Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations.

abstract：:A phenomenological theory for contracting muscle based on irreversible thermodynamics and the sliding filament theory is developed. The individual cross bridges, considered as subunits, are viewed as linear energy converters with constant transport coefficients. With this view of the subunits, phenomenological equatio...

journal_title：Biophysical journal

authors： Bornhorst WJ,Minardi JE

更新日期：1970-02-01 00:00:00

abstract：:DNA represents a promising therapeutic and prophylactic macromolecule in treating genetic diseases, infectious diseases and cancers. The therapeutic potential of DNA is directly related to how DNA transports within the targeted tissue. In this study, fluorescence photobleaching recovery was used to examine the diffusi...

journal_title：Biophysical journal

authors： Shen H,Hu Y,Saltzman WM

更新日期：2006-07-15 00:00:00

abstract：:We investigated the origins of greater clot rigidity associated with FXIIIa-dependent cross-linking. Fibrin clots were examined in which cross-linking was controlled through the use of two inhibitors: a highly specific active-center-directed synthetic inhibitor of FXIIIa, 1,3-dimethyl-4,5-diphenyl-2[2(oxopropyl)thio]i...

journal_title：Biophysical journal

authors： Ryan EA,Mockros LF,Stern AM,Lorand L

更新日期：1999-11-01 00:00:00

abstract：:We have examined the kinetics and thermodynamics of the exchange of a fluorescent amphiphile derived from a phospholipid, NBD-DMPE, between serum albumin and the serum lipoproteins of high density (HDL2 and HDL3), LDL, and VLDL. Binding of the fluorescent lipid amphiphile to bovine serum albumin is characterized, at 3...

journal_title：Biophysical journal

authors： Estronca LM,Moreno MJ,Laranjinha JA,Almeida LM,Vaz WL

更新日期：2005-01-01 00:00:00

abstract：:Universal features of the peptide aggregation process suggest a common mechanism, with a first-order phase transition in aqueous solutions of the peptides being the driving force. Small system sizes strongly affect the stability of the minor phase in the two-phase region. We show manifestations of this effect in aqueo...

journal_title：Biophysical journal

authors： Singh G,Brovchenko I,Oleinikova A,Winter R

更新日期：2008-10-01 00:00:00

abstract：:Structure-function studies of the Cys loop family of ionotropic neurotransmitter receptors (GABA, nACh, 5-HT(3), and glycine receptors) have resulted in a six-loop (A-F) model of the agonist-binding site. Key amino acids have been identified in these loops that associate with, and stabilize, bound ligand. The next ste...

journal_title：Biophysical journal

authors： Khatri A,Sedelnikova A,Weiss DS

更新日期：2009-01-01 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 analyze a two-state stochastic corral model for regulation of protein diffusion in a cell membrane. This model could mimic control of protein transport in the membrane by the cytoskeleton. The dynamic corral acts as a gate which when open permits an otherwise trapped protein to escape to a neighboring corral in the...

journal_title：Biophysical journal

authors： Leitner DM,Brown FL,Wilson KR

更新日期：2000-01-01 00:00:00

abstract：:The Ca(2+)-permeable cation channel TRPA1 acts as an ionotropic receptor for various pungent compounds and as a noxious cold sensor in sensory neurons. It is unclear what proportion of the TRPA1-mediated current is carried by Ca(2+) ions and how the permeation pathway changes during stimulation. Here, based on the rel...

journal_title：Biophysical journal

authors： Karashima Y,Prenen J,Talavera K,Janssens A,Voets T,Nilius B

更新日期：2010-03-03 00:00:00

abstract：:Red blood cells aggregate face-to-face to form long, cylindrical, straight chains and sometimes branched structures called rouleaux. Here we extend a kinetic model developed by R. W. Samsel and A. S. Perelson (1982, Biophys. J. 37:493-514) to include both the formation and dissociation of rouleaux. We examine thermody...

journal_title：Biophysical journal

authors： Samsel RW,Perelson AS

更新日期：1984-04-01 00:00:00

abstract：:Quasilongitudinal sound velocities and the second-order elastic moduli of tetragonal hen egg-white lysozyme crystals were determined as a function of relative humidity (RH) by Brillouin scattering. In hydrated crystals the measured sound velocities in the [110] plane vary between 2.12 +/- 0.03 km/s along the [001] dir...

