List of works - Syma Khalid

A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway

scientific article published on 17 May 2018

A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion

scientific article

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

scientific article published on 20 November 2020

An accurate in vitro model of the E. coli envelope.

scientific article

Atomistic and Coarse Grain Simulations of the Cell Envelope of Gram-Negative Bacteria: What Have We Learned?

scientific article published on 18 December 2018

Bookshelf: a simple curation system for the storage of biomolecular simulation data

scientific article (publication date: 2010)

Both interaction surfaces within cohesin's hinge domain are essential for its stable chromosomal association

scientific article

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

scientific article

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

scientific article published on 20 October 2006

Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations.

scientific article

Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: a molecular dynamics simulation study

scientific article

Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study.

scientific article

Correction to "Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm"

scientific article published on 23 August 2018

Correction to Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

scientific article published on 16 March 2017

DNA and lipid bilayers: self-assembly and insertion

scientific article published in December 2008

DNA lipoplexes: formation of the inverse hexagonal phase observed by coarse-grained molecular dynamics simulation

scientific article published on 01 July 2010

DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants

scientific article published on 10 August 2015

Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm

scientific article published on 06 July 2018

Distinct Intramolecular Hydrogen Bonding Dictates Antimicrobial Action of Membrane-Targeting Amphiphiles

scientific article published on 05 February 2019

Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition

scientific article

Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores

scientific article published on 19 July 2018

Electroporation of the E. coli and S. Aureus membranes: molecular dynamics simulations of complex bacterial membranes.

scientific article

Enantiomeric resolution of supramolecular helicates with different surface topographies

scientific article published on 20 November 2006

Encapsulated membrane proteins: A simplified system for molecular simulation.

scientific article published on 2 March 2016

Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study ⬇️

scientific article published on February 24, 2011

Free-energy calculations reveal the subtle differences in the interactions of DNA bases with α-hemolysin.

scientific article published in February 2015

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

scientific article published on October 2016

Influence of surface shape on DNA binding of bimetallo helicates.

scientific article

Interaction between the NS4B amphipathic helix, AH2, and charged lipid headgroups alters membrane morphology and AH2 oligomeric state--Implications for the Hepatitis C virus life cycle.

scientific article published on 02 May 2015

Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study

scientific article (publication date: April 2015)

Intramolecular DNA coiling mediated by metallo-supramolecular cylinders: differential binding of P and M helical enantiomers.

scientific article

It Is Complicated: Curvature, Diffusion, and Lipid Sorting within the Two Membranes of Escherichia coli

scientific article

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.

scientific article

Molecular Dynamics Simulations Predict the Pathways via Which Pristine Fullerenes Penetrate Bacterial Membranes

scientific article published on 20 October 2016

Molecular Dynamics Simulations Reveal the Conformational Flexibility of Lipid II and Its Loose Association with the Defensin Plectasin in the Staphylococcus aureus Membrane.

scientific article published on 9 May 2016

Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

scientific article published on 25 September 2012

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

scientific article (publication date: 4 August 2015)

Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation

scientific article published on 13 April 2011

Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis.

scientific article

Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?

scientific article published on 01 July 2020

Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: a comparative study

scientific article published on 28 February 2007

Movement of Arginine through OprD: The Energetics of Permeation and the Role of Lipopolysaccharide in Directing Arginine to the Protein

scientific article published on 19 March 2019

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment.

scientific article published on 8 November 2016

On the ability of PAMAM dendrimers and dendrimer/DNA aggregates to penetrate POPC model biomembranes

scientific article published on 01 June 2010

Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints

scientific article published on 21 March 2019

Outer membrane protein G: Engineering a quiet pore for biosensing

scientific article

Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers.

scientific article

Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes

scientific article

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories

scientific article

Role of O-Antigen in Response to Mechanical Stress of the E. coli Outer Membrane: Insights from Coarse-Grained MD Simulations

scientific article published on 23 April 2019

Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.

scientific article published on 11 July 2008

Shape effects on the activity of synthetic major-groove binding ligands

scientific article published on 11 July 2006

Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove

scientific article published on 01 April 2006

Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study ⬇️

scientific article published on September 5, 2012

Stability and membrane orientation of the fukutin transmembrane domain: a combined multiscale molecular dynamics and circular dichroism study

scientific article

Structural basis for Mep2 ammonium transceptor activation by phosphorylation.

scientific article published on 18 April 2016

The Free Energy of Small Solute Permeation through the Escherichia coli Outer Membrane Has a Distinctly Asymmetric Profile.

scientific article published on 12 August 2016

The NorM MATE transporter from N. gonorrhoeae: insights into drug and ion binding from atomistic molecular dynamics simulations

scientific article published on July 2014

The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

scientific article published on April 2015

The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization

scientific article published on 01 June 2018

Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes

scientific article

List of works by Syma Khalid

A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway

A positively charged channel within the Smc1/Smc3 hinge required for sister chromatid cohesion

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

An accurate in vitro model of the E. coli envelope.

