Computational methods for generating models of denatured and partially folded proteins.
Partially folded and denatured proteins can give important insights into protein folding, misfolding, and aggregation. Such non-native states of proteins are however very difficult to characterise in detail as they are dynamic, heterogeneous systems comprising of ensembles of interconverting conformers. This article describes methods that produce models for non-native proteins in atomic detail. A variety of molecular dynamics based protocols are discussed together with some recent procedures that include restraints from experimental data. These models provide an important framework for interpreting experimental data from studies of non-native states using nuclear magnetic resonance spectroscopy, fluorescence, circular dichroism, and small angle scattering techniques.
Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK. lorna.smith@chem.ox.ac.uk
Lorna J
LJ
Smith
D000818:Animals; D007611:Aprotinin / Q000737:chemistry; D002417:Cattle; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D006801:Humans; D007768:Lactalbumin / Q000737:chemistry; D008958:Models, Molecular; D011489:Protein Denaturation; D017510:Protein Folding; D012997:Solvents / Q000737:chemistry; D013696:Temperature
D012997:Solvents; D007768:Lactalbumin; D007611:Aprotinin