Exploring the ion selectivity properties of a large number of simplified binding site models.

abstract：:The E5 oncoprotein is the major transforming protein of bovine papillomavirus type 1. This 44-residue transmembrane protein can interact with the platelet-derived growth factor receptor β, leading to ligand-independent activation and cell transformation. For productive interaction, E5 needs to dimerize via a C-termina...

journal_title：Biophysical journal

authors： Windisch D,Hoffmann S,Afonin S,Vollmer S,Benamira S,Langer B,Bürck J,Muhle-Goll C,Ulrich AS

更新日期：2010-09-22 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：:Electrostatics-based calculations have been performed to examine the proton uptake upon reduction of the terminal electron acceptor Q(B) in the photosynthetic reaction center of Rhodobacter sphaeroides as a function of pH and the associated conformational equilibrium. Two crystal structures of the reaction center were...

journal_title：Biophysical journal

authors： Taly A,Sebban P,Smith JC,Ullmann GM

更新日期：2003-03-01 00:00:00

abstract：:Many proteins "bind" DNA through positively charged amino acids on their surfaces. However, to overcome significant energetic and topological obstacles, proteins that bend or package DNA might also modulate the stiffness that is generated by repulsions between phosphates within DNA. Much previous work describes how io...

journal_title：Biophysical journal

authors： Podestà A,Indrieri M,Brogioli D,Manning GS,Milani P,Guerra R,Finzi L,Dunlap D

更新日期：2005-10-01 00:00:00

abstract：:Interactions between amyloid-β peptide (Aβ) and the cell membrane include interaction with membrane lipids and binding to membrane receptors, both of which are considered to be the toxicity mechanisms of Aβ. However, it is unclear whether both mechanisms lead to cytotoxicity. Thus, we aimed to analyze these two mechan...

journal_title：Biophysical journal

authors： Shi JM,Zhu L,Lan X,Zhao DW,He YJ,Sun ZQ,Wu D,Li HY

更新日期：2020-09-15 00:00:00

abstract：:The interaction of an amphiphilic, 40-amino acid beta-amyloid (Abeta) peptide with liposomal membranes as a function of sterol mole fraction (X(sterol)) was studied based on the fluorescence anisotropy of a site-specific membrane sterol probe, dehydroergosterol (DHE), and fluorescence resonance energy transfer (FRET) ...

journal_title：Biophysical journal

authors： Qiu L,Lewis A,Como J,Vaughn MW,Huang J,Somerharju P,Virtanen J,Cheng KH

更新日期：2009-05-20 00:00:00

abstract：:We have used confocal microscopy to examine the [Ca2+]i increase in the albino eggs of the frog Xenopus laevis after fertilization. Eggs were placed in agar wells with their animal poles downward so that fertilization occurred preferentially in the equatorial plane, and confocal microscopy was used to provide a two-di...

journal_title：Biophysical journal

authors： Fontanilla RA,Nuccitelli R

更新日期：1998-10-01 00:00:00

abstract：:In cardiac muscle, troponin (Tn) and tropomyosin inhibit actin and myosin interactions through the steric blocking of myosin binding to F-actin. Ca2+ binding to Tn C modulates this inhibition. Thin filaments become activated upon Ca2+ binding, which enables strong binding of myosin with a concomitant release of ATP hy...

journal_title：Biophysical journal

authors： Solís C,Kim GH,Moutsoglou ME,Robinson JM

更新日期：2018-11-06 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：: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：:During postnatal development, major changes in mechanical properties of skeletal muscle occur. We investigated passive properties of skeletal muscle in mice and rabbits that varied in age from 1 day to approximately 1 year. Neonatal skeletal muscle expressed large titin isoforms directly after birth, followed by a gra...

journal_title：Biophysical journal

authors： Ottenheijm CA,Knottnerus AM,Buck D,Luo X,Greer K,Hoying A,Labeit S,Granzier H

