Comparison of Protein Backbone Entropy and β-Sheet Stability:  NMR-Derived Dynamics of Protein G B1 Domain Mutants

Role of Entropy in Protein Thermostability: Folding Kinetics of a Hyperthermophilic Cold Shock Protein at High Temperatures Using 19F NMR

“…The only currently available experimental methods with the potential capability of addressing some of these issues are nuclear spin relaxation rate measurements (50, 51; for a review, see ref 52). In a recent study, Stone and co-workers (53) found a striking correlation between the stability and backbone flexibility of several protein G B1 domain mutants, suggesting that increased backbone conformational entropy is a means of protein stabilization. Similar analyses might be able to clarify whether related mechanisms are utilized to achieve the remarkable stability of proteins from thermophilic organisms.…”

Procrustean rotation in concert with principal component analysis of molecular dynamics trajectories: Quantifying global and local differences between conformational samples

“…The temperature at which the protein is half folded/half unfolded ͑T m ͒ was measured to be 89°C. 11,16 This small protein domain maintains its folded structure without disulfide cross-links or tight ligand binding. 17 The densely packed hydrophobic core is what is assumed to give the domain its high thermal stability.…”

“…The chosen mutants cover a wide range of thermal stabilities and their backbone dynamics ͑with the exception of the T53P mutation which disrupts folding of the domain entirely͒ has been investigated by NMR. 16 Previous groups have tried to quantify the trend in decreasing thermal stability due to mutation at the Thr53 site and explain the result. Goehlert et al 20 investigated the contribution of methyl group side chain conformational entropy to the relative stabilities of ten of the 20 mutants.…”

“…However, their results were inconclusive due to limitations of the ͗S 2 ͘ order parameter, and the need to analyze additional mutants before this explanation can be generalized. 16 Due to its small size and interesting thermal stability, PG␤1 has been the subject of a number of computational investigations. 12,[24][25][26][27] Here, we perform short MD simulations on models for wild-type PG␤1 ͑WT͒ and four mutants TM, T53M, T53A, and T53P in order to obtain conformational samples, which we then subject to PCA, followed by Procrustean rotation of the mutant variance matrices to the target wild-type matrix.…”

Applications of NMR Spin Relaxation Methods for Measuring Biological Motions

“…22,23 Additionally, NMR spin relaxation methods have revealed that picosecond to nanosecond time scale motions contribute to the thermodynamics of biomolecular folding and structure. [24][25][26][27][28][29][30][31][32][33] For example, Akke et al 34 developed an analytical expression that relates the changes in backbone mobility derived from NMR spin relaxation data to the Gibbs free energy of a process. The approach was applied to the cooperative Ca 2+ binding to the protein calbindin D 9k in which significant contributions to the free energy of cooperativity were demonstrated to arise from motions of the protein backbone on the nanosecond to picosecond time scale.…”