Analysis of single-molecule FRET trajectories using hidden Markov modeling.

abstract：:The chemical unfolding transition of a protein was simulated, including the presence of an intermediate (I) in equilibrium with the native (N) and unfolded (U) states. The calculations included free energies of unfolding, DeltaGuw, in the range of 1.4 kcal/mol to 10 kcal/mol and three different global m-values. The si...

journal_title：Biophysical journal

authors： Soulages JL

更新日期：1998-07-01 00:00:00

abstract：:Molecular chaperone Hsp70 plays important roles in the pathology of amyloid diseases by inhibiting aberrant aggregation of proteins. However, the biophysical mechanism of the interaction of Hsp70 with the intrinsically disordered proteins (IDPs) is unclear. Here, we report that Hsp70 inhibits aggregation of islet amyl...

journal_title：Biophysical journal

authors： Chilukoti N,Sil TB,Sahoo B,Deepa S,Cherakara S,Maddheshiya M,Garai K

更新日期：2021-01-06 00:00:00

abstract：:Cysteine residues introduced by site-directed mutagenesis have been used to probe the conformation and dynamics of two receptors in the E. coli chemotaxis pathway. (a) Thermal motions of the polypeptide backbone were investigated in the periplasmic D-galactose and D-glucose receptor, a globular protein of known struct...

journal_title：Biophysical journal

authors： Careaga CL,Falke JJ

更新日期：1992-04-01 00:00:00

abstract：:The structure and biophysical properties of lipid membranes are important for cellular functions in health and disease. In Alzheimer's disease, the neuronal membrane is a target for toxic amyloid-β (Aβ). Melatonin is an important pineal gland hormone that has been shown to protect against Aβ toxicity in cellular and a...

journal_title：Biophysical journal

authors： Mei N,Robinson M,Davis JH,Leonenko Z

更新日期：2020-12-15 00:00:00

abstract：:We introduce dual-color time-integrated fluorescence cumulant analysis (TIFCA) to analyze fluorescence fluctuation spectroscopy data. Dual-color TIFCA utilizes the bivariate cumulants of the integrated fluorescent intensity from two detection channels to extract the brightness in each channel, the occupation number, a...

journal_title：Biophysical journal

authors： Wu B,Chen Y,Müller JD

更新日期：2006-10-01 00:00:00

abstract：:The physical forces that underlie the exclusion of solutes from macromolecular surfaces can be probed in a similar way as the measurement of forces between macromolecules in condensed arrays using the osmotic stress technique and x-ray scattering. We report here the dependence of alcohol exclusion or, equivalently, th...

journal_title：Biophysical journal

authors： Stanley C,Rau DC

更新日期：2006-08-01 00:00:00

abstract：:Coarse-grained (CG) models of biomolecules have recently attracted considerable interest because they enable the simulation of complex biological systems on length-scales and timescales that are inaccessible for atomistic molecular dynamics simulation. A CG model is defined by a map that transforms an atomically detai...

journal_title：Biophysical journal

authors： Zhang Z,Lu L,Noid WG,Krishna V,Pfaendtner J,Voth GA

更新日期：2008-12-01 00:00:00

abstract：:Coat protein (COP) I and COP II complexes are involved in the transport of proteins between the endoplasmic reticulum and the Golgi apparatus in eukaryotic cells. The formation of COP I/II complexes at membrane surfaces is an early step in vesicle formation and is mastered by p24, a type I transmembrane protein. Oligo...

journal_title：Biophysical journal

authors： Pannwitt S,Stangl M,Schneider D

更新日期：2019-11-05 00:00:00

abstract：:Motions through the energy landscape of proteins lead to biological function. At temperatures below a dynamical transition (150-250 K), some of these motions are arrested and the activity of some proteins ceases. Here, we introduce the technique of temperature-derivative fluorescence microspectrophotometry to investig...

journal_title：Biophysical journal

authors： Weik M,Vernede X,Royant A,Bourgeois D

更新日期：2004-05-01 00:00:00

abstract：:Efficient and rapid immune response upon challenge by an infectious agent is vital to host defense. The encounter of leukocytes (white blood cells of the immune system) with their targets is the first step in this response. Analysis of the kinetics of this process is essential not only to understanding dynamic behavio...

