Abstract:
:Fourier-transform infrared spectroscopy is a method of choice for the experimental determination of protein secondary structure. Numerous approaches have been developed during the past 15 years. A critical parameter that has not been taken into account systematically is the selection of the wavenumbers used for building the mathematical models used for structure prediction. The high quality of the current Fourier-transform infrared spectrometers makes the absorbance at every single wavenumber a valid and almost noiseless type of information. We address here the question of the amount of independent information present in the infrared spectra of proteins for the prediction of the different secondary structure contents. It appears that, at most, the absorbance at three distinct frequencies of the spectra contain all the nonredundant information that can be related to one secondary structure content. The ascending stepwise method proposed here identifies the relevance of each wavenumber of the infrared spectrum for the prediction of a given secondary structure and yields a particularly simple method for computing the secondary structure content. Using the 50-protein database built beforehand to contain as little fold redundancy as possible, the standard error of prediction in cross-validation is 5.5% for the alpha-helix, 6.6% for the beta-sheet, and 3.4% for the beta-turn.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Goormaghtigh E,Ruysschaert JM,Raussens Vdoi
10.1529/biophysj.105.072017subject
Has Abstractpub_date
2006-04-15 00:00:00pages
2946-57issue
8eissn
0006-3495issn
1542-0086pii
S0006-3495(06)72475-4journal_volume
90pub_type
杂志文章abstract::Protein kinases are key players in signal transduction pathways where they are crafted into two functional states. In response to growth factor binding stimulus, epidermal growth factor receptor (EGFR), which is physiologically populated in an autoinhibited inactive state, becomes active. Here, we outline a simple all...
journal_title:Biophysical journal
pub_type: 杂志文章,评审
doi:10.1016/j.bpj.2019.05.021
更新日期:2019-07-09 00:00:00
abstract::Small-angle neutron scattering (SANS) is used to probe the solution structure of two protein therapeutics (monoclonal antibodies 1 and 2 (MAb1 and MAb2)) and their protein-protein interaction (PPI) at high concentrations. These MAbs differ by small sequence alterations in the complementarity-determining region but sho...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2013.06.043
更新日期:2013-08-06 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
pub_type: 杂志文章
doi:10.1016/S0006-3495(87)83315-5
更新日期:1987-01-01 00:00:00
abstract::Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped by dual-beam lasers and the other was held by a micropipette. Several experimen...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.106.094052
更新日期:2007-05-01 00:00:00
abstract::We have previously studied single, voltage-dependent, saxitoxin-(STX) blockable sodium channels from rat brain in planar lipid bilayers, and found that channel block by STX was voltage-dependent. Here we describe the effect of voltage on the degree of block and on the kinetics of the blocking reaction. From their volt...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(84)84156-9
更新日期:1984-01-01 00:00:00
abstract::Voltage-sensitive fluorescent dyes are commonly used to measure cardiac electrical activity. Recent studies indicate, however, that optical action potentials (OAPs) recorded from the myocardial surface originate from a widely distributed volume beneath the surface and may contain useful information regarding intramura...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74690-6
更新日期:2003-10-01 00:00:00
abstract::Ca2+ regulates ryanodine receptor's (RyR) activity through an activating and an inhibiting Ca2+-binding site located on the cytoplasmic side of the RyR channel. Their altered sensitivity plays an important role in the pathology of malignant hyperthermia and heart failure. We used lanthanide ions (Ln3+) as probes to in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2017.03.023
更新日期:2017-05-23 00:00:00
abstract::Topical microbicide products are being developed for the prevention of sexually transmitted infections. These include vaginally-applied gels that deliver anti-HIV molecules. Gels may also provide partial barriers that slow virion diffusion from semen to vulnerable epithelium, increasing the time during which anti-HIV ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2009.08.010
更新日期:2009-11-04 00:00:00
abstract::We demonstrate the first, to our knowledge, integration of stimulated emission depletion (STED) with selective plane illumination microscopy (SPIM). Using this method, we were able to obtain up to 60% improvements in axial resolution with lateral resolution enhancements in control samples and zebrafish embryos. The in...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.12.3748
更新日期:2011-04-20 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::The role of the extracellular Glu side chains of bacteriorhodopsin in the proton transport mechanism has been studied using the single mutants E9Q, E74Q, E194Q, and E204Q; the triple mutant E9Q/E194Q/E204Q; and the quadruple mutant E9Q/E74Q/E194Q/E204Q. Steady-state difference and deconvoluted Fourier transform infrar...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(00)76749-X
更新日期:2000-04-01 00:00:00
abstract::The presence of tryptophan residues as intrinsic fluorophores in most proteins makes them an obvious choice for fluorescence spectroscopic analyses of such proteins. Membrane proteins have been reported to have a significantly higher tryptophan content than soluble proteins. The role of tryptophan residues in the stru...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(97)78116-5
更新日期:1997-08-01 00:00:00
abstract::We have measured the rates of insertion into, desorption from, and spontaneous interlayer translocation (flip-flop) in liquid-disordered and liquid-ordered phase lipid bilayer membranes, of the fluorescent phospholipid derivative NBD-dimyristoylphosphatidyl ethanolamine. This study made use of a recently described met...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.104.040576
更新日期:2004-07-01 00:00:00
abstract::The most probable source of force generation in muscle fibers in the rotation of the myosin head when bound to actin. This laboratory has demonstrated that ATP induces microsecond rotational motions of spin-labeled myosin heads bound to actin (Berger, C. L. E. C. Svensson, and D. D. Thomas. 1989. Proc. Natl. Acad. Sci...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(91)82338-4
