Normal mode analysis with simplified models to investigate the global dynamics of biological systems
- PMID: 12678809
- DOI: 10.2174/0929866033479077
Normal mode analysis with simplified models to investigate the global dynamics of biological systems
Abstract
Dynamical properties of macromolecules are increasingly being recognized as significantly contributing to biological functions, including catalysis, regulation of activity, etc. In this review, theoretical approaches to the study of dynamics of biological systems and their application are discussed. In particular, simplified models for the normal mode analysis are described.
Similar articles
-
Symmetry, form, and shape: guiding principles for robustness in macromolecular machines.Annu Rev Biophys Biomol Struct. 2006;35:115-33. doi: 10.1146/annurev.biophys.35.040405.102010. Annu Rev Biophys Biomol Struct. 2006. PMID: 16689630 Review.
-
Determination of kinetic rate and equilibrium binding constants for macromolecular interactions: a critique of the surface plasmon resonance literature.Curr Opin Biotechnol. 1994 Feb;5(1):65-71. doi: 10.1016/s0958-1669(05)80072-2. Curr Opin Biotechnol. 1994. PMID: 7764646 Review.
-
Theoretical approaches for dynamical ordering of biomolecular systems.Biochim Biophys Acta Gen Subj. 2018 Feb;1862(2):212-228. doi: 10.1016/j.bbagen.2017.10.001. Epub 2017 Oct 6. Biochim Biophys Acta Gen Subj. 2018. PMID: 28988931 Review.
-
Statistical kinetics of macromolecular dynamics.Biophys J. 2005 Oct;89(4):2277-85. doi: 10.1529/biophysj.105.064295. Epub 2005 Jul 22. Biophys J. 2005. PMID: 16040752 Free PMC article.
-
Normal mode analysis using the driven molecular dynamics method. II. An application to biological macromolecules.J Chem Phys. 2004 Sep 22;121(12):5646-53. doi: 10.1063/1.1777573. J Chem Phys. 2004. PMID: 15366988
Cited by
-
Intrinsic dynamics study identifies two amino acids of TIMP-1 critical for its LRP-1-mediated endocytosis in neurons.Sci Rep. 2017 Jul 14;7(1):5375. doi: 10.1038/s41598-017-05039-z. Sci Rep. 2017. PMID: 28710453 Free PMC article.
-
Calculation of the infrared spectra of proteins.Eur Biophys J. 2015 Apr;44(3):103-12. doi: 10.1007/s00249-014-1005-6. Epub 2014 Dec 24. Eur Biophys J. 2015. PMID: 25538002
-
An intracellular interaction network regulates conformational transitions in the dopamine transporter.J Biol Chem. 2008 Jun 20;283(25):17691-701. doi: 10.1074/jbc.M800475200. Epub 2008 Apr 21. J Biol Chem. 2008. PMID: 18426798 Free PMC article.
-
Alzheimer's abeta(1-40) amyloid fibrils feature size-dependent mechanical properties.Biophys J. 2010 May 19;98(10):2053-62. doi: 10.1016/j.bpj.2009.12.4317. Biophys J. 2010. PMID: 20483312 Free PMC article.
-
Explicit versus implicit consideration of binding partners in protein-protein complex to elucidate intrinsic dynamics.Biophys Rev. 2022 Dec 17;14(6):1379-1392. doi: 10.1007/s12551-022-01026-5. eCollection 2022 Dec. Biophys Rev. 2022. PMID: 36659985 Free PMC article. Review.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources