D. Peter Tieleman

University of Calgary

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‪Siewert J. Marrink

University of Groningen

Valentina Corradi

University of Calgary

Svetlana Baoukina

University of Calgary

Mark S.P. Sansom

University of Oxford

William F. Bennett

Lawrence Livermore National Laboratory

Luca Monticelli

Centre National de la Recherche Scientifique

Justin L. MacCallum

University of Calgary

Helgi I. Ingólfsson

Lawrence Livermore National Laboratory

Gurpreet Singh

Binghamton University

Tsjerk A. Wassenaar

University of Groningen

Cooperative Institutions

Institute of Molecular Biology and Biophysics

260

University of Calgary

143

Centre National de la Recherche Scientifique

University of British Columbia

University of Groningen

University of Oxford

National Institutes of Health

Simon Fraser University

Harvard University

University of Illinois Urbana-Champaign

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Computer Simulation of Antimicrobial Peptides

Current Medicinal Chemistry (2007)

Edit Mátyus Christian Kandt D. Peter Tieleman

Naturally occurring and synthetic peptides may be a novel class of clinically useful antibiotics. A large body of experimental data on structure function relationships for such peptides is available, but the molecular mechanism of their action remains elusive in most cases. Computer simulations can give detailed insights into the interactions between peptides and lipid bilayers, at least one crucial step in the antimicrobial mechanism. Here we review recent simulations of antimicrobial peptides and discuss potential future contributions of computer simulations in understanding and ultimately designing antimicrobial peptides.

10.2174/092986707782360105

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Citations (106)

Martini 3: a general purpose force field for coarse-grained molecular dynamics

Nature Methods (2021)

Paulo C. T. Souza Riccardo Alessandri Jonathan Barnoud Sebastian Thallmair Ignacio Faustino

Force Field

Miscibility

Electrostatics

10.1038/s41592-021-01098-3

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Citations (932)

Structure and Stability of Carbohydrate–Lipid Interactions. Methylmannose Polysaccharide–Fatty Acid Complexes

ChemBioChem (2016)

Lan Liu Iwona Siuda Michele R. Richards Justin B. Renaud Elena N. Kitova

We report a detailed study of the structure and stability of carbohydrate-lipid interactions. Complexes of a methylmannose polysaccharide (MMP) derivative and fatty acids (FAs) served as model systems. The dependence of solution affinities and gas-phase dissociation activation energies (Ea ) on FA length indicates a dominant role of carbohydrate-lipid interactions in stabilizing (MMP+FA) complexes. Solution (1) H NMR results reveal weak interactions between MMP methyl groups and FA acyl chain; MD simulations suggest the complexes are disordered. The contribution of FA methylene groups to the Ea is similar to that of heats of transfer of n-alkanes from the gas phase to polar solvents, thus suggesting that MMP binds lipids through dipole-induced dipole interactions. The MD results point to hydrophobic interactions and H-bonds with the FA carboxyl group. Comparison of collision cross sections of deprotonated (MMP+FA) ions with MD structures suggests that the gaseous complexes are disordered.

Methylene

10.1002/cbic.201600123

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Citations (5)

Lipid Mixing in Model Membranes

Biophysical Journal (2017)

Ruo‐Xu Gu Svetlana Baoukina D. Peter Tieleman

POPC

Lipid raft

10.1016/j.bpj.2016.11.490

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Citations (0)

Effect of late endosomal DOBMP lipid and traditional model lipids of electrophysiology on the anthrax toxin channel activity

Biochimica et Biophysica Acta (BBA) - Biomembranes (2018)

Nnanya Kalu Yoav Atsmon‐Raz Sanaz Momben Abolfath Laura H. Lucas Clare Kenney

Anthrax toxin

Transmembrane channels

10.1016/j.bbamem.2018.08.011

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Citations (4)

Faculty Opinions recommendation of Localization of multidrug transporter substrates within model membranes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature (2007)

D. Peter Tieleman

10.3410/f.1058853.510786

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Citations (0)

Curvature-Induced Lipid Sorting in Plasma Membrane Tethers

Biophysical Journal (2017)

Svetlana Baoukina Helgi I. Ingólfsson ‪Siewert J. Marrink D. Peter Tieleman

Membrane Curvature

10.1016/j.bpj.2016.11.2506

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Improved Parameters for the Martini Coarse-Grained Protein Force Field

Journal of Chemical Theory and Computation (2012)

Djurre H. de Jong Gurpreet Singh William F. Bennett Clément Arnarez Tsjerk A. Wassenaar

The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here, we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley-White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.

Force Field

Polarity (international relations)

10.1021/ct300646g

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Citations (1,429)

Coarse Grained Models: The Martini Force Field

Elsevier eBooks (2023)

Hanif M. Khan D. Peter Tieleman

Force Field

Popularity

Ranging

10.1016/b978-0-12-821978-2.00087-8

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Citations (0)

Proline‐induced hinges in transmembrane helices: Possible roles in ion channel gating

Proteins Structure Function and Bioinformatics (2001)

D. Peter Tieleman Indira H. Shrivastava Martin R. Ulmschneider Mark S.P. Sansom

Abstract A number of ion channels contain transmembrane (TM) α‐helices that contain proline‐induced molecular hinges. These TM helices include the channel‐forming peptide alamethicin (Alm), the S6 helix from voltage‐gated potassium (Kv) channels, and the D5 helix from voltage‐gated chloride (CLC) channels. For both Alm and KvS6, experimental data implicate hinge‐bending motions of the helix in an aspect of channel gating. We have compared the hinge‐bending motions of these TM helices in bilayer‐like environments by multi‐nanosecond MD simulations in an attempt to describe motions of these helices that may underlie possible modes of channel gating. Alm is an α‐helical channel‐forming peptide, which contains a central kink associated with a Gly‐x‐x‐Pro motif in its sequence. Simulations of Alm in a TM orientation for 10 ns in an octane slab indicate that the Gly‐x‐x‐Pro motif acts as a molecular hinge. The S6 helix from Shaker Kv channels contains a Pro‐Val‐Pro motif. Modeling studies and recent experimental data suggest that the KvS6 helix may be kinked in the vicinity of this motif. Simulations (10 ns) of an isolated KvS6 helix in an octane slab and in a POPC bilayer reveal hinge‐bending motions. A pattern‐matching approach was used to search for possible hinge‐bending motifs in the TM helices of other ion channel proteins. This uncovered a conserved Gly‐x‐Pro motif in TM helix D5 of CLC channels. MD simulations of a model of hCLC1‐D5 spanning an octane slab suggest that this channel also contains a TM helix that undergoes hinge‐bending motion. In conclusion, our simulations suggest a model in which hinge‐bending motions of TM helices may play a functional role in the gating mechanisms of several different families of ion channels. Proteins 2001;44:63–72. © 2001 Wiley‐Liss, Inc.

Helix (gastropod)

Structural motif

10.1002/prot.1073

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Citations (149)