Understanding protein dynamics using conformational ensembles.
Conformational ensembles are powerful tools to represent the range of conformations that can be sampled by proteins. They can be generated by using purely theoretical methods or, as is most often the case, by fitting ensembles of conformations to experimental data that report on the amplitude of protein dynamics. Conformational ensembles have been useful instruments to study fundamental properties of proteins such as the mechanism of molecular recognition, the early stages of protein folding and the mechanism by which structural information propagates through the structures of globular proteins structures via correlated backbone motions. In this chapter I will review the various approaches that have been put forward in the literature to generate conformation ensembles for proteins and present a selection of examples of how such representations of the structural heterogeneity of proteins have been used to explore the fundamental properties of these macromolecules. Finally, I will look ahead at likely future developments in this area, which is important for structural and chemical biology as well as for biophysics.
Joint BSC-IRB Research Programme in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Barcelona, Spain, xavier.salvatella@irbbarcelona.org.
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Salvatella
D000465:Algorithms; D000494:Allosteric Regulation; D016229:Amyloid beta-Peptides / Q000737:chemistry*; D001550:Benzamidines / Q000737:chemistry; D006801:Humans; D056004:Molecular Dynamics Simulation / Q000706:statistics & numerical data* / Q000639:trends; D019906:Nuclear Magnetic Resonance, Biomolecular; D010446:Peptide Fragments / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D014357:Trypsin / Q000737:chemistry; D025801:Ubiquitin / Q000737:chemistry
D016229:Amyloid beta-Peptides; D001550:Benzamidines; D010446:Peptide Fragments; D025801:Ubiquitin; C078592:amyloid beta-protein (1-40); C075222:amyloid beta-protein (1-42); D014357:Trypsin; C032157:benzamidine