Correlation times and adiabatic barriers for methyl rotation in SNase.
The relation of rotational correlation times to adiabatic rotational barriers for alanine methyl groups in staphylococcal nuclease (SNase) is investigated. The hypothesis that methyl rotational barriers may be useful probes of local packing in proteins is supported by an analysis of ten X-ray crystal structures of SNase mutants. The barrier heights are consistent across a set of ten structures of a native SNase and mutants containing single-point mutations or single or double insertions, most in a ternary SNase complex. The barriers for different methyls have a range of 7.5 kcal/mol, which at 300 K would correspond to a five-order-of-magnitude range in correlation time. It is demonstrated that adiabatic rotational barriers can fluctuate significantly during an MD simulation of hydrated SNase, but that a Boltzmann weighted average is predictive of rotational correlation times determined from correlation functions. Even if a given methyl is on average quite sterically hindered, infrequently sampled low-barrier conformations may dominate the Boltzmann distribution. This result is consistent with the observed uniformity of NMR correlation times for (13)C-labeled methyls. The methyl barriers in simulation fluctuate on multiple time scales, which can make the precise relationship between methyl rotational correlation time and methyl rotation barriers complicated. The implications of these issues for the interpretation of correlation times determined from NMR and simulation are discussed.
Chatfield
David C
DC
Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA. David.Chatfield@fiu.edu
Augsten
Alberto
A
D'Cunha
Cassian
C
D000409:Alanine / Q000737:chemistry; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008836:Micrococcal Nuclease / Q000737:chemistry*; D008962:Models, Theoretical; D009154:Mutation; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013997:Time Factors
D008836:Micrococcal Nuclease; D000409:Alanine