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 relative to the nearest cluster, which is stabilized by the SH...S bond. Although such bonds are generally considered weak, indications that Fe-S redox site sulfurs are better hydrogen-bond acceptors than most sulfurs include the numerous amide NH...S bonds noted by Adman and our quantum mechanical calculations. Furthermore, electrostatic potential calculations of 11 experimental ferredoxin structures indicate that the extra cysteine decreases the reduction potential relative to an alanine by approximately 60 mV, in agreement with experimental mutational studies. Moreover, the decrease in potential is due to a shift in the polar backbone stabilized by the SH...S bond rather than to the slightly polar cysteinyl side chain. Thus, these cysteines can "tune" the reduction potential, which could optimize electron flow in an electron transport chain. More generally, hydrogen bonds involving sulfur can be important in protein structure/function, and mutations causing polar backbone shifts can alter electrostatics and thus affect redox properties or even enzymatic activity of a protein.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Beck BW,Xie Q,Ichiye Tdoi
10.1016/s0006-3495(01)75726-8subject
Has Abstractpub_date
2001-08-01 00:00:00pages
601-13issue
2eissn
0006-3495issn
1542-0086pii
S0006-3495(01)75726-8journal_volume
81pub_type
杂志文章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
pub_type： 杂志文章
doi：10.1529/biophysj.106.094698
更新日期：2007-03-01 00:00:00
abstract：:In its most restrictive interpretation, the notion of chromatin remodeling refers to the action of chromatin-remodeling enzymes on nucleosomes with the aim of displacing and removing them from the chromatin fiber (the effective polymer formed by a DNA molecule and proteins). This local modification of the fiber struct...
journal_title：Biophysical journal
pub_type： 杂志文章,评审
doi：10.1016/j.bpj.2017.12.008
更新日期：2018-05-22 00:00:00
abstract：:Small RNA-mRNA binding is an essential step in RNA interference, an important cellular regulatory process. Calculations of binding free energy have been used in binding site prediction, but the cost of stretching the mRNA loop when the small RNA-mRNA duplex forms requires further exploration. Here, using both polymer ...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2012.12.017
更新日期：2013-01-22 00:00:00
abstract：:Simulations of two distinct systems, one a planar bilayer, the other the inverse hexagonal phase, indicate consistent mechanical properties and curvature preferences, with single DOPE leaflets having a spontaneous curvature, R0 = -26 Å (experimentally ~ -29.2 Å) and DOPC leaflets preferring to be approximately flat (R...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2013.03.048
更新日期：2013-05-21 00:00:00
abstract：:We have chemically modified a fraction of the monomers in actin filaments, and then measured the effects on the functional interaction of myosin with unmodified monomers within the same filament. Two modifications were used: (a) covalent attachment of various amounts of myosin subfragment-1 (S1) with the bifunctional ...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(93)81057-9
更新日期：1993-07-01 00:00:00
abstract：:Differential scanning calorimetry provides a new window into the plasma proteome. Plasma from normal individuals yields a characteristic, reproducible thermogram that appears to represent the weighted sum of denaturation profiles of the most abundant constituent plasma proteins. Plasma from diseased individuals yields...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.107.119453
更新日期：2008-02-15 00:00:00
abstract：:We use optical tweezers microrheology and fluorescence microscopy to apply nonlinear microscale strains to entangled and cross-linked actin networks, and measure the resulting stress and actin filament deformations. We couple nonlinear stress response and relaxation to the velocities and displacements of individual fl...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2017.01.012
更新日期：2017-10-03 00:00:00
abstract：:Many essential processes in eukaryotic cells depend on regulated molecular exchange between its two major compartments, the cytoplasm and the nucleus. In general, nuclear import of macromolecular complexes is dependent on specific peptide signals and their recognition by receptors that mediate translocation through th...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.105.060160
更新日期：2005-09-01 00:00:00
abstract：:In adherent and motile neutrophils NAD(P)H concentration, flavoprotein redox potential, and production of reactive oxygen species and nitric oxide, are all periodic and exhibit defined phase relationships to an underlying metabolic oscillation of approximately 20 s. Utilizing fluorescence microscopy, we have shown in ...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.104.056663
更新日期：2005-05-01 00:00:00
abstract：:Plasma insulin measurements from mice, rats, dogs, and humans indicate that insulin levels are oscillatory, reflecting pulsatile insulin secretion from individual islets. An unanswered question, however, is how the activity of a population of islets is coordinated to yield coherent oscillations in plasma insulin. Here...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2009.05.016
更新日期：2009-08-05 00:00:00
abstract：:N-methyl-d-aspartate (NMDA) receptors are glutamate- and glycine-gated channels that flux Na+ and Ca2+ into postsynaptic neurons during synaptic transmission. The resulting intracellular Ca2+ transient is essential to physiological and pathological processes related to synaptic development, plasticity, and apoptosis. ...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2017.06.035
更新日期：2017-11-21 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
pub_type： 杂志文章
doi：10.1529/biophysj.106.086181
更新日期：2006-10-01 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：:Calcium channels in neurons mediate a wide variety of essential functions. In addition to contributing to action potential shape, they furnish a substrate that acts as an intracellular second messenger. This study shows that the shape of the neuronal action potential has characteristics that promote long openings of L...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(92)81669-7
更新日期：1992-10-01 00:00:00
abstract：:A delay ( approximately 10 min) in the appearance of intracellular phage is caused by preincubating the infecting phage T4o(1) in proflavine, acridine orange, or ethidium, but not polyamines. No significant delay in attachment is observed. Apparently the presence of the dye is required inside the permeability barrier ...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(72)86144-7
