Siewert J Marrink

Siewert J Marrink

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Siewert J Marrink

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Emerging Diversity in Lipid-Protein Interactions.

Chem Rev 2019 Feb 13. Epub 2019 Feb 13.

Centre for Molecular Simulation and Department of Biological Sciences , University of Calgary , 2500 University Drive NW , Calgary , Alberta T2N 1N4 , Canada.

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http://dx.doi.org/10.1021/acs.chemrev.8b00451DOI Listing
February 2019

Computational Modeling of Realistic Cell Membranes.

Chem Rev 2019 Jan 9. Epub 2019 Jan 9.

Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K.

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http://dx.doi.org/10.1021/acs.chemrev.8b00460DOI Listing
January 2019

Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models.

J Phys Chem Lett 2018 Sep 11;9(18):5527-5533. Epub 2018 Sep 11.

Groningen Biomolecular Sciences and Biotechnology Institute and The Zernike Institute for Advanced Material , University of Groningen , Nijenborgh 7 , 9747 AG Groningen , Netherlands.

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http://pubs.acs.org/doi/10.1021/acs.jpclett.8b01877
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http://dx.doi.org/10.1021/acs.jpclett.8b01877DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6151656PMC
September 2018

Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers.

Biophys J 2018 Aug 20;115(3):494-502. Epub 2018 Jun 20.

Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Groningen, the Netherlands; Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.06.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6084417PMC
August 2018

Fluorinated Alcohols' Effects on Lipid Bilayer Properties.

Biophys J 2018 Aug 1;115(4):679-689. Epub 2018 Aug 1.

Department Physiology and Biophysics, Weill Cornell Medicine, New York City, New York; Groningen Biomolecular Science and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands; Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.07.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104562PMC
August 2018

Transferable MARTINI Model of Poly(ethylene Oxide).

J Phys Chem B 2018 Jul 13;122(29):7436-7449. Epub 2018 Jul 13.

Molecular Microbiology and Structural Biochemistry, UMR 5086 , CNRS and University of Lyon , Lyon , France.

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http://dx.doi.org/10.1021/acs.jpcb.8b04760DOI Listing
July 2018

The N-terminal amphipathic helix of Pex11p self-interacts to induce membrane remodelling during peroxisome fission.

Biochim Biophys Acta Biomembr 2018 Jun 1;1860(6):1292-1300. Epub 2018 Mar 1.

Molecular Dynamics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands; Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal. Electronic address:

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http://dx.doi.org/10.1016/j.bbamem.2018.02.029DOI Listing
June 2018

Lipid-Protein Interactions Are Unique Fingerprints for Membrane Proteins.

ACS Cent Sci 2018 Jun 13;4(6):709-717. Epub 2018 Jun 13.

Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada.

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http://dx.doi.org/10.1021/acscentsci.8b00143DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028153PMC
June 2018

Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments.

Chem Soc Rev 2018 May;47(10):3470-3489

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1039/c8cs00040aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5961611PMC
May 2018

Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2.

Biophys J 2018 Apr;114(8):1858-1868

Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2018.02.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5936973PMC
April 2018

Multiscale Simulation of Protein Hydration Using the SWINGER Dynamical Clustering Algorithm.

J Chem Theory Comput 2018 Mar 21;14(3):1754-1761. Epub 2018 Feb 21.

Laboratory for Molecular Modeling , National Institute of Chemistry , Hajdrihova 19 , SI-1001 Ljubljana , Slovenia.

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http://dx.doi.org/10.1021/acs.jctc.7b01129DOI Listing
March 2018

Structural insights into K48-linked ubiquitin chain formation by the Pex4p-Pex22p complex.

Biochem Biophys Res Commun 2018 02 28;496(2):562-567. Epub 2017 Dec 28.

Molecular Cell Biology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747AG, The Netherlands. Electronic address:

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https://www.rug.nl/research/portal/files/56327242/Structural
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https://linkinghub.elsevier.com/retrieve/pii/S0006291X173255
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http://dx.doi.org/10.1016/j.bbrc.2017.12.150DOI Listing
February 2018

Enhancing Molecular n-Type Doping of Donor-Acceptor Copolymers by Tailoring Side Chains.

