Local Interaction Signal Analysis Predicts Protein-Protein Binding Affinity
Copyright © 2018 Elsevier Ltd. All rights reserved..
Several models estimating the strength of the interaction between proteins in a complex have been proposed. By exploring the geometry of contact distribution at protein-protein interfaces, we provide an improved model of binding energy. Local interaction signal analysis (LISA) is a radial function based on terms describing favorable and non-favorable contacts obtained by density functional theory, the support-core-rim interface residue distribution, non-interacting charged residues and secondary structures contribution. The three-dimensional organization of the contacts and their contribution on localized hot-sites over the entire interaction surface were numerically evaluated. LISA achieves a correlation of 0.81 (and a root-mean-square error of 2.35 ± 0.38 kcal/mol) when tested on 125 complexes for which experimental measurements were realized. LISA's performance is stable for subsets defined by functional composition and extent of conformational changes upon complex formation. A large-scale comparison with 17 other functions demonstrated the power of the geometrical model in the understanding of complex binding.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2018 |
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| Erschienen: |
2018 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:26 |
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| Enthalten in: |
Structure (London, England : 1993) - 26(2018), 6 vom: 05. Juni, Seite 905-915.e4 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Raucci, Raffaele [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 08.03.2019 Date Revised 08.03.2019 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1016/j.str.2018.04.006 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM284259144 |
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| 520 | |a Copyright © 2018 Elsevier Ltd. All rights reserved. | ||
| 520 | |a Several models estimating the strength of the interaction between proteins in a complex have been proposed. By exploring the geometry of contact distribution at protein-protein interfaces, we provide an improved model of binding energy. Local interaction signal analysis (LISA) is a radial function based on terms describing favorable and non-favorable contacts obtained by density functional theory, the support-core-rim interface residue distribution, non-interacting charged residues and secondary structures contribution. The three-dimensional organization of the contacts and their contribution on localized hot-sites over the entire interaction surface were numerically evaluated. LISA achieves a correlation of 0.81 (and a root-mean-square error of 2.35 ± 0.38 kcal/mol) when tested on 125 complexes for which experimental measurements were realized. LISA's performance is stable for subsets defined by functional composition and extent of conformational changes upon complex formation. A large-scale comparison with 17 other functions demonstrated the power of the geometrical model in the understanding of complex binding | ||
| 650 | 4 | |a Journal Article | |
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| 650 | 4 | |a atom-atom contact | |
| 650 | 4 | |a binding affinity | |
| 650 | 4 | |a density functional theory | |
| 650 | 4 | |a electron density | |
| 650 | 4 | |a favorable contact | |
| 650 | 4 | |a non-covalent interaction | |
| 650 | 4 | |a non-interacting surface | |
| 650 | 4 | |a protein interface | |
| 650 | 4 | |a protein-protein interaction | |
| 650 | 4 | |a reduced density gradient | |
| 650 | 7 | |a Proteins |2 NLM | |
| 700 | 1 | |a Laine, Elodie |e verfasserin |4 aut | |
| 700 | 1 | |a Carbone, Alessandra |e verfasserin |4 aut | |
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