A systematic methodology for defining coarse-grained sites in large biomolecules.

abstract：:We present a two-component coarse-grained molecular-dynamics model for simulating the erythrocyte membrane. The proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton, thus showing both the fluidic behavior of the lipid bilayer and the elastic properties of the erythrocy...

journal_title：Biophysical journal

authors： Li H,Lykotrafitis G

更新日期：2012-01-04 00:00:00

abstract：:Epigenetic modifications can extend over long genomic regions to form domain-level chromatin states that play critical roles in gene regulation. The molecular mechanism for the establishment and maintenance of these states is not fully understood and remains challenging to study with existing experimental techniques. ...

journal_title：Biophysical journal

authors： Xie WJ,Zhang B

更新日期：2019-05-21 00:00:00

abstract：:A newly developed microscope using acousto-optic tunable filters (AOTFs) was used to generate in vivo hemoglobin saturation (SO2) and oxygen tension (PO2) maps in the cerebral cortex of mice. SO2 maps were generated from the spectral analysis of reflected absorbance images collected at different wavelengths, and PO2 m...

journal_title：Biophysical journal

authors： Shonat RD,Wachman ES,Niu W,Koretsky AP,Farkas DL

更新日期：1997-09-01 00:00:00

abstract：:We describe the use of asymmetric Ru-ligand complexes as a new class of luminescent probes that can be used to measure rotational motions of proteins. These complexes are known to display luminescent lifetimes ranging from 10 to 4000 ns. In this report, we show that the asymmetric complex Ru(bpy)2(dcbpy) (PF6)2 displa...

journal_title：Biophysical journal

authors： Terpetschnig E,Szmacinski H,Malak H,Lakowicz JR

更新日期：1995-01-01 00:00:00

abstract：:TWIK-1 two-pore domain K(+) channels generally produce nonmeasurable or very low levels of K(+) currents in heterologous expression systems under physiologically ionic conditions. Two controversial mechanisms have been proposed to account for this behavior: TWIK-1 K(+) channels are expressed in the cell surface but si...

journal_title：Biophysical journal

authors： Ma L,Xie YP,Zhou M,Chen H

更新日期：2012-04-18 00:00:00

abstract：:The aggregation of alpha-synuclein (α-syn) and huntingtin (htt) into fibrillar assemblies in nerve and glial cells is a molecular hallmark of Parkinson's and Huntington's diseases. Within the aggregation process, prefibrillar and fibrillar oligomeric species form. Prefibrillar assemblies rather than fibrils are nowada...

journal_title：Biophysical journal

authors： Pieri L,Madiona K,Bousset L,Melki R

更新日期：2012-06-20 00:00:00

abstract：:The motility of Amoeba proteus was examined using the technique of passive particle tracking microrheology, with the aid of newly developed particle tracking software, a fast digital camera, and an optical microscope. We tracked large numbers of endogeneous particles in the amoebae, which displayed subdiffusive motion...

journal_title：Biophysical journal

authors： Rogers SS,Waigh TA,Lu JR

更新日期：2008-04-15 00:00:00

abstract：:Using molecular dynamics simulations, we examine the behavior of lipids whose preferred curvature can be systematically varied. This curvature is imposed by controlling the headgroup size of a coarse-grained lipid model recently developed by us. To validate this approach, we examine self-assembly of each individual li...

journal_title：Biophysical journal

authors： Cooke IR,Deserno M

更新日期：2006-07-15 00:00:00

abstract：:Protein/lipid coassembly is an understudied phenomenon that is important to the function of antimicrobial peptides as well as the pathological effects of amyloid. Here, we study the coassembly process of PAP248-286, a seminal peptide that displays both amyloid-forming and antimicrobial activity. PAP248-286 is a peptid...

journal_title：Biophysical journal

authors： Vane EW,He S,Maibaum L,Nath A

更新日期：2020-09-01 00:00:00

abstract：:The circadian clocks keeping time in many living organisms rely on self-sustained biochemical oscillations entrained by external cues, such as light, to the 24-h cycle induced by Earth's rotation. However, environmental cues are unreliable due to the variability of habitats, weather conditions, or cue-sensing mechanis...

journal_title：Biophysical journal

authors： Pfeuty B,Thommen Q,Lefranc M

更新日期：2011-06-08 00:00:00

abstract：:In this study, we used microbeam grazing-incidence small-angle x-ray scattering (muGISAXS) to investigate in situ protein nucleation and crystal growth assisted by a protein nanotemplate, and introduced certain innovations to improve the method. Our aim was to understand the protein nanotemplate method in detail, as t...