Adv Mater 2018 Feb 11;30(7). Epub 2018 Jan 11.

Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen, NL-9747, AG, The Netherlands.

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http://doi.wiley.com/10.1002/adma.201704630
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http://dx.doi.org/10.1002/adma.201704630DOI Listing
February 2018

Energetics Underlying Twist Polymorphisms in Amyloid Fibrils.

J Phys Chem B 2018 01 5;122(3):1081-1091. Epub 2018 Jan 5.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Groningen 9747 AG, The Netherlands.

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http://dx.doi.org/10.1021/acs.jpcb.7b10233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5857390PMC
January 2018

Prediction of Thylakoid Lipid Binding Sites on Photosystem II.

Biophys J 2017 Dec;113(12):2669-2681

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.

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http://dx.doi.org/10.1016/j.bpj.2017.09.039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5770566PMC
December 2017

Computational Lipidomics of the Neuronal Plasma Membrane.

Biophys J 2017 Nov 4;113(10):2271-2280. Epub 2017 Nov 4.

Biosciences and Biotechnology Division, Physical and Life Sciences Directorate. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.10.017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5700369PMC
November 2017

Alcohol Interactions with Lipid Bilayers.

Molecules 2017 Nov 28;22(12). Epub 2017 Nov 28.

Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University in Bratislava, 832 32 Bratislava, Slovakia.

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http://dx.doi.org/10.3390/molecules22122078DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6149720PMC
November 2017

Structural and Spectroscopic Properties of Assemblies of Self-Replicating Peptide Macrocycles.

ACS Nano 2017 08 21;11(8):7858-7868. Epub 2017 Jul 21.

University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute , Nijenborgh 7, 9747AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/acsnano.7b02211DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5616102PMC
August 2017

Martini Coarse-Grained Force Field: Extension to RNA.

Biophys J 2017 Jul 17;113(2):246-256. Epub 2017 Jun 17.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.

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http://dx.doi.org/10.1016/j.bpj.2017.05.043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5529176PMC
July 2017

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex.

Nat Commun 2017 05 10;8:15214. Epub 2017 May 10.

Groningen Biomolecular Sciences and Biotechnology Institute &Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1038/ncomms15214DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5436218PMC
May 2017

Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding.

Biophys J 2017 May;112(9):1929-1939

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands. Electronic address:

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http://dx.doi.org/10.1016/j.bpj.2017.04.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5425406PMC
May 2017

Ganglioside-Lipid and Ganglioside-Protein Interactions Revealed by Coarse-Grained and Atomistic Molecular Dynamics Simulations.

J Phys Chem B 2017 04 4;121(15):3262-3275. Epub 2016 Oct 4.

Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , 2500 University Drive, N.W., Calgary, Alberta T2N 1N4, Canada.

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http://pubs.acs.org/doi/10.1021/acs.jpcb.6b07142
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http://dx.doi.org/10.1021/acs.jpcb.6b07142DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5402298PMC
April 2017

Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane.

J Phys Chem B 2017 04 28;121(15):3237-3249. Epub 2016 Sep 28.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands.

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http://dx.doi.org/10.1021/acs.jpcb.6b06865DOI Listing
April 2017

Lipid and Peptide Diffusion in Bilayers: The Saffman-Delbrück Model and Periodic Boundary Conditions.

J Phys Chem B 2017 04 6;121(15):3443-3457. Epub 2017 Jan 6.

Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health , Bethesda, Maryland 20892, United States.

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http://dx.doi.org/10.1021/acs.jpcb.6b09111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6326097PMC
April 2017

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations.

J Am Chem Soc 2017 03 7;139(10):3697-3705. Epub 2017 Mar 7.

Ghent Quantum Chemistry Group, Department of Inorganic and Physical Chemistry, Ghent University , Krijgslaan 281 (S3), B-9000 Gent, Belgium.

