Photoinduced conformational dynamics of a photoswitchable peptide: a nonequilibrium molecular dynamics simulation study.

abstract：:K(ATP) channels are comprised of a pore-forming protein, Kir6.x, and the sulfonylurea receptor, SURx. Interaction of adenine nucleotides with Kir6.2 positively charged amino acids such as K185 and R201 on the C-terminus causes channel closure. Substitution of these amino acids with other positively charged residues ha...

journal_title：Biophysical journal

authors： Ribalet B,John SA,Weiss JN

更新日期：2003-01-01 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：:We perform single-molecule spatial tracking measurements of a DNA repair protein, the C-terminal domain of Ada (C-Ada) from Escherichia coli, moving on DNA extended by flow. The trajectories of single proteins labeled with a fluorophore are constructed. We analyze single-protein dwell times on DNA for different flow r...

journal_title：Biophysical journal

authors： Lin Y,Zhao T,Jian X,Farooqui Z,Qu X,He C,Dinner AR,Scherer NF

更新日期：2009-03-04 00:00:00

abstract：:The development of scanning probe techniques has made it possible to examine protein-protein interactions at the level of individual molecular pairs. A calibrated optical tweezers, along with immunoglobulin G (IgG)-coated polystyrene microspheres, has been used to detect individual surface-linked Staphylococcus protei...

journal_title：Biophysical journal

authors： Stout AL

更新日期：2001-06-01 00:00:00

abstract：:Tension and dynamic stiffness of passive rabbit psoas, rabbit semitendinosus, and waterbug indirect flight muscles were investigated to study the contribution of weak-binding cross-bridges and elastic filaments (titin and minititin) to the passive mechanical behavior of these muscles. Experimentally, a functional diss...

journal_title：Biophysical journal

authors： Granzier HL,Wang K

更新日期：1993-11-01 00:00:00

abstract：:The potassium selective, inward rectifier current (IK1) is known to be responsible for maintaining the resting membrane potential of quiescent ventricular myocytes. However, the contribution of this current to the different phases of the cardiac action potential has not been adequately established. In the present stud...

journal_title：Biophysical journal

authors： Ibarra J,Morley GE,Delmar M

更新日期：1991-12-01 00:00:00

abstract：:L-type (alpha(1C)) calcium channels inactivate rapidly in response to localized elevation of intracellular Ca(2+), providing negative Ca(2+) feedback in a diverse array of biological contexts. The dominant Ca(2+) sensor for such Ca(2+)-dependent inactivation has recently been identified as calmodulin, which appears to...

journal_title：Biophysical journal

authors： Peterson BZ,Lee JS,Mulle JG,Wang Y,de Leon M,Yue DT

更新日期：2000-04-01 00:00:00

abstract：:The binding mechanism of sweet proteins to their receptor, a G-protein-coupled receptor, is not supported by direct structural information. In principle, the key groups responsible for biological activity (glucophores) can be localized on a small structural unit (sweet finger) or spread on a larger surface area. A rec...

journal_title：Biophysical journal

authors： De Simone A,Spadaccini R,Temussi PA,Fraternali F

更新日期：2006-05-01 00:00:00

abstract：:One of the central tasks in systems biology is to understand how cells regulate their metabolism. Hierarchical regulation analysis is a powerful tool to study this regulation at the metabolic, gene-expression, and signaling levels. It has been widely applied to study steady-state regulation, but analysis of the metabo...

journal_title：Biophysical journal

authors： He F,Stumpf MPH

更新日期：2019-05-21 00:00:00

abstract：:Studies in Shaker, a voltage-dependent potassium channel, suggest a coupling between activation and inactivation. This coupling is controversial in hERG, a fast-inactivating voltage-dependent potassium channel. To address this question, we transferred to hERG the S3-S4 linker of the voltage-independent channel, rolf, ...

journal_title：Biophysical journal

authors： Choveau FS,El Harchi A,Rodriguez N,Louérat-Oriou B,Baró I,Demolombe S,Charpentier F,Loussouarn G

更新日期：2009-09-02 00:00:00

abstract：:Large-conductance Ca(2+)-activated K(+) channels (BK) play a fundamental role in modulating membrane potential in many cell types. The gating of BK channels and its modulation by Ca(2+) and voltage has been the subject of intensive research over almost three decades, yielding several of the most complicated kinetic me...

