Browsing by Author "Prajapati, Jigneshkumar D."

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Brownian dynamics approach including explicit atoms for studying ion permeation and substrate translocation across nanopores
(ACS, 2018-11) Prajapati, Jigneshkumar D.
A Brownian dynamics (BD) approach including explicit atoms called BRODEA is presented to model ion permeation and molecule translocation across a nanopore confinement. This approach generalizes our previous hybrid molecular dynamics–Brownian dynamics framework (J. Chem. Theory Comput. 2016, 12, 2401) by incorporating a widespread and enhanced set of simulation schemes based on several boundary conditions and electrostatic models, as well as a temperature accelerated method for sampling free energy surfaces and determining substrate translocation pathways. As a test case, BRODEA was applied to study the ion diffusion as well as to ciprofloxacin and enrofloxacin transport through the outer membrane porin OmpC from E. coli. The equivalence between the different simulation schemes was demonstrated and their computational efficiency evaluated. The BRODEA results are able to reproduce the main features of the ion currents and free energy surfaces determined by all-atom molecular dynamics simulations and validated by experiments. Furthermore, the BRODEA results are able to determine the ciprofloxacin and enrofloxacin permeation pathways showing a remarkable agreement with the results obtained from a computational protocol that combines metadynamics and a zero-temperature string method (J. Chem. Theory Comput. 2017, 13, 4553; J. Phys. Chem. B2018, 122, 1417). To our knowledge, this is the first time such antibiotic permeation pathways have been characterized by a technique based on Brownian dynamics.
Ribosome hyper-swivel head domain motions are required for translocation and resetting
(Elsevier, 2023-02) Prajapati, Jigneshkumar D.
Translocation of messenger RNA (mRNA) and transfer RNA (tRNA) substrates through the ribosome during protein synthesis, an exemplar of directional molecular movement in biology, entails a complex interplay of conformational, compositional, and chemical changes. The molecular determinants of early translocation steps have been investigated rigorously. However, the elements enabling the ribosome to complete translocation and reset for subsequent protein synthesis reactions remain poorly understood. Here, we have combined molecular simulations with single-molecule fluorescence resonance energy transfer imaging to gain insights into the rate-limiting events of the translocation mechanism.1 We find that diffusive motions of the ribosomal small subunit head domain to hyper-swivelled positions, governed by universally conserved rRNA, can maneuver the mRNA and tRNAs to their fully translocated positions. Subsequent engagement of peptidyl-tRNA and disengagement of deacyl-tRNA from mRNA, within their respective small subunit binding sites, facilitate the ribosome resetting mechanism after translocation has occurred to enable protein synthesis to resume
Transport through bacterial membrane pores: insights from enhanced sampling simulations
(Elsevier, 2022-02) Prajapati, Jigneshkumar D.
Channels in the outer membrane of Gram-negative bacteria provide essential pathways for the controlled and unidirectional transport of ions, nutrients and metabolites into the cell. At the same time, the outer membrane serves as a physical barrier for the penetration of noxious substances such as antibiotics into the bacteria. In this contribution the simulation of ion and substrate transport across such bacterial channels will be detailed. As examples, the translocations of the antibiotics fosfomycin, ciprofloxacin and enrofloxacin through the major diffusion channels OmpF and OmpC have recently been computed using metadynamics and the temperature-accelerated sliced sampling approach (Chem. Rev. 121, 5158 (2021); J. Chem. Theory Comput. 17, 4564 (2021); J. Chem. Theory Comput. 17, 549 (2021)). The results will be compared to experimental findings when possible. A main focus of this contribution is on the testing and application of enhanced sampling approaches, their effective sampling and the inclusion of an enlarged number of degrees of freedom.
Understanding the structure and function of the Dcap channel from acinetobacter baumannii using MD simulations
(Elsevier, 2018-02) Prajapati, Jigneshkumar D.
DcaP is putative dicarboxylate specific channel, located in the outer membrane of the pathogen Acinetobacter baumannii. The X-ray crystal structure reveals that DcaP is the first trimeric channel identified in Acinetobacter baumannii and could play an important role in substrate and antibiotic permeation. To characterize the permeation properties of this channel, we have carried out the applied field MD simulations in the presence of ions (KCl), substrates (phthalic acid, succinic acid) and a β-lactam antibiotic (sulbactam). Additionally, free energy calculation have been carried out using metadynamics simulations to identify the lowest energy permeation path along the 2D free energy surfaces and the most prominent residues during translocation. These simulations clearly suggest that the DcaP channel is involved in the permeation of these solutes and results are complemented with electrophysiology experiments. Furthermore, the crystal structure reveals that DcaP have an extended N-terminus domain in the periplasmic space, which is presumably known to form the coiled-coil structure (uniprot entry: A0A0B9X9I7). As the N-terminus domain was not resolved in the crystal structure, we have predicted the structure using an extensive modeling approach. Moreover, the simulations and electrophysiology experiments suggest that the N-terminus might play an important role in the formation of a stable trimer. Overall, we have built the so far unknown structure-function relationship for the DcaP channel which could help in designing next generation antibiotics efficiently permeating through this channel.
Understanding the translocation of fluoroquinolones through OmpC using the metadynamics
(Cell Press, 2015-01) Prajapati, Jigneshkumar D.
The outer membrane of Gram-negative bacteria such as Escherichia coli acts as a selective permeable barrier between cell and external environment. Water filled outer membrane proteins called as porins were identified for exchange of hydrophilic solutes and hydrophilic antibiotics. One of the most abundant outer membrane porins in E. coli is OmpC and many studies revealed that down-regulation or mutation of this porin shows reduced accumulation of antibacterials in bacterial cells [1]. Fluoroquinolones, used since 1980, are the most common treatment for urinary tract infection caused by E. coli and today this treatment is ineffective in more than half of the patients globally due to widespread resistance. So far the influx kinetics of fluoroquinolones with OmpC has been characterized on free standing lipid bilayers formed on a glass substrate [2]. In particular, detailed analysis of antibiotic interaction with a single OmpC channel using electrophysiology can provide a kinetic description. Here we have investigated two fluoroquinolones, Ciprofloxacin and Enrofloxacin, using an advanced molecular dynamics technique, i.e., metadynamics [3,4]. These free energy calculations help to identify the most favorable paths and activation energies required for molecules to translocate through the OmpC channel. Furthermore, we have also investigated the translocation of the same molecules in the presence of different salts to understand the altered translocation kinetics [5]. Moreover, the identification of favorable interactions networks is important to determine the most prominent residues required for translocation.