journal_title：Biophysical journal

authors： Speziale S,Jiang F,Caylor CL,Kriminski S,Zha CS,Thorne RE,Duffy TS

更新日期：2003-11-01 00:00:00

abstract：:A new general method for the determination of electrostatic potentials at biological surfaces is presented. The approach is based on measurement of the collision frequency of a charged nitroxide in solution with a nitroxide fixed to the surface at the point of interest. The collision frequency is determined with 14N:1...

journal_title：Biophysical journal

authors： Shin YK,Hubbell WL

更新日期：1992-06-01 00:00:00

abstract：:The genetic map of T4 (and T2) bacteriophage is circular but the DNA molecule that is liberated by phenol extraction is a linear duplex of polynucleotide chains. If the genetic map is related to the physical structure of the DNA molecule, the problem arises as to how a linear molecule can give rise to a circular map. ...

journal_title：Biophysical journal

authors： THOMAS CA Jr,RUBENSTEIN I

更新日期：1964-03-01 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：:In striated muscle thin filament activation is initiated by Ca(2+) binding to troponin C and augmented by strong myosin binding to actin (cross-bridge formation). Several lines of evidence have led us to hypothesize that thin filament properties may limit the level and rate of force development in cardiac muscle at al...

journal_title：Biophysical journal

authors： Regnier M,Martin H,Barsotti RJ,Rivera AJ,Martyn DA,Clemmens E

更新日期：2004-09-01 00:00:00

abstract：:The mechanosensitive channel of small conductance (MscS) is a bacterial mechanosensitive channel that opens in response to rapid hypoosmotic stress. Since MscS can be opened solely by membrane stretch without help from any accessory protein, the lipid-protein interface must play a crucial role in sensing membrane tens...

journal_title：Biophysical journal

authors： Nomura T,Sokabe M,Yoshimura K

更新日期：2006-10-15 00:00:00

abstract：:We have examined the distribution of ryanodine receptors, L-type Ca(2+) channels, calsequestrin, Na(+)/Ca(2+) exchangers, and voltage-gated Na(+) channels in adult rat ventricular myocytes. Enzymatically dissociated cells were fixed and dual-labeled with specific antibodies using standard immunocytochemistry protocols...

journal_title：Biophysical journal

authors： Scriven DR,Dan P,Moore ED

更新日期：2000-11-01 00:00:00

abstract：:This paper reports on a coupled approach to determining the structure of the gramicidin A ion channel, utilizing solid state nuclear magnetic resonance (NMR) of isotopically labeled gramicidin channels aligned parallel to the magnetic field direction, and molecular dynamics (MD). MD computations using an idealized rig...

journal_title：Biophysical journal

authors： Chiu SW,Nicholson LK,Brenneman MT,Subramaniam S,Teng Q,McCammon JA,Cross TA,Jakobsson E

更新日期：1991-10-01 00:00:00

abstract：:In addition to the annular or boundary lipids that surround the transmembrane surface of the potassium channel KcsA from Streptomyces lividans, x-ray crystallographic studies have detected one anionic lipid molecule bound at each protein-protein interface in the homotetrameric structure, at sites referred to as nonann...

journal_title：Biophysical journal

authors： Marius P,Zagnoni M,Sandison ME,East JM,Morgan H,Lee AG

更新日期：2008-03-01 00:00:00

abstract：:Oriented purple membranes were equilibrated under controlled (2)H(2)O relative humidity ranging from 15% to 93% and introduced into the magnetic field of an NMR spectrometer with the membrane normal parallel to the magnetic field direction. Deuterium solid-state NMR spectra of these samples resolved four deuteron popu...

journal_title：Biophysical journal

authors： Bechinger B,Weik M

更新日期：2003-07-01 00:00:00

abstract：:We developed a kinetic model for a single-substrate trimolecular enzymatic system, where a receptor binds and stretches a substrate to expose its cleavage site, allowing an enzyme to bind and cleave it into product. We demonstrated that the general kinetics of the trimolecular enzymatic system is more complex than the...

