Syma Khalid: search on Z-Library

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1

Coarse-grained molecular dynamics simulations of membrane proteins and peptides

Peter J. Bond, John Holyoake, Anthony Ivetac, Syma Khalid, Mark S.P. Sansom

Journal:

Journal of Structural Biology

Year:

2007

Language:

english

File:

PDF, 2.38 MB

english, 2007

2

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

Jefferies, Damien, Hsu, Pin-Chia, Khalid, Syma

Journal:

Year:

2017

Language:

english

File:

PDF, 1.68 MB

english, 2017

3

Molecular Simulations of Gram-Negative Bacterial Membranes Come of Age

Im, Wonpil, Khalid, Syma

Journal:

Annual Review of Physical Chemistry

Year:

2020

Language:

english

File:

PDF, 4.11 MB

english, 2020

4

Combining native and âomicsâ mass spectrometry to identify endogenous ligands bound to membrane proteins

Gault, Joseph, Liko, Idlir, Landreh, Michael, Shutin, Denis, Bolla, Jani Reddy, Jefferies, Damien, Agasid, Mark, Yen, Hsin-Yung, Ladds, Marcus J. G. W., Lane, David P., Khalid, Syma, Mullen, Christoph

Journal:

Year:

2020

File:

PDF, 11.21 MB

2020

5

OmpA: Gating and dynamics via molecular dynamics simulations

Syma Khalid, Peter J. Bond, Timothy Carpenter, Mark S.P. Sansom

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2008

Language:

english

File:

PDF, 1.20 MB

english, 2008

6

The Fukutin Transmembrane Domain: Capturing the Complexity of the Golgi Apparatus Membrane via Multiscale MD Simulations

Holdbrook, Daniel A., Piggot, Thomas J., Marius, Phedra, Williamson, Philip T.F., Khalid, Syma

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 32 KB

english, 2011

7

Conformational Dynamics of PorB, a Helical Outer Membrane Protein from C. glutamicum: a Multi-scale MD Simulation Study

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 44 KB

english, 2009

8

Atomistic and Coarse-Grained Simulations of Membrane Proteins: A Practical Guide

Jefferies, Damien, Khalid, Syma

Journal:

Year:

2020

Language:

english

File:

PDF, 3.97 MB

english, 2020

9

Molecular Dynamics Simulations of Inwardly Rectifying (Kir) Potassium Channels: A Comparative Study †

Haider, Shozeb, Khalid, Syma, Tucker, Stephen J., Ashcroft, Frances M., Sansom, Mark S. P.

Journal:

Year:

2007

Language:

english

File:

PDF, 862 KB

english, 2007

10

Simulation Studies of Transport of Hydrophobic Compounds through Outer Membrane Proteins of Gram Negative Bacteria

Chohan, Pragya, Khalid, Syma, Sansom, Mark

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 78 KB

english, 2012

11

Molecular Dynamics Simulations of Membrane Proteins: Getting the Details Right

Piggot, Thomas J., Piñeiro, Ángel, Khalid, Syma

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 105 KB

english, 2012

12

Atomistic Simulations of OmpA: A Step Towards the Virtual Bacterial Envelope

Samsudin, Firdaus, Ortiz-Suarez, Maite L., Piggot, Thomas J., Bond, Peter J., Khalid, Syma

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 48 KB

english, 2017

13

Chiral discrimination in mobile phases for HPLC

Renato Lukač, Andrew J. Clark, Syma Khalid, Alison Rodger, Alan Snedden, P. Mark Rodger

Journal:

Journal of Molecular Liquids

Year:

2002

File:

PDF, 1.18 MB

2002

14

Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment

Daniel A. Holdbrook, Thomas J. Piggot, Mark S.P. Sansom, Syma Khalid

Journal:

Biochimica et Biophysica Acta (BBA) - Biomembranes

Year:

2013

Language:

english

File:

PDF, 1.57 MB

english, 2013

15

Self-Assembly of a Simple Membrane Protein: Coarse-Grained Molecular Dynamics Simulations of the Influenza M2 Channel

Carpenter, Timothy, Bond, Peter J., Khalid, Syma, Sansom, Mark S.P.

