ArticlePLoS computational biology2010
Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 31 citations in OpenAlex.
- Design of Protein Segments and Peptides for Binding to Protein Targets.Biodesign research · 2022Review
- Sequence-structure-function relationships in class I MHC: A local frustration perspective.PloS one · 2020Article
- Gaussian network model can be enhanced by combining solvent accessibility in proteins.Scientific reports · 2017Article
- Identification of Hot Spots in Protein Structures Using Gaussian Network Model and Gaussian Naive Bayes.BioMed research international · 2016Article
- Recent findings and future directions for interpolar mitotic kinesin inhibitors in cancer therapy.Future medicinal chemistry · 2016Review
- 'MHC-I-opathy'-unified concept for spondyloarthritis and Behçet disease.Nature reviews. Rheumatology · 2015Review
- Conformational Motions and Functionally Key Residues for Vitamin B12 Transporter BtuCD-BtuF Revealed by Elastic Network Model with a Function-Related Internal Coordinate.International journal of molecular sciences · 2015Article
- The role of binding site on the mechanical unfolding mechanism of ubiquitin.Scientific reports · 2015Article
- Article
- Study, by use of coarse-grained models, of the functionally crucial residues and allosteric pathway of anesthetic regulation of the Gloeobacter violaceus ligand-gated ion channel.European biophysics journal : EBJ · 2014Article
- Specialized Dynamical Properties of Promiscuous Residues Revealed by Simulated Conformational Ensembles.Journal of chemical theory and computation · 2013Article
- Hot spots in a network of functional sites.PloS one · 2013Article
- Article
- VitAL: Viterbi algorithm for de novo peptide design.PloS one · 2010Article
Corrections and comments
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Authors and funding
3 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A statistical thermodynamics approach is proposed to determine structurally and functionally important residues in native proteins that are involved in energy exchange with a ligand and other residues along an interaction pathway. The structure-function relationships, ligand binding and allosteric activities of ten structures of HLA Class I proteins of the immune system are studied by the Gaussian Network Model. Five of these models are associated with inflammatory rheumatic disease and the remaining five are properly functioning. In the Gaussian Network Model, the protein structures are modeled as an elastic network where the inter-residue interactions are harmonic. Important residues and the interaction pathways in the proteins are identified by focusing on the largest eigenvalue of the residue interaction matrix. Predicted important residues match those known from previous experimental and clinical work. Graph perturbation is used to determine the response of the important residues along the interaction pathway. Differences in response patterns of the two sets of proteins are identified and their relations to disease are discussed.
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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.