Computer modelling of glycolipids at membrane surfaces.


:Interactions of membrane anchored molecules such as glycolipids with a membrane surface are important in determining headgroup conformation. It is therefore essential to represent these membrane surface interactions in molecular modeling studies of glycolipids and other membrane bound molecules. We introduce here an energy term that represents the interaction of molecules with a membrane bilayer. This membrane interaction energy term has been added to the potential energy function of a molecular dynamics and mechanics program and has been parameterized using partition coefficients between an aqueous solution and a vesicular membrane for two model glycolipids.


Biophys J


Biophysical journal


Ram P,Kim E,Thomson DS,Howard KP,Prestegard JH




Has Abstract


1992-12-01 00:00:00














  • Calcium transients in cerebellar granule cell presynaptic terminals.

    abstract::Calcium ions act presynaptically to modulate synaptic strength and to trigger neurotransmitter release. Here we detect stimulus-evoked changes in residual free calcium ([Ca2+]i) in rat cerebellar granule cell presynaptic terminals. Granule cell axons, known as parallel fibers, and their associated boutons, were labele...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Regehr WG,Atluri PP

    更新日期:1995-05-01 00:00:00

  • GB1 is not a two-state folder: identification and characterization of an on-pathway intermediate.

    abstract::The folding pathway of the small α/β protein GB1 has been extensively studied during the past two decades using both theoretical and experimental approaches. These studies provided a consensus view that the protein folds in a two-state manner. Here, we reassessed the folding of GB1, both by experiments and simulations...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Morrone A,Giri R,Toofanny RD,Travaglini-Allocatelli C,Brunori M,Daggett V,Gianni S

    更新日期:2011-10-19 00:00:00

  • Hydrophobic Characteristic Is Energetically Preferred for Cysteine in a Model Membrane Protein.

    abstract::The naturally occurring amino acid cysteine has often been implicated with a crucial role in maintaining protein structure and stability. An intriguing duality in the intrinsic hydrophobicity of the cysteine side chain is that it exhibits both polar as well as hydrophobic characteristics. Here, we have utilized a cyst...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Iyer BR,Mahalakshmi R

    更新日期:2019-07-09 00:00:00

  • Nanoparticles as fluorescence labels: is size all that matters?

    abstract::Fluorescent labels are often used in bioassays as a means to detect and characterize ligand-receptor binding. This is due in part to the inherently high sensitivity of fluorescence-based technology and the relative accessibility of the technique. There is often little concern raised as to whether or not the fluorescen...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Swift JL,Cramb DT

    更新日期:2008-07-01 00:00:00

  • 2H NMR determination of the global correlation time of the gramicidin channel in a lipid bilayer.

    abstract::A detailed experimental description of molecular dynamics requires an accurate description of the global correlation time. For the gramicidin cation-selective channel the local dynamics of the polypeptide backbone are thought to play a very significant role in the functional process of this channel which occurs on the...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Lee KC,Hu W,Cross TA

    更新日期:1993-09-01 00:00:00

  • Modeling of the three-dimensional structure of polypeptides in solution using potential-scaled/hot-solute molecular dynamics.

    abstract::We present here an efficient and accurate procedure for modeling of the three-dimensional structures of polypeptides in the explicit solvent water based on molecular dynamics calculations. Using the toxic domain analog of heat-stable enterotoxin as a model peptide, we examined the utilities of two molecular dynamics t...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Tsujishita H,Moriguchi I,Hirono S

    更新日期:1994-06-01 00:00:00

  • Transmembrane exchange of hyperpolarized 13C-urea in human erythrocytes: subminute timescale kinetic analysis.

    abstract::The rate of exchange of urea across the membranes of human erythrocytes (red blood cells) was quantified on the 1-s to 2-min timescale. (13)C-urea was hyperpolarized and subjected to rapid dissolution and the previously reported (partial) resolution of (13)C NMR resonances from the molecules inside and outside red blo...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Pagès G,Puckeridge M,Liangfeng G,Tan YL,Jacob C,Garland M,Kuchel PW

    更新日期:2013-11-05 00:00:00

  • Voltage and temperature dependence of single K+ channels isolated from canine cardiac sarcoplasmic reticulum.

    abstract::The temperature and voltage dependence of gating and conductance of sarcoplasmic reticulum K+ channels (S-R K+) isolated from adult canine hearts were studied using the reconstituted bilayer technique. Fusion of vesicles from this preparation frequently resulted in the incorporation of a single channel. Only bilayers ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Shen WK,Rasmusson RL,Liu QY,Crews AL,Strauss HC

    更新日期:1993-08-01 00:00:00

  • Reassessment of the Basis of Cell Size Control Based on Analysis of Cell-to-Cell Variability.

    abstract::Fundamental mechanisms governing cell size control and homeostasis are still poorly understood. The relationship between sizes at division and birth in single cells is used as a metric to categorize the basis of size homeostasis. Cells dividing at a fixed size regardless of birth size (sizer) are expected to show a di...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Facchetti G,Knapp B,Chang F,Howard M

    更新日期:2019-11-05 00:00:00

  • The effect of salt on self-assembled actin-lysozyme complexes.