Atomistic and Coarse Grain Simulations of the Cell Envelope of Gram-Negative Bacteria: What Have We Learned?

Bookshelf: a simple curation system for the storage of biomolecular simulation data

Both interaction surfaces within cohesin's hinge domain are essential for its stable chromosomal association

Coarse-grained MD simulations of membrane protein-bilayer self-assembly.

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

Communication between the leaflets of asymmetric membranes revealed from coarse-grain molecular dynamics simulations.

Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: a molecular dynamics simulation study

Conformational dynamics of the mitochondrial ADP/ATP carrier: a simulation study.

Correction to "Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm"

Correction to Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

DNA and lipid bilayers: self-assembly and insertion

DNA lipoplexes: formation of the inverse hexagonal phase observed by coarse-grained molecular dynamics simulation

DNA sequencing with MspA: Molecular Dynamics simulations reveal free-energy differences between sequencing and non-sequencing mutants

Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm

Distinct Intramolecular Hydrogen Bonding Dictates Antimicrobial Action of Membrane-Targeting Amphiphiles

Dynamics of Crowded Vesicles: Local and Global Responses to Membrane Composition

Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores

Electroporation of the E. coli and S. Aureus membranes: molecular dynamics simulations of complex bacterial membranes.

Enantiomeric resolution of supramolecular helicates with different surface topographies

Encapsulated membrane proteins: A simplified system for molecular simulation.

Exploring the conformational dynamics and membrane interactions of PorB from C. glutamicum: A multi-scale molecular dynamics simulation study ⬇️

Free-energy calculations reveal the subtle differences in the interactions of DNA bases with α-hemolysin.

Full-Length OmpA: Structure, Function, and Membrane Interactions Predicted by Molecular Dynamics Simulations

Influence of surface shape on DNA binding of bimetallo helicates.

Interaction between the NS4B amphipathic helix, AH2, and charged lipid headgroups alters membrane morphology and AH2 oligomeric state--Implications for the Hepatitis C virus life cycle.

Interaction of the antimicrobial peptide polymyxin B1 with both membranes of E. coli: a molecular dynamics study

Intramolecular DNA coiling mediated by metallo-supramolecular cylinders: differential binding of P and M helical enantiomers.

It Is Complicated: Curvature, Diffusion, and Lipid Sorting within the Two Membranes of Escherichia coli

Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory.

Molecular Dynamics Simulations Predict the Pathways via Which Pristine Fullerenes Penetrate Bacterial Membranes

Molecular Dynamics Simulations Reveal the Conformational Flexibility of Lipid II and Its Loose Association with the Defensin Plectasin in the Staphylococcus aureus Membrane.

Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

Molecular Simulations of Gram-Negative Bacterial Membranes: A Vignette of Some Recent Successes

Molecular dynamics simulations of DNA within a nanopore: arginine-phosphate tethering and a binding/sliding mechanism for translocation

Molecular dynamics simulations of a bacterial autotransporter: NalP from Neisseria meningitidis.

Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling?

Molecular dynamics simulations of inwardly rectifying (Kir) potassium channels: a comparative study

Movement of Arginine through OprD: The Energetics of Permeation and the Role of Lipopolysaccharide in Directing Arginine to the Protein

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment.

On the ability of PAMAM dendrimers and dendrimer/DNA aggregates to penetrate POPC model biomembranes

Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints

Outer membrane protein G: Engineering a quiet pore for biosensing

Probing the oligomeric state and interaction surfaces of Fukutin-I in dilauroylphosphatidylcholine bilayers.

Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes

PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories

Role of O-Antigen in Response to Mechanical Stress of the E. coli Outer Membrane: Insights from Coarse-Grained MD Simulations

Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel.

Shape effects on the activity of synthetic major-groove binding ligands

Simulations of DNA coiling around a synthetic supramolecular cylinder that binds in the DNA major groove

Single-Stranded DNA within Nanopores: Conformational Dynamics and Implications for Sequencing; a Molecular Dynamics Simulation Study ⬇️

Stability and membrane orientation of the fukutin transmembrane domain: a combined multiscale molecular dynamics and circular dichroism study

Structural basis for Mep2 ammonium transceptor activation by phosphorylation.

The Free Energy of Small Solute Permeation through the Escherichia coli Outer Membrane Has a Distinctly Asymmetric Profile.

The NorM MATE transporter from N. gonorrhoeae: insights into drug and ion binding from atomistic molecular dynamics simulations

The membranes of Gram-negative bacteria: progress in molecular modelling and simulation

The role of the jaw subdomain of peptidoglycan glycosyltransferases for lipid II polymerization

Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes