ArticleBiophysical journal2005
How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues.
Article in Biophysical journal, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Article
- Revealing Allosteric Mechanism of Amino Acid Binding Proteins from Open to Closed State.Molecules (Basel, Switzerland) · 2023Article
- Normal Mode Analysis of KRas4B Reveals Partner Specific Dynamics.The journal of physical chemistry. B · 2021Article
- Recognition of Potential COVID-19 Drug Treatments through the Study of Existing Protein-Drug and Protein-Protein Structures: An Analysis of Kinetically Active Residues.Biomolecules · 2020Article
- Probing the Structural Dynamics of theFrontiers in molecular biosciences · 2020Article
- Article
- Local and global anatomy of antibody-protein antigen recognition.Journal of molecular recognition : JMR · 2018Article
- Heterodimer Binding Scaffolds Recognition via the Analysis of Kinetically Hot Residues.Pharmaceuticals (Basel, Switzerland) · 2018Article
- Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell.Chemical reviews · 2016Review
- Identification of Hot Spots in Protein Structures Using Gaussian Network Model and Gaussian Naive Bayes.BioMed research international · 2016Article
- The Chromosomal parDE2 Toxin-Antitoxin System of Mycobacterium tuberculosis H37Rv: Genetic and Functional Characterization.Frontiers in microbiology · 2016Article
- Domain Motions and Functionally-Key Residues of L-Alanine Dehydrogenase Revealed by an Elastic Network Model.International journal of molecular sciences · 2015Article
- Analysis of core-periphery organization in protein contact networks reveals groups of structurally and functionally critical residues.Journal of biosciences · 2015Article
- Analysis of conformational motions and residue fluctuations for Escherichia coli ribose-binding protein revealed with elastic network models.International journal of molecular sciences · 2013Article
- Substrate recognition and motion mode analyses of PFV integrase in complex with viral DNA via coarse-grained models.PloS one · 2013Article
- Hot spots in a network of functional sites.PloS one · 2013Article
- Stability and folding behavior analysis of zinc-finger using simple models.International journal of molecular sciences · 2010Article
- Induced fit, conformational selection and independent dynamic segments: an extended view of binding events.Trends in biochemical sciences · 2010Article
- Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins.PLoS computational biology · 2010Article
- DNABINDPROT: fluctuation-based predictor of DNA-binding residues within a network of interacting residues.Nucleic acids research · 2010Article
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4 authors.
Funding
Abstract
The underlying physico-chemical principles of the interactions between domains in protein folding are similar to those between protein molecules in binding. Here we show that conserved residues and experimental hot spots at intermolecular binding interfaces overlap residues that vibrate with high frequencies. Similarly, conserved residues and hot spots are found in protein cores and are also observed to vibrate with high frequencies. In both cases, these residues contribute significantly to the stability. Hence, these observations validate the proposition that binding and folding are similar processes. In both packing plays a critical role, rationalizing the residue conservation and the experimental alanine scanning hot spots. We further show that high-frequency vibrating residues distinguish between protein binding sites and the remainder of the protein surface.
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