    abstract::We present a combined experimental and computational study of the bundling of F-actin filaments induced by lysozyme proteins. Synchrotron small-angle x-ray scattering results show that these bundles consist of close-packed columnar complexes in which the actin is held together by incommensurate, one-dimensional arrays...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Guáqueta C,Sanders LK,Wong GC,Luijten E

    更新日期:2006-06-15 00:00:00

  • Cholesterol-sphingomyelin interactions: a molecular dynamics simulation study.

    abstract::Stearoylsphingomyelin (SSM) bilayers containing 0, 22, and 50 mol % cholesterol (Chol) and a pentadecanoyl-stearoylphosphatidylcholine (15SPC) bilayer containing 22 mol % Chol were molecular dynamics simulated at two temperatures (37 degrees C and 60 degrees C). 15SPC is the best PC equivalent of SSM. The Chol effect ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Róg T,Pasenkiewicz-Gierula M

    更新日期:2006-11-15 00:00:00

  • Does the use of DM-nitrophen, nitr-5, or diazo-2 interfere with the measurement of indo-1 fluorescence?

    abstract::Emission spectra of the photolabile Ca2+ chelators DM-nitrophen, nitr-5, and diazo-2 were studied alone, and in the presence of indo-1, to investigate potential interactions that would make the simultaneous manipulation and ratiometric measurement of the intracellular Ca2+ concentration difficult. Neither diazo-2 nor ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Hadley RW,Kirby MS,Lederer WJ,Kao JP

    更新日期:1993-12-01 00:00:00

  • Bacteriorhodopsin/amphipol complexes: structural and functional properties.

    abstract::The membrane protein bacteriorhodopsin (BR) can be kept soluble in its native state for months in the absence of detergent by amphipol (APol) A8-35, an amphiphilic polymer. After an actinic flash, A8-35-complexed BR undergoes a complete photocycle, with kinetics intermediate between that in detergent solution and that...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Gohon Y,Dahmane T,Ruigrok RW,Schuck P,Charvolin D,Rappaport F,Timmins P,Engelman DM,Tribet C,Popot JL,Ebel C

    更新日期:2008-05-01 00:00:00

  • Copper-based pulsed dipolar ESR spectroscopy as a probe of protein conformation linked to disease states.

    abstract::We demonstrate the ability of pulsed dipolar electron spin resonance (ESR) spectroscopy (PDS) to report on the conformation of Cu-Zn superoxide dismutase (SOD1) through the sensitive measurement of dipolar interactions between inherent Cu(2+) ions. Although the extent and the anisotropy of the Cu ESR spectrum provides...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Merz GE,Borbat PP,Pratt AJ,Getzoff ED,Freed JH,Crane BR

    更新日期:2014-10-07 00:00:00

  • Intermediates and kinetics of membrane fusion.

    abstract::Recently, it has become clear that the influenza virus fusion protein, hemagglutinin (HA), produces membrane destabilization and fusion by a multistep process, which involves the aggregation of the HAs to form a fusion site. While the details of this process are under debate, it is important to recognize that proposin...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Bentz J

    更新日期:1992-08-01 00:00:00

  • Force spectroscopy with dual-trap optical tweezers: molecular stiffness measurements and coupled fluctuations analysis.

    abstract::Dual-trap optical tweezers are often used in high-resolution measurements in single-molecule biophysics. Such measurements can be hindered by the presence of extraneous noise sources, the most prominent of which is the coupling of fluctuations along different spatial directions, which may affect any optical tweezers s...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Ribezzi-Crivellari M,Ritort F

    更新日期:2012-11-07 00:00:00

  • Effects of codon distributions and tRNA competition on protein translation.

    abstract::Translation is a central cellular process and the complexity of its mechanism necessitates mathematical frameworks to better understand system properties and make quantitative predictions. We have developed a gene sequence-specific mechanistic model for translation which accounts for all the elementary steps of transl...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Zouridis H,Hatzimanikatis V

    更新日期:2008-08-01 00:00:00

  • The dependence of the shapes of fluorescence induction curves in chloroplasts on the duration of illumination pulses.

    abstract::The shapes of fluorescence induction curves in spinach chloroplasts, measured using double-flash pump-probe techniques, are shown to depend on the duration of the actinic flashes. For flash durations tau(0)

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Valkunas L,Geacintov NE,France L,Breton J

    更新日期:1991-02-01 00:00:00

  • Covalent immobilization of native biomolecules onto Au(111) via N-hydroxysuccinimide ester functionalized self-assembled monolayers for scanning probe microscopy.

    abstract::We have worked out a procedure for covalent binding of native biomacromolecules on flat gold surfaces for scanning probe microscopy in aqueous buffer solutions and for other nanotechnological applications, such as the direct measurement of interaction forces between immobilized macromolecules, of their elastomechanica...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Wagner P,Hegner M,Kernen P,Zaugg F,Semenza G

    更新日期:1996-05-01 00:00:00

  • Recoil after severing reveals stress fiber contraction mechanisms.

