A computational assessment of pH-dependent differential interaction of T7 lysozyme with T7 RNA polymerase

Abstract

BackgroundT7 lysozyme (T7L), also known as N-acetylmuramoyl-L-alanine amidase, is a T7 bacteriophage gene product. It involves two functions: It can cut amide bonds in the bacterial cell wall and interacts with T7 RNA polymerase (T7RNAP) as a part of transcription inhibition. In this study, with the help of molecular dynamics (MD) calculations and computational interaction studies, we investigated the effect of varying pH conditions on conformational flexibilities of T7L and their influence on T7RNAP -T7L interactions.ResultsFrom the MD studies of the T7L at three different pH strengths viz. 5, neutral and 7.9 it was observed that T7L structure at pH 5 exhibited less stable nature with more residue level fluctuations, decrease of secondary structural elements and less compactness as compared to its counterparts: neutral pH and pH 7.9. The T-pad analysis of the MD trajectories identified local fluctuations in few residues that influenced the conformational differences in three pH strengths. From the docking of the minimum energy representative structures of T7L at different pH strengths (obtained from the free energy landscape analysis) with T7RNAP structures at same pH strengths, we saw strong interaction patterns at pH 7.9 and pH 5. The MD analysis of these complexes also confirmed the observations of docking study. From the combined in silico studies, it was observed that there are conformational changes in N-terminal and near helix 1 of T7L at different pH strengths, which are involved in the T7RNAP interaction, thereby varying the interaction pattern.ConclusionSince T7L has been used for developing novel therapeutics and T7RNAP one of the most biologically useful protein in both in-vitro and in vivo experiments, this in silico study of pH dependent conformational differences in T7L and the differential interaction with T7RNAP at different pH can provide a significant insight into the structural investigations on T7L and T7RNAP in varying pH environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s12900-017-0077-9) contains supplementary material, which is available to authorized users.

Structural and molecular dynamics ofMycobacterium tuberculosismalic enzyme, a potential anti-TB drug target

“…Previous studies of MEZ homologs suggest that MEs can adopt open and closed states [13,31]. In our simulations we also observe expansion and contraction of the MEZ active site, which can be tracked by recording the distance between αC atoms on two neighboring helices ( Figure S6).…”

“…With Mn 2+ , malate and NAD + , we observe two stable conformations of MEZ: one elongated and the other collapsed ( Figure 6B). Indeed, multiple conformations of NAD(H) have been observed and described previously in crystallographic, solution NMR, and MD studies [31][32][33][34]. Specifically, the collapsed form is commonly observed for unbound NAD(H) in solution [35], but has also been observed in holo structures, including in the exo-site of human mitochondrial ME (PDB ID:1PJ3, 1PJL [36,37]).…”

“…Domain D, and especially domain C, exhibit the greatest instability; residues in Domain D have RMSF values ranging from 1.5-3.5 Å while domain C has the broadest range from 1-7 Å for the apo MEZ simulation. When compared to RMSF values of other systems, domains C and D are particularly flexible; RMSF values computed from simulations of the highly compact and stable lysozyme are below 1 Å [31], while dimers of Amyloid β(1-40), a highly mobile and flexible protein range from 1-6 Å [33]. Interestingly, though binding might typically be expected to modestly stabilize fluctuations the addition of malate, Mn 2+ and NAD(P) + to the simulations had no impact on the overall stability of the MEZ protein backbone, apart from some reduction in computed αC RMSF values for residues between Gln355 and Ala430 ( Figure S5B).…”

Target-activated transcription for the amplified sensing of protease biomarkers

“…To describe the high amplitude concerted motion in a trajectory, principal components (PCs) extracted with a cosine content of 0.28, PC1 and PC2 for individual trajectories, were utilized to generate free energy landscape (FEL) maps. 46 The coordinates from the FEL maps with a minimum energy cluster at 33.9 ns were used to retrieve the low energy representative structure (Fig. 1a).…”

Molecular Dynamic Simulations and Binding Free Energy Evaluations of Thiazolo-[2,3-b] Quinazolinone Derivatives With wtEGFR-TKD and "TMLR" Mutant EGFR-TKD

“…Both Ligand and protein topologies les are incorporated in a single gromacs le. Gradually, this complex le is placed in the simulation box, which is 1 nm apart from the walls of the periodic boundary and solvates the box 30 . The prepared system is neutralized by using Na + and Cl.…”