Syma Khalid

ResearcherID ORCID

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 54

Top Venues

The journal of physical chemistry. B

Journal of chemical theory and computation

Nature

eLife

University of Southampton

This page only lists publications with an associated author ORCID identifier.

Affiliation History

University of Southampton Oct 01 2016

United Kingdom

Full Professor :: Chemistry

Publications

Iain Peter Shand Smith, Conrado Pedebos, Syma Khalid
Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli : Insights from Molecular Dynamics. The journal of physical chemistry. B 128 (11) (2024)
Iain Peter Shand Smith, Conrado Pedebos, Syma Khalid
Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli : Insights from Molecular Dynamics. The journal of physical chemistry. B (2024)
Astrid F Brandner, Dheeraj Prakaash, Alexandre Blanco González, Fergus Waterhouse, Syma Khalid
Faster but Not Sweeter: A Model of Escherichia coli Re-level Lipopolysaccharide for Martini 3 and a Martini 2 Version with Accelerated Kinetics. Journal of chemical theory and computation (2024)
Astrid F Brandner, Dheeraj Prakaash, Alexandre Blanco González, Fergus Waterhouse, Syma Khalid
Faster but Not Sweeter: A Model of Escherichia coli Re-level Lipopolysaccharide for Martini 3 and a Martini 2 Version with Accelerated Kinetics. Journal of chemical theory and computation 20 (15) (2024)
Iain Peter Shand Smith, Conrado Pedebos, Syma Khalid
Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli : Insights from Molecular Dynamics. The journal of physical chemistry. B 128 (11) (2024)
Robert Clark, Kahlan E Newman, Syma Khalid
Titratable residues that drive RND efflux: Insights from molecular simulations. QRB discovery 5 (2024)
Iain Peter Shand Smith, Conrado Pedebos, Syma Khalid
Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli : Insights from Molecular Dynamics. The journal of physical chemistry. B 128 (11) (2024)
Astrid F Brandner, Dheeraj Prakaash, Alexandre Blanco González, Fergus Waterhouse, Syma Khalid
Faster but Not Sweeter: A Model of Escherichia coli Re-level Lipopolysaccharide for Martini 3 and a Martini 2 Version with Accelerated Kinetics. Journal of chemical theory and computation 20 (15) (2024)
Iain Peter Shand Smith, Conrado Pedebos, Syma Khalid
Molecular Crowding Alters the Interactions of Polymyxin Lipopeptides within the Periplasm of E. coli : Insights from Molecular Dynamics. The journal of physical chemistry. B 128 (11) (2024)
Robert Clark, Kahlan E Newman, Syma Khalid
Titratable residues that drive RND efflux: Insights from molecular simulations. QRB discovery 5 (2024)
Astrid F Brandner, Dheeraj Prakaash, Alexandre Blanco González, Fergus Waterhouse, Syma Khalid
Faster but Not Sweeter: A Model of Escherichia coli Re-level Lipopolysaccharide for Martini 3 and a Martini 2 Version with Accelerated Kinetics. Journal of chemical theory and computation 20 (15) (2024)
Kahlan E Newman, Syma Khalid
Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. PLoS computational biology 19 (1) (2023)
Kahlan E Newman, Sarah N Tindall, Sophie L Mader, Syma Khalid, Gavin Hugh Thomas, Marjan W Van der Woude
A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer. eLife 12 (2023)
Rhys W Grinter, Ashleigh Kropp, Hari Venugopal, Moritz Senger, Jack Badley, Princess R Cabotaje, Ruyu Jia, Zehui Duan, Ping Huang, Sven Timo Stripp, Christopher K Barlow, Matthew Belousoff, Hannah S Shafaat, Gregory M Cook, Ralf Bernd Schittenhelm, Kylie A Vincent, Syma Khalid, Gustav Berggren, Chris Greening
