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Factors Stabilizing beta-Sheets in Protein Structures from a Quantum-Chemical Perspective
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SYSNO ASEP 0508834 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Factors Stabilizing beta-Sheets in Protein Structures from a Quantum-Chemical Perspective Author(s) Culka, Martin (UOCHB-X) ORCID
Rulíšek, Lubomír (UOCHB-X) RID, ORCIDSource Title Journal of Physical Chemistry B. - : American Chemical Society - ISSN 1520-6106
Roč. 123, č. 30 (2019), s. 6453-6461Number of pages 9 s. Language eng - English Country US - United States Keywords energy landscape ; WW domains ; dynamics Subject RIV CF - Physical ; Theoretical Chemistry OECD category Physical chemistry R&D Projects GA17-24155S GA ČR - Czech Science Foundation (CSF) Method of publishing Limited access Institutional support UOCHB-X - RVO:61388963 UT WOS 000479326100008 EID SCOPUS 85070551693 DOI 10.1021/acs.jpcb.9b04866 Annotation 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. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418 Year of Publishing 2020 Electronic address https://pubs.acs.org/doi/10.1021/acs.jpcb.9b04866
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