Time-resolved rapid-scan Fourier transform infrared difference spectroscopy on a noncyclic photosystem: rhodopsin photointermediates from Lumi to Meta II.


:The visual pigment rhodopsin has been extensively studied for the kinetics of its photointermediates by various spectroscopic methods. Unlike such archaeal retinal proteins as bacteriorhodopsin, visual rhodopsin does not thermally recover its dark state after photoexcitation, which precludes repeated excitation of a single sample and thereby complicates time-resolved experiments. Kinetic data on the late rhodopsin photointermediates have so far been available mainly from time-resolved ultraviolet (UV)-visible spectroscopy, but not from Fourier transform infrared (FTIR) spectroscopy. The latter has the advantage of being informative of structural changes of both chromophore and protein, but does not allow the highly reproducible, automated sample exchange procedures available to UV-visible spectroscopy. Using rapid-scan FTIR difference spectroscopy, we obtained time-resolved data sets that were analyzed by a maximum entropy inverse Laplace-transform. Covering the time range from 8 ms to 15 s at temperatures of 0 and -7 degrees C, the transitions from the Lumi to the Meta I and from the Meta I to the Meta II photoproduct states could be resolved. In the transition from Meta I to Meta II, our data reveal a partial deprotonation of the retinal Schiff base preceding the conformational change of the receptor protein to Meta II. The technique and the results are discussed in regard to its advantages as well as its limitations.






Lüdeke S,Lórenz Fonfría VA,Siebert F,Vogel R




Has Abstract


2006-10-05 00:00:00












  • NMR studies of RNA dynamics and structural plasticity using NMR residual dipolar couplings.

    abstract::An increasing number of RNAs are being discovered that perform their functions by undergoing large changes in conformation in response to a variety of cellular signals, including recognition of proteins and small molecular targets, changes in temperature, and RNA synthesis itself. The measurement of NMR residual dipol...


    pub_type: 杂志文章,评审


    authors: Getz M,Sun X,Casiano-Negroni A,Zhang Q,Al-Hashimi HM

    更新日期:2007-08-05 00:00:00

  • Synthesis and characterization of new biodegradable hyaluronan alkyl derivatives.

    abstract::Several new biocompatible and degradable materials were prepared by chemical modification of sodium hyaluronate. The method of activation of hyaluronate by cyanogen bromide was used and subsequent reaction with nucleophile led to the formation of carbamate. This modification of hydroxyl groups of glycosaminoglycans pr...


    pub_type: 杂志文章


    authors: Mlcochová P,Bystrický S,Steiner B,Machová E,Koós M,Velebný V,Krcmár M

    更新日期:2006-05-01 00:00:00

  • Helical side chain chemistry of a peptoid-based SP-C analogue: Balancing structural rigidity and biomimicry.

    abstract::Surfactant protein C (SP-C) is an important constituent of lung surfactant (LS) and, along with SP-B, is included in exogenous surfactant replacement therapies for treating respiratory distress syndrome (RDS). SP-C's biophysical activity depends upon the presence of a rigid C-terminal helix, of which the secondary str...


    pub_type: 杂志文章


    authors: Brown NJ,Lin JS,Barron AE

    更新日期:2019-06-01 00:00:00

  • Tooth enamel protein, amelogenin, has a probable beta-spiral internal channel, Gln112-Leu138, within a single polypeptide chain: preliminary molecular mechanics and dynamics studies.

    abstract::Molecular dynamics simulation, with backbone constraints for 20 ps of equilibration and simulation, of a repeating polypeptide segment, Gln-Pro-His-Gln-Pro-Leu-Gln-Pro-His-Gln-Pro-Leu-Gln-Pro-Met-(Gln-Pro-Leu )4, constituting residues 112-138 of bovine amelolgenin, a 19.35 kD hydrophobic protein, are discussed. It is ...


    pub_type: 杂志文章


    authors: Renugopalakrishnan V,Pattabiraman N,Prabhakaran M,Strawich E,Glimcher MJ

    更新日期:1989-01-01 00:00:00

  • Platform technology to generate broadly cross-reactive antibodies to α-helical epitopes in hemagglutinin proteins from influenza A viruses.

    abstract::We have utilized a de novo designed two-stranded α-helical coiled-coil template to display conserved α-helical epitopes from the stem region of hemagglutinin (HA) glycoproteins of influenza A. The immunogens have all the surface-exposed residues of the native α-helix in the native HA protein of interest displayed on t...


    pub_type: 杂志文章


    authors: Jiang Z,Gera L,Mant CT,Hirsch B,Yan Z,Shortt JA,Pollock DD,Qian Z,Holmes KV,Hodges RS

    更新日期:2016-03-01 00:00:00

  • Theoretical CD studies of polypeptide helices: examination of important electronic and geometric factors.

    abstract::An improved model for calculating the CD of polypeptides has been developed. Excited state wavefunctions were derived from CNDO/S (complete neglect of differential overlap, spectroscopic) calculations on N-methylacetamide. Four discrete peptide-localized transitions were employed: pi 0 pi* (NV1), pi* + pi* (NV2), n pi...


