Pathways for conformational change in nitrogen regulatory protein C from discrete path sampling.
Pathways corresponding to the conformational change in nitrogen regulatory protein C are calculated using the CHARMM19 force field with an implicit solvation model. Our analysis employs the discrete path sampling approach to grow a database of local minima and transition states from the potential energy surface that contains kinetically relevant pathways. The pathways with the largest contribution to the phenomenological two-state rate constants are found to exhibit a number of structural features that agree with experimental observations. Further details of the calculated pathways for conformational change may therefore provide useful predictions of how this large-scale motion is achieved.
Khalili
Mey
M
University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, UK.
Wales
David J
DJ
D018360:Crystallography, X-Ray; D008958:Models, Molecular; D051922:PII Nitrogen Regulatory Proteins / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
D051922:PII Nitrogen Regulatory Proteins; D012997:Solvents