Molecular dynamics simulations of barley and maize lipid transfer proteins show different ligand binding preferences in agreement with experimental data.

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dc.contributor.author Smith, Lorna J
dc.contributor.author Roby, Ysobel
dc.contributor.author Allison, Jane R
dc.contributor.author van Gunsteren, Wilfred F
dc.coverage.spatial United States
dc.date.accessioned 2022-05-25T04:18:24Z
dc.date.available 2022-05-25T04:18:24Z
dc.date.issued 2013-07-18
dc.identifier.citation (2013). Biochemistry, 52(30), 5029-5038.
dc.identifier.issn 0006-2960
dc.identifier.uri https://hdl.handle.net/2292/59498
dc.description.abstract Experimental studies of barley and maize lipid transfer proteins (LTPs) show that the two proteins bind the ligand palmitate in opposite orientations in their internal cavities. Moreover, maize LTP is reported to bind the ligand caprate in the internal cavity in a mixture of two orientations with approximately equal occupancy. Six 30 ns molecular dynamics (MD) simulations of maize and barley LTP with ligands bound in two orientations (modes M and B) have been used to understand the different ligand binding preferences. The simulations show that both maize and barley LTP could bind palmitate in the orientation observed experimentally for maize LTP (mode M), with the predominant interaction being a salt bridge between the ligand carboxylate headgroup and a conserved arginine side chain. However, the simulation of barley LTP with palmitate in the mode B orientation shows the most favorable protein-ligand interaction energy. In contrast, the simulations of maize LTP with palmitate and with caprate in the mode B orientation show no persistent ligand binding, the ligands leaving the cavity during the simulations. Sequence differences between maize and barley LTP in the AB loop region, in residues at the base of the hydrophobic cavity, and in the helix A region are identified as contributing to the different behavior. The simulations reproduce well the experimentally observed binding preferences for palmitate and suggest that the experimental data for maize LTP with caprate reflect ligand mobility in binding mode M rather than the population of binding modes M and B.
dc.format.medium Print-Electronic
dc.language eng
dc.publisher American Chemical Society (ACS)
dc.relation.ispartofseries Biochemistry
dc.rights Items in ResearchSpace are protected by copyright, with all rights reserved, unless otherwise indicated. Previously published items are made available in accordance with the copyright policy of the publisher.
dc.rights.uri https://researchspace.auckland.ac.nz/docs/uoa-docs/rights.htm
dc.subject Hordeum
dc.subject Zea mays
dc.subject Decanoic Acids
dc.subject Palmitic Acid
dc.subject Arginine
dc.subject Carrier Proteins
dc.subject Plant Proteins
dc.subject Ligands
dc.subject Reproducibility of Results
dc.subject Sequence Alignment
dc.subject Binding Sites
dc.subject Amino Acid Sequence
dc.subject Molecular Conformation
dc.subject Structural Homology, Protein
dc.subject Sequence Homology, Amino Acid
dc.subject Surface Properties
dc.subject Models, Molecular
dc.subject Molecular Sequence Data
dc.subject Fatty Acid-Binding Proteins
dc.subject Antigens, Plant
dc.subject Molecular Dynamics Simulation
dc.subject Hydrophobic and Hydrophilic Interactions
dc.subject Science & Technology
dc.subject Life Sciences & Biomedicine
dc.subject Biochemistry & Molecular Biology
dc.subject CRYSTAL-STRUCTURE
dc.subject RESOLUTION
dc.subject COMPLEXES
dc.subject FLUORESCENCE
dc.subject PALMITATE
dc.subject MUTATIONS
dc.subject EVOLUTION
dc.subject SOFTWARE
dc.subject RESIDUES
dc.subject SEQUENCE
dc.subject 0601 Biochemistry and Cell Biology
dc.subject 0304 Medicinal and Biomolecular Chemistry
dc.subject 1101 Medical Biochemistry and Metabolomics
dc.title Molecular dynamics simulations of barley and maize lipid transfer proteins show different ligand binding preferences in agreement with experimental data.
dc.type Journal Article
dc.identifier.doi 10.1021/bi4006573
pubs.issue 30
pubs.begin-page 5029
pubs.volume 52
dc.date.updated 2022-04-28T03:20:43Z
dc.rights.holder Copyright: The author en
dc.identifier.pmid 23834513 (pubmed)
pubs.author-url https://www.ncbi.nlm.nih.gov/pubmed/23834513
pubs.end-page 5038
pubs.publication-status Published
dc.rights.accessrights http://purl.org/eprint/accessRights/RetrictedAccess en
pubs.subtype Comparative Study
pubs.subtype Research Support, Non-U.S. Gov't
pubs.subtype Journal Article
pubs.elements-id 739589
pubs.org-id Science
pubs.org-id Biological Sciences
dc.identifier.eissn 1520-4995
pubs.record-created-at-source-date 2022-04-28
pubs.online-publication-date 2013-07-18


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