更新日期：2009-10-21 00:00:00

abstract：:Directly measured forces between DNA helices in ordered arrays have been reduced to simple force coefficients and mathematical expressions for the interactions between pairs of molecules. The tabulated force parameters and mathematical expressions can be applied to parallel molecules or, by transformation, to skewed m...

journal_title：Biophysical journal

authors： Podgornik R,Rau DC,Parsegian VA

更新日期：1994-04-01 00:00:00

abstract：:Single-particle tracking is an important technique in the life sciences to understand the kinetics of biomolecules. The analysis of apparent diffusion coefficients in vivo, for example, enables researchers to determine whether biomolecules are moving alone, as part of a larger complex, or are bound to large cellular c...

journal_title：Biophysical journal

authors： Vink JNA,Brouns SJJ,Hohlbein J

更新日期：2020-11-17 00:00:00

abstract：:We have previously observed that the hydrophobic polyelectrolyte poly(2-ethylacrylic acid) solubilizes lipid membranes in a pH-dependent manner, and we have exploited this phenomenon to prepare lipid vesicles that release their contents in response to pH, light, or glucose (Thomas, J. L., and D. A. Tirrell. Acc. Chem....

journal_title：Biophysical journal

authors： Thomas JL,Barton SW,Tirrell DA

更新日期：1994-09-01 00:00:00

abstract：:Cell adhesion provides not only physical linkage but also communication between the cell and its environment. As such, it is important to many cellular functions. Recently, the probability distribution of forming a low number of specific adhesive bonds in a short-duration contact has been described (Chesla et al., Bio...

journal_title：Biophysical journal

authors： Zhu C,Williams TE

更新日期：2000-10-01 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：:A recurring motif in gene regulatory networks is transcription factors (TFs) that regulate each other and then bind to overlapping sites on DNA, where they interact and synergistically control transcription of a target gene. Here, we suggest that this motif maximizes information flow in a noisy network. Gene expressio...

journal_title：Biophysical journal

authors： Hormoz S

更新日期：2013-03-05 00:00:00

abstract：:Globotriaosylceramide (Gb3), a glycosphingolipid found in the plasma membrane of animal cells, is the endocytic receptor of the bacterial Shiga toxin. Using x-ray reflectivity (XR) and grazing incidence x-ray diffraction (GIXD), lipid monolayers containing Gb3 were investigated at the air-water interface. XR probed Gb...

journal_title：Biophysical journal

authors： Watkins EB,Gao H,Dennison AJC,Chopin N,Struth B,Arnold T,Florent JC,Johannes L

更新日期：2014-09-02 00:00:00

abstract：:We report that voltage-gated Na+ channels (Na(V)) from rat muscle (mu1) expressed in HEK293 cells exhibit anomalous rectification of whole-cell outward current under conditions of symmetrical Na+. This behavior gradually fades with time after membrane break-in, as if a diffusible blocking substance in the cytoplasm is...

journal_title：Biophysical journal

authors： Huang CJ,Moczydlowski E

更新日期：2001-03-01 00:00:00

abstract：:Far infrared (FIR) spectral measurements of wild-type (WT) and D96N mutant bacteriorhodopsin thin films have been carried out using terahertz time domain spectroscopy as a function of hydration, temperature, and conformational state. The results are compared to calculated spectra generated via normal mode analyses usi...

journal_title：Biophysical journal

authors： Whitmire SE,Wolpert D,Markelz AG,Hillebrecht JR,Galan J,Birge RR

更新日期：2003-08-01 00:00:00

abstract：:A one-dimensional version of the model recently proposed by Läuger (1988) to explain the closed-time distribution of ionic channels in cell membranes is solved analytically. While the probability density f(t) for closed-time lengths may show a well-defined exponential behavior at short times, a power-law decay is pred...

