Inactivation by ionizing radiation of ion channels formed by polyene antibiotics amphotericin B and nystatin in lipid membranes: an inverse dose-rate behavior.

abstract：:We study the folding mechanism of a triple beta-strand WW domain from the Formin binding protein 28 (FBP28) at atomic resolution with explicit water model using replica exchange molecular dynamics computer simulations. Extended sampling over a wide range of temperatures to obtain the free energy, enthalpy, and entropy...

journal_title：Biophysical journal

authors： Mu Y,Nordenskiöld L,Tam JP

更新日期：2006-06-01 00:00:00

abstract：:Reversible blockage of the voltage-dependent anion channel (VDAC) of the mitochondrial outer membrane by dimeric tubulin is being recognized as a potent regulator of mitochondrial respiration. The tubulin-blocked state of VDAC is impermeant for ATP but only partially closed for small ions. This residual conductance al...

journal_title：Biophysical journal

authors： Gurnev PA,Queralt-Martin M,Aguilella VM,Rostovtseva TK,Bezrukov SM

更新日期：2012-05-02 00:00:00

abstract：:In this article, optimization-based frameworks are introduced for elucidating the input-output structure of signaling networks and for pinpointing targeted disruptions leading to the silencing of undesirable outputs in therapeutic interventions. The frameworks are demonstrated on a large-scale reconstruction of a sign...

journal_title：Biophysical journal

authors： Dasika MS,Burgard A,Maranas CD

更新日期：2006-07-01 00:00:00

abstract：:It is now known that the flexibility of the troponin T (TnT) tail determines thin filament conformation and hence cross-bridge cycling properties, expanding the classic structural role of TnT to a dynamic role regulating sarcomere function. Here, using transgenic mice bearing R-92W and R-92L missense mutations in card...

journal_title：Biophysical journal

authors： He H,Javadpour MM,Latif F,Tardiff JC,Ingwall JS

更新日期：2007-09-01 00:00:00

abstract：:Formation of liquid-ordered domains in model membranes can be linked to raft formation in cellular membranes. The lipid stoichiometry has a governing influence on domain formation and consequently, biochemical hydrolysis of specific lipids has the potential to remodel domain features. Activation of phospholipase A(2) ...

journal_title：Biophysical journal

authors： Simonsen AC

更新日期：2008-05-15 00:00:00

abstract：:A model is presented for the steric interaction between a plasma membrane protein and the membrane cytoskeleton in the human erythrocyte. The cytoskeleton is treated as a network of polymer chains attached to a flat bilayer, and the membrane protein is a hemisphere of effective radius R(e) with center on the bilayer e...

journal_title：Biophysical journal

authors： Boal DH,Boey SK

更新日期：1995-08-01 00:00:00

abstract：:Synchrotron radiation circular dichroism, Fourier transform infrared, and nuclear magnetic resonance spectroscopies, and small-angle x-ray scattering were used to monitor the reversible thermal unfolding of hen egg white lysozyme. The results were compared with crystal structures and high- and low-temperature structur...

journal_title：Biophysical journal

authors： Meersman F,Atilgan C,Miles AJ,Bader R,Shang W,Matagne A,Wallace BA,Koch MH

更新日期：2010-10-06 00:00:00

abstract：:Scanning ion conductance microscopy (SICM) is a super-resolution live imaging technique that uses a glass nanopipette as an imaging probe to produce three-dimensional (3D) images of cell surface. SICM can be used to analyze cell morphology at nanoscale, follow membrane dynamics, precisely position an imaging nanopipet...

journal_title：Biophysical journal

authors： Shevchuk A,Tokar S,Gopal S,Sanchez-Alonso JL,Tarasov AI,Vélez-Ortega AC,Chiappini C,Rorsman P,Stevens MM,Gorelik J,Frolenkov GI,Klenerman D,Korchev YE

更新日期：2016-05-24 00:00:00

abstract：:A new method, weighted-ensemble Brownian dynamics, is proposed for the simulation of protein-association reactions and other events whose frequencies of outcomes are constricted by free energy barriers. The method features a weighted ensemble of trajectories in configuration space with energy levels dictating the prop...

journal_title：Biophysical journal

authors： Huber GA,Kim S

更新日期：1996-01-01 00:00:00

abstract：:The solution structures of the N-terminal domains of protein S, a plasma vitamin K-dependent glycoprotein, and its homolog growth arrest specific protein 6 (Gas6) were predicted by molecular dynamics computer simulations. The initial structures were based on the x-ray crystallographic structure of the corresponding re...

