Molecular dynamics simulations of the photoactive protein nitrile hydratase.

abstract：:Small, icosahedral double-stranded DNA bacteriophage pack their genomes tightly into preformed protein capsids using an ATP-driven motor. Coarse-grain molecular-mechanics models provide a detailed picture of DNA packaging in bacteriophage, revealing how conformation depends on capsid size and shape, and the presence o...

journal_title：Biophysical journal

authors： Petrov AS,Harvey SC

更新日期：2008-07-01 00:00:00

abstract：:The problem of the desorption of a lipid molecule from a lipid vesicle (donor) and its incorporation into another vesicle (acceptor) at high acceptor concentrations, which has been investigated experimentally (Jones, J. D. and Thompson, T. E., 1990. Biochemistry, 29:1593-1600), is analyzed here from a theoretical poin...

journal_title：Biophysical journal

authors： Almeida PF

更新日期：1999-04-01 00:00:00

abstract：:13C alpha chemical shifts and site-specific unfolding curves are reported for 12 sites on a 33-residue, GCN4-like leucine zipper peptide (GCN4-lzK), ranging over most of the chain and sampling most heptad positions. Data were derived from NMR spectra of nine synthetic, isosequential peptides bearing 99% 13C alpha at s...

journal_title：Biophysical journal

authors： Holtzer ME,Lovett EG,d'Avignon DA,Holtzer A

更新日期：1997-08-01 00:00:00

abstract：:Very high dielectric constants have been observed for bacteria at low frequencies. High dielectric constants such as these can be explained by a theory which has been developed for the low-frequency dielectric dispersion of porous charged particles and which has been tested successfully through measurements with ion e...

journal_title：Biophysical journal

authors： Einolf CW Jr,Carstensen EL

更新日期：1973-01-01 00:00:00

abstract：:Here it is reported that aggrecan, the highly negatively charged macromolecule in the cartilage extracellular matrix, undergoes Ca(2+)-mediated self-adhesion after static compression even in the presence of strong electrostatic repulsion in physiological-like solution conditions. Aggrecan was chemically end-attached o...

journal_title：Biophysical journal

authors： Han L,Dean D,Daher LA,Grodzinsky AJ,Ortiz C

更新日期：2008-11-15 00:00:00

abstract：:Calmodulin (CaM) expression is upregulated upon HIV-1 infection and interacts with proteins involved in viral processing, including the multifunctional HIV-1 MA protein. We present here the results of studies utilizing small-angle neutron scattering with contrast variation that, when considered in the light of earlier...

journal_title：Biophysical journal

authors： Taylor JE,Chow JYH,Jeffries CM,Kwan AH,Duff AP,Hamilton WA,Trewhella J

更新日期：2012-08-08 00:00:00

abstract：:Calculations based on the known dimensions of bull spermatozoa show that the scattered light intensity is strongly dependent upon the relative orientation of the particle to the incident beam. The magnitude of this effect of apparently much greater than for other systems where motility has been investigated by dynamic...

journal_title：Biophysical journal

authors： Harvey JD,Woolford MW

更新日期：1980-07-01 00:00:00

abstract：:The two glycosphingolipids galactosylceramide (GalC) and its sulfated form, cerebroside sulfate (CBS), are present at high concentrations in the multilayered myelin sheath and are involved in carbohydrate-carbohydrate interactions between the lipid headgroups. In order to study the structure of the complex of these tw...

journal_title：Biophysical journal

authors： Boggs JM,Menikh A,Rangaraj G

更新日期：2000-02-01 00:00:00

abstract：:In this work, boundary element modeling is used to study the transport of highly charged rod-like model polyions of various length under a variety of different aqueous salt conditions. Transport properties considered include free solution electrophoretic mobility, translational diffusion, and the components of the "te...

journal_title：Biophysical journal

authors： Allison S,Chen C,Stigter D

更新日期：2001-11-01 00:00:00

abstract：:The primary drivers of yeast endocytosis are actin polymerization and curvature-generating proteins, such as clathrin and BAR domain proteins. Previous work has indicated that these factors may not be capable of generating the forces necessary to overcome turgor pressure. Thus local reduction of the turgor pressure, v...