journal_title：Biophysical journal

authors： Condat CA,Jäckle J

更新日期：1989-05-01 00:00:00

abstract：:We report on a molecular dynamics (MD) simulation of carboxy-myoglobin (MbCO) embedded in a water-trehalose system. The mean square fluctuations of protein atoms, calculated at different temperatures in the 100-300 K range, are compared with those from a previous MD simulation on an H2O-solvated MbCO and with experime...

journal_title：Biophysical journal

authors： Cottone G,Cordone L,Ciccotti G

更新日期：2001-02-01 00:00:00

abstract：:The Qx-Qy splitting observed in the fluorescence excitation spectra of Mg-mesoporphyrin-IX substituted horseradish peroxidase (MgMP-HRP) and of its complex with naphthohydroxamic acid (NHA) was studied by spectral hole burning techniques. The width of a hole directly burnt in the Qy band and that of a satellite hole i...

journal_title：Biophysical journal

authors： Suisalu A,Mauring K,Kikas J,Herenyi L,Fidy J

更新日期：2001-01-01 00:00:00

abstract：:Electric field pulses have been reported to induce long-lived permeabilization and fusogenicity on cell membranes. The two membrane property alterations are under the control of the field strength, the pulse duration, and the number of pulses. Experiments on mammalian cells pulsed by square wave form pulses and then b...

journal_title：Biophysical journal

authors： Teissié J,Ramos C

更新日期：1998-04-01 00:00:00

abstract：:In an open circuit there can be no net cation flux through membranes containing only cation-selective channels, because electroneutrality must be maintained. If the channels are so narrow that water and cations cannot pass by each other, then the net water flux through those "single-file" channels that contain a catio...

journal_title：Biophysical journal

authors： Dani JA,Levitt DG

更新日期：1981-08-01 00:00:00

abstract：:In this article, optimization-based frameworks are introduced for elucidating the input-output structure of signaling networks and for pinpointing targeted disruptions leading to the silencing of undesirable outputs in therapeutic interventions. The frameworks are demonstrated on a large-scale reconstruction of a sign...

journal_title：Biophysical journal

authors： Dasika MS,Burgard A,Maranas CD

更新日期：2006-07-01 00:00:00

abstract：:Ion channels assist and control the diffusion of ions through biological membranes. The conduction process depends on the structural characteristics of these nanopores, among which are the hydrophobicity and the afforded diameter of the conduction pathway. In this contribution, we use full atomistic free-energy molecu...

journal_title：Biophysical journal

authors： Treptow W,Tarek M

更新日期：2006-08-01 00:00:00

abstract：:Monolayers of a functional pulmonary surfactant (PS) can reach very low surface tensions well below their equilibrium value. The mechanism by which PS monolayers reach such low surface tensions and maintain film stability remains unknown. As shown previously by fluorescence microscopy, phospholipid phase transition an...

journal_title：Biophysical journal

authors： Zuo YY,Keating E,Zhao L,Tadayyon SM,Veldhuizen RA,Petersen NO,Possmayer F

更新日期：2008-05-01 00:00:00

abstract：:Na(+) conductance through cloned K(+) channels has previously allowed characterization of inactivation and K(+) binding within the pore, and here we have used Na(+) permeation to study recovery from C-type inactivation in human Kv1.5 channels. Replacing K(+) in the solutions with Na(+) allows complete Kv1.5 inactivati...

journal_title：Biophysical journal

authors： Wang Z,Hesketh JC,Fedida D

更新日期：2000-11-01 00:00:00

abstract：:Late-onset heart failure (HF) is a known side effect of doxorubicin chemotherapy. Typically, patients are diagnosed when already at an irreversible stage of HF, which allows few or no treatment options. Identifying the causes of compromised cardiac function in this patient group may improve early patient diagnosis and...

journal_title：Biophysical journal

authors： Lewalle A,Land S,Merken JJ,Raafs A,Sepúlveda P,Heymans S,Kleinjans J,Niederer SA

更新日期：2019-12-17 00:00:00