journal_title：Biophysical journal

authors： Perera L,Li L,Darden T,Monroe DM,Pedersen LG

更新日期：1997-10-01 00:00:00

abstract：:Protein solution rheology data in the biophysics literature have incompletely identified factors that govern hydrodynamics. Whereas spontaneous protein adsorption at the air/water (A/W) interface increases the apparent viscosity of surfactant-free globular protein solutions, it is demonstrated here that irreversible c...

journal_title：Biophysical journal

authors： Pathak JA,Sologuren RR,Narwal R

更新日期：2013-02-19 00:00:00

abstract：:Uracil DNA Glycosylase (UNG2) is the primary enzyme in humans that prevents the stable incorporation of deoxyuridine monophosphate into DNA in the form of U/A basepairs. During S-phase, UNG2 remains associated with the replication fork through its interactions with two proteins, Proliferating Cell Nuclear Antigen (PCN...

journal_title：Biophysical journal

authors： Weiser BP,Stivers JT,Cole PA

更新日期：2017-07-25 00:00:00

abstract：:Molecular dynamics simulations of wild-type bacteriorhodopsin (bR) and of its D85N, D85T, D212N, and Y57F mutants have been carried out to investigate possible differences in the photoproducts of these proteins. For each mutant, a series of 50 molecular dynamics simulations of the photoisomerization and subsequent rel...

journal_title：Biophysical journal

authors： Humphrey W,Bamberg E,Schulten K

更新日期：1997-03-01 00:00:00

abstract：:Fourier transform infrared (FTIR) spectroscopy was used to monitor secondary structural changes associated with binding of bovine prothrombin and prothrombin fragment 1 to acidic lipid membranes. Prothrombin and prothrombin fragment 1 were examined under four different conditions: in the presence of (a) Na2EDTA, (b) 5...

journal_title：Biophysical journal

authors： Wu JR,Lentz BR

更新日期：1991-07-01 00:00:00

abstract：:The pathway to membrane fusion in synthetic and biological systems is thought to pass through hemifusion, in which the outer leaflets are fused while the inner leaflets engage in a hemifusion diaphragm (HD). Fusion has been proposed to be completed by lysis of the expanded HD that matures from a localized stalklike in...

journal_title：Biophysical journal

authors： Warner JM,O'Shaughnessy B

更新日期：2012-08-22 00:00:00

abstract：:We have used chemical synthesis, electron paramagnetic resonance (EPR), and circular dichroism to detect and analyze the structural dynamics of a ryanodine receptor (RyR) peptide bound to calmodulin (CaM). The skeletal muscle calcium release channel RyR1 is activated by Ca2+-free CaM and inhibited by Ca2+-bound CaM. T...

journal_title：Biophysical journal

authors： Her C,McCaffrey JE,Thomas DD,Karim CB

更新日期：2016-12-06 00:00:00

abstract：:Small single-domain proteins often exhibit only a single free-energy barrier, or transition state, between the denatured and the native state. The folding kinetics of these proteins is usually explored via mutational analysis. A central question is which structural information on the transition state can be derived fr...

journal_title：Biophysical journal

authors： Weikl TR

更新日期：2008-02-01 00:00:00

abstract：:Recent experimental evidence from a number of preparations indicates that sodium channel inactivation may be intrinsically voltage sensitive. Intrinsically voltage sensitive inactivation should produce a charge movement. Crayfish giant axons provide a unique opportunity to reexamine the slower components of gating cur...

journal_title：Biophysical journal

authors： Swenson RP Jr

更新日期：1983-03-01 00:00:00

abstract：:We describe a combined use of experimental and simulation techniques to configure side chains in a coiled coil structure. As already demonstrated in a previous work, x-ray diffraction patterns from hard alpha-keratin fibers in the 5.15 A meridian zone reflect the global configuration of the chi(1) dihedral angle of th...

journal_title：Biophysical journal

authors： Briki F,Doucet J,Etchebest C

更新日期：2002-10-01 00:00:00

abstract：:We argue that membrane viscosity, η(m), plays a prominent role in the thermal fluctuation dynamics of micron-scale lipid domains. A theoretical expression is presented for the timescales of domain shape relaxation, which reduces to the well-known η(m) = 0 result of Stone and McConnell in the limit of large domain size...