Structural basis for bacterial energy extraction from atmospheric hydrogen. Nature 615 (7952) (2023)
Rhys W Grinter, Ashleigh Kropp, Hari Venugopal, Moritz Senger, Jack Badley, Princess R Cabotaje, Ruyu Jia, Zehui Duan, Ping Huang, Sven Timo Stripp, Christopher K Barlow, Matthew Belousoff, Hannah S Shafaat, Gregory M Cook, Ralf Bernd Schittenhelm, Kylie A Vincent, Syma Khalid, Gustav Berggren, Chris Greening
Structural basis for bacterial energy extraction from atmospheric hydrogen. Nature 615 (7952) (2023)
Dheeraj Prakaash, Syma Khalid
All-Atom Mesoscale Simulations Predict the Conformational Dynamics of Influenza Virus Surface Glycoproteins. ACS central science 9 (1) (2023)
Rhys W Grinter, Ashleigh Kropp, Hari Venugopal, Moritz Senger, Jack Badley, Princess R Cabotaje, Ruyu Jia, Zehui Duan, Ping Huang, Sven Timo Stripp, Christopher K Barlow, Matthew Belousoff, Hannah S Shafaat, Gregory M Cook, Ralf Bernd Schittenhelm, Kylie A Vincent, Syma Khalid, Gustav Berggren, Chris Greening
Structural basis for bacterial energy extraction from atmospheric hydrogen. Nature (2023)
Kahlan E Newman, Sarah N Tindall, Sophie L Mader, Syma Khalid, Gavin Hugh Thomas, Marjan W Van der Woude
A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer. eLife 12 (2023)
Dheeraj Prakaash, Syma Khalid
All-Atom Mesoscale Simulations Predict the Conformational Dynamics of Influenza Virus Surface Glycoproteins. ACS central science 9 (1) (2023)
Kahlan E Newman, Syma Khalid
Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. PLoS computational biology 19 (1) (2023)
Kahlan E Newman, Syma Khalid
Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. PLoS computational biology 19 (1) (2023)
Kahlan E Newman, Sarah N Tindall, Sophie L Mader, Syma Khalid, Gavin Hugh Thomas, Marjan W Van der Woude
A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer. eLife 12 (2023)
Benjamin F Cooper, Robert Clark, Anju Kudhail, Gira Bhabha, Damian C Ekiert, Syma Khalid, Georgia L Isom
Phospholipid transport to the bacterial outer membrane through an envelope-spanning bridge. bioRxiv : the preprint server for biology (2023)
Rhys W Grinter, Ashleigh Kropp, Hari Venugopal, Moritz Senger, Jack Badley, Princess R Cabotaje, Ruyu Jia, Zehui Duan, Ping Huang, Sven Timo Stripp, Christopher K Barlow, Matthew Belousoff, Hannah S Shafaat, Gregory M Cook, Ralf Bernd Schittenhelm, Kylie A Vincent, Syma Khalid, Gustav Berggren, Chris Greening
Structural basis for bacterial energy extraction from atmospheric hydrogen. Nature 615 (7952) (2023)
Kahlan E Newman, Syma Khalid
Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. PLoS computational biology 19 (1) (2023)
Rhys W Grinter, Ashleigh Kropp, Hari Venugopal, Moritz Senger, Jack Badley, Princess R Cabotaje, Ruyu Jia, Zehui Duan, Ping Huang, Sven Timo Stripp, Christopher K Barlow, Matthew Belousoff, Hannah S Shafaat, Gregory M Cook, Ralf Bernd Schittenhelm, Kylie A Vincent, Syma Khalid, Gustav Berggren, Chris Greening
Structural basis for bacterial energy extraction from atmospheric hydrogen. Nature 615 (7952) (2023)
Kahlan E Newman, Sarah N Tindall, Sophie L Mader, Syma Khalid, Gavin Hugh Thomas, Marjan W Van der Woude
A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer. eLife 12 (2023)
Augustinas Silale, Yiling Zhu, Jerzy Witwinowski, Robert E Smith, Kahlan E Newman, Satya P Bhamidimarri, Arnaud Baslé, Syma Khalid, Christophe Beloin, Simonetta Gribaldo, Bert van den Berg
Dual function of OmpM as outer membrane tether and nutrient uptake channel in diderm Firmicutes. Nature communications 14 (1) (2023)
