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445
The voltage sensor in voltage-dependent ion channels
- Physiol. Rev
, 2000
"... A. The pore and the voltage sensor 556 II. Theoretical Background 559 A. Electric charge movement reflects the operation of the sensor 559 B. Coupling energetics of the sensor and the pore 559 ..."
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Cited by 94 (5 self)
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A. The pore and the voltage sensor 556 II. Theoretical Background 559 A. Electric charge movement reflects the operation of the sensor 559 B. Coupling energetics of the sensor and the pore 559
A coarse-grained normal mode approach for macromolecules: an efficient implementation and application to Ca(2+)-ATPase
- Biophys. J
, 2002
"... ABSTRACT A block normal mode (BNM) algorithm, originally proposed by Tama et al., (Proteins Struct. Func. Genet. 41:1–7, 2000) was implemented into the simulation program CHARMM. The BNM approach projects the hessian matrix into local translation/rotation basis vectors and, therefore, dramatically r ..."
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Cited by 56 (4 self)
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ABSTRACT A block normal mode (BNM) algorithm, originally proposed by Tama et al., (Proteins Struct. Func. Genet. 41:1–7, 2000) was implemented into the simulation program CHARMM. The BNM approach projects the hessian matrix into local translation/rotation basis vectors and, therefore, dramatically reduces the size of the matrix involved in diagonalization. In the current work, by constructing the atomic hessian elements required in the projection operation on the fly, the memory requirement for the BNM approach has been significantly reduced from that of standard normal mode analysis and previous implementation of BNM. As a result, low frequency modes, which are of interest in large-scale conformational changes of large proteins or protein-nucleic acid complexes, can be readily obtained. Comparison of the BNM results with standard normal mode analysis for a number of small proteins and nucleic acids indicates that many properties dominated by low frequency motions are well reproduced by BNM; these include atomic fluctuations, the displacement covariance matrix, vibrational entropies, and involvement coefficients for conformational transitions. Preliminary application to a fairly large system, Ca2-ATPase (994 residues), is described as an example. The structural flexibility of the cytoplasmic domains (especially domain N), correlated motions among residues on domain interfaces and displacement patterns for the trans-membrane helices observed in the BNM results are discussed in relation to the function of Ca2-ATPase. The current implementation of the BNM approach has paved the way for developing efficient sampling algorithms with molecular dynamics or Monte Carlo for studying long-time scale dynamics of macromolecules.
Helix-Helix Packing and Interfacial Pairwise Interactions of Residues in Membrane Proteins
- J. Mol. Biol
, 2001
"... this paper. Here, we are interested in the packing of peptide chains, therefore all ligands and water molecules are removed before computation. Voids and pockets in the TM regions are identied and measured with a probe radius of 1.4 A using the CAST method ..."
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Cited by 48 (17 self)
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this paper. Here, we are interested in the packing of peptide chains, therefore all ligands and water molecules are removed before computation. Voids and pockets in the TM regions are identied and measured with a probe radius of 1.4 A using the CAST method
2001, "Emerging issues of connexin channels: biophysics fills the gap
- Q Rev Biophys
"... 1.1 What? Terminology and general properties 327 ..."
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Tests of Continuum Theories as Models of Ion Channels. II. Poisson-Nernst-Planck Theory versus Brownian Dynamics
- BIOPHYS. J
, 2000
"... We test the validity of the mean-field approximation in Poisson-Nernst-Planck theory by contrasting its predictions with those of Brownian dynamics simulations in schematic cylindrical channels and in a realistic potassium channel. Equivalence of the two theories in bulk situations is demonstrated i ..."
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Cited by 42 (9 self)
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We test the validity of the mean-field approximation in Poisson-Nernst-Planck theory by contrasting its predictions with those of Brownian dynamics simulations in schematic cylindrical channels and in a realistic potassium channel. Equivalence of the two theories in bulk situations is demonstrated in a control study. In simple cylindrical channels, considerable differences are found between the two theories with regard to the concentration profiles in the channel and its conductance properties. These differences are at a maximum in narrow channels with a radius smaller than the Debye length and diminish with increasing radius. Convergence occurs when the channel radius is over 2 Debye lengths. These tests unequivocally demonstrate that the mean-field approximation in the Poisson-Nernst-Planck theory breaks down in narrow ion channels that have radii smaller than the Debye length.