journal_title：Biophysical journal

authors： Gebhardt R,Pechkova E,Riekel C,Nicolini C

更新日期：2010-08-09 00:00:00

abstract：:A beat-to-beat variation in the cardiac action potential duration is a phenomenon known as alternans. Alternans has been linked to ventricular fibrillation, and thus the ability to predict the onset of alternans could be clinically beneficial. Theoretically, it has been proposed that the slope of a restitution curve, ...

journal_title：Biophysical journal

authors： Cram AR,Rao HM,Tolkacheva EG

更新日期：2011-02-16 00:00:00

abstract：:Supercoiled DNA polymer models for which the torsional energy depends on the total twist of molecules (Tw) are a priori well suited for thermodynamic analysis of long molecules. So far, nevertheless, the exact determination of Tw in these models has been based on a computation of the writhe of the molecules (Wr) by ex...

journal_title：Biophysical journal

authors： Lepage T,Képès F,Junier I

更新日期：2015-07-07 00:00:00

abstract：:The physical characteristics which govern the water relations of the giant-celled sporangiophore of Phycomyces blakesleeanus were measured with the pressure probe technique and with nanoliter osmometry. These properties are important because they govern water uptake associated with cell growth and because they may in...

journal_title：Biophysical journal

authors： Cosgrove DJ,Ortega JK,Shropshire W Jr

更新日期：1987-03-01 00:00:00

abstract：:Microbes inhabiting Earth have adapted to diverse environments of water, air, soil, and often at the interfaces of multiple media. In this study, we focus on the behavior of Caulobacter crescentus, a singly flagellated bacterium, at the air/water interface. Forward swimming C. crescentus swarmer cells tend to get phys...

journal_title：Biophysical journal

authors： Morse M,Huang A,Li G,Maxey MR,Tang JX

更新日期：2013-07-02 00:00:00

abstract：:We examined the effect of temperature (12-40°C) on local and global Ca2+ signals mediated by inositol trisphosphate receptor/channels (IP3R) in human neuroblastoma (SH-SY5Y) cells. The amplitudes and spatial spread of local signals arising from single IP3R (blips) and clusters of IP3R (puffs) showed little temperature...

journal_title：Biophysical journal

authors： Dickinson GD,Parker I

更新日期：2013-01-22 00:00:00

abstract：:The effects of low pH, and of alkaline earth cations, were examined on calcium uptake by pinched-off nerve terminals (synaptosomes). This uptake appears to be mediated by voltage-sensitive Ca channels (J. Physiol. 247:617, 1975). Ca uptake was measured in low (5 mM) or high (77 mM) potassium media. The extra uptake pr...

journal_title：Biophysical journal

authors： Nachshen DA,Blaustein MP

更新日期：1979-05-01 00:00:00

abstract：:We combine ensemble and single-molecule spectroscopy to gain insight into the energy transfer between chlorophylls (Chls) in peridinin-chlorophyll-protein (PCP) complexes reconstituted with Chl a, Chl b, as well as both Chl a and Chl b. The main focus is the heterochlorophyllous system (Chl a/b-N-PCP), and reference i...

journal_title：Biophysical journal

authors： Mackowski S,Wörmke S,Brotosudarmo TH,Jung C,Hiller RG,Scheer H,Bräuchle C

更新日期：2007-11-01 00:00:00

abstract：:The molecular basis of the activation of G-proteins by the G-protein coupled receptor for parathyroid hormone (PTH) is unknown. Employing a combination of NMR methods and computer-based structural refinement, structural features involved in the activation of Galpha(s) by the PTH receptor (PTH1R) have been determined. ...

journal_title：Biophysical journal

authors： Plati J,Tsomaia N,Piserchio A,Mierke DF

更新日期：2007-01-15 00:00:00

abstract：:We describe a statistical technique, the joint peristimulus time (PST) scatter diagram, for the analysis of data from simultaneously recorded neurons subjected to repeated stimulation. Distinguishable features in the scatter diagram are related to effects of the stimulus on the observed neurons and to functional relat...

