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Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residuesCarl, Nejc ...A protocol was developed for the computational determination of the contribution of interfacial amino acid residues to the free energy of protein-protein binding. Thermodynamic integration, based on ... molecular dynamics simulation in CHARMM, was used to determine the free energy associated with single point mutations to glycine in a protein-protein interface. The hot spot amino acids found in this way were then correlated to structural similarity scores detected by the ProBiS algorithm for local structural alignment. We find that amino acids with high structural similarity scores contribute on average -3.19 kcal/mol to the free energy of protein-protein binding and are thus correlated with hot spot residues, while residues with low similarity scores contribute on average only -0.43 kcal/mol. This suggests that the local structural alignment method provides a good approximation of the contribution of a residue to the free energy of binding and is particularly useful for detection of hot spots in proteins with known structures but undetermined protein-protein complexes.Source: Journal of chemical information and modeling. - ISSN 1549-9596 (VOl. 52, issue 10, 2012, str. 2541-2549)Type of material - article, component partPublish date - 2012Language - englishCOBISS.SI-ID - 5069594
Author
Carl, Nejc |
Hodošček, Milan |
Vehar, Blaž |
Konc, Janez |
Brooks, Bernard R. |
Janežič, Dušanka, 1952-
Topics
analizna kemija |
proteini |
simulacije
source: Journal of chemical information and modeling. - ISSN 1549-9596 (VOl. 52, issue 10, 2012, str. 2541-2549)
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Database name | Field | Year |
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Links to authors' personal bibliographies | Links to information on researchers in the SICRIS system |
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Carl, Nejc | 28560 |
Hodošček, Milan | 02287 |
Vehar, Blaž | 30286 |
Konc, Janez | 25435 |
Brooks, Bernard R. | |
Janežič, Dušanka, 1952- | 06734 |
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