journal_title：Biophysical journal

authors： Chen W,Zhu C

更新日期：2010-05-19 00:00:00

abstract：:The kinetics of redistribution of lipid-like molecules between the membranes of two fused spherical vesicles is studied by solving the time-dependent diffusion equation of the system. The effects on the probe redistribution rate of pore size at the fusion junction and the relative sizes of the vesicles are examined. I...

journal_title：Biophysical journal

authors： Rubin RJ,Chen YD

更新日期：1990-11-01 00:00:00

abstract：:The bile acid-sensitive ion channel is activated by amphiphilic substances such as bile acids or artificial detergents via membrane alterations; however, the mechanism of membrane sensitivity of the bile acid-sensitive ion channel is not known. It has also not been systematically investigated whether other members of ...

journal_title：Biophysical journal

authors： Schmidt A,Alsop RJ,Rimal R,Lenzig P,Joussen S,Gervasi NN,Khondker A,Gründer S,Rheinstädter MC,Wiemuth D

更新日期：2018-03-27 00:00:00

abstract：:Air dried films of purple membranes (PM) from Halobacterium halobium containing the photochromic protein bacteriorhodopsin (BR) were prepared and the BR-photocycle of this material analyzed. The absorption maxima of the initial state B (lambda(max) = 570 nm) and the photochemical intermediate M (lambda(max) = 412 nm),...

journal_title：Biophysical journal

authors： Hampp N,Bräuchle C,Oesterhelt D

更新日期：1990-07-01 00:00:00

abstract：:A continuum model is provided of the free energy terms that contribute to the molecular association of ricin A-chain (RTA) with the rRNA substrate and several small ligands. The model for RTA interactions with the RNA was taken from a previously proposed complex containing a 29-mer oligonucleotide hairpin (. Proteins ...

journal_title：Biophysical journal

authors： Olson MA,Cuff L

更新日期：1999-01-01 00:00:00

abstract：:Cord factor (trehalose 6,6'-dimycolate, CF) is a glycolipid located in the outer mycobacterial cell wall that is implicated in the pathogenesis of mycobacteria. Furthermore, CF is a convenient model for studying mycolic acid residues, the major lipid constituents of the mycobacterial cell wall that are believed to for...

journal_title：Biophysical journal

authors： Almog R,Mannella CA

更新日期：1996-12-01 00:00:00

abstract：:Precise information regarding the transmembrane topology of mitochondrial porin is essential for understanding the mechanisms by which this protein functions. Porin acts as a channel in the outer membrane and interacts with small solutes and proteins to regulate mitochondrial function. The acquisition of high-resoluti...

journal_title：Biophysical journal

authors： Bay DC,O'Neil JD,Court DA

更新日期：2008-01-15 00:00:00

abstract：:Downstream processes that discriminate between DNA adducts of a third generation platinum antitumor drug oxaliplatin and conventional cisplatin are believed to be responsible for the differences in their biological effects. These different biological effects are explained by the ability of oxaliplatin to form DNA addu...

journal_title：Biophysical journal

authors： Malina J,Novakova O,Vojtiskova M,Natile G,Brabec V

更新日期：2007-12-01 00:00:00

abstract：:A challenge in the understanding of creatine kinase (CK) fluxes reflected by NMR magnetization transfer in the perfused rat heart is the choice of a kinetic model of analysis. The complexity of the energetic pathways, due to the presence of adenosine triphosphate (ATP)-inorganic phosphate (Pi) exchange, of metabolite ...

journal_title：Biophysical journal

authors： Joubert F,Hoerter JA,Mazet JL

更新日期：2001-12-01 00:00:00

abstract：:This paper describes the relation between the quantum yield of photosynthesis in the red alga Porphyridium cruentum, and the spectral composition of light, changed by filtering white light through aqueous phycobilin solutions of increasing optical density. At sufficiently high densities of the filter solution, no meas...

journal_title：Biophysical journal

authors： THOMAS JB,GOVINDJEE

更新日期：1960-09-01 00:00:00