Cooperativity and specificity in enzyme kinetics: a single-molecule time-based perspective.

abstract：:The redox-driven proton pump cytochrome c oxidase is that enzymatic machinery of the respiratory chain that transfers electrons from cytochrome c to molecular oxygen and thereby splits molecular oxygen to form water. To investigate the reaction mechanism of cytochrome c oxidase on the single vibrational level, we used...

journal_title：Biophysical journal

authors： Heitbrink D,Sigurdson H,Bolwien C,Brzezinski P,Heberle J

更新日期：2002-01-01 00:00:00

abstract：:Molecular machines fueled by NTP play pivotal roles in a wide range of cellular activities. One common feature among NTP-driven molecular machines is that NTP binding is a major force-generating step among the elementary reaction steps comprising NTP hydrolysis. To understand the mechanism in detail,in this study, we ...

journal_title：Biophysical journal

authors： Arai HC,Yukawa A,Iwatate RJ,Kamiya M,Watanabe R,Urano Y,Noji H

更新日期：2014-07-01 00:00:00

abstract：:A method for fabricating biomimetic surfaces from intact cell membranes is described. A monolayer of alkanethiol on gold is covered by a second layer derived from the components of erythrocyte membranes either by self-assembly or by Langmuir-Blodgett methods. The resulting asymmetric hybrid layer was characterized by ...

journal_title：Biophysical journal

authors： Rao NM,Plant AL,Silin V,Wight S,Hui SW

更新日期：1997-12-01 00:00:00

abstract：:The ability to discriminate between different cations efficiently is essential for the proper physiological functioning of many membrane transport proteins. One obvious mechanism of ion selectivity is when a binding site is structurally constrained by the protein architecture and its geometry is precisely adapted to f...

journal_title：Biophysical journal

authors： Roux B

更新日期：2010-06-16 00:00:00

abstract：:Many animals regulate power generation for locomotion by varying the number of muscle fibers used for movement. However, insects with asynchronous flight muscles may regulate the power required for flight by varying the calcium concentration ([Ca(2+)]). In vivo myoplasmic calcium levels in Drosophila flight muscle hav...

journal_title：Biophysical journal

authors： Wang Q,Zhao C,Swank DM

更新日期：2011-11-02 00:00:00

abstract：:Stochastic effects in gene expression may result in different physiological states of individual cells, with consequences for pathogen survival and artificial gene network design. We studied the contributions of a regulatory factor to gene expression noise in four basic mechanisms of negative gene expression control: ...

journal_title：Biophysical journal

authors： Komorowski M,Miekisz J,Kierzek AM

更新日期：2009-01-01 00:00:00

abstract：:Some membrane peptides, such as Alamethicin, form barrel-stave aggregates with a broad probability distribution of size (number of peptides in the aggregate). This distribution has been shown to depend on the characteristics of the lipid bilayer. A mechanism for this influence is suggested, in analogy to earlier work ...

journal_title：Biophysical journal

authors： Cantor RS

更新日期：2002-05-01 00:00:00

abstract：:The closed-state crystal structure of prokaryotic inward rectifier, KirBac1.1, has implicated four inner helical phenylalanines near the cytoplasmic side as a possible locus of the channel gate. In the present study, we investigate whether this structural feature corresponds to the physiological pH gate of the renal i...

journal_title：Biophysical journal

authors： Sackin H,Nanazashvili M,Palmer LG,Krambis M,Walters DE

更新日期：2005-04-01 00:00:00

abstract：:Enterococcus hirae V1-ATPase is a molecular motor composed of the A3B3 hexamer ring and the central stalk. In association with ATP hydrolysis, three catalytic AB pairs in the A3B3 ring undergo conformational changes, which lead to a 120° rotation of the central stalk. To understand how the conformational changes of th...

journal_title：Biophysical journal

authors： Isaka Y,Ekimoto T,Kokabu Y,Yamato I,Murata T,Ikeguchi M

更新日期：2017-03-14 00:00:00

abstract：:Amantadine is known to block the M2 proton channel of the Influenza A virus. Here, we present a structure of the M2 trans-membrane domain blocked with amantadine, built using orientational constraints obtained from solid-state NMR polarization-inversion-spin-exchange-at-the-magic-angle experiments. The data indicates ...