Thibaud Dieudonné, Felix Kümmerer, Michelle Juknaviciute Laursen, Charlott Stock, Rasmus Kock Flygaard, Syma Khalid, Guillaume Lenoir, Joseph Anthony Lyons, Kresten Lindorff-Larsen, Poul Nissen
Activation and substrate specificity of the human P4-ATPase ATP8B1. Nature communications 14 (1) (2023)
Kahlan E Newman, Syma Khalid
Conformational dynamics and putative substrate extrusion pathways of the N-glycosylated outer membrane factor CmeC from Campylobacter jejuni. PLoS computational biology 19 (1) (2023)
Kahlan E Newman, Sarah N Tindall, Sophie L Mader, Syma Khalid, Gavin Hugh Thomas, Marjan W Van der Woude
A novel fold for acyltransferase-3 (AT3) proteins provides a framework for transmembrane acyl-group transfer. eLife 12 (2023)
Conrado Pedebos, Syma Khalid
Simulations of the spike: molecular dynamics and SARS-CoV-2. Nature reviews. Microbiology 20 (4) (2022)
Jan Böhning, Mnar Ghrayeb, Conrado Pedebos, Daniel K Abbas, Syma Khalid, Liraz Chai, Tanmay A M Bharat
Donor-strand exchange drives assembly of the TasA scaffold in Bacillus subtilis biofilms. Nature communications 13 (1) (2022)
Christopher M Miles, Pin-Chia Hsu, Ann M Dixon, Syma Khalid, Gabriele Cesare Sosso
Lipid bilayers as potential ice nucleating agents. Physical chemistry chemical physics : PCCP 24 (11) (2022)
Bert van den Berg, Augustinas Silale, Arnaud Basle, Astrid F Brandner, Sophie L Mader, Syma Khalid
Structural basis for host recognition and superinfection exclusion by bacteriophage T5. Proceedings of the National Academy of Sciences of the United States of America 119 (42) (2022)
Melissa N Webby, Abraham Olusegun Oluwole, Conrado Pedebos, Patrick G Inns, Anna Olerinyova, Dheeraj Prakaash, Nicholas G Housden, Georgina Benn, Dawei Sun, Bart W Hoogenboom, Philipp Kukura, Shabaz Mohammad, Carol V Robinson, Syma Khalid, Colin Kleanthous
Lipids mediate supramolecular outer membrane protein assembly in bacteria. Science advances 8 (44) (2022)
Dhanushka Weerakoon, Kamen Petrov, Conrado Pedebos, Syma Khalid
Polymyxin B1 within the E. coli c ell envelope: insights from molecular dynamics simulations. Biophysical reviews 13 (6) (2021)
Ya Gao, Jumin Lee, Iain Peter Shand Smith, Hwayoung Lee, Seonghoon Kim, John Z H Zhang, Jeffery B Klauda, Göran Widmalm, Syma Khalid, Wonpil Im
CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides. Journal of chemical information and modeling 61 (2) (2021)
Abigail C Dommer, Lorenzo Casalino, Fiona L Kearns, Mia A Rosenfeld, Nicholas A Wauer, Surl-Hee Ahn, John D Russo, Sofia Oliveira, Clare Morris, Anthony T Bogetti, Anda Trifan, Alexander Brace, Terra Sztain, Austin Clyde, Heng Ma, Chakra Chennubhotla, Hyungro Lee, Matteo Turilli, Syma Khalid, Teresa Tamayo-Mendoza, Matthew Welborn, Anders Christensen, Daniel G A Smith, Zhuoran Qiao, Sai Krishna Sirumalla, Michael O'Connor, Frederick R Manby, Anima Anandkumar, David Hardy, James Phillips, Abraham Stern, Josh Romero, David Clark, Mitchell Dorrell, Tom Maiden, Lei Huang, John McCalpin, Christopher Woods, Alan Gray, Matt Williams, Bryan Barker, Harinda Rajapaksha, Richard Pitts, Tom Gibbs, John E Stone, Daniel M Zuckerman, Adrian Mulholland, Thomas Miller, Shantenu Jha, Arvind Ramanathan, Lillian T Chong, Rommie Elizabeth Amaro
#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol. bioRxiv : the preprint server for biology (2021)
Jonathan Shearer, Jan K Marzinek, Peter John Bond, Syma Khalid
Molecular dynamics simulations of bacterial outer membrane lipid extraction: Adequate sampling? The Journal of chemical physics 153 (4) (2021)
