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

0508834 - ÚOCHB 2020 RIV US eng J - Článek v odborném periodiku
Culka, Martin - Rulíšek, Lubomír
Factors Stabilizing beta-Sheets in Protein Structures from a Quantum-Chemical Perspective.
Journal of Physical Chemistry B. Roč. 123, č. 30 (2019), s. 6453-6461. ISSN 1520-6106. E-ISSN 1520-5207
Grant CEP: GA ČR(CZ) GA17-24155S
Institucionální podpora: RVO:61388963
Klíčová slova: energy landscape * WW domains * dynamics
Obor OECD: Physical chemistry
Impakt faktor: 2.857, rok: 2019
Způsob publikování: Omezený přístup
https://pubs.acs.org/doi/10.1021/acs.jpcb.9b04866

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.
Trvalý link: http://hdl.handle.net/11104/0299637