更新日期：1972-08-01 00:00:00
abstract：:Amperometry recording reveals the exocytosis of catecholamine from individual vesicles as a sequential process, typically beginning slowly with a prespike foot, accelerating sharply to initiate a spike, reaching a peak, and then decaying. This complex sequence reflects the interplay between diffusion, flux through a f...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2020.06.001
更新日期：2020-07-07 00:00:00
abstract：:In Shaker-like channels, the activation gate is formed at the bundle crossing by the convergence of the inner S6 helices near a conserved proline-valine-proline motif, which introduces a kink that allows for electromechanical coupling with voltage sensor motions via the S4-S5 linker. Human ether-a-go-go-related gene (...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2014.01.035
更新日期：2014-03-04 00:00:00
abstract：:The stability of the structure of double-stranded DNA in the salt-free solution is discussed on the basis of the polyelectrolyte theory. Assuming that DNA is an infinitely long rod, and the formation of double strands is divided into combining process and folding process, the free energy changes required in these proc...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/s0006-3495(63)86831-9
更新日期：1963-11-01 00:00:00
abstract：:Plant light-harvesting complex II (LHCII) is the key antenna complex for plant photosynthesis. We present coarse-grained molecular dynamics simulations of monomeric and trimeric LHCII in a realistic thylakoid membrane environment based on the Martini force field. The coarse-grained protein model has been optimized wit...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2019.03.009
更新日期：2019-04-23 00:00:00
abstract：:The muscle nicotinic receptor (AChR) is a pentamer of four different subunits, each of which contains four transmembrane domains (M1-M4). We recently showed that channel opening and closing rates of the AChR depend on a hydrogen bond involving a threonine at position 14' of the M4 domain in the alpha-subunit. To deter...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(02)75541-0
更新日期：2002-04-01 00:00:00
abstract：:The opening of basepairs plays a key role in DNA replication and transcription, and in the action of DNA repair and modification enzymes. In this article, we have used proton exchange to define the energetics of the pathways for basepair opening in two DNA 17-mer duplexes. The rates of exchange of imino protons with s...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1529/biophysj.105.065763
更新日期：2005-11-01 00:00:00
abstract：:A simulation of the function of the human heart and heart muscle has been developed in the form of a digital computer code. For a given set of values for the input variables, realistic values of the cardiac output variables are predicted. A detailed discussion of the simulation and some results obtained from its appli...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(73)86011-4
更新日期：1973-07-01 00:00:00
abstract：:A review is given of the structure and dynamics of the flagellar rotary motor. Force-generating elements in a motor driving a tethered bacterium (a cell fixed to the substratum by a single flagellum) exert forces of order 20 pN while moving at speeds of order 1 micron/s. Force-generating elements in a motor driving a ...
journal_title：Biophysical journal
pub_type： 杂志文章,评审
doi：
更新日期：1995-04-01 00:00:00
abstract：:The outer membrane (OM) of Gram-negative bacteria is composed of lipopolysaccharide (LPS) in the outer leaflet and phospholipids in the inner leaflet. The outer membrane protein H (OprH) of Pseudomonas aeruginosa provides an increased stability to the OMs by directly interacting with LPS. Here we report the influence ...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2016.12.006
更新日期：2017-01-24 00:00:00
abstract：:The channel-forming properties of two analogs of gramicidin, gramicidin-ethylenediamine (gram-EDA), and gramicidin-N,N-dimethylethylenediamine (gram-DMEDA) were studied in planar lipid bilayers, using protons as the permeant ion. These peptides have positively charged amino groups tethered to their C-terminal ends via...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(97)78275-4
更新日期：1997-11-01 00:00:00
abstract：:Helical beta-peptides have been shown to fold into well-defined structures. In aqueous solution, some beta-peptides self-assemble into nanoscale fibers, aggregates, and liquid crystalline phases. Molecular simulations, at an atomistic level, are used to examine, in a systematic manner, the interactions between distinc...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2008.11.076
更新日期：2009-06-03 00:00:00
abstract：:Mechanosensitivity in voltage-gated calcium channels could be an asset to calcium signaling in healthy cells or a liability during trauma. Recombinant N-type channels expressed in HEK cells revealed a spectrum of mechano-responses. When hydrostatic pressure inflated cells under whole-cell clamp, capacitance was unchan...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(02)75267-3
更新日期：2002-11-01 00:00:00
abstract：:Multiphasic kinetics are often observed in stopped-flow investigations. To characterize further these kinetic phases, we have developed a methodology whereby fluorescence total intensity and anisotropy stopped-flow data can be combined in a single analysis. Fluorescence total intensity and anisotropy are highly interr...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(94)80741-6
更新日期：1994-12-01 00:00:00
abstract：:Actin, a highly conserved cytoskeletal protein found in all eukaryotic cells, facilitates cell motility and membrane remodeling via a directional polymerization cycle referred to as treadmilling. The nucleotide bound at the core of each actin subunit regulates this process. Although the biochemical kinetics of treadmi...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/j.bpj.2014.03.012
更新日期：2014-04-15 00:00:00
abstract：:Aggregated Markov models are a widely used tool to model patch clamp data measured from single ion channels. These channels must obey the principle of detailed balance in thermodynamic equilibrium; otherwise, the channel is driven by an external source of energy. We investigate the power of a likelihood ratio test for...
journal_title：Biophysical journal
pub_type： 杂志文章
doi：10.1016/S0006-3495(00)76529-5
更新日期：2000-12-01 00:00:00
