Factors Stabilizing beta-Sheets in Protein Structures from a Quantum-Chemical Perspective

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F19%3A00508834" target="_blank" >RIV/61388963:_____/19:00508834 - isvavai.cz</a>

Result on the web

<a href="https://pubs.acs.org/doi/10.1021/acs.jpcb.9b04866" target="_blank" >https://pubs.acs.org/doi/10.1021/acs.jpcb.9b04866</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1021/acs.jpcb.9b04866" target="_blank" >10.1021/acs.jpcb.9b04866</a>

Result language

angličtina

Original language name

Factors Stabilizing beta-Sheets in Protein Structures from a Quantum-Chemical Perspective

Original language description

Protein folds are determined by the interplay between various (de)stabilizing forces, which can be broadly divided into a local strain of the protein chain and intramolecular interactions. In contrast to the alpha-helix, the beta-sheet secondary protein structure is significantly stabilized by long-range interactions between the individual beta-strands. It has been observed that quite diverse amino acid sequences can form a very similar small beta-sheet fold, such as in the three-beta-strand WW domain. Employing 'calibrated' quantum-chemical methods, we show herein on two sequentially diverse examples of the WW domain that the internal strain energy is higher in the beta-strands and lower in the loops, while the interaction energy has an opposite trend. Low strain energy computed for peptide sequences in the loop 1 correlates with its postulated early formation in the folding process. The relatively high strain energy within the beta-strands (up to 8 kcal mol(-1) per amino acid residue) is compensated by even higher intramolecular interaction energy (up to 15 kcal mol(-1) per residue). It is shown in a quantitative way that the most conserved residues across the structural family of WW domains have the highest contributions to the intramolecular interaction energy. On the other hand, the residues in the regions with the lowest strain are not conserved. We conclude that the internal interaction energy is the physical quantity tuned by evolution to define the beta-sheet protein fold.

Czech name

—

Czech description

—

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/GA17-24155S" target="_blank" >GA17-24155S: Exploring Conformational Space of Short Peptides by Advanced Quantum Chemical and Solvation Methods: A Key to Understand Protein Structures?</a><br>

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2019

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

123

Issue of the periodical within the volume

30

Country of publishing house

US - UNITED STATES

Number of pages

9

Pages from-to

6453-6461

UT code for WoS article

000479326100008

EID of the result in the Scopus database

2-s2.0-85070551693