Martin B Ulmschneider

Martin B Ulmschneider

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Martin B Ulmschneider

Martin B Ulmschneider

Publications by authors named "Martin B Ulmschneider"

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Understanding and modelling the interactions of peptides with membranes: from partitioning to self-assembly.

Curr Opin Struct Biol 2020 Apr 30;61:160-166. Epub 2020 Jan 30.

Department of Chemistry, King's College London, London, UK. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2019.12.021DOI Listing
April 2020

Simulation-Guided Rational de Novo Design of a Small Pore-Forming Antimicrobial Peptide.

J Am Chem Soc 2019 03 13;141(12):4839-4848. Epub 2019 Mar 13.

Department of Chemistry , King's College London , London , U.K.

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http://dx.doi.org/10.1021/jacs.8b11939DOI Listing
March 2019

The importance of the membrane interface as the reference state for membrane protein stability.

Biochim Biophys Acta Biomembr 2018 12 20;1860(12):2539-2548. Epub 2018 Sep 20.

Department of Chemistry, King's College London, UK. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00052736183027
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http://dx.doi.org/10.1016/j.bbamem.2018.09.012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6309459PMC
December 2018

Predicting drug delivery efficiency into tumor tissues through molecular simulation of transport in complex vascular networks.

J Control Release 2018 12 8;292:221-234. Epub 2018 Nov 8.

Department of Chemistry, King's College London, London, UK; University of Exeter Medical School, Exeter, UK; Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD, USA; Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01683659183064
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http://dx.doi.org/10.1016/j.jconrel.2018.11.010DOI Listing
December 2018

Role of the Interaction Motif in Maintaining the Open Gate of an Open Sodium Channel.

Biophys J 2018 11 4;115(10):1920-1930. Epub 2018 Oct 4.

Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303419PMC
November 2018

Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method.

J Membr Biol 2018 06 8;251(3):345-356. Epub 2018 Mar 8.

Department of Physics and the Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.

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http://dx.doi.org/10.1007/s00232-018-0026-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6030508PMC
June 2018

Correction to: Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method.

J Membr Biol 2018 06;251(3):357

Department of Physics and the Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, 200240, China.

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http://dx.doi.org/10.1007/s00232-018-0038-7DOI Listing
June 2018

Molecular Dynamics Simulations Are Redefining Our View of Peptides Interacting with Biological Membranes.

Acc Chem Res 2018 05 18;51(5):1106-1116. Epub 2018 Apr 18.

Department of Chemistry , King's College , London SE1 1DB , U.K.

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http://dx.doi.org/10.1021/acs.accounts.7b00613DOI Listing
May 2018

Proline-Rich Chaperones Are Compared Computationally and Experimentally for Their Abilities to Facilitate Recombinant Butyrylcholinesterase Tetramerization in CHO Cells.

Biotechnol J 2018 Mar 17;13(3):e1700479. Epub 2017 Nov 17.

Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 221 Maryland Hall, 3400 N. Charles St. Baltimore, Maryland, 21218, USA.

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http://dx.doi.org/10.1002/biot.201700479DOI Listing
March 2018

Statistically derived asymmetric membrane potentials from α-helical and β-barrel membrane proteins.

Sci Rep 2018 03 13;8(1):4446. Epub 2018 Mar 13.

Medical School, University of Exeter, Exeter, EX1 2 LU, UK.

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http://dx.doi.org/10.1038/s41598-018-22476-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5849751PMC
March 2018

Transmembrane helices containing a charged arginine are thermodynamically stable.

Eur Biophys J 2017 Oct 13;46(7):627-637. Epub 2017 Apr 13.

Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California, Irvine, CA, 92697-4560, USA.

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http://dx.doi.org/10.1007/s00249-017-1206-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5640460PMC
October 2017

Spontaneous formation of structurally diverse membrane channel architectures from a single antimicrobial peptide.

Nat Commun 2016 11 22;7:13535. Epub 2016 Nov 22.

Institute of Natural Sciences, Shanghai Jiao-Tong University, 800 Dongchuan Road, Shanghai 200240, China.

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http://dx.doi.org/10.1038/ncomms13535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121426PMC
November 2016

Mechanisms of Membrane Pore Formation by Amyloidogenic Peptides in Amyotrophic Lateral Sclerosis.

Chemistry 2016 Jul 16;22(29):9958-61. Epub 2016 Jun 16.

Department of Materials Science and Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218-2608, USA.

