ArticleJournal of molecular biology2020
Characterizing and Predicting Protein Hinges for Mechanistic Insight.
Article in Journal of molecular biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Structural Dynamics of the Afamin/Wnt3a Complex Mediated by the Afamin Hydrophobic Pocket.Nano letters · 2026Article
- Investigation of potential hinge region forbioRxiv : the preprint server for biology · 2026Article
- Highly Optimized Simulation of Atomic Resolution Cell-Like Protein Environment.The journal of physical chemistry. B · 2025Article
- Diffusion of proteins in crowded solutions studied by docking-based modeling.The Journal of chemical physics · 2024Article
- Computational remodeling of an enzyme conformational landscape for altered substrate selectivity.Nature communications · 2023Article
- Docking-based long timescale simulation of cell-size protein systems at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Article
- Coarse-graining protein structures into their dynamic communities with DCI, a dynamic community identifier.Bioinformatics (Oxford, England) · 2022Article
- PACKMAN-Molecule: Python toolbox for structural bioinformatics.Bioinformatics advances · 2022Article
- hdANM: a new comprehensive dynamics model for protein hinges.Biophysical journal · 2021Article
- Hinge-shift mechanism as a protein design principle for the evolution of β-lactamases from substrate promiscuity to specificity.Nature communications · 2021Article
- SAP130 and CSN1 interact and regulate male gametogenesis in Arabidopsis thaliana.Journal of plant research · 2021Article
- Structural compliance: A new metric for protein flexibility.Proteins · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The functioning of proteins requires highly specific dynamics, which depend critically on the details of how amino acids are packed. Hinge motions are the most common type of large motion, typified by the opening and closing of enzymes around their substrates. The packing and geometries of residues are characterized here by graph theory. This characterization is sufficient to enable reliable hinge predictions from a single static structure, and notably, this can be from either the open or the closed form of a structure. This new method to identify hinges within protein structures is called PACKMAN. The predicted hinges are validated by using permutation tests on B-factors. Hinge prediction results are compared against lists of manually curated hinge residues, and the results suggest that PACKMAN is robust enough to reproduce the known conformational changes and is able to predict hinge regions equally well from either the open or the closed forms of a protein. A group of 167 protein pairs with open and closed structures has been investigated Examples are shown for several additional proteins, including Zika virus nonstructured (NS) proteins where there are 6 hinge regions in the NS5 protein, 5 hinge regions in the NS2B bound in the NS3 protease complex and 5 hinges in the NS3- helicase protein. Results obtained from this method can be important for generating conformational ensembles of protein targets for drug design. PACKMAN is freely accessible at (https://PACKMAN.bb.iastate.edu/).
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