Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme.

abstract：:Noncanonical DNA structures that retain programmability and structural predictability are increasingly being used in DNA nanotechnology applications, in which they offer versatility beyond traditional Watson-Crick interactions. The d(CGA) triplet repeat motif is structurally dynamic and can transition between parallel...

journal_title：Biophysical journal

authors： Luteran EM,Kahn JD,Paukstelis PJ

更新日期：2020-10-20 00:00:00

abstract：:Proteins fold and function in cellular environments that are crowded with other macromolecules. As a consequence of excluded volume effects, compact folded states of proteins should be indirectly stabilized due to destabilization of extended unfolded conformations. Here, we assess the role of excluded volume in terms ...

journal_title：Biophysical journal

authors： Mikaelsson T,Adén J,Johansson LB,Wittung-Stafshede P

更新日期：2013-02-05 00:00:00

abstract：:A recent theory for the long time dynamics of flexible chain molecules is applied for the first time to a peptide of biological importance, the neurotransmitter met-enkephalin. The dynamics of met-enkephalin is considerably more complicated than that of the previously studied glycine oligomers; met-enkephalin contains...

journal_title：Biophysical journal

authors： Kostov KS,Freed KF

更新日期：1999-01-01 00:00:00

abstract：:Here we model the Alzheimer beta-peptide ion channel with the goal of obtaining insight into the mechanism of amyloid toxicity. The models are built based on NMR data of the oligomers, with the universal U-shaped (strand-turn-strand) motif. After 30-ns simulations in the bilayer, the channel dimensions, shapes and sub...

journal_title：Biophysical journal

authors： Jang H,Zheng J,Nussinov R

更新日期：2007-09-15 00:00:00

abstract：:The oxygen concentration in tissue can vary on several length scales. The basic scale of variation is determined by capillary spacing. It is this scale that is manifest in the simplest Krogh cylinder model. A second, smaller scale of variation is associated with the consumption of oxygen by mitochondria. This paper gi...

journal_title：Biophysical journal

authors： Clark A Jr,Clark PA

更新日期：1985-12-01 00:00:00

abstract：:The UV-visible absorption and magnetic circular dichroism (MCD) spectra of the ferric, ferrous, CO-ligated forms and kinetic photolysis intermediates of the tetraheme electron-transfer protein cytochrome c3 (Cc3) are reported. Consistent with bis-histidinyl axial coordination of the hemes in this Class III c-type cyto...

journal_title：Biophysical journal

authors： O'Connor DB,Goldbeck RA,Hazzard JH,Kliger DS,Cusanovich MA

更新日期：1993-10-01 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：:We present a theoretical and experimental analysis of the effects of nonlinear flow in a cone-plate viscometer. The analysis predicts that flow in the viscometer is a function of two parameters, the Reynolds number and the cone angle. Nonlinear flow occurs at high shear rates and causes spatial variations in wall shea...

journal_title：Biophysical journal

authors： Shankaran H,Neelamegham S

更新日期：2001-06-01 00:00:00

abstract：:We have constructed a model of the upper part of the glycolysis in the pancreatic beta-cell. The model comprises the enzymatic reactions from glucokinase to glyceraldehyde-3-phosphate dehydrogenase (GAPD). Our results show, for a substantial part of the parameter space, an oscillatory behavior of the glycolysis for a ...

journal_title：Biophysical journal

authors： Westermark PO,Lansner A

更新日期：2003-07-01 00:00:00

abstract：:A sequence determinant of reduction potentials is reported for bacterial [4Fe-4S]-type ferredoxins. The residue that is four residues C-terminal to the fourth ligand of either cluster is generally an alanine or a cysteine. In five experimental ferredoxin structures, the cysteine has the same structural orientation rel...

journal_title：Biophysical journal

authors： Beck BW,Xie Q,Ichiye T

更新日期：2001-08-01 00:00:00

abstract：:Formation of amyloid oligomers, the most toxic species of amyloids in degenerative diseases, is critically coupled to the interplay with surrounding water. The hydrophobic force driving the oligomerization causes water removal from interfaces, changing the surface-hydration properties. Here, we show that such effects ...