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http://dx.doi.org/10.1002/chem.201601765DOI Listing
July 2016

Quantitative Analysis of the Enhanced Permeation and Retention (EPR) Effect.

PLoS One 2015 4;10(5):e0123461. Epub 2015 May 4.

Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America; Institute for Nanobiotechnology (INBT), Johns Hopkins University, Baltimore, Maryland, United States of America; Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0123461PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418820PMC
April 2016

Mathematical models of the steps involved in the systemic delivery of a chemotherapeutic to a solid tumor: From circulation to survival.

J Control Release 2015 Aug 20;212:78-84. Epub 2015 Jun 20.

Department of Materials Science and Engineering, Institute for Nanobiotechnology (INBT), Johns Hopkins University, Baltimore, MD 21218, United States; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21231. Electronic address:

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http://dx.doi.org/10.1016/j.jconrel.2015.06.026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4508231PMC
August 2015

Peptide Folding in Translocon-Like Pores.

J Membr Biol 2015 Jun 28;248(3):407-17. Epub 2015 May 28.

Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA,

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http://dx.doi.org/10.1007/s00232-015-9808-7DOI Listing
June 2015

Lipid headgroups modulate membrane insertion of pHLIP peptide.

Biophys J 2015 Feb;108(4):791-794

Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, Kansas. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2015.01.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4336367PMC
February 2015

Computational modeling of membrane proteins.

Proteins 2015 Jan 19;83(1):1-24. Epub 2014 Nov 19.

Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, 21218.

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http://dx.doi.org/10.1002/prot.24703DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4270820PMC
January 2015

Absorption and folding of melittin onto lipid bilayer membranes via unbiased atomic detail microsecond molecular dynamics simulation.

Biochim Biophys Acta 2014 Sep 21;1838(9):2243-9. Epub 2014 Apr 21.

Department of Materials Science and Engineering, Johns Hopkins University, Baltimore MD, USA. Electronic address:

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http://dx.doi.org/10.1016/j.bbamem.2014.04.012DOI Listing
September 2014

Spontaneous transmembrane helix insertion thermodynamically mimics translocon-guided insertion.

Nat Commun 2014 Sep 10;5:4863. Epub 2014 Sep 10.

Department of Physiology &Biophysics and the Center for Biomembrane Systems, University of California, Irvine, California 92697-4560, USA.

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http://dx.doi.org/10.1038/ncomms5863DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4161982PMC
September 2014

Mechanisms of molecular transport through the urea channel of Helicobacter pylori.

Nat Commun 2013 ;4:2900

1] Center for Biomembrane Systems & Department of Molecular Biology & Biochemistry, University of California, Irvine, California 92697, USA [2].

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http://dx.doi.org/10.1038/ncomms3900DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3863980PMC
July 2014

Efficient Characterization of Protein Cavities within Molecular Simulation Trajectories: trj_cavity.

J Chem Theory Comput 2014 May;10(5):2151-64

Unilever Centre for Molecular Science Informatics, Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom.

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http://dx.doi.org/10.1021/ct401098bDOI Listing
May 2014

Molecular dynamics of ion transport through the open conformation of a bacterial voltage-gated sodium channel.

Proc Natl Acad Sci U S A 2013 Apr 29;110(16):6364-9. Epub 2013 Mar 29.

Institute of Structural and Molecular Biology, Birkbeck College, University of London, London WC1E 7HX, United Kingdom.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1214667110
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http://dx.doi.org/10.1073/pnas.1214667110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631666PMC
April 2013

Conformational states of melittin at a bilayer interface.

Biophys J 2013 Mar 19;104(6):L12-4. Epub 2013 Mar 19.

Department of Physiology and Biophysics, University of California, Irvine, CA, USA.

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http://dx.doi.org/10.1016/j.bpj.2013.02.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602767PMC
March 2013

Assembly and Stability of α-Helical Membrane Proteins.

Soft Matter 2012 Aug;8(30):7742-7752

Department of Chemistry, University of California, Irvine, CA 92697, U.S.A.

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http://dx.doi.org/10.1039/C2SM25402FDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500387PMC
August 2012

Determining peptide partitioning properties via computer simulation.

J Membr Biol 2011 Jan 25;239(1-2):15-26. Epub 2010 Nov 25.

IWR, University of Heidelberg, Heidelberg, Germany.

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http://dx.doi.org/10.1007/s00232-010-9324-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3030940PMC
January 2011

Mechanism and kinetics of peptide partitioning into membranes from all-atom simulations of thermostable peptides.

