Membrane Insertion of a Voltage Sensor Helix
Tóm tắt
Từ khóa
Tài liệu tham khảo
Nilsson, 2005, Comparative analysis of amino acid distributions in integral membrane proteins from 107 genomes, Proteins, 60, 606, 10.1002/prot.20583
Terstappen, 2001, In silico research in drug discovery, Trends Pharmacol. Sci., 22, 23, 10.1016/S0165-6147(00)01584-4
Killian, 2000, How proteins adapt to a membrane-water interface, Trends Biochem. Sci., 25, 429, 10.1016/S0968-0004(00)01626-1
Krepkiy, 2009, Structure and hydration of membranes embedded with voltage-sensing domains, Nature, 462, 473, 10.1038/nature08542
Long, 2005, Crystal structure of a mammalian voltage-dependent Shaker family K+ channel, Science, 309, 897, 10.1126/science.1116269
Long, 2007, Atomic structure of a voltage-dependent K+ channel in a lipid membrane-like environment, Nature, 450, 376, 10.1038/nature06265
Parsegian, 1969, Energy of an ion crossing a low dielectric membrane: solutions to four relevant electrostatic problems, Nature, 221, 844, 10.1038/221844a0
Hessa, 2005, Membrane insertion of a potassium-channel voltage sensor, Science, 307, 1427, 10.1126/science.1109176
Freites, 2005, Interface connections of a transmembrane voltage sensor, Proc. Natl. Acad. Sci. USA, 102, 15059, 10.1073/pnas.0507618102
Allen, 2007, Modeling charged protein side chains in lipid membranes, J. Gen. Physiol., 130, 237, 10.1085/jgp.200709850
Dorairaj, 2007, On the thermodynamic stability of a charged arginine side chain in a transmembrane helix, Proc. Natl. Acad. Sci. USA, 104, 4943, 10.1073/pnas.0610470104
MacCallum, 2008, Distribution of amino acids in a lipid bilayer from computer simulations, Biophys. J., 94, 3393, 10.1529/biophysj.107.112805
Ayton, 2007, Multiscale modeling of biomolecular systems: in serial and in parallel, Curr. Opin. Struct. Biol., 17, 192, 10.1016/j.sbi.2007.03.004
Bond, 2008, Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer, Biochemistry, 47, 11321, 10.1021/bi800642m
Marrink, 2004, Coarse grained model for semiquantitative lipid simulations, J. Phys. Chem. B., 108, 750, 10.1021/jp036508g
Monticelli, 2008, The MARTINI coarse grained force field: extension to proteins, J. Chem. Theory Comput., 4, 819, 10.1021/ct700324x
Shih, 2006, Coarse grained protein-lipid model with application to lipoprotein particles, J. Phys. Chem. B., 110, 3674, 10.1021/jp0550816
Shelley, 2001, A coarse grain model for phospholipid simulations, J. Phys. Chem. B., 105, 4464, 10.1021/jp010238p
Izvekov, 2005, A multiscale coarse-graining method for biomolecular systems, J. Phys. Chem. B., 109, 2469, 10.1021/jp044629q
Tozzini, 2005, Coarse-grained models for proteins, Curr. Opin. Struct. Biol., 15, 144, 10.1016/j.sbi.2005.02.005
Wee, 2010, Membrane/toxin interaction energetics via serial multi-scale molecular dynamics simulations, J. Chem. Theory Comput., 6, 966, 10.1021/ct900652s
Sands, 2007, How does a voltage sensor interact with a lipid bilayer? Simulations of a potassium channel domain, Structure, 15, 235, 10.1016/j.str.2007.01.004
Schow, 2010, Down-state model of the voltage-sensing domain of a potassium channel, Biophys. J., 98, 2857, 10.1016/j.bpj.2010.03.031
Jiang, 2003, X-ray structure of a voltage-dependent K+ channel, Nature, 423, 33, 10.1038/nature01580
Sali, 1993, Comparative protein modelling by satisfaction of spatial restraints, J. Mol. Biol., 234, 779, 10.1006/jmbi.1993.1626
Sánchez, 2000, Comparative protein structure modeling. Introduction and practical examples with modeller, Methods Mol. Biol., 143, 97
van Gunsteren, 1996
Berger, 1997, Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature, Biophys. J., 72, 2002, 10.1016/S0006-3495(97)78845-3
Marrink, 1998, Adhesion forces of lipids in a phospholipid membrane studied by molecular dynamics simulations, Biophys. J., 74, 931, 10.1016/S0006-3495(98)74016-0
Kumar, 1992, The weighted histogram analysis method for free-energy calculations on biomolecules. 1. The method, J. Comput. Chem., 13, 1011, 10.1002/jcc.540130812
Berendsen, 1984, Molecular dynamics with coupling to an external bath, J. Chem. Phys., 81, 3684, 10.1063/1.448118
Darden, 1993, Particle mesh Ewald: an N.log(N) method for Ewald sums in large systems, J. Chem. Phys., 98, 10089, 10.1063/1.464397
Hess, 1997, LINCS: A linear constraint solver for molecular simulations, J. Comput. Chem., 18, 1463, 10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
Miyamoto, 1992, Settle: an analytical version of the Shake and Rattle algorithm for rigid water models, J. Comput. Chem., 13, 952, 10.1002/jcc.540130805
