Flowchart describing the operation of NMRdyn.

Abstract

<p>Panel A shows that the system being studied may be a monomeric protein or may include oligomers. The types of parameters that describe the dynamics of the system are labeled. In the monomeric case, relaxation data are usually measured at different magnetic field strengths and at one concentration, for a series of n nuclei (typically the backbone amide nitrogen for each amino acid, or backbone/sidechain <sup>13</sup>C labeled sites) as shown in panel B. To study self-association, data at multiple concentrations are required. Relaxation data, molecular parameters, and physical constants are used as input into NMRdyn. Panel C (left side) shows that in the case of a monomeric protein, NMRdyn performs a ‘classical’ analysis, where the AIC value is minimized until it and all microdynamic parameters converge with model optimization and model selection performed at each minimization step. For studies of protein self-association (Panel C, right side), a grid-search approach can be applied, resulting in a set of microdynamic parameters describing the monomeric protein and the oligomer.</p

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