ArticleBiophysics and physicobiology2016
Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes.
Article in Biophysics and physicobiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Druggability Simulations and X-Ray Crystallography Reveal a Ligand-Binding Site in the GluA3 AMPA Receptor N-Terminal Domain.Structure (London, England : 1993) · 2019Article
- Engineered control of enzyme structural dynamics and function.Protein science : a publication of the Protein Society · 2018Review
- Theoretical framework for analyzing structural compliance properties of proteins.Biophysics and physicobiology · 2018Article
- Preface of Special Issue "Protein-Ligand Interactions".Biophysics and physicobiology · 2016Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We examine the dynamic features of non-trivial allosteric binding sites to elucidate potential drug binding sites. These allosteric sites were previously found to be allosteric after determination of the protein-drug co-crystal structure. After comprehensive search in the Protein Data Bank, we identify 10 complex structures with allosteric ligands whose structures are very similar to their functional forms. Then, possible pockets on the protein surface are searched as potential ligand binding sites. To mimic ligand binding to the pocket, complex models are generated to fill out each pocket with pseudo ligand blocks consisting of spheres. Normal mode analysis of the elastic network model is performed for the complex models and unbound structures to assess the change of protein dynamics induced by ligand binding. We examine nine profiles to describe the dynamic and positional characteristics of the pockets, and identify the change of fluctuation around the ligand, Δ
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