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• W2146332813 endingPage "437" @default.
• W2146332813 startingPage "425" @default.
• W2146332813 abstract "Model-free methods are introduced to determine quantities pertaining to protein domain motions from normal mode analyses and molecular dynamics simulations. For the normal mode analysis, the methods are based on the assumption that in low frequency modes, domain motions can be well approximated by modes of motion external to the domains. To analyze the molecular dynamics trajectory, a principal component analysis tailored specifically to analyze interdomain motions is applied. A method based on the curl of the atomic displacements is described, which yields a sharp discrimination of domains, and which defines a unique interdomain screw-axis. Hinge axes are defined and classified as twist or closure axes depending on their direction. The methods have been tested on lysozyme. A remarkable correspondence was found between the first normal mode axis and the first principal mode axis, with both axes passing within 3 A of the alpha-carbon atoms of residues 2, 39, and 56 of human lysozyme, and near the interdomain helix. The axes of the first modes are overwhelmingly closure axes. A lesser degree of correspondence is found for the second modes, but in both cases they are more twist axes than closure axes. Both analyses reveal that the interdomain connections allow only these two degrees of freedom, one more than provided by a pure mechanical hinge." @default.
• W2146332813 created "2016-06-24" @default.
• W2146332813 creator A5023268539 @default.
• W2146332813 creator A5035351286 @default.
• W2146332813 creator A5083564020 @default.
• W2146332813 date "1997-03-01" @default.
• W2146332813 modified "2023-10-18" @default.
• W2146332813 title "Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme" @default.
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• W2146332813 doi "https://doi.org/10.1002/(sici)1097-0134(199703)27:3<425::aid-prot10>3.0.co;2-n" @default.
• W2146332813 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/9094744" @default.
• W2146332813 hasPublicationYear "1997" @default.
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