Factors Stabilizing beta-Sheets in Protein Structures from a Quantum-Chemical Perspective
Identifikátory výsledku
Kód výsledku v 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>
Výsledek na webu
<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>
Alternativní jazyky
Jazyk výsledku
angličtina
Název v původním jazyce
Factors Stabilizing beta-Sheets in Protein Structures from a Quantum-Chemical Perspective
Popis výsledku v původním jazyce
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.
Název v anglickém jazyce
Factors Stabilizing beta-Sheets in Protein Structures from a Quantum-Chemical Perspective
Popis výsledku anglicky
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.
Klasifikace
Druh
J<sub>imp</sub> - Článek v periodiku v databázi Web of Science
CEP obor
—
OECD FORD obor
10403 - Physical chemistry
Návaznosti výsledku
Projekt
<a href="/cs/project/GA17-24155S" target="_blank" >GA17-24155S: Mapování konformačního prostoru krátkých peptidů pokročilými kvantově-chemickými a solvatačními metodami: klíč k pochopení struktury proteinů?</a><br>
Návaznosti
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Ostatní
Rok uplatnění
2019
Kód důvěrnosti údajů
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Údaje specifické pro druh výsledku
Název periodika
Journal of Physical Chemistry B
ISSN
1520-6106
e-ISSN
—
Svazek periodika
123
Číslo periodika v rámci svazku
30
Stát vydavatele periodika
US - Spojené státy americké
Počet stran výsledku
9
Strana od-do
6453-6461
Kód UT WoS článku
000479326100008
EID výsledku v databázi Scopus
2-s2.0-85070551693