journal_title：Biophysical journal

authors： Walton JH,Berry RS,Despa F

更新日期：2011-05-04 00:00:00

abstract：:Spin inversion transfer (SIT) NMR experiments are reported probing the thermodynamics and kinetics of interconversion of two folded forms of a GCN4-like leucine zipper near room temperature. The peptide is 13Calpha-labeled at position V9(a) and results are compared with prior findings for position L13(e). The SIT data...

journal_title：Biophysical journal

authors： d'Avignon DA,Bretthorst GL,Holtzer ME,Holtzer A

更新日期：1999-05-01 00:00:00

abstract：:Ion channel behavior can depend strongly on temperature, with faster kinetics at physiological temperatures leading to considerable changes in currents relative to room temperature. These temperature-dependent changes in voltage-dependent ion channel kinetics (rates of opening, closing, inactivating, and recovery) are...

journal_title：Biophysical journal

authors： Lei CL,Clerx M,Beattie KA,Melgari D,Hancox JC,Gavaghan DJ,Polonchuk L,Wang K,Mirams GR

更新日期：2019-12-17 00:00:00

abstract：:In high light conditions, cyanobacteria dissipate excess absorbed energy as heat in the light-harvesting phycobilisomes (PBs) to protect the photosynthetic system against photodamage. This process requires the binding of the red active form of the Orange Carotenoid Protein (OCP(r)), which can effectively quench the ex...

journal_title：Biophysical journal

authors： Tian L,Gwizdala M,van Stokkum IH,Koehorst RB,Kirilovsky D,van Amerongen H

更新日期：2012-04-04 00:00:00

abstract：:The nuclear magnetic resonance (NMR) of water protons in live and glycerinated muscle, suspensions of glycerinated myofibrils, and solutions of several muscle proteins has been studied. T(1) and T(2), measured on partially hydrated proteins by pulsed spin-echo techniques, decreased as the ratio of water to protein dec...

journal_title：Biophysical journal

authors： Cooke R,Wien R

更新日期：1971-12-01 00:00:00

abstract：:By combining a description of the coupled solute and water flows through the in vivo cornea with a set of appropriate mechanical equilibrium conditions, it is possible to calculate directly the corneal thickness, given the corneal temperature, the state of the aqueous and tears, the swelling pressure-hydration relatio...

journal_title：Biophysical journal

authors： Friedman MH

更新日期：1972-06-01 00:00:00

abstract：:The average sizes of fluid and gel domains in the two-component, two-phase system formed from mixtures of dimyristoyl phosphatidylcholine and distearoyl phosphatidylcholine were determined from an analysis of the electron spin resonance spectral lineshapes of a dimyristoyl phosphatidylcholine-nitroxide spin label as a...

journal_title：Biophysical journal

authors： Sankaram MB,Marsh D,Thompson TE

更新日期：1992-08-01 00:00:00

abstract：:A phenomenological theory for contracting muscle based on irreversible thermodynamics and the sliding filament theory is developed. The individual cross bridges, considered as subunits, are viewed as linear energy converters with constant transport coefficients. With this view of the subunits, phenomenological equatio...

journal_title：Biophysical journal

authors： Bornhorst WJ,Minardi JE

更新日期：1970-02-01 00:00:00

abstract：:Nonconfluent fibroblasts are relatively depolarized when compared with confluent fibroblasts, and transient hyperpolarizations result from a range of external stimuli as well as internal cellular activities. This electrical activity ceases, along with growth and mitogenic activity, when the cells become confluent. A c...

journal_title：Biophysical journal

authors： Stockbridge LL,French AS

更新日期：1988-07-01 00:00:00

abstract：:Cells in a cloned population of coliform bacteria exhibit a wide range of swimming behaviors--a form of non-genetic individuality. We used computer models to examine the proposition that these variations are due to differences in the number of chemotaxis signaling molecules from one cell to the next. Simulations were ...

