The study of protein conformational dynamics is motivated in large part by a desire to understand the forces present at different sites throughout the molecular structure. The generalized order parameter determined by NMR spectroscopy has played a central role in the study of protein dynamics on the picosecond-nanosecond time scale. A modeling procedure is presented for analysis of the temperature dependence of the generalized order parameter that extends a previous analysis (Massi and Palmer, J Am Chem Soc 2003;125:11158-11159). As part of this procedure, the potential of mean force is characterized for the N-H bond vectors of the protein backbone. This procedure accounts for the observed temperature dependence of the generalized order parameter in a representative data set from the B1 domain of Streptococcal protein G (Seewald, Pichumani, Stowell, Tibbals, Regan, and Stone, Protein Sci 2000;9:1177-1193). The results indicate a general trend, in which the force constants associated with the potential of mean force decrease with increasing temperature. The analysis also provides evidence for variations in the potential of mean force for different secondary structural elements.
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