Abstract:
:The results of a 3-ns molecular dynamics simulation of the dodecamer duplex d(TATGGATCCATA)(2) recognized by the BamHI endonuclease are presented here. The DNA has been simulated as a flexible molecule using an AMBER force field and the Ewald summation method, which eliminates the undesired effects of truncation and permits evaluation of the full effects of electrostatic forces. The starting B conformation evolves toward a configuration quite close to that observed through x-ray diffraction in its complex with BamHI. This configuration is fairly stable and the Watson-Crick hydrogen bonds are well maintained over the simulation trajectory. Hydration analysis indicates a preferential hydration for the phosphate rather than for the ester oxygens. Hydration shells in both the major and minor groove were observed. In both grooves the C-G pairs were found to be more hydrated than A-T pairs. The "spine of hydration" in the minor groove was clear. Water residence times are longer in the minor groove than in the major groove, although relatively short in both cases. No special long values are observed for sites where water molecules were observed by x-ray diffraction, indicating that water molecules having a high probability of being located in a specific site are also fast-exchanging.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Castrignanò T,Chillemi G,Desideri Adoi
10.1016/S0006-3495(00)76380-6subject
Has Abstractpub_date
2000-09-01 00:00:00pages
1263-72issue
3eissn
0006-3495issn
1542-0086pii
S0006-3495(00)76380-6journal_volume
79pub_type
杂志文章abstract::In most studied microbial rhodopsins two conserved carboxylic acid residues (the homologs of Asp-85 and Asp-212 in bacteriorhodopsin) and an arginine residue (the homolog of Arg-82) form a complex counterion to the protonated retinylidene Schiff base, and neutralization of the negatively charged carboxylates causes re...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2014.03.002
更新日期:2014-04-15 00:00:00
abstract::Previous mathematical modeling of beta cell electrical activity has involved single cells or, recently, clusters of identical cells. Here we model clusters of heterogeneous cells that differ in size, channel density, and other parameters. We use gap-junctional electrical coupling, with conductances determined by an ex...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81539-X
更新日期:1993-06-01 00:00:00
abstract::We have used resonance Raman spectroscopy to probe the heme environment of a recently discovered NOS from the pathogenic bacterium Staphylococcus aureus, named SANOS. We detect two forms of the CO complex in the absence of L-arginine, with nu(Fe-CO) at 482 and 497 cm(-1) and nu(C-O) at 1949 and 1930 cm(-1), respective...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.042119
更新日期:2004-09-01 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
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.05.060
更新日期:2011-07-20 00:00:00
abstract::Many different cell types are able to migrate by formation of a thin actin-based cytoskeletal extension. Recently, it became evident that this extension consists of two distinct substructures, designated lamellipodium and lamellum, which differ significantly in their kinetic and kinematic properties as well as their b...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.108.134817
更新日期:2008-12-15 00:00:00
abstract::Ca2+ release from the endoplasmic reticulum (ER) contributes to Ca2+ transients in frog sympathetic ganglion neurons. Here we use video-rate confocal fluo-4 fluorescence imaging to show that single action potentials reproducibly trigger rapidly rising Ca2+ transients at 1-3 local hot spots within the peripheral ER-ric...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74094-1
更新日期:2004-01-01 00:00:00
abstract::The pores of ion channel proteins are often modeled as static structures. In this view, selectivity reflects rigidly constrained backbone orientations. Such a picture is at variance with the generalization that biological proteins are flexible, capable of major internal motions on biologically relevant time scales. We...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78096-2
更新日期:1997-08-01 00:00:00
abstract::Chimeras consisting of the homologous skeletal dihydropyridine receptor (DHPR) beta1a subunit and the heterologous cardiac/brain beta2a subunit were used to determine which regions of beta1a were responsible for the skeletal-type excitation-contraction (EC) coupling phenotype. Chimeras were transiently transfected in ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.043810
更新日期:2004-08-01 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
pub_type: 杂志文章
doi:10.1529/biophysj.104.051474
更新日期:2005-04-01 00:00:00
abstract::The polyunsaturated fatty acid docosahexaenoic acid (DHA) makes up approximately 50% of the lipid chains in the retinal rod outer segment disk membranes and a large fraction of the lipid chains in the membranes of neuronal tissues. There is an extensive literature concerned with the dietary requirements for essential ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76344-2
更新日期:2000-08-01 00:00:00
abstract::The influence of basic open-loop synaptic connections on the firing of simultaneously recorded neurons has been investigated with auto- and cross-correlation histograms, using experimental records and computer simulations. The basic connections examined were direct synaptic excitation, direct synaptic inhibition, and ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(70)86341-X
更新日期:1970-09-01 00:00:00
abstract::The TRPV1 cation nonselective ion channel plays an essential role in thermosensation and perception of other noxious stimuli. TRPV1 can be activated by low extracellular pH, high temperature, or naturally occurring pungent molecules such as allicin, capsaicin, or resiniferatoxin. Its noxious thermal sensitivity makes ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.10.041
更新日期:2020-02-25 00:00:00
abstract::Proliferation of mammalian cells, even under conditions of unlimited growth, presents a complex problem because of the interaction of deterministic and stochastic processes. Division of the cell cycle into a finite number of parts establishes a multidimensional vector space. In this space an arbitrary culture can be r...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(66)86656-0
更新日期:1966-05-01 00:00:00
abstract::Two mechanisms have been proposed to account for solute permeation of lipid bilayers. Partitioning into the hydrophobic phase of the bilayer, followed by diffusion, is accepted by many for the permeation of water and other small neutral solutes, but transient pores have also been proposed to account for both water and...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(96)79575-9
更新日期:1996-01-01 00:00:00
abstract::In the absence of atomic structures of high-density lipoproteins in their lipid-bound states, many molecular models have been produced based on experimental data. Using molecular dynamics, we show that a recently proposed "solar-flares" model of discoidal high-density lipoprotein is implausible. Our simulations show a...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1529/biophysj.108.131581
更新日期:2008-06-01 00:00:00
abstract::Label-free imaging techniques such as differential interference contrast (DIC) allow the observation of cells and large subcellular structures in their native, unperturbed states with minimal exposure to light. The development of robust computational image-analysis routines is vital to quantitative label-free imaging....
