Evolutionary analysis is a powerful complement to energy calculations for protein stabilization

DOI: 10.1021/acscatal.8b01677

Authors: Koen Beerens (Masaryk University) , Stanislav Mazurenko (Masaryk University) , Antonin Kunka (Masaryk University) , Sérgio M. Marques (Masaryk University; St. Anne's University Hospital Brno) , Niels Hansen (University of Stuttgart) , Milos Musil (Masaryk University; Brno University of Technology) , Radka Chaloupkova (Masaryk University) , Jitka Waterman (Diamond Light Source) , Jan Brezovsky (Masaryk University) , David Bednar (Masaryk University; St. Anne's University Hospital Brno) , Zbynek Prokop (Masaryk University; St. Anne's University Hospital Brno) , Jiri Damborsky (Masaryk University; St. Anne's University Hospital Brno)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Acs Catalysis

State: Published (Approved)
Published: August 2018
Diamond Proposal Number(s): 11175

Abstract: Stability is one of the most important characteristics of proteins employed as biocatalysts, biotherapeutics and biomaterials, and the role of computational approaches in modifying protein stability is rapidly expanding. We have recently identified stabilizing mutations in haloalkane dehalogenase DhaA using phylogenetic analysis but were not able to reproduce the effects of these mutations using force-field calculations. Here we tested four different hypotheses to explain the molecular basis of stabilization using structural, biochemical, biophysical and computational analyses. We demonstrate that stabilization of DhaA by the mutations identified using the phylogenetic analysis is driven by both entropy and enthalpy-contributions, in contrast to primarily enthalpy- driven stabilization by mutations designed by the force-field calculations. Comprehensive bioinformatics analysis revealed that more than half (53%) of 1,099 evolution-based stabilizing mutations would be evaluated as destabilizing by force-field calculations. Thermodynamic integration considers both folded and unfolded states and can describe the entropic component of stabilization, yet it is not suitable for predictive purposes due to computational demands. Altogether, our results strongly suggest that energetic calculations should be complemented by a phylogenetic analysis in protein stabilization endeavors.

Journal Keywords: Protein Stabilization; Thermostability; Evolutionary Analysis; Force-Field Calculations; Computational Tools; Entropy; Enthalpy; Thermodynamic integration

Subject Areas: Biology and Bio-materials, Chemistry


Instruments: I04-Macromolecular Crystallography

Added On: 03/09/2018 08:31

Discipline Tags:

Biochemistry Chemistry Structural biology Biophysics Life Sciences & Biotech

Technical Tags:

Diffraction Macromolecular Crystallography (MX)