Mutagenesis of DsbAss is Crucial for the Signal Recognition Particle Mechanism in Escherichia coli: Insights from Molecular Dynamics Simulations

Abstract

The disulfide bond signal sequence (DsbAss) protein is characterized as an important virulence factor in gram-negative bacteria. This study aimed to analyze the “alanine” alteration in the hydrophobic (H) region of DsbAss and to understand the conformational DsbAss alteration(s) inside the fifty-four homolog (Ffh)-binding groove which were revealed to be crucial for translocation of ovine growth hormone (OGH) to the periplasmic space in Escherichia coli via the secretory (Sec) pathway. An experimental design was used to explore the hydrophobicity and alteration of alanine (Ala) to isoleucine (Ile) in the tripartite structure of DsbAss. As a result, two DsbAss mutants (Ala at positions -11 and -13) with same hydrophobicity of 1.539 led to the conflicting translocation of the active OGH gene. We performed molecular dynamics (MD) simulations and molecular mechanics generalized born surface area (MM-GBSA) binding free energy calculations to examine the interaction energetic and dynamic aspects of DsbAss/signal repetition particle 54 (SRP54) binding, which has a principle role in Escherichia coli Sec pathways. Although both DsbAss mutants retained helicity, the MD simulation analysis evidenced that altering Ala-13 changed the orientation of the signal peptide in the Ffh M binding domain groove, favored more stable interaction energies (MM-GBSA ΔGtotal = −140.62 kcal mol−1), and hampered the process of OGH translocation, while Ala-11 pointed outward due to unstable conformation and less binding energy (ΔGtotal = −124.24 kcal mol−1). Here we report the dynamic behavior of change of “alanine” in the H-domain of DsbAss which affects the process of translocation of OGH, where MD simulation and MM-GBSA can be useful initial tools to investigate the virulence of bacteria.

In Vitro Antidiabetic, Anti-Obesity and Antioxidant Analysis of Ocimum basilicum Aerial Biomass and in Silico Molecular Docking Simulations with Alpha-Amylase and Lipase Enzymes

“…Molecular docking coupled with MD simulations is an important method to elucidate the mode of interaction of ligands with specific targets, such as enzymes, and to comprehend the enzyme inhibition mechanisms [18,21,23,24,48]. Our in-silico molecular modeling study revealed a favorable binding affinity of linalool and estragole, the two major constituents of this plant, with PPA and PPL ( Figures 6 and 7) and both compounds showed a similar conformation and interactions pattern as reported with their co-crystalized inhibitors.…”

“…The AMBER16 simulation package was employed for molecular dynamic simulations which uses the AMBER ff99SB force field [35,36]. The same stepwise energy minimization and equilibration protocol was utilized as described in previous studies [18,21,23,24]. The solvated system with explicit water molecular (TIP3 system) was submitted to a production run of 20ns at constant 300 K temperature and 1 bar pressure.…”

“…In-silico molecular docking is a rapidly emerging field to understand and predict possible mode of interaction between a ligand and a target biomolecule [14][15][16][17][18], while molecular dynamics simulations presented a plausible way to estimate the dynamic stability and interaction energetics of a protein-ligand complex [18][19][20][21][22][23][24]. It was, therefore, planned to conduct docking analysis of the major constituents of O. basilicum, linalool and estragole, with alpha-amylase and lipase together with their inhibitors.…”

Pharmacoinformatics and molecular dynamics simulation studies reveal potential covalent and FDA-approved inhibitors of SARS-CoV-2 main protease 3CLpro

“…The approach is typically based on MD simulations of protein-ligand complexes. It has been applied to numerous systems with varying success (Chen et al, 2016;Durrani et al, 2019;Parveen et al, 2019;Sirin et al, 2014) and better covered in various reviews (Chen et al, 2016;Gohlke & Case, 2004;Gohlke et al, 2003). The AMBER MM-GBSA energetic components for each complex are tabulated in Table 1.…”

Enhanced Thermostability and Enzymatic Activity of cel6A Variants from Thermobifida fusca by Empirical Domain Engineering

“…The accessory roles of non-catalytic domains (CBMs) on thermal stability and insoluble substrate degrading efficiencies have been extensively reported by removing or grafting from respective catalytic domain/s [ 17 , 18 , 19 , 20 , 21 , 22 ]. MD simulations (molecular dynamics, is used to analyze physical movements of atoms and molecules by using computational tools) have been used in several studies to evaluate the factors regulating thermostability of enzymes [ 11 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 ] and to investigate the stability of the biomolecular complex and interaction attributes [ 31 , 32 ]. These include the thermal stable mechanisms of rubredoxin [ 33 ], nuclease [ 34 ], barnase [ 35 ], nitrile hydratase [ 36 ], adenylate kinase [ 37 ], carbonic anhydrase [ 38 ], carboxylesterase from Geobacillus stearothermophilus [ 39 ], psychrophilic esterase from Pseudoalteromonas haloplanktis [ 40 ], hyperthermophilic esterase from Archaeoglobus fulgidus [ 41 ], thermostable para-nitrobenzyl esterase from Bacillus subtilis [ 42 ], and CBMs from Clostridium cellulovorans [ 43 , 44 ].…”