Elucidating the Effects of Mutation upon C-Type Lysozyme through Quantitative Stability/Flexibility Relationships

Abstract

The Distance Constraint Model (DCM) [1, 2] is a computational modeling scheme that integrates thermodynamic and mechanical descriptions to compute Quantitative Stability/Flexibility Relationships (QSFR) of protein structure. We have previously employed the mDCM to predict melting temperatures of c-type lysozyme mutants with a maximum error of 4.3% [3]. Going further, we now assess the differences in other QSFR quantities across the dataset. The model is parameterized by fitting to experimental heat capacity curves. Subsequently, a large number of mechanical descriptions of protein flexibility are calculated. Pronounced changes in rigidity and flexibility at sites remote from the mutation are common. Drastic changes occur in the backbone flexibility at the mutation site and neighboring residues within 6Å. Increases in rigidity and flexibility are nearly equal, and collectively occur more than sites without change. Interestingly, the β-domain becomes flexible in all cases, likely leading to domain unfolding related to aggregation [4]. We also present changes in pairwise residue-to-residue couplings that can affect functional collective motions. [1] Jacobs, D.J., and Dallakyan, S. Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity. Biophys. J, 2005. 88: p. 903-15. [2] Livesay, D.R., Dallakyan, S., Wood, G.G. and Jacobs, D.J. A flexible approach for understanding protein stability. FEBS Lett, 2004. 576: p. 468-67. [3] Verma, D., Jacobs, D.J. and Livesay, D.R. Predicting the melting point of human c-type lysozyme mutants. Current Protein and Peptide Science, 2010, In press. [4] Canet, D., Last, A.M., Tito, P., Sunde, M., Spencer, A., Archer, D.B., Redfield, C., Robinson, C.V. and Dobson, C.M. Local cooperativity in the unfolding of an amyloidogenic variant of human lysozyme. Nature Structure Biology 9, 2002, 308-315.