acs.jpcb.9b11784</a>

Result language

angličtina

Original language name

Interplay between Conformational Strain and Intramolecular Interaction in Protein Structures: Which of Them Is Evolutionarily Conserved?

Original language description

By computing strain energies of peptide fragments within protein structures and their intramolecular interaction energies, we attempt to reveal general biophysical trends behind the secondary structure formation in the context of protein evolution. Our “protein basis set” consisted of 1143 representatives of different folds obtained from curated SCOPe database, and for each member of the set, the strain and intramolecular energy was calculated on the “rolling tripeptide” basis, employing the DFT-D3/COSMO-RS method for the former and the QM-calibrated force field method (MM) for the latter. The calculated data, strain and interactions, were correlated with the conservation of amino acid residues in secondary structure elements and also with the level of the residue burial within the protein three-dimensional structure. It allowed us to formulate several observations concerning fundamental differences between two main secondary structure motifs: α-helices and β-strands. We have shown that a strong interaction is one of the determining characteristics of the β-sheet formation, at least at the level of tripeptides (and likely penta- or heptapeptides, too), and that the β-strand is a prevailing secondary structure in the strongly-interacting regions of the protein folds conserved by evolution. On the other hand, low strain was neither proven to be an important physicochemical property conserved by evolution nor does it correlate with the propensity for the α-helix and β-strand. Finally, it has been demonstrated that the strong interaction has a certain level of connection with residue burial, however, we demonstrate that these two characteristics should be rather regarded as two complementary factors. These findings represent an important contribution to understanding protein folding from first principles, which is a complementary approach to ongoing efforts to solve the protein folding problem by knowledge-based approaches and machine-learning.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

—

OECD FORD branch

10403 - Physical chemistry

Project

<a href="/en/project/GA20-08772S" target="_blank" >GA20-08772S: Fundamental Principles of Protein Folding and Protein-Ligand Interactions Revealed by High-Level Quantum Chemical Calculations</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2020

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Physical Chemistry B

ISSN

1520-6106

e-ISSN

—

Volume of the periodical

124

Issue of the periodical within the volume

16

Country of publishing house

US - UNITED STATES

Number of pages

9

Pages from-to

3252-3260

UT code for WoS article

000529216600002

EID of the result in the Scopus database

2-s2.0-85084027819