Albany 2001

category image Biomolecular
SUNY at Albany
June 19-23, 2001

Methyl groups as probes of structure and dynamics in peptides and proteins

Dynamical NMR has enabled measurement of correlation times for the dynamics of methyl groups in proteins and crystalline amino acids. These data may yield important information concerning the structure (packing) and dynamics of proteins. We have undertaken simulations to elucidate the relationship between structure and methyl dynamics. We report results of simulations of crystalline amino acids, a 13-residue peptide, and staphylococcal nuclease (SNase). The agreement between NMR and simulated methyl correlation times is quite good across a set of four crystalline amino acids, which supports the use of simulation to interpret the NMR data. However, some alanine methyl correlation times for SNase are much longer in simulation than in NMR. We show that the simulated correlation times are strongly correlated with adiabatic rotational barriers. The barriers can vary by several kcal/mol over the 11 ns simulation, and furthermore it is likely that the simulation time scale precludes sampling some important conformations. We will address the hypothesis that for proteins under physiological conditions, in most conformations some methyl groups are relatively free to rotate, while others are sterically hindered. Our research suggests that methyl correlation times measured by NMR reflect an an average environment that may not be representative of any particular folded conformation.

David Chatfield,

Florida International University Chemistry Department Florida International University Miami, FL 33199
tel (305) 348-3977; fax (305) 348-3772; chatfiel@fiu.edu