Thermostability of Enzymes from Molecular Dynamics Simulations

Abstract

Thermodynamic stability is a central requirement for protein function and one goal of protein engineering is improvement of stability, particularly for applications in biotechnology. Herein, molecular dynamics simulations are used to predict in vitro thermostability of members of the bacterial Ribonuclease HI (RNase H) family of endonucleases. The temperature dependence of the generalized order parameter, S, for four RNase H homologs, from psychrotrophic, mesophilic and thermophilic organisms, is highly correlated with experimentally determined melting temperatures and with calculated free energies of folding at the midpoint temperature of the simulations. This study provides an approach for in silico mutational screens to improve thermostability of biologically and industrially relevant enzymes.

Heat-resistant cytosolic malate dehydrogenases (cMDHs) of thermophilic intertidal snails (genus Echinolittorina): protein underpinnings of tolerance to body temperatures reaching 55°C

“…Binding involves residues 92-98, the active site loop comprises residues 91-101, and the region important for subunitsubunit interactions comprises residues 230, 238, 243, 244 and 248 (Chapman et al, 1999;Dong and Somero, 2009). These are sites where evolutionary trade-off between activity and stability may be especially important (Tattersall et al, 2012;Zeiske et al, 2016). A potential general pattern in temperature adaptation of enzymes was proposed that conjectured that the sensitivity of an enzyme to temperature and, thereby, the intensity of selection for temperature adaptation of structure depends on the degree of conformational change that the enzyme undergoes during catalysis (Lockwood and Somero, 2012).…”

Role of simple descriptors and applicability domain in predicting change in protein thermostability

“…Inclusion of even more complex descriptors, e.g. conformational flexibility [ 21 , 62 – 65 ], may enhance predictive capabilities, however the limited and unbalanced experimental dataset available to train models is shown, herein, to be a major obstacle for prospective predictions. Our results suggest that most published models built with the available datasets would suffer from the same ill fate of having narrow applicability domain (i.e.…”

“…Differences in structural fluctuations of molecular dynamics (MD) trajectories have been shown to correlate with changes in thermostability. [ 21 , 22 ] However, MD is not tractable for mutant triage. Additionally, calculated ddG of unfolding has been used to predict the classification of change in thermostability as a result of single point mutations.…”

How to Lengthen the Long-Term Stability of Enzyme Membranes: Trends and Strategies

“…However, knowledge of the relationships between protein structures and their properties is still lacking at this stage. Though thermo-stability prediction of enzymes combined with known protein sequences has been carried out with molecular dynamics simulations [25,26], and the complete design of amino acid sequences cannot be feasible.…”