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 1.06 MB

english, 2008

16

Obituary

Chohan, Pragya, Khalid, Syma, Sansom, Mark

Journal:

Year:

1989

Language:

english

File:

PDF, 157 KB

english, 1989

17

Membrane Recognition and Dynamics of the RNA Degradosome

Strahl, Henrik, Turlan, Catherine, Khalid, Syma, Bond, Peter J., Kebalo, Jean-Marie, Peyron, Pascale, Poljak, Leonora, Bouvier, Marie, Hamoen, Leendert, Luisi, Ben F., Carpousis, Agamemnon J., Viollie

Journal:

Year:

2015

Language:

english

File:

PDF, 1.72 MB

english, 2015

18

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

Shearer, Jonathan, Jefferies, Damien, Khalid, Syma

Journal:

Journal of Chemical Theory and Computation

Year:

2019

Language:

english

File:

PDF, 6.35 MB

english, 2019

19

A Computational Swiss Army Knife Approach toÂ Unraveling the Secrets of Proton Movement through SERCA

Khalid, Syma, Newstead, Simon

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 193 KB

2020

20

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

Somboon, Kamolrat, Doble, Anne, Bulmer, David, BaslÃ©, Arnaud, Khalid, Syma, van den Berg, Bert

Journal:

Nature Communications

Year:

2020

File:

PDF, 3.60 MB

2020

21

Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove

Syma Khalid, Michael J. Hannon, Alison Rodger, P. Mark Rodger

Journal:

Chemistry - A European Journal

Year:

2006

Language:

english

File:

PDF, 1.33 MB

english, 2006

22

The Complexities of the E.Coli Cell Envelope: Details Revealed by MD Simulations

Khalid, Syma, Piggot, Thomas J., Holdbrook, Daniel A., Parkin, Jamie

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 40 KB

english, 2013

23

OmpA: A Flexible Clamp for Bacterial Cell Wall Attachment

Samsudin, Firdaus, Ortiz-Suarez, Maite L., Piggot, Thomas J., Bond, Peter J., Khalid, Syma

Journal:

Year:

2016

Language:

english

File:

PDF, 3.49 MB

english, 2016

24

Braun’s Lipoprotein Facilitates OmpA Interaction with the Escherichia coli Cell Wall

Samsudin, Firdaus, Boags, Alister, Piggot, Thomas J., Khalid, Syma

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 2.33 MB

english, 2017

25

A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway

Huber, Roland G., Berglund, Nils A., Kargas, Vasileios, Marzinek, Jan K., Holdbrook, Daniel A., Khalid, Syma, Piggot, Thomas J., Schmidtchen, Artur, Bond, Peter J.

Journal:

Year:

2018

Language:

english

File:

PDF, 4.35 MB

english, 2018

26

Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR

Saunders, Graham M., Bruce Macdonald, Hannah E., Essex, Jonathan W., Khalid, Syma

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 2.79 MB

english, 2018

27

Simulation of subcellular structures

Khalid, Syma, Rouse, Sarah L

Journal:

Current Opinion in Structural Biology

Year:

2020

Language:

english

File:

PDF, 2.11 MB

english, 2020

28

Melittin vs E.coli: Insights from Molecular Dynamics Simulations

Khalid, Syma, Piggot, Thomas J.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 47 KB

english, 2011

29

The Autotransporter β Domain: Insights into Structure and Function through Molecular Dynamics Simulations

Holdbrook, Daniel A., Piggot, Thomas J., Khalid, Syma

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 41 KB

english, 2012

30

The Nucleotide Capture Region of Alpha Hemolysin: Insights into Nanopore Design for DNA Sequencing from Molecular Dynamics Simulations

Manara, Richard, Tomasio, Susana, Khalid, Syma

Journal:

Year:

2015

Language:

english

File:

PDF, 3.22 MB

english, 2015

31

Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR

Saunders, Graham M., Bruce Macdonald, Hannah E., Essex, Jonathan W., Khalid, Syma

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 51 KB

2019

32

Interactions of a Bacterial RND Transporter with a Transmembrane Small Protein in a Lipid Environment

Du, Dijun, Neuberger, Arthur, Orr, Mona Wu, Newman, Catherine E., Hsu, Pin-Chia, Samsudin, Firdaus, Szewczak-Harris, Andrzej, Ramos, Leana M., Debela, Mekdes, Khalid, Syma, Storz, Gisela, Luisi, Ben F

Journal:

Year:

2020

File:

PDF, 4.51 MB

2020

33

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

Shearer, Jonathan, Marzinek, Jan K., Bond, Peter J., Khalid, Syma

Journal:

The Journal of Chemical Physics

Year:

2020

File:

PDF, 3.54 MB

2020

34

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

Shearer, Jonathan, Khalid, Syma

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 1.44 MB

english, 2018

35

Environmental Influences on the Conformational Dynamics of Tonb-Dependent Transporters: Molecular Dynamics Simulations of Complex Membrane Models

Piggot, Thomas J., Holdbrook, Daniel A., Khalid, Syma

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 37 KB

english, 2011

36

The NorM MATE Transporter from N. gonorrhoeae: Insights into Drug and Ion Binding from Atomistic Molecular Dynamics Simulations

