Quasi-harmonic analysis of mode coupling in fluctuating native proteins

Why are large conformational changes well described by harmonic normal modes?

Low-frequency normal modes generated by elastic network models tend to correlate strongly with large conformational changes of proteins, despite their reliance on the harmonic approximation, which is only valid in close proximity of the native structure. We consider 12 variants of the torsional network model (TNM), an elastic network model in torsion angle space, that adopt different sets of torsion angles as degrees of freedom and reproduce with similar quality the thermal fluctuations of proteins but present drastic differences in their agreement with conformational changes. We show that these differences are related to the extent of the deviations from the harmonic approximation, assessed through an anharmonic energy function whose harmonic approximation coincides with the TNM. Our results indicate that mode anharmonicity is more strongly related to its collectivity, i.e., the number of atoms displaced by the mode, than to its amplitude; low-frequency modes can remain harmonic even at large amplitudes, provided they are sufficiently collective. Finally, we assess the potential benefits of different strategies to minimize the impact of anharmonicity. The reduction of the number of degrees of freedom or their regularization by a torsional harmonic potential significantly improves the collectivity and harmonicity of normal modes and the agreement with conformational changes. In contrast, the correction of normal mode frequencies to partially account for anharmonicity does not yield substantial benefits. The TNM program is freely available at https://github.com/ugobas/tnm.

Molecular dynamics simulations of site point mutations in the TPR domain of cyclophilin 40 identify conformational states with distinct dynamic and enzymatic properties

Cyclophilin 40 (Cyp40) is a member of the immunophilin family that acts as a peptidyl-prolyl-isomerase enzyme and binds to the heat shock protein 90 (Hsp90). Its structure comprises an N-terminal cyclophilin domain and a C-terminal tetratricopeptide (TPR) domain. Cyp40 is overexpressed in prostate cancer and certain T-cell lymphomas. The groove for Hsp90 binding on the TPR domain includes residues Lys227 and Lys308, referred to as the carboxylate clamp, and is essential for Cyp40-Hsp90 binding. In this study, the effect of two mutations, K227A and K308A, and their combinative mutant was investigated by performing a total of 5.76 μs of all-atom molecular dynamics (MD) simulations in explicit solvent. All simulations, except the K308A mutant, were found to adopt two distinct (extended or compact) conformers defined by different cyclophilin-TPR interdomain distances. The K308A mutant was only observed in the extended form which is observed in the Cyp40 X-ray structure. The wild-type, K227A, and combined mutant also showed bimodal distributions. The experimental melting temperature, Tm, values of the mutants correlate with the degree of compactness with the K308A extended mutant having a marginally lower melting temperature. Another novel measure of compactness determined from the MD data, the "coordination shell volume," also shows a direct correlation with Tm. In addition, the MD simulations show an allosteric effect with the mutations in the remote TPR domain having a pronounced effect on the molecular motions of the enzymatic cyclophilin domain which helps rationalise the experimentally observed increase in enzyme activity measured for all three mutations.

Mode coupling points to functionally important residues in myosin II

Relevance of mode coupling to energy/information transfer during protein function, particularly in the context of allosteric interactions is widely accepted. However, existing evidence in favor of this hypothesis comes essentially from model systems. We here report a novel formal analysis of the near-native dynamics of myosin II, which allows us to explore the impact of the interaction between possibly non-Gaussian vibrational modes on fluctutational dynamics. We show that an information-theoretic measure based on mode coupling alone yields a ranking of residues with a statistically significant bias favoring the functionally critical locations identified by experiments on myosin II.