Literature DB >> 24655203

More than the sum of its parts: coarse-grained peptide-lipid interactions from a simple cross-parametrization.

Tristan Bereau1, Zun-Jing Wang1, Markus Deserno1.   

Abstract

Interfacial systems are at the core of fascinating phenomena in many disciplines, such as biochemistry, soft-matter physics, and food science. However, the parametrization of accurate, reliable, and consistent coarse-grained (CG) models for systems at interfaces remains a challenging endeavor. In the present work, we explore to what extent two independently developed solvent-free CG models of peptides and lipids--of different mapping schemes, parametrization methods, target functions, and validation criteria--can be combined by only tuning the cross-interactions. Our results show that the cross-parametrization can reproduce a number of structural properties of membrane peptides (for example, tilt and hydrophobic mismatch), in agreement with existing peptide-lipid CG force fields. We find encouraging results for two challenging biophysical problems: (i) membrane pore formation mediated by the cooperative action of several antimicrobial peptides, and (ii) the insertion and folding of the helix-forming peptide WALP23 in the membrane.

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Year:  2014        PMID: 24655203      PMCID: PMC3977883          DOI: 10.1063/1.4867465

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  67 in total

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5.  Mixed atomistic and coarse-grained molecular dynamics: simulation of a membrane-bound ion channel.

Authors:  Qiang Shi; Sergei Izvekov; Gregory A Voth
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6.  A systematically coarse-grained solvent-free model for quantitative phospholipid bilayer simulations.

Authors:  Zun-Jing Wang; Markus Deserno
Journal:  J Phys Chem B       Date:  2010-09-02       Impact factor: 2.991

7.  Parameterization of PACE Force Field for Membrane Environment and Simulation of Helical Peptides and Helix-Helix Association.

Authors:  Cheuk-Kin Wan; Wei Han; Yun-Dong Wu
Journal:  J Chem Theory Comput       Date:  2011-12-01       Impact factor: 6.006

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Authors:  Nathan Hyunjoong Joh; Andrew Min; Salem Faham; Julian P Whitelegge; Duan Yang; Virgil L Woods; James U Bowie
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9.  Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane.

Authors:  Igor Vorobyov; Libo Li; Toby W Allen
Journal:  J Phys Chem B       Date:  2008-07-18       Impact factor: 2.991

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Authors:  O G Mouritsen; M Bloom
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  8 in total

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Authors:  Tristan Bereau; Markus Deserno
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Review 5.  Molecular dynamics simulations in photosynthesis.

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Review 6.  Computational Modeling of Realistic Cell Membranes.

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7.  Model parameters for simulation of physiological lipids.

Authors:  Ronald D Hills; Nicholas McGlinchey
Journal:  J Comput Chem       Date:  2016-02-11       Impact factor: 3.376

8.  Refining amino acid hydrophobicity for dynamics simulation of membrane proteins.

Authors:  Ronald D Hills
Journal:  PeerJ       Date:  2018-01-10       Impact factor: 2.984

  8 in total

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