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http://pubs.acs.org/doi/10.1021/jacs.6b11717
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http://dx.doi.org/10.1021/jacs.6b11717DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5355903PMC
March 2017

Stability and dynamics of membrane-spanning DNA nanopores.

Nat Commun 2017 03 20;8:14784. Epub 2017 Mar 20.

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.

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http://dx.doi.org/10.1038/ncomms14784DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5364398PMC
March 2017

High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating.

J Am Chem Soc 2017 02 10;139(7):2664-2671. Epub 2017 Feb 10.

Groningen Biomolecular Science and Biotechnology Institute, University of Groningen , Nijenborgh 7, 9747 AG, Groningen, The Netherlands.

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http://dx.doi.org/10.1021/jacs.6b11091DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5343553PMC
February 2017

Coupled binding mechanism of three sodium ions and aspartate in the glutamate transporter homologue Glt.

Nat Commun 2016 11 10;7:13420. Epub 2016 Nov 10.

University of Groningen, Groningen Biomolecular Sciences and Biotechnology Institute, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1038/ncomms13420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5110648PMC
November 2016

Adaptive Resolution Simulation of Supramolecular Water: The Concurrent Making, Breaking, and Remaking of Water Bundles.

J Chem Theory Comput 2016 Aug 25;12(8):4138-45. Epub 2016 Jul 25.

Department of Molecular Modeling, National Institute of Chemistry , Hajdrihova 19, SI-1001 Ljubljana, Slovenia.

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http://dx.doi.org/10.1021/acs.jctc.6b00536DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5008762PMC
August 2016

Intramolecular photostabilization via triplet-state quenching: design principles to make organic fluorophores "self-healing".

Faraday Discuss 2015 9;184:221-35. Epub 2015 Oct 9.

Molecular Microscopy Research Group & Single-molecule Biophysics, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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http://xlink.rsc.org/?DOI=C5FD00114E
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http://dx.doi.org/10.1039/c5fd00114eDOI Listing
July 2016

Computational 'microscopy' of cellular membranes.

J Cell Sci 2016 Jan 7;129(2):257-68. Epub 2016 Jan 7.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, Groningen 9747 AG, The Netherlands

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http://dx.doi.org/10.1242/jcs.176040DOI Listing
January 2016

From light-harvesting to photoprotection: structural basis of the dynamic switch of the major antenna complex of plants (LHCII).

Sci Rep 2015 Oct 23;5:15661. Epub 2015 Oct 23.

Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.

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http://www.nature.com/articles/srep15661
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http://dx.doi.org/10.1038/srep15661DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4616226PMC
October 2015

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field.

J Chem Theory Comput 2015 Sep 27;11(9):4486-94. Epub 2015 Aug 27.

Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas , 2030 Becker Drive, Lawrence, Kansas 66047, United States.

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http://dx.doi.org/10.1021/acs.jctc.5b00513DOI Listing
September 2015

Martini Coarse-Grained Force Field: Extension to DNA.

J Chem Theory Comput 2015 Aug 23;11(8):3932-45. Epub 2015 Jul 23.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/acs.jctc.5b00286DOI Listing
August 2015

Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations.

Biochim Biophys Acta 2015 Jun 5;1848(6):1319-30. Epub 2015 Mar 5.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1016/j.bbamem.2015.02.025DOI Listing
June 2015

Atomistic and Coarse Grain Topologies for the Cofactors Associated with the Photosystem II Core Complex.

J Phys Chem B 2015 Jun 8;119(25):7791-803. Epub 2015 Jun 8.

‡Department of Physics and Astronomy and Institute for Lasers, Life and Biophotonics, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.

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http://dx.doi.org/10.1021/acs.jpcb.5b00809DOI Listing
June 2015

Adaptive resolution simulation of polarizable supramolecular coarse-grained water models.

J Chem Phys 2015 Jun;142(24):244118

Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.

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http://dx.doi.org/10.1063/1.4923008DOI Listing
June 2015

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations.

