S. Khalid

Phospholipid transport to the bacterial outer membrane through an envelope-spanning bridge

This study identifies YhdP as a phospholipid transporter spanning the bacterial cell envelope, using AlphaFold, electron microscopy, and simulations to show its structure and function.

An ancestral dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes

This study identifies OmpM as a dual-function protein in diderm Firmicutes that tethers the outer membrane to peptidoglycan and facilitates nutrient uptake.

Activation and substrate specificity of the human P4-ATPase ATP8B1

This study presents cryo-EM structures and functional analysis of the human ATP8B1-CDC50A complex, revealing its mechanism of action, substrate specificity, and regulation by phosphoinositides.

Energy extraction from air: structural basis of atmospheric hydrogen oxidation

This paper determines the structure of a mycobacterial hydrogenase and explains how it selectively oxidizes atmospheric H2 while avoiding O2, enabling energy extraction from air.

Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni

This study uses molecular dynamics simulations to analyze the conformational dynamics and substrate extrusion pathways of N-glycosylated CmeC in Campylobacter jejuni, revealing the role of glycans and cations in antibiotic and bile resistance.

Impact on S. aureus and E. coli membranes of treatment with chlorhexidine and alcohol solutions: insights from molecular simulations and nuclear magnetic resonance.

This study uses molecular simulations and NMR to examine how chlorhexidine and alcohol affect S. aureus and E. coli membranes, showing chlorhexidine's role in membrane partitioning.

A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer

This study identifies a novel fold for the AT3 domain in bacterial acetyltransferases, revealing a mechanism for transmembrane acyl-group transfer and providing a framework for inhibitor development.

Structural basis for host recognition and superinfection exclusion by bacteriophage T5

This study reveals the structural basis of host recognition and superinfection exclusion by bacteriophage T5 through cryo-EM and crystal structures of its receptor and SE proteins.

Molecular architecture of the TasA biofilm scaffold in Bacillus subtilis

This study reveals the molecular structure of TasA biofilm scaffolds in Bacillus subtilis, showing they form β-sheet-rich filaments through donor strand complementation, essential for biofilm formation.

#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol

This paper uses AI-enabled multiscale computational microscopy to study SARS-CoV-2 Delta variant in respiratory aerosols, revealing atomic-level insights into airborne transmission.

Effects of early life adversity on meningeal mast cells and proinflammatory gene expression in male and female Mus musculus

This study investigates how early life adversity affects meningeal mast cells and inflammatory gene expression in male and female mice, finding sex-specific effects and a role for mast cells in disease susceptibility.

Uncovering cryptic pockets in the SARS-CoV-2 spike glycoprotein

This study identifies a novel cryptic pocket on the SARS-CoV-2 spike protein using molecular dynamics simulations and validates its druggable potential through experimental methods.

Dynamic interplay between a TonB dependent heme transporter and a TonB protein in a membrane environment

The paper uses molecular dynamics simulations to study the interaction between a heme transporter and a TonB-like protein in E. coli, revealing dynamic interactions and validating them experimentally.

Structural basis for silicon uptake by higher plants

This study presents the X-ray structure and molecular dynamics simulations of OsNIP2;1, revealing how silicon is taken up by plant roots through aquaporins.

Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion

The paper shows that Pseudomonas putida F1 uses FadL channels for lateral diffusion of monoaromatic hydrocarbons, bypassing the outer membrane's polar barrier.

AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics

This paper develops an AI-driven workflow to simulate SARS-CoV-2 spike protein dynamics, revealing glycan shield structure, spike glycans' role in infectivity, and spike-ACE2 interactions.

Structure-based modelling and dynamics of MurM, a Streptococcus pneumoniae penicillin resistance determinant that functions at the cytoplasmic membrane interface

The paper models MurM's structure and dynamics to show its interaction with phospholipids and Lipid II, revealing its role in penicillin resistance in Streptococcus pneumoniae.

Molecular Dynamics Simulations of Bacterial Outer Membrane Lipid Extraction: Adequate Sampling?

This study evaluates simulation protocols for accurately sampling lipopolysaccharide dynamics in bacterial membranes, finding that decoupling cations improves convergence while lateral mixing remains slow.

The Hitchhiker's Guide to the Periplasm: Unexpected Molecular Interactions of Antibiotics Revealed by Considering Crowding Effects in E. coli

This study uses molecular dynamics simulations to show that the antibiotic polymyxin B1 forms transient and long-lived interactions with periplasmic proteins and lipoproteins, suggesting it hitchhikes through the periplasm rather than diffusing freely.

Structure and lipid dynamics in the A. baumannii maintenance of lipid asymmetry (MLA) inner membrane complex

This study reports cryo-EM structures of the A. baumannii MLA complex in different states and proposes a molecular mechanism for lipid transport.

Translocation of flexible and tensioned ssDNA through in silico de-signed hydrophobic nanopores with two constrictions.

This study investigates how hydrophobic nanopores with two constrictions affect ssDNA translocation, showing that aromatic residues slow translocation and influence DNA conformation and variability under tension.

Interactions of a bacterial RND transporter with a transmembrane small protein in a lipid environment

The paper reports cryo-EM structures of AcrB and the AcrBZ complex, showing how AcrZ and lipid interactions modulate AcrB activity.

Pal stabilises the bacterial outer membrane during constriction by a mobilisation-and-capture mechanism

The paper shows the Tol system in E. coli actively mobilizes and captures Pal to coordinate outer membrane constriction with cell division.

To infect or not to infect: molecular determinants of bacterial outer membrane vesicle internalization by host membranes

This study uses molecular dynamics simulations to show that lipopolysaccharide length affects OMV shape and internalization by host membranes.

Binding From both sides: TolR and full-length OmpA bind and maintain the local structure of the E. coli cell wall

This study uses molecular modeling to show TolR and OmpA bind the E. coli cell wall from opposite sides, maintaining its structure without Brauns lipoprotein.

The outer membrane proteins OmpA, FhuA, OmpF, EstA, BtuB and OmpX have unique lipopolysaccharide fingerprints.

The paper uses molecular dynamics simulations to show that six E. coli outer membrane proteins have unique interactions with lipopolysaccharide, influenced by membrane composition and lipid mobility.

Prediction of the closed conformation and insights into the mechanism of the membrane enzyme LpxR

The paper uses simulations to predict the closed conformation of LpxR and elucidate its mechanism of substrate binding.