Structure of the bacterial cell envelope and interactions with antimicrobials: insights from molecular dynamics simulations
Bacteria have evolved over 3 billion years, sha** our intrinsic and symbiotic coexistence
with these single-celled organisms. With rising populations of drug-resistant strains, the …
with these single-celled organisms. With rising populations of drug-resistant strains, the …
Atomistic simulation of molecules interacting with biological nanopores: from current understanding to future directions
Biological nanopores have been at the focus of numerous studies due to their role in many
biological processes as well as their (prospective) technological applications. Among many …
biological processes as well as their (prospective) technological applications. Among many …
Conformational dynamics of loop L3 in OmpF: implications toward antibiotic translocation and voltage gating
In the present work, we delineate the molecular mechanism of a bulky antibiotic permeating
through a bacterial channel and uncover the role of conformational dynamics of the …
through a bacterial channel and uncover the role of conformational dynamics of the …
Converging PMF Calculations of Antibiotic Permeation across an Outer Membrane Porin with Subkilocalorie per Mole Accuracy
The emergence of multidrug-resistant pathogens led to a critical need for new antibiotics. A
key property of effective antibiotics against Gram-negative bacteria is their ability to …
key property of effective antibiotics against Gram-negative bacteria is their ability to …
Antibiotic charge profile determines the extent of L3 dynamics in OmpF: an expedited passage for molecules with a positive charge
Efficient permeation into Gram-negative bacterial cells is a much-desired property in the
design of antibacterial agents. The goal is to arrive at one or more chemical modifications of …
design of antibacterial agents. The goal is to arrive at one or more chemical modifications of …
Boosting the conformational sampling by combining replica exchange with solute tempering and well‐sliced metadynamics
Methods that combine collective variable (CV) based enhanced sampling and global
tempering approaches are used in speeding‐up the conformational sampling and free …
tempering approaches are used in speeding‐up the conformational sampling and free …
Seeing is believing: Illuminating the Gram-negative outer membrane with molecular dynamics simulations
Recent advances in molecular dynamics (MD) simulations have led to rapid improvement in
our understanding of the molecular details of the outer membranes (OMs) of Gram-negative …
our understanding of the molecular details of the outer membranes (OMs) of Gram-negative …
Proton-exchange reaction in acidic zeolites: Mechanism and free energetics
Conversion of alkanes to liquid fuels and other chemicals has a great demand in many
industrial applications. The key challenge in the alkane conversion is the activation of the C …
industrial applications. The key challenge in the alkane conversion is the activation of the C …
Temperature Accelerated Sliced Sampling to Probe Ligand Dissociation from Protein
Modeling ligand unbinding in proteins to estimate the free energy of binding and probing the
mechanism presents several challenges. They primarily pertain to the entropic bottlenecks …
mechanism presents several challenges. They primarily pertain to the entropic bottlenecks …
Molecular Mechanism of Ciprofloxacin Translocation Through the Major Diffusion Channels of the ESKAPE Pathogens Klebsiella pneumoniae and Enterobacter …
Experimental studies on the translocation and accumulation of antibiotics in Gram-negative
bacteria have revealed details of the properties that allow efficient permeation through …
bacteria have revealed details of the properties that allow efficient permeation through …