journal_title：Biophysical journal

authors： Scher-Zagier JK,Carlsson AE

更新日期：2016-12-20 00:00:00

abstract：:The stability of the structure of double-stranded DNA in the salt-free solution is discussed on the basis of the polyelectrolyte theory. Assuming that DNA is an infinitely long rod, and the formation of double strands is divided into combining process and folding process, the free energy changes required in these proc...

journal_title：Biophysical journal

authors： OHNISHI T

更新日期：1963-11-01 00:00:00

abstract：:Mathematical modeling of the cardiac action potential has proven to be a powerful tool for illuminating various aspects of cardiac function, including cardiac arrhythmias. However, no currently available detailed action potential model accurately reproduces the dynamics of the cardiac action potential and intracellula...

journal_title：Biophysical journal

authors： Mahajan A,Shiferaw Y,Sato D,Baher A,Olcese R,Xie LH,Yang MJ,Chen PS,Restrepo JG,Karma A,Garfinkel A,Qu Z,Weiss JN

更新日期：2008-01-15 00:00:00

abstract：:A new method is presented to describe the low shear rate behavior of blood. We observed the response of a thin layer of sedimenting blood to a graded shear stress in a wedge-shaped chamber. The method allows quantitation of the degree of phase separation between red cells and plasma, and extracts the yield stress of t...

journal_title：Biophysical journal

authors： Morris CL,Smith CM 2nd,Blackshear PL Jr

更新日期：1987-08-01 00:00:00

abstract：:Equatorial x-ray diffraction patterns were obtained from single skinned rabbit psoas fibers during various degrees of activation under isometric conditions at ionic strength 170 mM and 6-9 degrees C. By direct calcium activation, contraction was homogeneous throughout the preparation, and by using a cycling technique ...

journal_title：Biophysical journal

authors： Brenner B,Yu LC

更新日期：1985-11-01 00:00:00

abstract：:The interactions between vitamin-A and beta-lactoglobulin have been investigated. We have found that two different complexes can be formed: one involving vitamin-A, and one involving a derivative of vitamin-A that most probably has a retro-beta-ionylidene structure. Room temperature absorption spectra for these comple...

journal_title：Biophysical journal

authors： Hemley R,Kohler BE,Siviski P

更新日期：1979-12-01 00:00:00

abstract：:We present an analysis of physical chemical constraints on the accuracy of DNA micro-arrays under equilibrium and nonequilibrium conditions. At the beginning of the article we describe an algorithm for choosing a probe set with high specificity for targeted genes under equilibrium conditions. The algorithm as well as ...

journal_title：Biophysical journal

authors： Bhanot G,Louzoun Y,Zhu J,DeLisi C

更新日期：2003-01-01 00:00:00

abstract：:The switch 1 region of myosin forms a lid over the nucleotide phosphates as part of a structure known as the phosphate-tube. The homologous region in kinesin-family motors is more open, not interacting with the nucleotide. We used molecular dynamics (MD) simulations to examine a possible displacement of switch 1 of th...

journal_title：Biophysical journal

authors： Minehardt TJ,Cooke R,Pate E,Kollman PA

更新日期：2001-03-01 00:00:00

abstract：:Synthetic filaments prepared from column-purified rabbit skeletal myosin by slow dialysis exhibit characteristic bipolar organization and 14-nm axial subunit spacing. Backbone substructure can be discerned in high resolution micrographs in the form of striations of 3--4-nm width and slight angular tilt from the direct...

journal_title：Biophysical journal

authors： Koretz JF

更新日期：1979-09-01 00:00:00

abstract：:Current methods for screening cell receptor internalization often require complex image analysis with limited sensitivity. Here we describe a novel bioassay based on detection of changes in global fluorescence lifetime above a gold substrate, with superresolution axial sensitivity and no need for image analysis. We sh...