    pub_type: 杂志文章


    authors: Manning MC,Woody RW

    更新日期:1991-04-01 00:00:00

  • Molecular mass and chain conformation of carboxymethylated derivatives of beta-glucan from sclerotia of Pleurotus tuber-regium.

    abstract::Seven water-insoluble (1 --> 3)-beta-D-glucan fractions TM8-1 to TM8-7 with weight-average molecular mass M(w) ranged from 2.22 to 77.4 x 10(4) obtained from the sclerotia of Pleurotus tuber-regium were carboxymethylated to produce the water-soluble fractions CTM8-1 to CTM8-7 with M(w) ranged from 3.87 to 87.8 x 10(4)...


    pub_type: 杂志文章


    authors: Zhang M,Zhang L,Cheung PC

    更新日期:2003-02-01 00:00:00

  • Dynamics and structures of DNA: long-range effects of a 16 base-pair (CG)8 sequence on secondary structure.

    abstract::The effects of inserting 16 base pair (bp) of alternating CG [(CG)8] near the middle of a much longer restriction fragment (1097 bp) are investigated by measuring various properties that are sensitive to secondary and tertiary structure. Results for this fragment are compared with those for a control fragment (1089 bp...


    pub_type: 杂志文章


    authors: Kim US,Fujimoto BS,Furlong CE,Sundstrom JA,Humbert R,Teller DC,Schurr JM

    更新日期:1993-11-01 00:00:00

  • X-ray solution scattering studies of the structural diversity intrinsic to protein ensembles.

    abstract::It is becoming increasingly clear that characterization of the protein ensemble-the collection of all conformations of which the protein is capable-will be a critical step in developing a full understanding of the linkage between structure, dynamics, and function. X-ray solution scattering in the small angle (SAXS) an...


    pub_type: 杂志文章


    authors: Makowski L,Gore D,Mandava S,Minh D,Park S,Rodi DJ,Fischetti RF

    更新日期:2011-08-01 00:00:00

  • Removal of kinetic traps and enhanced protein folding by strategic substitution of amino acids in a model alpha-helical hairpin peptide.

    abstract::The presence of non-native kinetic traps in the free energy landscape of a protein may significantly lengthen the overall folding time so that the folding process becomes unreliable. We use a computational model alpha-helical hairpin peptide to calculate structural free energy landscapes and relate them to the kinetic...


    pub_type: 杂志文章


    authors: Chapagain PP,Gerstman BS

    更新日期:2006-02-15 00:00:00

  • Conformational analysis of peptide T and of its C-pentapeptide fragment.

    abstract::The synthetic peptide of sequence H-Ala-Ser-Thr-Thr-Thr-Asn-Tyr-Thr-OH, termed peptide T, a competitor of the Human Immunodeficiency Virus in the binding to human T cells, and its C-terminal pentapeptide fragment, were studied by 1H-nmr in DMSO solution to determine conformational preferences. The observation of nucle...


    pub_type: 杂志文章


    authors: Motta A,Picone D,Temussi PA,Marastoni M,Tomatis R

    更新日期:1989-01-01 00:00:00

  • CD and fluorescence studies of the human granulocyte-macrophage colony-stimulating factor and related peptide conformations in aqueous solution.

    abstract::The absorption, CD, and fluorescence emission spectra, and the fluorescence emission and depolarization lifetimes of the human granulocyte-macrophage colony-stimulating factor (hGM-CSF) and related peptides previously tested for their immunological activity, were measured in water at various pHs and temperatures to ob...


    pub_type: 杂志文章


    authors: Casté L,Zandomeneghi M,Houben JL,Rovero P,Pegoraro S,Revoltella PR,Brochon JC

    更新日期:1995-07-01 00:00:00

  • Structural behavior of nanometric carbohydrate films transduced by a resonant technique.

    abstract::New optical nanoresonance effects enabled us to study the effect of ions on nanometric carbohydrate thin layers on chips. Immobilization was done via spin coating of the derivatized carbohydrate polymer at a metallized chip surface forming ultrathin films (about 50-300 nm thick) followed by photochemical cross-linking...


    pub_type: 杂志文章


    authors: Palkovits R,Mayer C,Bauer G,Winkler H,Pittner F,Schalkhammer T

    更新日期:2003-07-01 00:00:00

  • Flow linear dichroism and Fourier transform IR spectra reveal geometry for X-form DNA.

    abstract::Flow linear dichroism measurements extended into the vacuum uv region yield inclinations for the base normal from the helix axis of 21 degrees for dA and 40 degrees for dT in the X-form of poly(dAdT).poly(dAdT). These inclination angles are similar to the B form of the synthetic polymer, but the axes around which the ...


    pub_type: 杂志文章


    authors: Riazance-Lawrence JH,Kang H,Chou PJ,Johnson WC Jr,Vorlícková M

    更新日期:1994-11-01 00:00:00

  • Depsipeptide analogues of elastin repeating sequences: synthesis.

