Analysis of Correlations between Energy and Residue Fluctuations in Native Proteins and Determination of Specific Sites for Binding
Abstract
The Gaussian network model is used to derive the correlations between energy and residue fluctuations in native proteins. Residues are identified that respond strongly to energy fluctuations and that display correlations with the remaining residues of the protein at the highest modes. We postulate that these residues are located at specific sites for drug binding. We test the validity of this postulate on a data set of 33 structurally distinct proteins in the unbound state. Detailed results are presented for drug binding to the HIV protease.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Propagation of conformational change at certain locations can cause large-amplitude fluctuations of linked domains.
“The propagation of conformational change at certain locations228–230 can lead to large amplitude fluctuations of the linked domains.231”
From Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell (2016) · cites this paper as [231]
Cites
Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis
Tirion, M. M. (1996) · Physical Review Letters · doi:10.1103/physrevlett.77.1905 · Cited by 1,617 · see citing works
Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
Bahar, İ., Atılgan, A. R., & Erman, B. (1997) · Folding and Design · doi:10.1016/s1359-0278(97)00024-2 · Cited by 1,377 · see citing works
Self-citationQ-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
Laurie, A. T. R., & Jackson, R. M. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti315 · Cited by 1,049 · see citing works
STRUCTURE-BASED INHIBITORS OF HIV-1 PROTEASE
Wlodawer, A., & Erickson, J. W. (1993) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.62.070193.002551 · Cited by 828 · see citing works
Gaussian Dynamics of Folded Proteins
Haliloǧlu, T., Bahar, İ., & Erman, B. (1997) · Physical Review Letters · doi:10.1103/physrevlett.79.3090 · Cited by 761 · see citing works
Self-citationA structural model for the retroviral proteases
Pearl, L. H., & Taylor, W. R. (1987) · Nature · doi:10.1038/329351a0 · Cited by 601 · see citing works
Bahar, İ., Atılgan, A. R., Demirel, M. C., & Erman, B. (1998) · Physical Review Letters · doi:10.1103/physrevlett.80.2733 · Cited by 442 · see citing works
Self-citationComputational study of protein specificity: The molecular basis of HIV-1 protease drug resistance
Wang, W., & Kollman, P. A. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.251265598 · Cited by 251 · see citing works
Prediction of Human Immunodeficiency Virus Protease Cleavage Sites in Proteins
Chou, K. (1996) · Analytical Biochemistry · doi:10.1006/abio.1996.0001 · Cited by 247 · see citing works
Molecular characterization of gag proteins from simian immunodeficiency virus (SIVMne)
Henderson, L. E., Benveniste, R. E., Sowder, R. C., II, Copeland, T. D., Schultz, A. M., & Oroszlan, S. I. (1988) · Journal of Virology · doi:10.1128/jvi.62.8.2587-2595.1988 · Cited by 185 · see citing works
Wong, K. F., Selzer, T., Benkovic, S. J., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0408343102 · Cited by 143 · see citing works
Identification of kinetically hot residues in proteins
Demirel, M. C., Atılgan, A. R., Bahar, İ., Jernigan, R. L., & Erman, B. (1998) · Protein Science · doi:10.1002/pro.5560071205 · Cited by 122 · see citing works
Self-citationRevisiting Monomeric HIV-1 Protease
Louis, J. M., Ishima, R., Nesheiwat, I., et al. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m209726200 · Cited by 56 · see citing works
Blundell, T. L., & Pearl, L. H. (1989) · Nature · doi:10.1038/337596a0 · Cited by 52 · see citing works
Prediction of Binding Sites in Receptor-Ligand Complexes with the Gaussian Network Model
Haliloǧlu, T., Seyrek, E., & Erman, B. (2008) · Physical Review Letters · doi:10.1103/physrevlett.100.228102 · Cited by 45 · see citing works
Self-citationMolecular mechanics analysis of drug-resistant mutants of HIV protease
Weber, I. T., & Harrison, R. W. (1999) · Protein Engineering Design and Selection · doi:10.1093/protein/12.6.469 · Cited by 37 · see citing works
Louis, J. M., Smith, C. A., Wondrak, E. M., et al. (1989) · Biochemical and Biophysical Research Communications · doi:10.1016/0006-291x(89)91678-1 · Cited by 35 · see citing works
Association of putative concave protein‐binding sites with the fluctuation behavior of residues
Ertekin, A., Nussinov, R., & Haliloǧlu, T. (2006) · Protein Science · doi:10.1110/ps.051815006 · Cited by 25 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Wei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436 · see citing works
Dynamic Allostery: Linkers Are Not Merely Flexible
Ma, B., Tsai, C.-J., Haliloğlu, T., & Nussinov, R. (2011) · Structure · doi:10.1016/j.str.2011.06.002 · Cited by 222 · see citing works
Self-citationLong-range energy transfer in proteins
Piazza, F., & Sanejouand, Y.-H. (2009) · Physical Biology · doi:10.1088/1478-3975/6/4/046014 · Cited by 58 · see citing works
- Authors
- Haliloglu, T., & Erman, B.
- Affiliations
- Koç University (TR)
- ORCID
- Erman, Burak
- Venue
- Physical Review Letters
- Publisher
- American Physical Society (APS)
- Published
- 2009-02-27
- Volume
- 102
- Issue
- 8
- Pages
- 088103-088103
- ISSN
- 0031-9007 (ISSN-L)
- 1079-7114
- OpenAlex
- W2062341807
- Cited by
- 38
- References
- 18
- Citations by year
- 2024: 1 · 2022: 1 · 2021: 1 · 2020: 3 · 2017: 2 · 2016: 5 · 2015: 3 · 2014: 3 · 2013: 4
- FWCI
- 2.01
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Physical Review Letters (publishedVersion)
- PubMed (publishedVersion)
- Digital Collections portal (Koç University) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Computational Drug Discovery Methods
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Interaction Studies and Fluorescence Analysis
- Keywords
- energy fluctuations, residue fluctuations, native proteins, Gaussian network model, drug binding sites, HIV protease, drug-protein binding
- MeSH terms
- Binding Sites, Models, Chemical, Models, Molecular, Protein Binding, Proteins, Thermodynamics, HIV-1, Normal Distribution, HIV Protease
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
