ArticleScientific reports2016
Surface energetics and protein-protein interactions: analysis and mechanistic implications.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Design of multi-target peptide modulators for protein chaperone networks.Structure (London, England : 1993) · 2025Article
- Nanoparticle stereochemistry-dependent endocytic processing improves in vivo mRNA delivery.Nature chemistry · 2023Article
- Molecular recognition of SARS-CoV-2 spike protein with three essential partners: exploring possible immune escape mechanisms of viral mutants.Journal of molecular modeling · 2023Article
- Spatial organization of hydrophobic and charged residues affects protein thermal stability and binding affinity.Scientific reports · 2022Article
- Modeling the Dynamics of Protein-Protein Interfaces, How and Why?Molecules (Basel, Switzerland) · 2022Review
- Surface charge of Merkel cell polyomavirus small T antigen determines cell transformation through allosteric FBW7 WD40 domain targeting.Oncogenesis · 2020Article
- A spatial similarity of stereochemical environments formed by amino acid residues defines a common epitope of two non-homologous proteins.Scientific reports · 2019Article
- Water follows polar and nonpolar protein surface domains.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- A Recombinant Affinity Reagent Specific for a Phosphoepitope of Akt1.International journal of molecular sciences · 2018Article
- PD-L1 Nanobody Competitively Inhibits the Formation of the PD-1/PD-L1 Complex: Comparative Molecular Dynamics Simulations.International journal of molecular sciences · 2018Article
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Authors and funding
3 authors.
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Abstract
Understanding protein-protein interactions (PPI) at the molecular level is a fundamental task in the design of new drugs, the prediction of protein function and the clarification of the mechanisms of (dis)regulation of biochemical pathways. In this study, we use a novel computational approach to investigate the energetics of aminoacid networks located on the surface of proteins, isolated and in complex with their respective partners. Interestingly, the analysis of individual proteins identifies patches of surface residues that, when mapped on the structure of their respective complexes, reveal regions of residue-pair couplings that extend across the binding interfaces, forming continuous motifs. An enhanced effect is visible across the proteins of the dataset forming larger quaternary assemblies. The method indicates the presence of energetic signatures in the isolated proteins that are retained in the bound form, which we hypothesize to determine binding orientation upon complex formation. We propose our method, BLUEPRINT, as a complement to different approaches ranging from the ab-initio characterization of PPIs, to protein-protein docking algorithms, for the physico-chemical and functional investigation of protein-protein interactions.
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