    abstract::Stress fibers are cellular contractile actomyosin machines central to wound healing, shear stress response, and other processes. Contraction mechanisms have been difficult to establish because stress fibers in cultured cells typically exert isometric tension and present little kinetic activity. In a recent study, livi...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Stachowiak MR,O'Shaughnessy B

    更新日期:2009-07-22 00:00:00

  • Subsecond proton-hole propagation in bacteriorhodopsin.

    abstract::The dynamics of proton transfer between the surface of purple membrane and the aqueous bulk have recently been investigated by the Laser Induced Proton Pulse Method. Following a Delta-function release of protons to the bulk, the system was seen to regain its state of equilibrium within a few hundreds of microseconds. ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Schätzler B,Dencher NA,Tittor J,Oesterhelt D,Yaniv-Checover S,Nachliel E,Gutman M

    更新日期:2003-01-01 00:00:00

  • Glycosphingolipid fatty acid arrangement in phospholipid bilayers: cholesterol effects.

    abstract::Deuterium wide line NMR spectroscopy was used to study cholesterol effects on the ceramide portions of two glycosphingolipids (GSLs) distributed as minor components in fluid membranes. The common existence of very long fatty acids on GSLs was taken into account by including one glycolipid species with fatty acid chain...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Morrow MR,Singh D,Lu D,Grant CW

    更新日期:1995-01-01 00:00:00

  • Intrinsic cytosolic calcium buffering properties of single rat cardiac myocytes.

    abstract::Intracellular passive Ca2+, buffering was measured in voltage-clamped rat ventricular myocytes. Cells were loaded with indo-1 (K+ salt) to an estimated cytosolic concentration of 44 +/- 5 microM (Mean +/- SEM, n = 5), and accessible cell volume was estimated to be 24.5 +/- 3.6 pl. Ca2+ transport by the sarcoplasmic re...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Berlin JR,Bassani JW,Bers DM

    更新日期:1994-10-01 00:00:00

  • Patch electrode glass composition affects ion channel currents.

    abstract::The influence of patch electrode glass composition on macroscopic IV relations in inside-out patches of the cGMP-activated ion channel from rod photoreceptors was examined for a soda lime glass, a Kovar sealing glass, a borosilicate glass, and several soft lead glasses. In several glasses the shape or magnitude of the...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Furman RE,Tanaka JC

    更新日期:1988-02-01 00:00:00

  • Determination of cellular strains by combined atomic force microscopy and finite element modeling.

    abstract::Many organs adapt to their mechanical environment as a result of physiological change or disease. Cells are both the detectors and effectors of this process. Though many studies have been performed in vitro to investigate the mechanisms of detection and adaptation to mechanical strains, the cellular strains remain unk...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Charras GT,Horton MA

    更新日期:2002-08-01 00:00:00

  • PrP(106-126) does not interact with membranes under physiological conditions.

    abstract::Transmissible spongiform encephalopathies are neurodegenerative diseases characterized by the accumulation of an abnormal isoform of the prion protein PrP(Sc). Its fragment 106-126 has been reported to maintain most of the pathological features of PrP(Sc), and a role in neurodegeneration has been proposed based on the...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Henriques ST,Pattenden LK,Aguilar MI,Castanho MA

    更新日期:2008-08-01 00:00:00

  • Voltage-dependent block by saxitoxin of sodium channels incorporated into planar lipid bilayers.

    abstract::We have previously studied single, voltage-dependent, saxitoxin-(STX) blockable sodium channels from rat brain in planar lipid bilayers, and found that channel block by STX was voltage-dependent. Here we describe the effect of voltage on the degree of block and on the kinetics of the blocking reaction. From their volt...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: French RJ,Worley JF 3rd,Krueger BK

    更新日期:1984-01-01 00:00:00

  • The bound states of amphipathic drugs in lipid bilayers: study of curcumin.

    abstract::Drug-membrane interactions are well known but poorly understood. Here we describe dual measurements of membrane thickness change and membrane area change due to the binding of the amphipathic drug curcumin. The combined results allowed us to analyze the binding states of a drug to lipid bilayers, one on the water-memb...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Sun Y,Lee CC,Hung WC,Chen FY,Lee MT,Huang HW

    更新日期:2008-09-01 00:00:00

  • Molecular dynamics free energy calculations to assess the possibility of water existence in protein nonpolar cavities.

    abstract::Are protein nonpolar cavities filled with water molecules? Although many experimental and theoretical investigations have been done, particularly for the nonpolar cavity of IL-1 beta, the results are still conflicting. To study this problem from the thermodynamic point of view, we calculated hydration free energies of...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Oikawa M,Yonetani Y

    更新日期:2010-06-16 00:00:00

  • The nature of sources of bioelectric and biomagnetic fields.

    abstract::The goal of this paper is to examine the origins and relative importance of primary and secondary sources of electric and magnetic fields for excitable tissue. It is shown that for axonal and cardiac tissue a comparison of the relative field strength from both primary and secondary sources shows only the latter to be ...

    journal_title:Biophysical journal

    pub_type: 杂志文章


    authors: Plonsey R

    更新日期:1982-09-01 00:00:00