journal_title：Biophysical journal

authors： Charnick SB,Lauffenburger DA

更新日期：1990-05-01 00:00:00

abstract：:Actin polymerization is typically initiated at specific sites in a cell by membrane-bound protein complexes, and the resulting structures are involved in specialized cellular functions, such as migration, particle uptake, or mitotic division. Here we analyze the potential of the actin system to self-organize into wave...

journal_title：Biophysical journal

authors： Bretschneider T,Anderson K,Ecke M,Müller-Taubenberger A,Schroth-Diez B,Ishikawa-Ankerhold HC,Gerisch G

更新日期：2009-04-08 00:00:00

abstract：:Forces applied by intact mucus-propelling cilia were measured for the first time that we know of using a combined atomic force microscopy (AFM) and electrooptic system. The AFM probe was dipped into a field of beating cilia and its time-dependent deflection was recorded as it was struck by the cilia while the electroo...

journal_title：Biophysical journal

authors： Teff Z,Priel Z,Gheber LA

更新日期：2007-03-01 00:00:00

abstract：:During cytokinesis in Saccharomyces cerevisiae, damaged proteins are distributed unequally between the daughter and mother cells. The retention of these proteins is correlated with yeast aging. Even though evidence suggests that aggregates are retained due to an underlying molecular mechanism, the debate on whether an...

journal_title：Biophysical journal

authors： Andrade-Restrepo M

更新日期：2017-12-05 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：:A new form of metabolic flux analysis (MFA) called thermodynamics-based metabolic flux analysis (TMFA) is introduced with the capability of generating thermodynamically feasible flux and metabolite activity profiles on a genome scale. TMFA involves the use of a set of linear thermodynamic constraints in addition to th...

journal_title：Biophysical journal

authors： Henry CS,Broadbelt LJ,Hatzimanikatis V

更新日期：2007-03-01 00:00:00

abstract：:We measured the influence of alternative versions of the Drosophila melanogaster myosin heavy chain relay domain on muscle mechanical properties. We exchanged relay domain regions (encoded by alternative versions of exon 9) between an embryonic (EMB) isoform and the indirect flight muscle isoform (IFI) of myosin. Prev...

journal_title：Biophysical journal

authors： Yang C,Ramanath S,Kronert WA,Bernstein SI,Maughan DW,Swank DM

更新日期：2008-12-01 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：:Segmentation of the Drosophila melanogaster embryo results from the dynamic establishment of spatial mRNA and protein patterns. Here, we exploit recent temporal mRNA and protein expression measurements on the full surface of the blastoderm to calibrate a dynamical model of the gap gene network on the entire embryo cor...

journal_title：Biophysical journal

authors： Bieler J,Pozzorini C,Naef F

更新日期：2011-07-20 00:00:00

abstract：:Cochlear outer hair cells undergo reversible changes in shape when externally stimulated. This response, known as OHC motility, is a central component of the cochlear amplifier, the mechanism responsible for the high sensitivity of mammalian hearing. We report that actin depolymerization, as regulated by activation/in...

journal_title：Biophysical journal

authors： Matsumoto N,Kitani R,Maricle A,Mueller M,Kalinec F

更新日期：2010-10-06 00:00:00

abstract：:Voltage-dependent G-protein inhibition of N-type calcium channels reduces presynaptic calcium entry, sharply attenuating neurotransmitter release. Studies in neurons demonstrate that G-proteins have multiple modulatory effects on N-type channels. The observed changes may reflect genuine complexity in G-protein action ...

journal_title：Biophysical journal

authors： Patil PG,de Leon M,Reed RR,Dubel S,Snutch TP,Yue DT

更新日期：1996-11-01 00:00:00

abstract：:Protein solution rheology data in the biophysics literature have incompletely identified factors that govern hydrodynamics. Whereas spontaneous protein adsorption at the air/water (A/W) interface increases the apparent viscosity of surfactant-free globular protein solutions, it is demonstrated here that irreversible c...