更新日期:1991-06-01 00:00:00
abstract::The diffusion of plastoquinol and its binding to the cytochrome bf complex, which occurs during linear photosynthetic electron transport and is analogous to reaction sequences found in most energy-converting membranes, has been studied in intact thylakoid membranes. The flash-induced electron transfer between the late...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(90)82445-0
更新日期:1990-10-01 00:00:00
abstract::Cartilage stiffness was measured ex vivo at the micrometer and nanometer scales to explore structure-mechanical property relationships at smaller scales than has been done previously. A method was developed to measure the dynamic elastic modulus, |E(*)|, in compression by indentation-type atomic force microscopy (IT A...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(04)74375-1
更新日期:2004-05-01 00:00:00
abstract::Transport of large proteins into the nucleus involves two events, binding of the cargo protein to a transport receptor in the cytoplasm and passage of the cargo-transporter complex through the selective permeability barrier of the nuclear pore complex. The permeability barrier is formed by largely disordered polypepti...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2010.02.049
更新日期:2010-06-02 00:00:00
abstract::Steady-state and time-resolved fluorescence spectroscopy was used to follow the local and global changes in structure and dynamics during chemical and thermal denaturation of unlabeled human serum albumin (HSA) and HSA with an acrylodan moiety bound to Cys34. Acrylodan fluorescence was monitored to obtain information ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77598-8
更新日期:1998-08-01 00:00:00
abstract::Stepwise two-photon excitation of chlorophyll a and b in the higher plant main light-harvesting complex (LHC II) and the minor complex CP29 (as well as in organic solution) with 100-fs pulses in the Q(y) region results in a weak blue fluorescence. The dependence of the spectral shape of the blue fluorescence on excita...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75509-4
更新日期:2002-03-01 00:00:00
abstract::Cardiac excitation-contraction coupling is initialized by the release of Ca from the sarcoplasmic reticulum (SR) in response to a sudden increase in local cytosolic [Ca] ([Ca]i) within the junctional cleft. We have tested the hypothesis that functional ryanodine receptor (RyR) regulation plays a major role in the regu...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1529/biophysj.105.068734
更新日期:2005-12-01 00:00:00
abstract::Regulation of the F-actin severing activity of gelsolin by Ca2+ has been investigated under physiologic ionic conditions. Tryptophan fluorescence intensity measurements indicate that gelsolin contains at least two Ca2+ binding sites with affinities of 2.5 x 10(7) M-1 and 1.5 x 10(5) M-1. At F-actin and gelsolin concen...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(98)77751-3
更新日期:1998-12-01 00:00:00
abstract::Biological membranes are constantly exposed to forces. The stress-strain relation in membranes determines the behavior of many integral membrane proteins or other membrane related-proteins that show a mechanosensitive behavior. Here, we studied by force spectroscopy the behavior of supported lipid bilayers (SLBs) subj...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2012.05.039
更新日期:2012-07-03 00:00:00
abstract::Photosystem II catalyzes photosynthetic water oxidation in plants, green algae, and cyanobacteria. The manganese-containing active site cycles through a series of five oxidation states, S(n), where n refers to the number of oxidizing equivalents stored. In this report, reaction-induced Fourier transform infrared and e...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74680-3
更新日期:2003-10-01 00:00:00
abstract::The p7 protein from hepatitis C virus is critical for the assembly and secretion of infectious virus, making it an attractive drug target. It is thought to be a viroporin with a demonstrated ion channel activity when reconstituted into planar lipid bilayers. Electron microscopy experiments suggest that p7 oligomers co...
journal_title:Biophysical journal
pub_type: 信件
doi:10.1016/j.bpj.2008.10.004
更新日期:2009-01-01 00:00:00
abstract::Activation of skeletal muscle ryanodine receptors (RyRs) by suramin and disulfonic stilbene derivatives (Diisothiocyanostilbene-2',2'-disulfonic acid (DIDS), 4,4'-dibenzamidostilbene-2,2'-disulfonic acid (DBDS),and 4,4'-dinitrostilbene-2,2'-disulfonic acid (DNDS)) was investigated using planar bilayers. One reversible...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(03)74976-5
更新日期:2003-03-01 00:00:00
abstract::In two-color fluorescence correlation spectroscopy (TCFCS), the fluorescence intensities of two fluorescently-labeled species are cross-correlated over time and can be used to identify static and dynamic interactions. Generally, fluorophore labels are chosen that do not undergo Förster resonance energy transfer (FRET)...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(02)75189-8
更新日期:2002-07-01 00:00:00
abstract::Diffusional encounters between a dumbbell model of a cleft enzyme and a dumbbell model of an elongated ligand are simulated by Brownian dynamics. The simulations take into account electrostatic and hydrodynamic interactions between the molecules. It is shown that the primary effect of inclusion of hydrodynamic interac...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(95)79874-5
更新日期:1995-07-01 00:00:00
abstract::Based on the existence of ATP-sensitive potassium channels in the plasma membrane of pancreatic beta cells, we develop a quantitative explanation of the electrical activity observed in pancreatic islets. The proposed mechanism involves the voltage-dependent inward calcium and outward potassium currents described by Ro...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/S0006-3495(89)82669-4
更新日期:1989-08-01 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
pub_type: 杂志文章
doi:10.1016/j.bpj.2019.07.033
更新日期:2019-12-17 00:00:00
abstract::The lipid matrix present in the uppermost layer of the skin, the stratum corneum, plays a crucial role in the skin barrier function. The lipids are organized into two lamellar phases. To gain more insight into the molecular organization of one of these lamellar phases, we performed neutron diffraction studies. In the ...
journal_title:Biophysical journal
pub_type: 杂志文章
doi:10.1016/j.bpj.2011.02.001
更新日期:2011-03-16 00:00:00