journal_title：Biophysical journal

authors： Rosales RA,Varanda WA

更新日期：2009-05-20 00:00:00

abstract：:We present a quantitative analysis of conformational changes of the nucleotide-binding subunits, MalK(2), of the maltose ATP-binding cassette importer MalFGK(2) during the transport cycle. Distance changes occurring between selected residues were monitored in the full transporter by site-directed spin-labeling electro...

journal_title：Biophysical journal

authors： Grote M,Bordignon E,Polyhach Y,Jeschke G,Steinhoff HJ,Schneider E

更新日期：2008-09-15 00:00:00

abstract：:A novel combined approach of molecular dynamics (MD) and Monte Carlo simulations is developed to calculate various free-volume distributions as a function of position in a lipid bilayer membrane at 323 K. The model bilayer consists of 2 x 100 chain molecules with each chain molecule having 15 carbon segments and one h...

journal_title：Biophysical journal

authors： Xiang TX

更新日期：1993-09-01 00:00:00

abstract：:A new experimental approach has been developed to study the distribution of local electrostatic potential around specific protons in biologically important molecules. The approach is the development of a method denoted as "spin label/spin probe," which was proposed by one of us (. Mol. Biol. 6:498-507). The proposed m...

journal_title：Biophysical journal

authors： Likhtenshtein GI,Adin I,Novoselsky A,Shames A,Vaisbuch I,Glaser R

更新日期：1999-07-01 00:00:00

abstract：:The lateral distribution of N-[10(1-pyrenyl)decanoyl]-sphingomyelin (PyrSPM) and N-[10(1-pyrenyl)decanoyl]-glucocerebroside (PyrGlcCer) was studied in multilamellar vesicles of 1,2-dipalmitoyl-, 1,2-dimyristoyl-, and 1-palmitoyl-2-oleoyl-phosphatidylcholine (DPPC, DMPC, and POPC, respectively) under anaerobic conditio...

journal_title：Biophysical journal

authors： Hresko RC,Sugár IP,Barenholz Y,Thompson TE

更新日期：1987-05-01 00:00:00

abstract：:Kinesin is a motor protein that uses the energy derived from the hydrolysis of ATP to power the transport of organelles along microtubules. To probe the mechanism of this chemical-to-mechanical energy transduction reaction, the movement of microtubules across glass surfaces coated with kinesin was perturbed by raising...

journal_title：Biophysical journal

authors： Hunt AJ,Gittes F,Howard J

更新日期：1994-08-01 00:00:00

abstract：:Proteins that cross-link actin filaments can either form bundles of parallel filaments or isotropic networks of individual filaments. We have found that mixtures of actin filaments with alpha-actinin purified from either Acanthamoeba castellanii or chicken smooth muscle can form bundles or isotropic networks depending...

journal_title：Biophysical journal

authors： Wachsstock DH,Schwartz WH,Pollard TD

更新日期：1993-07-01 00:00:00

abstract：:Proteins are denatured in aqueous urea solution. The nature of the molecular driving forces has received substantial attention in the past, whereas the question how urea acts at different phases of unfolding is not yet well understood at the atomic level. In particular, it is unclear whether urea actively attacks fold...

journal_title：Biophysical journal

authors： Stumpe MC,Grubmüller H

更新日期：2009-05-06 00:00:00

abstract：:Voltage-gated sodium channels undergo transitions between open, closed, and inactivated states, enabling regulation of the translocation of sodium ions across membranes. A recently published crystal structure of the full-length prokaryotic NavMs crystal structure in the activated open conformation has revealed the pre...

journal_title：Biophysical journal

authors： Ke S,Ulmschneider MB,Wallace BA,Ulmschneider JP

更新日期：2018-11-20 00:00:00

abstract：:Cartilage stiffness was measured ex vivo at the micrometer and nanometer scales to explore structure-mechanical property relationships at smaller scales than has been done previously. A method was developed to measure the dynamic elastic modulus, |E(*)|, in compression by indentation-type atomic force microscopy (IT A...