journal_title：Biophysical journal

authors： Gerstein GL,Perkel DH

更新日期：1972-05-01 00:00:00

abstract：:Evidence is presented for the existence of two forms of low-potential cytochrome a3. One appears to be similar to the low-spin form reported by Nicholls, P., and V. Hildebrandt (1978 Biochem. J. 173:65-72) and Wrigglesworth, J. M., J. Elsden, A. Chapman, N. Van der Water, and M. F. Grahn (1988. Biochim. Biophys. Acta....

journal_title：Biophysical journal

authors： Sidhu GS,Hendler RW

更新日期：1990-06-01 00:00:00

abstract：:Dual-color fluorescence cross-correlation analysis is a powerful tool for probing interactions of different fluorescently labeled molecules in aqueous solution. The concept is the selective observation of coordinated spontaneous fluctuations in two separate detection channels that unambiguously reflect the existence o...

journal_title：Biophysical journal

authors： Heinze KG,Rarbach M,Jahnz M,Schwille P

更新日期：2002-09-01 00:00:00

abstract：:Determining the spatial relationship of individual proteins in dense assemblies remains a challenge for superresolution nanoscopy. The organization of aquaporin-4 (AQP4) into large plasma membrane assemblies provides an opportunity to image membrane-bound AQP4 antibodies (AQP4-IgG) and evaluate changes in their spatia...

journal_title：Biophysical journal

authors： Soltys JN,Meyer SA,Schumann H,Gibson EA,Restrepo D,Bennett JL

更新日期：2017-04-25 00:00:00

abstract：:Molecular recognition between biotinylated bovine serum albumin and polyclonal, biotin-directed IG antibodies has been measured directly under various buffer conditions using an atomic force microscope (AFM). It was found that even highly structured molecules such as IgG antibodies preserve their specific affinity to ...

journal_title：Biophysical journal

authors： Dammer U,Hegner M,Anselmetti D,Wagner P,Dreier M,Huber W,Güntherodt HJ

更新日期：1996-05-01 00:00:00

abstract：:Synchronous neurotransmitter release is mediated by the opening of voltage-gated Ca(2+) channels and the build-up of submembrane Ca(2+) microdomains. Previous models of Ca(2+) microdomains have neglected possible electrostatic interactions between Ca(2+) ions and negative surface charges on the inner leaflet of the pl...

journal_title：Biophysical journal

authors： Catacuzzeno L,Fioretti B,Franciolini F

更新日期：2008-09-01 00:00:00

abstract：:It is shown that if x(t) is the solution of a second order differential equation, with real negative characteristic roots (not necessarily distinct), which exhibits an extremum at t = T, then T|x(T)|/|A| [UNK] 1/e where A is the area under the x(t) curve. This result is compared to a special case previously derived by...

journal_title：Biophysical journal

authors： HEARON JZ

更新日期：1961-09-01 00:00:00

abstract：:Microbial capsules are important for virulence, but their architecture and physical properties are poorly understood. The human pathogenic fungus Cryptococcus neoformans has a large polysaccharide capsule that is necessary for virulence and is the target of protective antibody responses. To study the C. neoformans cap...

journal_title：Biophysical journal

authors： Frases S,Pontes B,Nimrichter L,Rodrigues ML,Viana NB,Casadevall A

更新日期：2009-08-19 00:00:00

abstract：:Some low molecular weight biomolecules, i.e., NAD(P)H, are unstable at high temperatures. The use of these biomolecules by thermophilic microorganisms has been scarcely analyzed. Herein, NADH stability has been studied at different temperatures and viscosities. NADH decay increased at increasing temperatures. At incre...

journal_title：Biophysical journal

authors： Cuecas A,Cruces J,Galisteo-López JF,Peng X,Gonzalez JM

更新日期：2016-08-23 00:00:00

abstract：:Ceramides have been implicated in the initiation of apoptosis by permeabilizing the mitochondrial outer membrane to small proteins, including cytochrome c. In addition, ceramides were shown to form large metastable channels in planar membranes and liposomes, indicating that these lipids permeabilize membranes directly...

journal_title：Biophysical journal

authors： Anishkin A,Sukharev S,Colombini M

更新日期：2006-04-01 00:00:00

abstract：:The tunneling transfer of electrons between two sites, appropriate to biological intermolecular electron transfer, contains physical considerations which are not important in the tunneling transfer between two metals. Analyses (such as the recent one by Hales) based on the well-known formula for the latter but applied...

journal_title：Biophysical journal

authors： Hopfield JJ

更新日期：1976-10-01 00:00:00