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Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis—application to the HIV-1 protease
- Source :
- Physical Chemistry Chemical Physics, Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2010, 12 (12), pp.2850. ⟨10.1039/b919148h⟩
- Publication Year :
- 2010
- Publisher :
- HAL CCSD, 2010.
-
Abstract
- International audience; Protein flexibility is essential for enzymatic function, ligand binding, and protein–protein or protein–nucleic acid interactions. Normal mode analysis has increasingly been shown to be well suited for studying such flexibility, as it can be used to identify favorable structural deformations that correspond to functional motions. However, normal modes are strictly relevant to a single structure, reflecting a particular minimum on a complex energy surface, and are thus susceptible to artifacts. We describe a new theoretical framework for determining ‘‘consensus’’ normal modes from a set of related structures, such as those issuing from a short molecular dynamics simulation. This approach is more robust than standard normal mode analysis, and provides higher collectivity and symmetry properties. In an application to HIV-1 protease, the low-frequency consensus modes describe biologically relevant motions including flap openingand closing that can be used in interpreting structural changes accompanying the bindingof widely differing inhibitors.
- Subjects :
- Models, Molecular
Magnetic Resonance Spectroscopy
Stereochemistry
General Physics and Astronomy
Molecular Dynamics Simulation
01 natural sciences
03 medical and health sciences
Molecular dynamics
HIV Protease
HIV-1 protease
Normal mode
0103 physical sciences
Humans
Physical and Theoretical Chemistry
[SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM]
030304 developmental biology
Flexibility (engineering)
0303 health sciences
010304 chemical physics
biology
Chemistry
Mode (statistics)
Function (mathematics)
Symmetry (physics)
HIV-1
biology.protein
Standard normal table
Biological system
Subjects
Details
- Language :
- English
- ISSN :
- 14639076 and 14639084
- Database :
- OpenAIRE
- Journal :
- Physical Chemistry Chemical Physics, Physical Chemistry Chemical Physics, Royal Society of Chemistry, 2010, 12 (12), pp.2850. ⟨10.1039/b919148h⟩
- Accession number :
- edsair.doi.dedup.....478e208fab6faad1909369dabacbd4fd