J Chem Theory Comput 2015 May 24;11(5):2144-55. Epub 2015 Apr 24.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/acs.jctc.5b00209DOI Listing
May 2015

High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach.

J Chem Theory Comput 2015 May 26;11(5):2278-91. Epub 2015 Mar 26.

Computational Biology, Department of Biology, Friedrich-Alexander University of Erlangen-Nürnberg , Staudtstrasse 5, 91058 Erlangen, Germany.

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http://dx.doi.org/10.1021/ct5010092DOI Listing
May 2015

Ironing out their differences: dissecting the structural determinants of a phenylalanine aminomutase and ammonia lyase.

ACS Chem Biol 2015 Apr 20;10(4):989-97. Epub 2015 Jan 20.

†Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands.

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http://dx.doi.org/10.1021/cb500794hDOI Listing
April 2015

Enantioselective enzymes by computational design and in silico screening.

Angew Chem Int Ed Engl 2015 Mar 4;54(12):3726-30. Epub 2015 Feb 4.

Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands).

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http://dx.doi.org/10.1002/anie.201411415DOI Listing
March 2015

MARTINI coarse-grained model for crystalline cellulose microfibers.

J Phys Chem B 2015 Jan 6;119(2):465-73. Epub 2015 Jan 6.

Theoretical Division, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States.

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http://dx.doi.org/10.1021/jp5105938DOI Listing
January 2015

Dry Martini, a coarse-grained force field for lipid membrane simulations with implicit solvent.

J Chem Theory Comput 2015 Jan 17;11(1):260-75. Epub 2014 Dec 17.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ct500477kDOI Listing
January 2015

Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry.

Proc Natl Acad Sci U S A 2014 Dec 17;111(48):17170-5. Epub 2014 Nov 17.

Department of Neuroscience, University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands

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http://dx.doi.org/10.1073/pnas.1413118111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4260606PMC
December 2014

Disaccharides impact the lateral organization of lipid membranes.

J Am Chem Soc 2014 Nov 5;136(46):16167-75. Epub 2014 Nov 5.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ja505476cDOI Listing
November 2014

The activation mode of the mechanosensitive ion channel, MscL, by lysophosphatidylcholine differs from tension-induced gating.

FASEB J 2014 Oct 23;28(10):4292-302. Epub 2014 Jun 23.

Groningen Biomolecular Sciences and Biotechnology Institute, Groningen, The Netherlands; Neuroscience Department, University Medical Centre Groningen, Groningen, The Netherlands

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http://dx.doi.org/10.1096/fj.14-251579DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4202108PMC
October 2014

Lipid organization of the plasma membrane.

J Am Chem Soc 2014 Oct 1;136(41):14554-9. Epub 2014 Oct 1.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ja507832eDOI Listing
October 2014

Hydrophobic compounds reshape membrane domains.

PLoS Comput Biol 2014 Oct 9;10(10):e1003873. Epub 2014 Oct 9.

IBCP, CNRS UMR 5086, Lyon, France; Université Claude Bernard Lyon I, Lyon, France.

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http://dx.doi.org/10.1371/journal.pcbi.1003873DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191877PMC
October 2014

Mechanisms shaping cell membranes.

Curr Opin Cell Biol 2014 Aug 18;29:53-60. Epub 2014 Apr 18.

MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK. Electronic address:

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http://dx.doi.org/10.1016/j.ceb.2014.03.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180517PMC
August 2014

Phytochemicals perturb membranes and promiscuously alter protein function.

ACS Chem Biol 2014 Aug 17;9(8):1788-98. Epub 2014 Jun 17.

Zernike Institute for Advanced Materials, ‡Groningen Biomolecular Science and Biotechnology Institute, University of Groningen , Groningen, The Netherlands.

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http://dx.doi.org/10.1021/cb500086eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4136704PMC
August 2014

Establishing conditions for simulating hydrophobic solutes in electric fields by molecular dynamics: effects of the long-range van der Waals treatment on the apparent particle mobility.

J Mol Model 2014 Aug 8;20(8):2359. Epub 2014 Aug 8.