journal_title：Biophysical journal

authors： Cade NI,Fruhwirth G,Archibald SJ,Ng T,Richards D

更新日期：2010-06-02 00:00:00

abstract：:Herein, we consider the process of force development along the adhesome within cell focal adhesions. Our model adhesome consists of the actin cytoskeleton-vinculin-talin-integrin-ligand-extracellular matrix-substrate force train. We specifically consider the effects of substrate stiffness on the force levels expected ...

journal_title：Biophysical journal

authors： Asaro RJ,Lin K,Zhu Q

更新日期：2019-11-05 00:00:00

abstract：:We have applied two-dimensional infrared (2D IR) and betanu correlation spectroscopy to in-situ IR spectroscopy of pulmonary surfactant proteins SP-B and SP-C in lipid-protein monolayers at the air-water interface. For both SP-B and SP-C, a statistical windowed autocorrelation method identified two separate surface pr...

journal_title：Biophysical journal

authors： Shanmukh S,Howell P,Baatz JE,Dluhy RA

更新日期：2002-10-01 00:00:00

abstract：:Glucagon solutions at pH 2.0 were subjected to mechanical agitation at 37 degrees C in the presence of a hydrophobic surface to explore the details of aggregation and fiber formation. High-resolution intermittent-contact atomic force microscopy performed in solution revealed the presence of aggregates after 0.5 h; how...

journal_title：Biophysical journal

authors： De Jong KL,Incledon B,Yip CM,DeFelippis MR

更新日期：2006-09-01 00:00:00

abstract：:The mechanical properties of living cells are a label-free biophysical marker of cell viability and health; however, their use has been greatly limited by low measurement throughput. Although examining individual cells at high rates is now commonplace with fluorescence activated cell sorters, development of comparable...

journal_title：Biophysical journal

authors： Sawetzki T,Eggleton CD,Desai SA,Marr DW

更新日期：2013-11-19 00:00:00

abstract：:Transcription factor (TF) proteins rapidly locate unique target sites on long genomic DNA molecules--and bind to them--during gene regulation. The search mechanism is known to involve a combination of three-dimensional diffusion through the bulk of the cell and one-dimensional sliding diffusion along the DNA. It is be...

journal_title：Biophysical journal

authors： Hu L,Grosberg AY,Bruinsma R

更新日期：2008-08-01 00:00:00

abstract：:Phospholipids have been treated as dimers on a hexagonal lattice, and a move has been introduced that allows the dimers to move and change their orientation on the lattice. Simulations have been performed in which phospholipid chains have been treated as being either independent or infinitely coupled thermodynamically...

journal_title：Biophysical journal

authors： Jerala R,Almeida PF,Biltonen RL

更新日期：1996-08-01 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：:Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a d...

journal_title：Biophysical journal

authors： Tjong H,Zhou HX

更新日期：2008-09-15 00:00:00

abstract：:Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped by dual-beam lasers and the other was held by a micropipette. Several experimen...

journal_title：Biophysical journal

authors： Wen JD,Manosas M,Li PT,Smith SB,Bustamante C,Ritort F,Tinoco I Jr

更新日期：2007-05-01 00:00:00

abstract：:In response to external stimuli, cells modulate their adhesive state by regulating the number and intrinsic affinity of receptor/ligand bonds. A number of studies have shown that cell adhesion is dramatically reduced at room or lower temperatures as compared with physiological temperature. However, the underlying mech...

journal_title：Biophysical journal

authors： Rico F,Chu C,Abdulreda MH,Qin Y,Moy VT

更新日期：2010-09-08 00:00:00

abstract：:Depending on the nucleotide sequence, the temperature, and other conditions, RNA hairpin-folding kinetics can be very complex. The complexity with a wide range of cooperative and noncooperative kinetic behaviors arises from the interplay between the formation of the loops, the disruption of the misfolded states, and t...

journal_title：Biophysical journal

authors： Zhang W,Chen SJ

更新日期：2006-02-01 00:00:00