Bond, 2007, Bilayer deformation by the Kv channel voltage sensor domain revealed by self-assembly simulations, Proc. Natl. Acad. Sci. USA, 104, 2631, 10.1073/pnas.0606822104
Schmidt, 2006, Phospholipids and the origin of cationic gating charges in voltage sensors, Nature, 444, 775, 10.1038/nature05416
Xu, 2008, Removal of phospho-head groups of membrane lipids immobilizes voltage sensors of K+ channels, Nature, 451, 826, 10.1038/nature06618
Vorobyov, 2008, Assessing atomistic and coarse-grained force fields for protein-lipid interactions: the formidable challenge of an ionizable side chain in a membrane, J. Phys. Chem. B., 112, 9588, 10.1021/jp711492h
Treptow, 2006, Environment of the gating charges in the Kv1.2 Shaker potassium channel, Biophys. J., 90, L64, 10.1529/biophysj.106.080754
Jogini, 2007, Dynamics of the Kv1.2 voltage-gated K+ channel in a membrane environment, Biophys. J., 93, 3070, 10.1529/biophysj.107.112540
Denning, 2008, Double bilayers and transmembrane gradients: a molecular dynamics study of a highly charged peptide, Biophys. J., 95, 3161, 10.1529/biophysj.108.134049
Treptow, 2008, Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations, J. Phys. Chem. B., 112, 3277, 10.1021/jp709675e
Hessa, 2005, Recognition of transmembrane helices by the endoplasmic reticulum translocon, Nature, 433, 377, 10.1038/nature03216
Enquist, 2009, Membrane-integration characteristics of two ABC transporters, CFTR and P-glycoprotein, J. Mol. Biol., 387, 1153, 10.1016/j.jmb.2009.02.035
Vostrikov, 2010, Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations, J. Am. Chem. Soc., 132, 5803, 10.1021/ja100598e
Fernández-Vidal, M., F. Castro-Roman, and S.H. White. 2006. Membrane insertion of a S4 potassium channel voltage sensor: an experimental study. 2006 Biophysical Society Meeting Abstracts. Biophys. J. Suppl. 20a. :1164–Pos.
Zhang, 2007, Contribution of hydrophobic and electrostatic interactions to the membrane integration of the Shaker K+ channel voltage sensor domain, Proc. Natl. Acad. Sci. USA, 104, 8263, 10.1073/pnas.0611007104
White, 2008, How translocons select transmembrane helices, Annu. Rev. Biophys., 37, 23, 10.1146/annurev.biophys.37.032807.125904
White, 1999, Membrane protein folding and stability: physical principles, Annu. Rev. Biophys. Biomol. Struct., 28, 319, 10.1146/annurev.biophys.28.1.319
Taylor, 1999, A calorimetric study of the folding-unfolding of an α-helix with covalently closed N and C-terminal loops, J. Mol. Biol., 291, 965, 10.1006/jmbi.1999.3025
Gnanakaran, 2005, Helix-coil transition of alanine peptides in water: force field dependence on the folded and unfolded structures, Proteins, 59, 773, 10.1002/prot.20439
Mattila, 1999, The alignment of a voltage-sensing peptide in dodecylphosphocholine micelles and in oriented lipid bilayers by nuclear magnetic resonance and molecular modeling, Biophys. J., 77, 2102, 10.1016/S0006-3495(99)77051-7
Lee, 2008, Transmembrane helix tilting: insights from calculating the potential of mean force, Phys. Rev. Lett., 100, 018103, 10.1103/PhysRevLett.100.018103
Johansson, 2009, Protein contents in biological membranes can explain abnormal solvation of charged and polar residues, Proc. Natl. Acad. Sci. USA, 106, 15684, 10.1073/pnas.0905394106
Nishizawa, 2008, Molecular dynamics simulation of Kv channel voltage sensor helix in a lipid membrane with applied electric field, Biophys. J., 95, 1729, 10.1529/biophysj.108.130658
Ramsey, 2010, An aqueous H+ permeation pathway in the voltage-gated proton channel Hv1, Nat. Struct. Mol. Biol., 17, 869, 10.1038/nsmb.1826
Chen, 2007, Proton transport behavior through the influenza A M2 channel: insights from molecular simulation, Biophys. J., 93, 3470, 10.1529/biophysj.107.105742
Yoo, 2008, Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations, Biophys. J., 94, L61, 10.1529/biophysj.107.122945
Treptow, 2009, Initial response of the potassium channel voltage sensor to a transmembrane potential, J. Am. Chem. Soc., 131, 2107, 10.1021/ja807330g
Gkeka, 2010, Interactions of phospholipid bilayers with several classes of amphiphilic α-helical peptides: insights from coarse-grained molecular dynamics simulations, J. Phys. Chem. B., 114, 826, 10.1021/jp908320b
Ulmschneider, 2010, Peptide partitioning properties from direct insertion studies, Biophys. J., 98, L60, 10.1016/j.bpj.2010.03.043
Schmidt, 2008, Voltage-dependent K+ channel gating and voltage sensor toxin sensitivity depend on the mechanical state of the lipid membrane, Proc. Natl. Acad. Sci. USA, 105, 19276, 10.1073/pnas.0810187105