Literature DB >> 21134351

An NMR database for simulations of membrane dynamics.

Avigdor Leftin1, Michael F Brown.   

Abstract

Computational methods are powerful in capturing the results of experimental studies in terms of force fields that both explain and predict biological structures. Validation of molecular simulations requires comparison with experimental data to test and confirm computational predictions. Here we report a comprehensive database of NMR results for membrane phospholipids with interpretations intended to be accessible by non-NMR specialists. Experimental ¹³C-¹H and ²H NMR segmental order parameters (S(CH) or S(CD)) and spin-lattice (Zeeman) relaxation times (T(1Z)) are summarized in convenient tabular form for various saturated, unsaturated, and biological membrane phospholipids. Segmental order parameters give direct information about bilayer structural properties, including the area per lipid and volumetric hydrocarbon thickness. In addition, relaxation rates provide complementary information about molecular dynamics. Particular attention is paid to the magnetic field dependence (frequency dispersion) of the NMR relaxation rates in terms of various simplified power laws. Model-free reduction of the T(1Z) studies in terms of a power-law formalism shows that the relaxation rates for saturated phosphatidylcholines follow a single frequency-dispersive trend within the MHz regime. We show how analytical models can guide the continued development of atomistic and coarse-grained force fields. Our interpretation suggests that lipid diffusion and collective order fluctuations are implicitly governed by the viscoelastic nature of the liquid-crystalline ensemble. Collective bilayer excitations are emergent over mesoscopic length scales that fall between the molecular and bilayer dimensions, and are important for lipid organization and lipid-protein interactions. Future conceptual advances and theoretical reductions will foster understanding of biomembrane structural dynamics through a synergy of NMR measurements and molecular simulations.
Copyright © 2010 Elsevier B.V. All rights reserved.

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Year:  2010        PMID: 21134351      PMCID: PMC5176272          DOI: 10.1016/j.bbamem.2010.11.027

Source DB:  PubMed          Journal:  Biochim Biophys Acta        ISSN: 0006-3002


  211 in total

1.  A unified model of protein dynamics.

Authors:  Hans Frauenfelder; Guo Chen; Joel Berendzen; Paul W Fenimore; Helén Jansson; Benjamin H McMahon; Izabela R Stroe; Jan Swenson; Robert D Young
Journal:  Proc Natl Acad Sci U S A       Date:  2009-02-27       Impact factor: 11.205

2.  Influence of docosahexaenoic acid and cholesterol on lateral lipid organization in phospholipid mixtures.

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Journal:  Biochemistry       Date:  1998-12-08       Impact factor: 3.162

3.  Molecular motion and order in single-bilayer vesicles and multilamellar dispersions of egg lecithin and lecithin-cholesterol mixtures. A deuterium nuclear magnetic resonance study of specifically labeled lipids.

Authors:  G W Stockton; C F Polnaszek; A P Tulloch; F Hasan; I C Smith
Journal:  Biochemistry       Date:  1976-03-09       Impact factor: 3.162

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Authors:  S Marcelja
Journal:  Biochim Biophys Acta       Date:  1974-10-29

5.  Deuterium nuclear magnetic resonance investigation of the dipalmitoyl lecithin-cholesterol-water system.

Authors:  R A Haberkorn; R G Griffin; M D Meadows; E Oldfield
Journal:  J Am Chem Soc       Date:  1977-10-26       Impact factor: 15.419

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Authors:  G W Stockton; I C Smith
Journal:  Chem Phys Lipids       Date:  1976-10       Impact factor: 3.329

7.  Effects of cholesterol on the properties of equimolar mixtures of synthetic phosphatidylethanolamine and phosphatidylcholine. A 31P NMR and differential scanning calorimetry study.

Authors:  P R Cullis; P W van Dijck; B de Kruijff; J de Gier
Journal:  Biochim Biophys Acta       Date:  1978-10-19

8.  Interaction of rhodopsin with two unsaturated phosphatidylcholines: a deuterium nuclear magnetic resonance study.

Authors:  A J Deese; E A Dratz; F W Dahlquist; M R Paddy
Journal:  Biochemistry       Date:  1981-10-27       Impact factor: 3.162

9.  Deuterium NMR studies of the interactions of polyhydroxyl compounds and of glycolipids with lipid model membranes.

Authors:  B Bechinger; P M Macdonald; J Seelig
Journal:  Biochim Biophys Acta       Date:  1988-08-18

10.  14N NMR of lipid bilayers: effects of ions and anesthetics.

Authors:  D J Siminovitch; M F Brown; K R Jeffrey
Journal:  Biochemistry       Date:  1984-05-22       Impact factor: 3.162

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  28 in total

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2.  Depolarization Laplace transform analysis of exchangeable hyperpolarized ¹²⁹Xe for detecting ordering phases and cholesterol content of biomembrane models.

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4.  Curvature forces in membrane lipid-protein interactions.

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Journal:  Biochemistry       Date:  2012-11-27       Impact factor: 3.162

5.  Deuterium NMR of raft model membranes reveals domain-specific order profiles and compositional distribution.

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6.  Computer simulations of protein-membrane systems.

Authors:  Jennifer Loschwitz; Olujide O Olubiyi; Jochen S Hub; Birgit Strodel; Chetan S Poojari
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7.  Markovian and Non-Markovian Modeling of Membrane Dynamics with Milestoning.

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Journal:  J Phys Chem B       Date:  2016-04-05       Impact factor: 2.991

Review 8.  Cholesterol-induced suppression of membrane elastic fluctuations at the atomistic level.

Authors:  Trivikram R Molugu; Michael F Brown
Journal:  Chem Phys Lipids       Date:  2016-05-03       Impact factor: 3.329

9.  Solid-state ¹³C NMR reveals annealing of raft-like membranes containing cholesterol by the intrinsically disordered protein α-Synuclein.

Authors:  Avigdor Leftin; Constantin Job; Klaus Beyer; Michael F Brown
Journal:  J Mol Biol       Date:  2013-04-11       Impact factor: 5.469

10.  Phase transitions in coarse-grained lipid bilayers containing cholesterol by molecular dynamics simulations.

Authors:  Qaiser Waheed; Richard Tjörnhammar; Olle Edholm
Journal:  Biophys J       Date:  2012-11-20       Impact factor: 4.033

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