journal_title：Biophysical journal

authors： Stolz M,Raiteri R,Daniels AU,VanLandingham MR,Baschong W,Aebi U

更新日期：2004-05-01 00:00:00

abstract：:Understanding the fundamentals of genome packaging in viral capsids is important for finding effective antiviral strategies and for utilizing benign viral particles for gene therapy. While the structure of encapsidated genomic materials has been routinely characterized with experimental techniques such as cryo-electro...

journal_title：Biophysical journal

authors： Kim J,Wu J

更新日期：2015-10-20 00:00:00

abstract：:Motor enzymes use energy from ATP dephosphorylation to generate movement by a mechanical cycle, moving and pushing in one direction while attached to their cytoskeletal substrate, and recovering by moving relative to their substrate to a new attachment site. Mainstream models assert that movement while attached to the...

journal_title：Biophysical journal

authors： Brokaw CJ

更新日期：1997-08-01 00:00:00

abstract：:The arrangement of side chains in alpha-helical regions of protein can be represented by helical net-diagrams. The addition of quantitative indices of the character of the residue at each net-point facilitates a straightforward examination of the groupings of residues of different character. As such the method complem...

journal_title：Biophysical journal

authors： Dunnill P

更新日期：1968-07-01 00:00:00

abstract：:Each gating mechanism controlling permeability in a membrane may be influenced by only a few charge binding sites on the membrane surface, so that fluctuations in the occupancy of these sites are important. Tow extreme cases arise. (a) The time scale of these fluctuations is much shorter than the gating time constant....

journal_title：Biophysical journal

authors： Attwell D,Eisner D

更新日期：1978-12-01 00:00:00

abstract：:The structural dynamics of bovine erythrocyte Cu, Zn superoxide dismutase (BSOD) was studied by time-resolved fluorescence spectroscopy. BSOD is a homodimer containing a single tyrosine residue (and no tryptophan) per subunit. Frequency-domain fluorometry revealed a heterogeneous fluorescence decay that could be descr...

journal_title：Biophysical journal

authors： Ferreira ST,Stella L,Gratton E

更新日期：1994-04-01 00:00:00

abstract：:Excitation-contraction coupling in atrial cells is mediated by calcium (Ca) signaling between L-type Ca channels and Ryanodine receptors that occurs mainly at the cell boundary. This unique architecture dictates essential aspects of Ca signaling under both normal and diseased conditions. In this study we apply laser s...

journal_title：Biophysical journal

authors： Shiferaw Y,Aistrup GL,Wasserstrom JA

更新日期：2017-08-08 00:00:00

abstract：:Fusion is a crucial event in the infection of animal cells by enveloped viruses (e.g., HIV or influenza). Viral fusion is mediated by glycoproteins, spanning the viral envelope, which attach to a membrane surface and induce fusion of the viral envelope to the cellular membrane. Influenza fusion protein (hemagglutinin)...

journal_title：Biophysical journal

authors： Longo ML,Waring AJ,Hammer DA

更新日期：1997-09-01 00:00:00

abstract：:A study on clonal growth in Chinese hamster ovary (CHO) cells was conducted after exposure to optical trapping wavelengths using Nd:YAG (1064 nm) and tunable titanium-sapphire (700-990 nm) laser microbeam optical traps. The nuclei of cells were exposed to optical trapping forces at various wavelengths, power densities...

journal_title：Biophysical journal

authors： Liang H,Vu KT,Krishnan P,Trang TC,Shin D,Kimel S,Berns MW

更新日期：1996-03-01 00:00:00

abstract：:Bistability is a major mechanism for cellular decision making and usually results from positive feedback in biochemical control systems. Here we show theoretically that bistability between unbound and bound states of adhesion clusters results from positive feedback mediated by structural rather than biochemical proces...

journal_title：Biophysical journal

authors： Erdmann T,Schwarz US

更新日期：2006-09-15 00:00:00

abstract：:A 3D model was developed and used to explore dynamics of phosphatidylinositol-4,5-bisphosphate (PIP2) signaling in cerebellar Purkinje neurons. Long-term depression in Purkinje neurons depends on coincidence detection of climbing fiber stimulus evoking extracellular calcium flux into the cell and parallel fiber stimul...

journal_title：Biophysical journal

authors： Brown SA,Morgan F,Watras J,Loew LM

更新日期：2008-08-01 00:00:00