Cluster of Excellence: Engineering of Advanced Materials, Friedrich-Alexander University Erlangen-Nuremberg, Nägelsbachstraße 49b, 91052, Erlangen, Germany.

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http://link.springer.com/10.1007/s00894-014-2359-5
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http://dx.doi.org/10.1007/s00894-014-2359-5DOI Listing
August 2014

Computationally efficient and accurate enantioselectivity modeling by clusters of molecular dynamics simulations.

J Chem Inf Model 2014 Jul 30;54(7):2079-92. Epub 2014 Jun 30.

Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ci500126xDOI Listing
July 2014

Computational library design for increasing haloalkane dehalogenase stability.

Chembiochem 2014 Jul 27;15(11):1660-72. Epub 2014 Jun 27.

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen (The Netherlands).

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http://dx.doi.org/10.1002/cbic.201402128DOI Listing
July 2014

Helfrich model of membrane bending: from Gibbs theory of liquid interfaces to membranes as thick anisotropic elastic layers.

Adv Colloid Interface Sci 2014 Jun 3;208:25-33. Epub 2014 Feb 3.

Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel. Electronic address:

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http://dx.doi.org/10.1016/j.cis.2014.01.018DOI Listing
June 2014

Adaptive Resolution Simulation of MARTINI Solvents.

J Chem Theory Comput 2014 Jun 6;10(6):2591-8. Epub 2014 May 6.

Laboratory for Molecular Modeling, National Institute of Chemistry , Hajdrihova 19, SI-1001 Ljubljana, Slovenia.

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http://dx.doi.org/10.1021/ct5001523DOI Listing
June 2014

The power of coarse graining in biomolecular simulations.

Wiley Interdiscip Rev Comput Mol Sci 2014 May;4(3):225-248

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen Groningen, The Netherlands.

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http://dx.doi.org/10.1002/wcms.1169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4171755PMC
May 2014

Simulation of polyethylene glycol and calcium-mediated membrane fusion.

J Chem Phys 2014 Mar;140(12):124905

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1063/1.4869176DOI Listing
March 2014

Computationally designed libraries for rapid enzyme stabilization.

Protein Eng Des Sel 2014 Feb 8;27(2):49-58. Epub 2014 Jan 8.

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1093/protein/gzt061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893934PMC
February 2014

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models.

J Chem Theory Comput 2014 Feb 21;10(2):676-90. Epub 2014 Jan 21.

Department of Biological Sciences, University of Calgary, 2500 University Drive NW , Calgary, Alberta, Canada T2N 1N4.

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http://dx.doi.org/10.1021/ct400617gDOI Listing
February 2014

Adaptive resolution simulation of an atomistic protein in MARTINI water.

J Chem Phys 2014 Feb;140(5):054114

Laboratory for Molecular Modeling, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia.

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http://dx.doi.org/10.1063/1.4863329DOI Listing
February 2014

Coarse-grain modelling of protein-protein interactions.

Curr Opin Struct Biol 2013 Dec 27;23(6):878-86. Epub 2013 Oct 27.

Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, Paris 75005, France. Electronic address:

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http://dx.doi.org/10.1016/j.sbi.2013.09.004DOI Listing
December 2013

Computational microscopy of cyclodextrin mediated cholesterol extraction from lipid model membranes.

Sci Rep 2013 ;3:2071

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1038/srep02071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3691568PMC
October 2013

Gaussian curvature elasticity determined from global shape transformations and local stress distributions: a comparative study using the MARTINI model.

Faraday Discuss 2013 ;161:365-82; discussion 419-59

Carnegie Mellon University, 5000 Forbes Avenue, Pittsburgh, PA 15213, USA.

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September 2013

Perspective on the Martini model.

Chem Soc Rev 2013 Aug;42(16):6801-22

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.

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http://xlink.rsc.org/?DOI=c3cs60093a
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http://dx.doi.org/10.1039/c3cs60093aDOI Listing
August 2013

Improved Angle Potentials for Coarse-Grained Molecular Dynamics Simulations.