Lorenzo Casalino, Abigail Dommer, Zied Gaieb, Emilia P Barros, Terra Sztain, Surl-Hee Ahn, Anda Trifan, Alexander Brace, Anthony Bogetti, Heng Ma, Hyungro Lee, Matteo Turilli, Syma Khalid, Lillian Chong, Carlos Simmerling, David J Hardy, Julio D C Maia, James C Phillips, Thorsten Kurth, Abraham Stern, Lei Huang, John McCalpin, Mahidhar Tatineni, Tom Gibbs, John E Stone, Shantenu Jha, Arvind Ramanathan, Rommie E Amaro
AI-Driven Multiscale Simulations Illuminate Mechanisms of SARS-CoV-2 Spike Dynamics. bioRxiv : the preprint server for biology (2020)
Firdaus Samsudin, Syma Khalid
Movement of Arginine through OprD: The Energetics of Permeation and the Role of Lipopolysaccharide in Directing Arginine to the Protein. The journal of physical chemistry. B 123 (13) (2019)
Jonathan Shearer, Damien Jefferies, Syma Khalid
Outer Membrane Proteins OmpA, FhuA, OmpF, EstA, BtuB, and OmpX Have Unique Lipopolysaccharide Fingerprints. Journal of chemical theory and computation 15 (4) (2019)
Madhurima Mitra, Mohammad Asad, Sandeep Kumar, Kavita Yadav, Sarika Chaudhary, Neel Sarovar Bhavesh, Syma Khalid, Lipi Thukral, Avinash Bajaj
Distinct Intramolecular Hydrogen Bonding Dictates Antimicrobial Action of Membrane-Targeting Amphiphiles. The journal of physical chemistry letters 10 (4) (2019)
Damien Jefferies, Jonathan Shearer, Syma Khalid
Role of O-Antigen in Response to Mechanical Stress of the E. coli Outer Membrane: Insights from Coarse-Grained MD Simulations. The journal of physical chemistry. B 123 (17) (2019)
Nicholas G Housden, Patrice Rassam, Sejeong Lee, Firdaus Samsudin, Renata Kaminska, Connor Sharp, Jonathan D Goult, Marie-Louise Francis, Syma Khalid, Hagan Bayley, Colin Kleanthous
Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm. Biochemistry 57 (29) (2018)
Syma Khalid, Thomas J Piggot, Firdaus Samsudin
Atomistic and Coarse Grain Simulations of the Cell Envelope of Gram-Negative Bacteria: What Have We Learned? Accounts of chemical research 52 (1) (2018)
Nicholas G Housden, Patrice Rassam, Sejeong Lee, Firdaus Samsudin, Renata Kaminska, Connor Sharp, Jonathan D Goult, Marie-Louise Francis, Syma Khalid, Hagan Bayley, Colin Kleanthous
Correction to "Directional Porin Binding of Intrinsically Disordered Protein Sequences Promotes Colicin Epitope Display in the Bacterial Periplasm". Biochemistry 57 (35) (2018)
Taylor Haynes, Iain P S Smith, E Jayne Wallace, Jemma L Trick, Mark S P Sansom, Syma Khalid
Electric-Field-Driven Translocation of ssDNA through Hydrophobic Nanopores. ACS nano 12 (8) (2018)
James A Graham, Jonathan W Essex, Syma Khalid
PyCGTOOL: Automated Generation of Coarse-Grained Molecular Dynamics Models from Atomistic Trajectories. Journal of chemical information and modeling 57 (4) (2017)
Alister Boags, Pin-Chia Hsu, Firdaus Samsudin, Peter J Bond, Syma Khalid
Progress in Molecular Dynamics Simulations of Gram-Negative Bacterial Cell Envelopes. The journal of physical chemistry letters 8 (11) (2017)
Thomas J Piggot, Ángel Piñeiro, Syma Khalid
Correction to Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study. Journal of chemical theory and computation 13 (4) (2017)
Pin-Chia Hsu, Firdaus Samsudin, Jonathan Shearer, Syma Khalid
It Is Complicated: Curvature, Diffusion, and Lipid Sorting within the Two Membranes of Escherichia coli. The journal of physical chemistry letters 8 (22) (2017)
Damien Jefferies, Pin-Chia Hsu, Syma Khalid
Through the Lipopolysaccharide Glass: A Potent Antimicrobial Peptide Induces Phase Changes in Membranes. Biochemistry 56 (11) (2017)

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Publication Activity (10 Years)

Top Topics

Top Venues

Syma Khalid