journal_title：Biophysical journal

authors： Hu J,Asbury T,Achuthan S,Li C,Bertram R,Quine JR,Fu R,Cross TA

更新日期：2007-06-15 00:00:00

abstract：:Rapid and robust methods are required to quantify the effect of hydrodynamic shear on protein conformation change. We evaluated such strategies in this work and found that the binding of the fluorescent probe 4,4'-dianilino-1,1'-binaphthyl-5,5'-disulfonic acid (bis-ANS) to hydrophobic pockets in the blood protein von ...

journal_title：Biophysical journal

authors： Themistou E,Singh I,Shang C,Balu-Iyer SV,Alexandridis P,Neelamegham S

更新日期：2009-11-04 00:00:00

abstract：:We study the effect of ergosterol on the physical properties of 1-[(2)H(31)]palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) multibilayers using deuterium nuclear magnetic resonance. NMR spectra were taken as a function of temperature and ergosterol concentration up to 70 mol %. The spectral first moments sh...

journal_title：Biophysical journal

authors： Hsueh YW,Weng CJ,Chen MT,Thewalt J,Zuckermann M

更新日期：2010-04-07 00:00:00

abstract：:Mechanosensitive ion channels (MSCs) which could provide for fast osmoregulatory responses in bacteria, remain unidentified as molecular entities. MSCs from Escherichia coli (strain AW740) were examined using the patch-clamp technique, either (a) in giant spheroplasts, (b) after reconstitution by fusing native membran...

journal_title：Biophysical journal

authors： Sukharev SI,Martinac B,Arshavsky VY,Kung C

更新日期：1993-07-01 00:00:00

abstract：:We accelerate protein folding in all-atom molecular dynamics simulations by introducing alternating hydrogen bond potentials as a supplement to the force field. The alternating hydrogen bond potentials result in accelerated hydrogen bond reordering, which leads to rapid formation of secondary structure elements. The m...

journal_title：Biophysical journal

authors： Wolf MG,de Leeuw SW

更新日期：2008-05-15 00:00:00

abstract：:Crystals have been grown of "sperm whale" myoglobin produced in Escherichia coli from a synthetic gene and the structure has been solved to 1.9 A resolution. Because of a remaining initiator methionine, this protein crystallizes in a different space group from native sperm whale myoglobin. The three-dimensional struct...

journal_title：Biophysical journal

authors： Phillips GN Jr

更新日期：1990-02-01 00:00:00

abstract：:We have constructed a theory for diffusion through the pore of a single-ion channel by taking a limit of a random walk around a cycle of states. Similar to Levitt's theory of single-ion diffusion, one obtains boundary conditions for the Nernst-Planck equation that guarantee that the pore is occupied by at most one ion...

journal_title：Biophysical journal

authors： McGill P,Schumaker MF

更新日期：1996-10-01 00:00:00

abstract：:Interpretation of fluorescence anisotropy decay for the case of restricted rotational diffusion often requires a model. To investigate the extent of model dependence, two models are compared: a strict cone model, in which a fluorescent probe wobbles uniformly within a cone, and a Gaussian model, where the stationary d...

journal_title：Biophysical journal

authors： Kinosita K Jr,Ikegami A,Kawato S

更新日期：1982-02-01 00:00:00

abstract：:Helical beta-peptides have been shown to fold into well-defined structures. In aqueous solution, some beta-peptides self-assemble into nanoscale fibers, aggregates, and liquid crystalline phases. Molecular simulations, at an atomistic level, are used to examine, in a systematic manner, the interactions between distinc...

journal_title：Biophysical journal

authors： Miller CA,Gellman SH,Abbott NL,de Pablo JJ

更新日期：2009-06-03 00:00:00

abstract：:A filopodium is a cytoplasmic projection, exquisitely built and regulated, which extends from the leading edge of the migrating cell, exploring the cell's neighborhood. Commonly, filopodia grow and retract after their initiation, exhibiting rich dynamical behaviors. We model the growth of a filopodium based on a stoch...

journal_title：Biophysical journal

authors： Lan Y,Papoian GA

更新日期：2008-05-15 00:00:00

abstract：:Two-dimensional solid-state 31P NMR has been used to investigate the orientational exchange of phospholipids in gel and liquid-crystalline aqueous multilamellar dispersions and oriented multibilayers, and in biological membranes. In liquid-crystalline L alpha multilamellar dispersions, orientational exchange originate...