J Am Chem Soc 2010 Mar;132(10):3452-60

Department of Chemistry, University of Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/ja909347xDOI Listing
March 2010

Membrane/Toxin Interaction Energetics via Serial Multiscale Molecular Dynamics Simulations.

J Chem Theory Comput 2010 Mar;6(3):966-76

Department of Biochemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom.

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http://dx.doi.org/10.1021/ct900652sDOI Listing
March 2010

Peptide Partitioning and Folding into Lipid Bilayers.

J Chem Theory Comput 2009 Sep;5(9):2202-5

IWR, University of Heidelberg, Germany, Department of Chemistry, University of Utrecht, Utrecht, The Netherlands, and Oak Ridge National Laboratory, Oak Ridge, Tennessee.

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http://dx.doi.org/10.1021/ct900256kDOI Listing
September 2009

United Atom Lipid Parameters for Combination with the Optimized Potentials for Liquid Simulations All-Atom Force Field.

J Chem Theory Comput 2009 Jul;5(7):1803-13

IWR, University of Heidelberg, Heidelberg, Germany, and Department of Chemistry, University of Utrecht, Utrecht, The Netherlands.

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http://dx.doi.org/10.1021/ct900086bDOI Listing
July 2009

Sampling efficiency in explicit and implicit membrane environments studied by peptide folding simulations.

Proteins 2009 May;75(3):586-97

Department of Biochemistry, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1002/prot.22270DOI Listing
May 2009

Folding Peptides into Lipid Bilayer Membranes.

J Chem Theory Comput 2008 Nov;4(11):1807-9

Department of Biochemistry, University of Oxford, Oxford OX1 1QU, U.K.

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http://dx.doi.org/10.1021/ct800100mDOI Listing
November 2008

Membrane adsorption, folding, insertion and translocation of synthetic trans-membrane peptides.

Mol Membr Biol 2008 Apr;25(3):245-57

Department of Biochemistry, University of Oxford, Oxford, UK.

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http://dx.doi.org/10.1080/09687680802020313DOI Listing
April 2008

Monte Carlo folding of trans-membrane helical peptides in an implicit generalized Born membrane.

Proteins 2007 Nov;69(2):297-308

Department of Chemistry, University of Rome La Sapienza, Rome, Italy.

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http://dx.doi.org/10.1002/prot.21519DOI Listing
November 2007

Folding Simulations of the Transmembrane Helix of Virus Protein U in an Implicit Membrane Model.

J Chem Theory Comput 2007 Nov;3(6):2335-46

Department of Chemistry, University of Rome "La Sapienza", Rome, Italy, and Department of Biochemistry, University of Oxford, Oxford, U.K.

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http://dx.doi.org/10.1021/ct700103kDOI Listing
November 2007

Dehydration-driven solvent exposure of hydrophobic surfaces as a driving force in peptide folding.

Proc Natl Acad Sci U S A 2007 Sep 19;104(39):15230-5. Epub 2007 Sep 19.

Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.

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http://dx.doi.org/10.1073/pnas.0701401104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2000556PMC
September 2007

A generalized born implicit-membrane representation compared to experimental insertion free energies.

Biophys J 2007 Apr 11;92(7):2338-49. Epub 2007 Jan 11.

Department of Biochemistry, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1529/biophysj.106.081810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1864825PMC
April 2007

Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations.

J Phys Chem B 2006 Aug;110(33):16733-42

Department of Chemistry, University of Rome "La Sapienza", Rome, Italy.

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http://dx.doi.org/10.1021/jp061619bDOI Listing
August 2006

Evaluating tilt angles of membrane-associated helices: comparison of computational and NMR techniques.

Biophys J 2006 Mar 9;90(5):1650-60. Epub 2005 Dec 9.

Department of Chemistry, University of Rome La Sapienza, I-00185 Rome, Italy.

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http://dx.doi.org/10.1529/biophysj.105.065367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1367316PMC
March 2006

The role of extra-membranous inter-helical loops in helix-helix interactions.

Protein Eng Des Sel 2005 Dec 26;18(12):563-70. Epub 2005 Oct 26.

Laboratory of Molecular Biophysics, The Rex Richards Building, Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.

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http://dx.doi.org/10.1093/protein/gzi059DOI Listing
December 2005

Properties of integral membrane protein structures: derivation of an implicit membrane potential.

Proteins 2005 May;59(2):252-65

Department of Chemistry, University of Rome La Sapienza, Rome, Italy.

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http://dx.doi.org/10.1002/prot.20334DOI Listing
May 2005