Coupling between voltage sensors and activation gate in voltage-gated K � channels
, 2002
"... abstract Current through voltage-gated K � channels underlies the action potential encoding the electrical signal in excitable cells. The four subunits of a voltage-gated K � channel each have six transmembrane segments (S1–S6), whereas some other K � channels, such as eukaryotic inward rectifier K ..."
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Cited by 39 (1 self)
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abstract Current through voltage-gated K � channels underlies the action potential encoding the electrical signal in excitable cells. The four subunits of a voltage-gated K � channel each have six transmembrane segments (S1–S6), whereas some other K � channels, such as eukaryotic inward rectifier K � channels and the prokaryotic KcsA channel, have only two transmembrane segments (M1 and M2). A voltage-gated K � channel is formed by an ion-pore module (S5–S6, equivalent to M1–M2) and the surrounding voltage-sensing modules. The S4 segments are the primary voltage sensors while the intracellular activation gate is located near the COOH-terminal end of S6, although the coupling mechanism between them remains unknown. In the present study, we found that two short, complementary sequences in voltage-gated K � channels are essential for coupling the voltage sensors to the intracellular activation gate. One sequence is the so called S4–S5 linker distal to the voltage-sensing S4, while the other is around the COOH-terminal end of S6, a region containing the actual gate-forming residues. key words: Shaker • DRK1 • KcsA • S4-S5 linker • S6
Permeation of Ions Across the Potassium Channel: Brownian Dynamics Studies
- Biophys. J
, 1999
"... The physical mechanisms underlying the transport of ions across a model potassium channel are described. The shape of the model channel corresponds closely to that deduced from crystallography. From electrostatic calculations, we show that an ion permeating the channel, in the absence of any residua ..."
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Cited by 35 (14 self)
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The physical mechanisms underlying the transport of ions across a model potassium channel are described. The shape of the model channel corresponds closely to that deduced from crystallography. From electrostatic calculations, we show that an ion permeating the channel, in the absence of any residual charges, encounters an insurmountable energy barrier arising from induced surface charges. Carbonyl groups along the selectivity filter, helix dipoles near the oval chamber, and mouth dipoles near the channel entrances together transform the energy barrier into a deep energy well. Two ions are attracted to this well, and their presence in the channel permits ions to diffuse across it under the influence of an electric field. Using Brownian dynamics simulations, we determine the magnitude of currents flowing across the channel under various conditions. The conductance increases with increasing dipole strength and reaches its maximum rapidly; a further increase in dipole strength causes a st...
Executive Summary
- Usability Inspection Methods
, 1994
"... The fact that membrane proteins are notoriously difficult to analyse using standard protocols for atomic-resolution structure determination methods have motivated adaptation of these techniques to membrane protein studies as well as development of new technologies. With this motivation, liquid-state ..."
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Cited by 32 (0 self)
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The fact that membrane proteins are notoriously difficult to analyse using standard protocols for atomic-resolution structure determination methods have motivated adaptation of these techniques to membrane protein studies as well as development of new technologies. With this motivation, liquid-state nuclear magnetic resonance (NMR) has recently been used with success for studies of peptides and membrane proteins in detergent micelles, and solid-state NMR has undergone a tremendous evolution towards characterization of membrane proteins in native membrane and oriented phospholipid bilayers. In this mini-review, we describe some of the technological challenges behind these efforts and provide examples on their use in membrane biology.
other authors
, 2006
"... This is an uncopyedited electronic version of an article accepted for publication in Diabetes. The American Diabetes Association, publisher of Diabetes, is not responsible for any errors or omissions in this version of the manuscript or any version derived from it by third parties. The definitive pu ..."
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Cited by 30 (3 self)
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This is an uncopyedited electronic version of an article accepted for publication in Diabetes. The American Diabetes Association, publisher of Diabetes, is not responsible for any errors or omissions in this version of the manuscript or any version derived from it by third parties. The definitive publisher-authenticated version will be available in a future issue of Diabetes in print and online at
Structural features of the glutamate transporter family
- Microbiol Mol Biol Rev
, 1999
"... Updated information and services can be found at: ..."
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