Identifying stabilizing key residues in proteins using interresidue interaction energy matrix

Proteins
Lada Bendová-BiedermannováJirí Vondrásek

Abstract

We are proposing an interresidue interaction energy map (IEM)--a new tool for protein structure analysis and protein bioinformatics. This approach employs the sum of pair-wise interaction energies of a particular residue as a measure of its structural importance. We will show that the IEM can serve as a means for identifying key residues responsible for the stability of a protein. Our method can be compared with the interresidue contact map but has the advantage of weighting the contacts by the stabilization energy content which they bring to the protein structure. For the theoretical adjustment of the proposed method, we chose the Trp-cage mini protein as a model system to compare a spectrum of computational methods ranging from the ab initio MP2 level through the DFT method to empirical force-field methods. The IEM method correctly identifies Tryptophane 6 as the key residue in the Trp-cage. The other residues with the highest stabilizing contributions correspond to the structurally important positions in the protein. We have further tested our method on the Trp2Cage miniprotein--a P12W mutant of the Trp-cage and on two proteins from the rubredoxin family that differ in their thermostability. Our method correctly identified t...Continue Reading

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Citations

Aug 9, 2012·Accounts of Chemical Research·Kevin E Riley, Pavel Hobza
Jan 13, 2011·Biochemistry·D Victoria WilliamsNiels H Andersen
Mar 2, 2013·The Journal of Physical Chemistry. B·Zaizhi LaiJin Wang
Mar 5, 2011·Organic & Biomolecular Chemistry·Xiaoqin HuangChang-Guo Zhan
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Oct 31, 2012·Journal of Molecular Recognition : JMR·Jiří Kysilka, Jiří Vondrášek
Oct 31, 2008·Physical Chemistry Chemical Physics : PCCP·Lada BiedermannovaJiri Vondrasek
May 5, 2017·Nucleic Acids Research·Jakub GalgonekJirí Vondrášek
May 11, 2021·Protein Science : a Publication of the Protein Society·Kristyna BousovaJiri Vondrasek
Apr 1, 2015·The Journal of Physical Chemistry. a·Yefei WangLishan Yao

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