journal_title：Biophysical journal

authors： Pathak JA,Sologuren RR,Narwal R

更新日期：2013-02-19 00:00:00

abstract：:The two-microelectrode, voltage-clamp technique was applied to rabbit cardiac Purkinje fibers to study the interaction of tetrodotoxin (TTX) with the slowly inactivating Na current. Binding of TTX to rested, inactivated, and activated channels was estimated by measuring the relative decrease of current at the beginnin...

journal_title：Biophysical journal

authors： Carmeliet E

更新日期：1987-01-01 00:00:00

abstract：:The phenomena reported are part of a study about the effects of ionizing radiation on membrane transport. We found that the conductance of lipid membranes in the presence of the polyene-antibiotics nystatin or amphotericin B is reduced to virtually zero following irradiation. Ion channels formed by these substances se...

journal_title：Biophysical journal

authors： Barth C,Stark G,Wilhelm M

更新日期：1993-01-01 00:00:00

abstract：:Thin filament regulation of contraction is thought to involve the binding of two activating ligands: Ca2+ and strongly bound cross-bridges. The specific cross-bridge states required to promote thin filament activation have not been identified. This study examines the relationship between cross-bridge cycling and thin ...

journal_title：Biophysical journal

authors： Wahr PA,Metzger JM

更新日期：1999-04-01 00:00:00

abstract：:Raman spectroscopic data indicate that the conformations of the two hydrocarbon chains of dipalmitoyl phosphatidylcholine in aqueous dispersions of the lipid differ signficantly. The compounds 1-palmitoyl, 2-palmitoyl-d31-3-sn-phosphatidylcholine and 1-palmitoyl-d31, 2-palmitoyl-3-sn-phosphatidylcholine were synthesiz...

journal_title：Biophysical journal

authors： Gaber BP,Yager P,Peticolas WL

更新日期：1978-12-01 00:00:00

abstract：:Red fluorescent proteins are important tools in fluorescence-based life science research. Recently, we have introduced eqFP611, a red fluorescent protein with advantageous properties from the sea anemone Entacmaea quadricolor. Here, we have studied the submillisecond light-driven intramolecular dynamics between bright...

journal_title：Biophysical journal

authors： Schenk A,Ivanchenko S,Röcker C,Wiedenmann J,Nienhaus GU

更新日期：2004-01-01 00:00:00

abstract：:Helix-coil transitions in polyalanine molecules of length 10 are studied by multi-canonical Monte Carlo simulations. The solvation effects are included by either a distance-dependent dielectric permittivity or by a term that is proportional to the solvent-accessible surface area of the peptide. We found a strong depen...

journal_title：Biophysical journal

authors： Peng Y,Hansmann UH

更新日期：2002-06-01 00:00:00

abstract：:Many complex cellular processes from mitosis to cell motility depend on the ability of the cytoskeleton to generate force. Force-generating systems that act on elastic cytoskeletal elements are prone to oscillating instabilities. In this work, we have measured spontaneous shape and movement oscillations in motile fish...

journal_title：Biophysical journal

authors： Barnhart EL,Allen GM,Jülicher F,Theriot JA

更新日期：2010-03-17 00:00:00

abstract：:As sketched in Fig. 1, a current molecular dynamics computer simulation of a lipid bilayer fails to capture significant features of the macroscopic system, including long wavelength undulations. Such fluctuations are intrinsically connected to the value of the macroscopic (or thermodynamic) surface tension (cf. Eqs. 1...

journal_title：Biophysical journal

authors： Feller SE,Pastor RW

更新日期：1996-09-01 00:00:00

abstract：:A complete mechanistic understanding of membrane-localized processes in vesicular transport, such as membrane budding and fission, requires their reconstitution with biochemically-defined components from a biochemically-defined substrate. Supported bilayers formed by vesicle fusion represent an attractive substrate fo...

journal_title：Biophysical journal

authors： Pucadyil TJ,Schmid SL

更新日期：2010-07-21 00:00:00