J Chem Theory Comput 2013 Aug 16;9(8):3282-92. Epub 2013 Jul 16.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ct400219nDOI Listing
August 2013

Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: a theoretical and computational study.

J Chem Phys 2013 Jun;138(23):234901

Dipartimento di Scienze Chimiche, Università di Catania, Viale A. Doria 6, 95125 Catania, Italy.

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http://dx.doi.org/10.1063/1.4809993DOI Listing
June 2013

Mixing MARTINI: electrostatic coupling in hybrid atomistic-coarse-grained biomolecular simulations.

J Phys Chem B 2013 Apr 6;117(13):3516-30. Epub 2013 Mar 6.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/jp311533pDOI Listing
April 2013

Martini Force Field Parameters for Glycolipids.

J Chem Theory Comput 2013 Mar 5;9(3):1694-708. Epub 2013 Feb 5.

Groningen Biomolecular Sciences and Biotechnology (GBB) Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ct3009655DOI Listing
March 2013

Evidence for cardiolipin binding sites on the membrane-exposed surface of the cytochrome bc1.

J Am Chem Soc 2013 Feb 13;135(8):3112-20. Epub 2013 Feb 13.

Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://pubs.acs.org/doi/10.1021/ja310577u
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February 2013

Vibrational Spectra of a Mechanosensitive Channel.

J Phys Chem Lett 2013 Feb 18;4(3):448-52. Epub 2013 Jan 18.

†Center for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/jz3019258DOI Listing
February 2013

Structural investigation of MscL gating using experimental data and coarse grained MD simulations.

PLoS Comput Biol 2012 20;8(9):e1002683. Epub 2012 Sep 20.

School of Biomedical, Biomolecular and Chemical Sciences, The University of Western Australia, Perth, Australia.

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http://dx.plos.org/10.1371/journal.pcbi.1002683
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http://dx.doi.org/10.1371/journal.pcbi.1002683DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3447979PMC
January 2013

Improved Parameters for the Martini Coarse-Grained Protein Force Field.

J Chem Theory Comput 2013 Jan 28;9(1):687-97. Epub 2012 Nov 28.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ct300646gDOI Listing
January 2013

Amylose folding under the influence of lipids.

Carbohydr Res 2012 Dec 17;364:1-7. Epub 2012 Oct 17.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1016/j.carres.2012.10.007DOI Listing
December 2012

Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers.

J Am Chem Soc 2012 Jul 25;134(26):10959-65. Epub 2012 Jun 25.

Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ja303286eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406292PMC
July 2012

Transmembrane helices can induce domain formation in crowded model membranes.

Biochim Biophys Acta 2012 Apr 22;1818(4):984-94. Epub 2011 Aug 22.

Groningen Biomolecular Sciences and Biotechnology Institute, and Zernike Institute for Advanced Materials, University of Groningen, Nijemborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1016/j.bbamem.2011.08.021DOI Listing
April 2012

Molecular structure of membrane tethers.

Biophys J 2012 Apr;102(8):1866-71

Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.

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http://dx.doi.org/10.1016/j.bpj.2012.03.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3328718PMC
April 2012

Dimerization of Amino Acid Side Chains: Lessons from the Comparison of Different Force Fields.

J Chem Theory Comput 2012 Mar 29;8(3):1003-14. Epub 2012 Feb 29.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ct200599dDOI Listing
March 2012

Lipid acrobatics in the membrane fusion arena.

Curr Top Membr 2011 ;68:259-94

Institute for Complex Molecular Systems & Biomodeling and Bioinformatics Group, Eindhoven University of Technology, Eindhoven, The Netherlands.

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http://dx.doi.org/10.1016/B978-0-12-385891-7.00011-8DOI Listing
January 2012

In silico design of robust bolalipid membranes.

Biomacromolecules 2012 Jan 1;13(1):196-205. Epub 2011 Dec 1.

Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1021/bm201454jDOI Listing
January 2012

Molecular view of the role of fusion peptides in promoting positive membrane curvature.