journal_title：Biophysical journal

authors： Camley BA,Esposito C,Baumgart T,Brown FL

更新日期：2010-09-22 00:00:00

abstract：:The structure and dynamics of soluble misfolded aggregates are poorly understood, despite their importance in protein science and disease. Water-soluble self-associated species that do not become insoluble over time are invaluable tools for high-resolution conformational studies aimed at dissecting the determinants of...

journal_title：Biophysical journal

authors： Rajagopalan S,Kurt N,Cavagnero S

更新日期：2011-02-02 00:00:00

abstract：:The process by which an organism changes the composition of its membranal fatty acids in response to growth temperature, so as to maintain optimal membrane functioning, is known as homeoviscous adaptation (HA). One expression of HA is the constancy of the fluorescence polarization (P) of the lipophilic probe 1,6-diphe...

journal_title：Biophysical journal

authors： Parola AH,Ibdah M,Gill D,Zaritsky A

更新日期：1990-03-01 00:00:00

abstract：:Protein-mediated DNA looping, such as that induced by the lactose repressor (LacI) of Escherichia coli, is a well-known gene regulation mechanism. Although researchers have given considerable attention to DNA looping by LacI, many unanswered questions about this mechanism, including the role of protein flexibility, re...

journal_title：Biophysical journal

authors： Hirsh AD,Lillian TD,Lionberger TA,Perkins NC

更新日期：2011-08-03 00:00:00

abstract：:Chemical synaptic transmission is a fundamental component of interneuronal communications in the central nervous system (CNS). Discharge of a presynaptic vesicle containing a few thousand molecules (a quantum) of neurotransmitter into the synaptic cleft generates a transmitter concentration signal that drives postsyna...

journal_title：Biophysical journal

authors： Uteshev VV,Pennefather PS

更新日期：1997-03-01 00:00:00

abstract：:Molecular dynamics simulations of the tripeptide Ala-Phe-Ala-O-tert-butyl interacting with dimyristoylphosphatidylcholine lipid bilayers have been carried out. The lipid and aqueous environments of the peptide, the alkyl chain order, and the lipid and peptide dynamics have been investigated with use of density profile...

journal_title：Biophysical journal

authors： Damodaran KV,Merz KM Jr,Gaber BP

更新日期：1995-10-01 00:00:00

abstract：:The amyloid fibrillar form of the protein Tau is involved in a number of neurodegenerative diseases, also known as tauopathies. In this work, six different fibrillar Tau isoforms were assembled in vitro. The morphological and nanomechanical properties of these isoforms were studied using atomic force microscopy at hig...

journal_title：Biophysical journal

authors： Makky A,Bousset L,Madiona K,Melki R

更新日期：2020-12-15 00:00:00

abstract：:The effect of Ca ion concentration on cross-bridge kinetics in a small bundle (one to three fibers) of chemically skinned rabbit psoas muscle is studied. The length of the muscle is oscillated in small amplitude sine waves (0.2% L0 peak-to-peak) at varying frequencies (0.125 -- 167 Hz), and the resulting amplitude and...

journal_title：Biophysical journal

authors： Kawai M,Cox RN,Brandt PW

更新日期：1981-08-01 00:00:00

abstract：:The wormlike-chain (WLC) model is widely used to describe the energetics of DNA bending. Motivated by recent experiments, alternative, so-called subelastic chain models were proposed that predict a lower elastic energy of highly bent DNA conformations. Until now, no unambiguous verification of these models has been ob...

journal_title：Biophysical journal

authors： Schöpflin R,Brutzer H,Müller O,Seidel R,Wedemann G

更新日期：2012-07-18 00:00:00

abstract：:We perform single-molecule flow experiments using confocal microscopy and a microfluidic device for shear rates up to 20,000 s-1 and present results for the shear-induced unraveling and elongation of tethered von Willebrand factor (VWF) multimers. Further, we employ companion Brownian dynamics simulations to help expl...

journal_title：Biophysical journal

authors： Wang Y,Morabito M,Zhang XF,Webb E 3rd,Oztekin A,Cheng X

更新日期：2019-06-04 00:00:00

abstract：:A systematic new approach to derive multiscale coarse-grained (MS-CG) models has been recently developed. The approach employs information from atomistically detailed simulations to derive CG forces and associated effective potentials. In this work, the MS-CG methodology is extended to study two peptides representing ...

journal_title：Biophysical journal

authors： Zhou J,Thorpe IF,Izvekov S,Voth GA

更新日期：2007-06-15 00:00:00