journal_title：Biophysical journal

authors： Levin MD,Morton-Firth CJ,Abouhamad WN,Bourret RB,Bray D

更新日期：1998-01-01 00:00:00

abstract：:Nisin is an antimicrobial peptide used as food preservative. To gain some insights into the hypothesis that its bactericidal activity is due to the perturbation of the lipid fraction of the bacterial plasmic membrane, we have investigated the effect of nisin on model phosphatidylcholine (PC) membranes. We show that ni...

journal_title：Biophysical journal

authors： El Jastimi R,Edwards K,Lafleur M

更新日期：1999-08-01 00:00:00

abstract：:Deuterium and phosphorus nuclear magnetic resonance (NMR) has been used to investigate the dynamics of slow motional processes induced in bilayer cardiolipin upon binding with cytochrome c. 31P NMR line shapes suggest that protein binding induces less restricted, isotropic-like motions in the lipid phosphates within t...

journal_title：Biophysical journal

authors： Spooner PJ,Duralski AA,Rankin SE,Pinheiro TJ,Watts A

更新日期：1993-07-01 00:00:00

abstract：:Previous studies on aurein 2.2 and 2.3 in DMPC/DMPG and POPC/POPG membranes have shown that bilayer thickness and phosphatidylglycerol content have a significant impact on the interaction of these peptides with membrane bilayers. Further examination with the DiSC(3)5 assay has indicated that aurein 2.2 induces greater...

journal_title：Biophysical journal

authors： Cheng JT,Hale JD,Kindrachuk J,Jenssen H,Elliott M,Hancock RE,Straus SK

更新日期：2010-11-03 00:00:00

abstract：:Actin dynamics is important in determining cell shape, tension, and migration. Methods such as fluorescent speckle microscopy and spatial temporal image correlation spectroscopy have been used to capture high-resolution actin turnover dynamics within cells in two dimensions. However, these methods are not directly app...

journal_title：Biophysical journal

authors： Chiu CL,Digman MA,Gratton E

更新日期：2013-10-15 00:00:00

abstract：:Fluorescence resonance energy transfer (FRET) was used to reveal aspects of the mechanism of signal transduction by epidermal growth factor receptors (EGFR). The superpositions of epidermal growth factor (EGF), transforming growth factor-alpha (TGFalpha) and an antibody fragment (29.1) to the carbohydrate extremity of...

journal_title：Biophysical journal

authors： Martin-Fernandez M,Clarke DT,Tobin MJ,Jones SV,Jones GR

更新日期：2002-05-01 00:00:00

abstract：:We have used optical tweezers to study the elasticity of red cell membranes; force was applied to a bead attached to a permeabilized spherical ghost and the force-extension relation was obtained from the response of a second bead bound at a diametrically opposite position. Interruption of the skeletal network by disso...

journal_title：Biophysical journal

authors： Sleep J,Wilson D,Simmons R,Gratzer W

更新日期：1999-12-01 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：:Crossover motifs are integral components for designing DNA-based nanostructures and nanomechanical devices due to their enhanced rigidity compared to the normal B-DNA. Although the structural rigidity of the double helix B-DNA has been investigated extensively using both experimental and theoretical tools, to date the...

journal_title：Biophysical journal

authors： Santosh M,Maiti PK

更新日期：2011-09-21 00:00:00

abstract：:Primary embryonic chick cells have been evaluated on the basis of their capacity to repair photochemical lesions produced in the deoxyribonucleic acid (DNA) by ultraviolet (UV) radiation. The fate of one prominent class of UV photoproducts, cyclobutane pyrimidine dimers, was monitored by an in vitro enzymatic assay. U...

journal_title：Biophysical journal

authors： Paterson MC,Lohman PH,de Weerd-Kastelein EA,Westerveld A

更新日期：1974-06-01 00:00:00

abstract：:Current viral docking models have relied upon the assumption that bond formation and breakage are independent of viral and docking surface geometry, as well as the forces exerted on the bonds. This assumption, known as the equivalent site hypothesis (ESH), is examined in detail using a newly developed simulation techn...

journal_title：Biophysical journal

authors： English TJ,Hammer DA

更新日期：2004-06-01 00:00:00