J Am Chem Soc 2012 Jan 10;134(3):1543-52. Epub 2012 Jan 10.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1021/ja207290bDOI Listing
January 2012

Structural basis for the enhanced activity of cyclic antimicrobial peptides: the case of BPC194.

Biochim Biophys Acta 2011 Sep 8;1808(9):2197-205. Epub 2011 May 8.

Department of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands.

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http://dx.doi.org/10.1016/j.bbamem.2011.05.001DOI Listing
September 2011

Determining equilibrium constants for dimerization reactions from molecular dynamics simulations.

J Comput Chem 2011 Jul 5;32(9):1919-28. Epub 2011 Apr 5.

Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.

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http://dx.doi.org/10.1002/jcc.21776DOI Listing
July 2011

Hybrid simulations: combining atomistic and coarse-grained force fields using virtual sites.

Phys Chem Chem Phys 2011 Jun 15;13(22):10437-48. Epub 2011 Apr 15.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1039/c0cp02981eDOI Listing
June 2011

The molecular basis for antimicrobial activity of pore-forming cyclic peptides.

Biophys J 2011 May;100(10):2422-31

Department of Biochemistry and Biophysical Chemistry, Groningen Biomolecular Sciences, Netherlands.

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http://dx.doi.org/10.1016/j.bpj.2011.03.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093570PMC
May 2011

Molecular mechanism of cyclodextrin mediated cholesterol extraction.

PLoS Comput Biol 2011 Mar 24;7(3):e1002020. Epub 2011 Mar 24.

Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1371/journal.pcbi.1002020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3063748PMC
March 2011

Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes.

Proc Natl Acad Sci U S A 2011 Jan 4;108(4):1343-8. Epub 2011 Jan 4.

Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.

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http://dx.doi.org/10.1073/pnas.1009362108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3029762PMC
January 2011

Partitioning of lipids at domain boundaries in model membranes.

Biophys J 2010 Dec;99(12):L91-3

Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1016/j.bpj.2010.08.072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3000497PMC
December 2010

Release of content through mechano-sensitive gates in pressurized liposomes.

Proc Natl Acad Sci U S A 2010 Nov 1;107(46):19856-60. Epub 2010 Nov 1.

Groningen Biomolecular Sciences and Biotechnology Institute, Department of Biophysical Chemistry, University of Groningen, Nijenborgh 4, 9747AG Groningen, The Netherlands.

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http://dx.doi.org/10.1073/pnas.1001316107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2993341PMC
November 2010

Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes.

Phys Chem Chem Phys 2010 Oct 23;12(40):12987-96. Epub 2010 Aug 23.

Groningen Biomolecular Sciences and Biotechnology Institute (GBB) and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, Netherlands.

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http://xlink.rsc.org/?DOI=c0cp00101e
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http://dx.doi.org/10.1039/c0cp00101eDOI Listing
October 2010

Cholesterol in bilayers with PUFA chains: doping with DMPC or POPC results in sterol reorientation and membrane-domain formation.

Biochemistry 2010 Sep;49(35):7485-93

Canadian Neutron Beam Centre, National Research Council, Chalk River, Ontario K0J 1J0, Canada.

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http://dx.doi.org/10.1021/bi100891zDOI Listing
September 2010

Influence of hydrophobic mismatch and amino acid composition on the lateral diffusion of transmembrane peptides.

Biophys J 2010 Sep;99(5):1447-54

Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, Netherlands Proteomics Centre, and Zernike Institute for Advanced Materials, University of Groningen, Groningen, The Netherlands.

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http://dx.doi.org/10.1016/j.bpj.2010.05.042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2931740PMC
September 2010

Polarizable water model for the coarse-grained MARTINI force field.

PLoS Comput Biol 2010 Jun 10;6(6):e1000810. Epub 2010 Jun 10.

Department of Physics of Biological Systems, Institute of Physics, National Academy of Sciences of Ukraine, Kiev, Ukraine.

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http://dx.plos.org/10.1371/journal.pcbi.1000810
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http://dx.doi.org/10.1371/journal.pcbi.1000810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2883601PMC
June 2010