Leung, Yuk Ming, Holdbrook, Daniel A., Piggot, Thomas J., Khalid, Syma

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 2.08 MB

english, 2014

37

An Accurate In Vitro Model of the E. coli Envelope

Clifton, Luke A., Holt, Stephen A., Hughes, Arwel V., Daulton, Emma L., Arunmanee, Wanatchaporn, Heinrich, Frank, Khalid, Syma, Jefferies, Damien, Charlton, Timothy R., Webster, John R. P., Kinane, Ch

Journal:

Angewandte Chemie

Year:

2015

Language:

english

File:

PDF, 3.67 MB

english, 2015

38

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

Boags, Alister T, Hsu, Pin Chia, Samsudin, Mohd Firdaus, Bond, Peter J, Khalid, Syma

Journal:

The Journal of Physical Chemistry Letters

Year:

2017

Language:

english

File:

PDF, 979 KB

english, 2017

39

DNA Lipoplexes: Formation of the Inverse Hexagonal Phase Observed by Coarse-Grained Molecular Dynamics Simulation

Corsi, Josephine, Hawtin, Robert W., Ces, Oscar, Attard, George S., Khalid, Syma

Journal:

Year:

2010

Language:

english

File:

PDF, 994 KB

english, 2010

40

Molecular Dynamics Simulations of DNA within a Nanopore: Arginine−Phosphate Tethering and a Binding/Sliding Mechanism for Translocation

Bond, Peter J., Guy, Andrew T., Heron, Andrew J., Bayley, Hagan, Khalid, Syma

Journal:

Year:

2011

Language:

english

File:

PDF, 4.38 MB

english, 2011

41

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

Johnston, Jennifer M., Johnston, Jennifer M., Khalid, Syma, Johnston, Jennifer M., Khalid, Syma, Sansom, Mark S. P.

Journal:

Molecular Membrame Biology

Year:

2008

Language:

english

File:

PDF, 4.08 MB

english, 2008

42

Directional porin binding of intrinsically disordered protein sequences promotes colicin epitope display in the bacterial periplasm

Housden, Nicholas, Rassam, Patrice, Lee, Sejeong, Samsudin, Firdaus, Kaminska, Renata, Sharp, Connor, Goult, Jonathan David, Francis, Marie-Louise, Khalid, Syma, Bayley, Hagan, Kleanthous, Colin

Journal:

Year:

2018

Language:

english

File:

PDF, 849 KB

english, 2018

43

Prediction of the Closed Conformation and Insights into the Mechanism of the Membrane Enzyme LpxR

Saunders, Graham M., Bruce Macdonald, Hannah E., Essex, Jonathan W., Khalid, Syma

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 51 KB

english, 2019

44

Simple Cell, Complex Envelope: Modeling the Heterogeneous Membranes of E.coli

Khalid, Syma, Piggot, Thomas J., Holdbrook, Daniel A.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 33 KB

english, 2011

45

The Role of Instantaneous Lipid “Flows” Within the E. coli Outer Membrane

Goose, Joseph, Holdbrook, Daniel A., Khalid, Syma, Sansom, Mark

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 55 KB

english, 2012

46

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

Ortiz-Suarez, Maite L., Samsudin, Firdaus, Piggot, Thomas J., Bond, Peter J., Khalid, Syma

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 2.23 MB

english, 2016

47

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

Piggot, Thomas J., Piñeiro, Ángel, Khalid, Syma

Journal:

Journal of Chemical Theory and Computation

Year:

2017

Language:

english

File:

PDF, 1015 KB

english, 2017

48

CHARMM-GUI Martini Maker for modeling and simulation of complex bacterial membranes with lipopolysaccharides

Hsu, Pin-Chia, Bruininks, Bart M. H., Jefferies, Damien, Cesar Telles de Souza, Paulo, Lee, Jumin, Patel, Dhilon S., Marrink, Siewert J., Qi, Yifei, Khalid, Syma, Im, Wonpil

Journal:

Journal of Computational Chemistry

Year:

2017

Language:

english

File:

PDF, 1.07 MB

english, 2017

49

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

Khalid, Syma, Piggot, Thomas J, Samsudin, Firdaus

Journal:

Accounts of Chemical Research

Year:

2018

Language:

english

File:

PDF, 8.29 MB

english, 2018

50

An Accurate In Vitro Model of the E. coli Envelope

Clifton, Luke A., Holt, Stephen A., Hughes, Arwel V., Daulton, Emma L., Arunmanee, Wanatchaporn, Heinrich, Frank, Khalid, Syma, Jefferies, Damien, Charlton, Timothy R., Webster, John R. P., Kinane, Ch

Journal:

Angewandte Chemie International Edition

Year:

2015

Language:

english

File:

PDF, 3.68 MB

english, 2015

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