Crystal structure of Thermus thermophilus methylenetetrahydrofolate dehydrogenase and determinants of thermostability

Abstract

The elucidation of mechanisms behind the thermostability of proteins is extremely important both from the theoretical and applied perspective. Here we report the crystal structure of methylenetetrahydrofolate dehydrogenase (MTHFD) from Thermus thermophilus HB8, a thermophilic model organism. Molecular dynamics trajectory analysis of this protein at different temperatures (303 K, 333 K and 363 K) was compared with homologous proteins from the less temperature resistant organism Thermoplasma acidophilum and the mesophilic organism Acinetobacter baumannii using several data reduction techniques like principal component analysis (PCA), residue interaction network (RIN) analysis and rotamer analysis. These methods enabled the determination of important residues for the thermostability of this enzyme. The description of rotamer distributions by Gini coefficients and Kullback-Leibler (KL) divergence both revealed significant correlations with temperature. The emerging view seems to indicate that a static salt bridge/charged residue network plays a fundamental role in the temperature resistance of Thermus thermophilus MTHFD by enhancing both electrostatic interactions and entropic energy dispersion. Furthermore, this analysis uncovered a relationship between residue mutations and evolutionary pressure acting on thermophilic organisms and thus could be of use for the design of future thermostable enzymes.

Development of thermostable sucrose phosphorylase by semi-rational design for efficient biosynthesis of alpha-D-glucosylglycerol

“…Tailoring such flexible regions might have a positive effect on the catalytic performance of SPase under harsh conditions. Similar behavior of RMSD and RMSF in the analysis of thermostable proteins is observed in studies for other enzymes like lipase (Wang et al 2020), trehalose synthase (Chen et al 2021), or methylenetetrahydrofolate dehydrogenase (Maiello et al 2020). Furthermore, the intermolecular interactions between the residues were analyzed.…”

A proteomics-MM/PBSA dual approach for the analysis of SARS-CoV-2 main protease substrate peptide specificity

“…Because this -TΔS value is similar, the task of ranking the binding can be thus in most cases simplified in first approximation to comparison of the other binding energy values. The somewhat atypical -TΔS value of 47.5 kcal/mol for the GETEQKRIRK peptide is possibly the result of its increased number of large, positively charged residues, which will induce more vibrational and rotational movements, including side-chain rotamer states [49] , [50] . These states are stabilized upon binding, leading to a reduction of conformational entropy.…”

Targeting allosteric binding site in methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) to identify natural product inhibitors via structure-based computational approach

“…The choice of simulation time and convergence criteria aims to strike a balance between capturing relevant dynamics and obtaining accurate and reliable results while efficiently using computational resources. The MD simulations were conducted for the time duration of 300 ns, as influenced by the biological questions being addressed for MTHFD2 protein as mentioned in previous studies 62 , 63 . VMD 64 and UCSF Chimera were used to visualise the MD simulation trajectories 65 .…”