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.12.013
更新日期:2021-01-11 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
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.01.029
更新日期:2017-03-14 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
pub_type: 杂志文章
doi:10.1529/biophysj.106.093138
更新日期:2007-03-01 00:00:00
abstract::The photocycle of salinarum halorhodopsin was investigated in the presence of azide. The azide binds to the halorhodopsin with 150 mM binding constant in the absence of chloride and with 250 mM binding constant in the presence of 1 M chloride. We demonstrate that the azide-binding site is different from that of chlori...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75521-5
更新日期:2002-04-01 00:00:00
abstract::Cofilin/ADF, beryllium fluoride complex (BeFx), and phalloidin have opposing effects on actin filament structure and dynamics. Cofilin/ADF decreases the stability of F-actin by enhancing disorder in subdomain 2, and by severing and accelerating the depolymerization of the filament. BeFx and phalloidin stabilize the su...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.087767
更新日期:2006-12-15 00:00:00
abstract::It has recently been observed in situ in mice that insulin takes approximately 10 min to be transported 20 microm into the t-tubule networks of skeletal muscle fibers. The mechanisms for this slow transport are unknown. It has been suggested that the biochemical composition of the t-tubular space that may include larg...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.107.107888
更新日期:2007-11-01 00:00:00
abstract::beta-Lactamase, which catalyzes beta-lactam antibiotics, is prototypical of large alpha/beta proteins with a scaffolding formed by strong noncovalent interactions. Experimentally, the enzyme is well characterized, and intermediates that are slightly less compact and having nearly the same content of secondary structur...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(93)81288-8
更新日期:1993-12-01 00:00:00
abstract::Nuclear receptor (NR) ligands occupy a pocket that lies within the core of the NR ligand-binding domain (LBD), and most NR LBDs lack obvious entry/exit routes upon the protein surface. Thus, significant NR conformational rearrangements must accompany ligand binding and release. The precise nature of these processes, h...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.063818
更新日期:2005-09-01 00:00:00
abstract::It is widely assumed that the decay of fluorescence in photosynthetic systems can be described as a sum of exponential components and that the amplitude of each component is directly related to the absorption cross-section of the antenna pigments coupled to the fluorescing species. We present exact calculations of exc...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(89)82767-5
更新日期:1989-12-01 00:00:00
abstract::Strain B(8-11) has been found to be very sensitive to postirradiation DNA degradation. Up to 98% of the DNA is degraded at optimum doses. The amount of residual DNA correlates with the retention of colony-forming ability (CFA). Studies of rates of degradation as a function of dose agree with the concept that a degradi...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(72)86076-4
更新日期:1972-02-01 00:00:00
abstract::In vitro and in situ tests have been run to characterize the reaction of the mettalochromic indicator, arsenazo III, with calcium. Job plots as well as plots of indicator absorbance vs. [Ca2+] at different indicator concentrations show a 1:1 reaction stoichiometry. Equilibrium analysis and analysis using Adair's equat...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(80)85025-9
更新日期:1980-12-01 00:00:00
abstract::Human apolipoprotein E (apoE) is a 299-amino-acid protein with a molecular weight of 34 kDa. The difference between the apoE3 and apoE4 isoforms is a single residue substitution involving a Cys-Arg replacement at residue 112. ApoE4 is positively associated with atherosclerosis and late-onset and sporadic Alzheimer's d...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.046813
更新日期:2005-01-01 00:00:00
abstract::The switch 1 region of myosin forms a lid over the nucleotide phosphates as part of a structure known as the phosphate-tube. The homologous region in kinesin-family motors is more open, not interacting with the nucleotide. We used molecular dynamics (MD) simulations to examine a possible displacement of switch 1 of th...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(01)76092-4
更新日期:2001-03-01 00:00:00
abstract::The effect of the presence of a minor antenna component in light-harvesting complexes of photosynthetic bacteria is investigated with numerical simulation employing the transition probability matrix method. A model antenna system of hexagonal symmetry is adopted, using as a working hypothesis that the minor component ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(92)81689-2
更新日期:1992-10-01 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
pub_type: 杂志文章
doi:10.1016/j.bpj.2020.07.035
更新日期:2020-09-15 00:00:00