journal_title：Biophysical journal

authors： Fenske DB,Jarrell HC

更新日期：1991-01-01 00:00:00

abstract：:The coupling between the mechanical properties of enzymes and their biological activity is a well-established feature that has been the object of numerous experimental and theoretical works. In particular, recent experiments show that enzymatic function can be modulated anisotropically by mechanical stress. We study s...

journal_title：Biophysical journal

authors： Sacquin-Mora S,Delalande O,Baaden M

更新日期：2010-11-17 00:00:00

abstract：:Previous data as well as new results are examined with a view to determining the boundary conditions which present experimental information places on a satisfactory polypeptide chain model for the structure of feather keratin. Our studies indicate these conditions to include the following: (1) A 189 A identity period,...

journal_title：Biophysical journal

authors： Schor R,Krimm S

更新日期：1961-07-01 00:00:00

abstract：:Solid phase amplification (SPA), a new method to amplify DNA, is characterized by the use of surface-bound primers. This limits the amplification to two-dimensional surfaces and therefore allows the easy parallelization of DNA amplification in a single system. SPA leads to the formation of small but dense DNA brushes,...

journal_title：Biophysical journal

authors： Mercier JF,Slater GW

更新日期：2005-07-01 00:00:00

abstract：:In the photocycle of bacteriorhodopsin at pH 7, a proton is ejected to the extracellular medium during the protonation of Asp-85 upon formation of the M intermediate. The group that releases the ejected proton does not become reprotonated until the prephotolysis state is restored from the N and O intermediates. In con...

journal_title：Biophysical journal

authors： Morgan JE,Vakkasoglu AS,Lanyi JK,Lugtenburg J,Gennis RB,Maeda A

更新日期：2012-08-08 00:00:00

abstract：:In this work, we present a protocol to reconstitute membrane proteins into giant unilamellar vesicles (GUV) via peptide-induced fusion. In principle, GUV provide a well-defined lipid matrix, resembling a close-to-native state for biophysical studies, including optical microspectroscopy, of transmembrane proteins at th...

journal_title：Biophysical journal

authors： Kahya N,Pécheur EI,de Boeij WP,Wiersma DA,Hoekstra D

更新日期：2001-09-01 00:00:00

abstract：:Solute transport through the extracellular matrix is essential for cellular activities in articular cartilage. Increased solute transport via fluid convection may be a mechanism by which dynamic compression stimulates chondrocyte metabolism. However, loading conditions that optimally augment transport likely vary for ...

journal_title：Biophysical journal

authors： Evans RC,Quinn TM

更新日期：2006-08-15 00:00:00

abstract：:It has long been appreciated that spatiotemporal dynamics of cell migration are under the control of intracellular signaling pathways, which are mediated by adhesion receptors and other transducers of extracellular cues. Further, there is ample evidence that aspects of cell migration are stochastic: how else could it ...

journal_title：Biophysical journal

authors： Weiger MC,Ahmed S,Welf ES,Haugh JM

更新日期：2010-01-06 00:00:00

abstract：:The bacterial flagellar motor couples the flow of protons across the cytoplasmic membrane to the rotation of a helical flagellar filament. Using tethered cells, we have measured the stall torque required to block this rotation and compared it with the torque of the running motor over a wide range of values of proton-m...

journal_title：Biophysical journal

authors： Meister M,Berg HC

更新日期：1987-09-01 00:00:00

abstract：:During inflammation, flowing leukocytes tether to and roll on vascular surfaces through the association and dissociation of selectin/ligand bonds. The interactions of P- and L- selectins with their respective ligands exhibit catch-slip bonds, such that increasing force initially prolongs and then shortens bond lifetim...

journal_title：Biophysical journal

authors： Wayman AM,Chen W,McEver RP,Zhu C

更新日期：2010-08-09 00:00:00

abstract：:Cytotoxic lymphocytes are key elements of the immune system that are primarily responsible for targeting cells infected with intracellular pathogens, or cells that have become malignantly transformed. Target cells are killed mainly via lymphocyte exocytosis of specialized lysosomes containing perforin, a pore-forming ...

journal_title：Biophysical journal

authors： Woodsworth DJ,Dunsing V,Coombs D

更新日期：2015-08-04 00:00:00