ArticleJournal of bioinformatics and computational biology2012
Structure fluctuations and conformational changes in protein binding.
Article in Journal of bioinformatics and computational biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
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- Multimeric protein interaction and complex prediction: Structure, dynamics and function.Computational and structural biotechnology journal · 2025Review
- Study of Allosteric Transitions of Human P-Glycoprotein by Using the Two-State Anisotropic Network Model.Frontiers in medicine · 2022Article
- Structural modelling of SARS-CoV-2 alpha variant (B.1.1.7) suggests enhanced furin binding and infectivity.Virus research · 2021Article
- An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid.Chemical science · 2021Article
- Exploring Evolutionary Constraints in the Proteomes of Zika, Dengue, and Other Flaviviruses to Find Fitness-Critical Sites.Journal of molecular evolution · 2020Article
- Computational Ways to Enhance Protein Inhibitor Design.Frontiers in molecular biosciences · 2020Article
- B-factor Guided Proline Substitutions in Chromobacterium violaceum Amine Transaminase: Evaluation of the Proline Rule as a Method for Enzyme Stabilization.Chembiochem : a European journal of chemical biology · 2019Article
- Modeling of Protein Structural Flexibility and Large-Scale Dynamics: Coarse-Grained Simulations and Elastic Network Models.International journal of molecular sciences · 2018Review
- Metal-catalyzed oxidation of human serum albumin does not alter the interactive binding to the two principal drug binding sites.Biochemistry and biophysics reports · 2018Article
- Specific stereochemistry of OP-1074 disrupts estrogen receptor alpha helix 12 and confers pure antiestrogenic activity.Nature communications · 2018Article
- Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.Protein science : a publication of the Protein Society · 2018Article
- Alanine mutation of the catalytic sites of Pantothenate Synthetase causes distinct conformational changes in the ATP binding region.Scientific reports · 2018Article
- Knowledge-based entropies improve the identification of native protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Local packing modulates diversity of iron pathways and cooperative behavior in eukaryotic and prokaryotic ferritins.The Journal of chemical physics · 2014Article
- B-factor Analysis and Conformational Rearrangement of Aldose Reductase.Current proteomics · 2014Article
- PreFRP: Prediction and visualization of fluctuation residues in proteins.Journal of natural science, biology, and medicineArticle
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers of mass in proteins and a statistical analysis of conformation changes in the side-chains upon binding. Normal mode analysis and an elastic network model were applied to a set of protein complexes to calculate the residue fluctuations and develop the residue classification. Comparison with a classification based on normalized B-factors suggests that the B-factors may underestimate protein flexibility in solvent. Our classification shows that protein loops and disordered fragments are enriched with highly fluctuating residues and depleted with weakly fluctuating residues. Strategies for engineering thermostable proteins are discussed. To calculate the dihedral angles distribution functions, the configuration space was divided into cells by a cubic grid. The effect of protein association on the distribution functions depends on the amino acid type and a grid step in the dihedral angles space. The changes in the dihedral angles increase from the near-backbone dihedral angle to the most distant one, for most residues. On average, one fifth of the interface residues change the rotamer state upon binding, whereas the rest of the interface residues undergo local readjustments within the same rotamer.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.