    abstract::Depsipeptide analogues of peptide sequences can help in elucidating the role of specific hydrogen bonds in determining the conformation in peptides. The repeating pentapeptide and hexapeptide sequences of elastin have been suggested to contain a type II beta-turn with a 4----1 hydrogen bond. Depsipeptide analogues of ...


    pub_type: 杂志文章


    authors: Arad O,Goodman M

    更新日期:1990-10-01 00:00:00

  • Homopurine and homopyrimidine strands complementary in parallel orientation form an antiparallel duplex at neutral pH with A-C, G-T, and T-C mismatched base pairs.

    abstract::DNA sequences d-TGAGGAAAGAAGGT (a 14-mer) and d-CTCCTTTCTTCC (a 12-mer) are complementary in parallel orientation forming either Donohue (reverse Watson-Crick) base pairing at neutral pH or Hoogsteen base pairing at slightly acidic pH. The structure of the complex formed by dissolving the two strands in equimolar rati...


    pub_type: 杂志文章


    authors: Bhaumik SR,Chary KV,Govil G,Liu K,Miles HT

    更新日期:1997-06-01 00:00:00

  • Synthesis of new hydrophilic microspheres: optimized carriers for microparticle-enhanced nephelometric immunoassays.

    abstract::To optimize antigen-antibody reactions, we have synthesized chemically well-defined hydrophilic microspheres. Proteins or haptens were covalently linked to these carriers. When the microsphere conjugates were agglutinated by the corresponding antiserum, the size of the complex artificially increased during the immunol...


    pub_type: 杂志文章


    authors: Marchand J,Varcin P,Riochet D,Montagne P,Cuilliere ML,Duheille J,Pau B

    更新日期:1992-08-01 00:00:00

  • Comparison of monovalent and divalent ion distributions around a DNA duplex with molecular dynamics simulation and a Poisson-Boltzmann approach.

    abstract::The ion atmosphere created by monovalent (Na(+) ) or divalent (Mg(2+) ) cations surrounding a B-form DNA duplex were examined using atomistic molecular dynamics (MD) simulations and the nonlinear Poisson-Boltzmann (PB) equation. The ion distributions predicted by the two methods were compared using plots of radial and...


    pub_type: 杂志文章


    authors: Robbins TJ,Ziebarth JD,Wang Y

    更新日期:2014-08-01 00:00:00

  • Gold nanoparticles crosslinking by peptides and amino acids: A tool for the colorimetric identification of amino acids.

    abstract::Gold nanoparticles are known to aggregate in the presence of proper multifunctional compounds. For those larger than 3 nm, the process can be followed with the naked eye because the surface plasmon absorption band of the particles shifts to longer wavelengths and the solution color changes from red to blue. To exploit...


    pub_type: 杂志文章


    authors: Martínez Á,Scrimin P

    更新日期:2018-08-01 00:00:00

  • Osmolyte-induced changes in protein conformational equilibria.

    abstract::Examining solute-induced changes in protein conformational equilibria is a long-standing method for probing the role of water in maintaining protein stability. Interpreting the molecular details governing the solute-induced effects, however, remains controversial. We present experimental and theoretical data for osmol...


    pub_type: 杂志文章


    authors: Saunders AJ,Davis-Searles PR,Allen DL,Pielak GJ,Erie DA

    更新日期:2000-04-05 00:00:00

  • FTIR study on heat-induced and pressure-assisted cold-induced changes in structure of bovine alpha-lactalbumin: stabilizing role of calcium ion.

    abstract::The second derivative FTIR study of heat-induced and pressure-assisted cold-induced changes in the secondary structure of bovine alpha-lactalbumin was carried out for native holoprotein and calcium ion depleted apoprotein. The secondary structure and compactness of alpha-lactalbumin were examined in a temperature rang...


    pub_type: 杂志文章


    authors: Dzwolak W,Kato M,Shimizu A,Taniguchi Y

    更新日期:2001-01-01 00:00:00

  • Structure-activity studies of peptidomimetics based on kinase-inhibitory region of suppressors of cytokine signaling 1.

    abstract::Suppressors of Cytokine Signaling (SOCS) proteins are negative regulators of JAK proteins that are receptor-associated tyrosine kinases, which play key roles in the phosphorylation and subsequent activation of several transcription factors named STATs. Unlike the other SOCS proteins, SOCS1 and 3 show, in the N-termina...


    pub_type: 杂志文章


    authors: La Manna S,Lopez-Sanz L,Leone M,Brandi P,Scognamiglio PL,Morelli G,Novellino E,Gomez-Guerrero C,Marasco D

    更新日期:2017-11-20 00:00:00

  • Reactive oxygen species responsive nanoplatforms as smart drug delivery systems for gastrointestinal tract targeting.

    abstract::The pharmacological therapy for gastrointestinal (GI) diseases, such as inflammatory bowel diseases, continues to present challenges in targeting efficacy. The need for maximal local drug exposure at the inflamed regions of the GI tract has led research to focus on a disease-targeted drug delivery approach. Smart nano...


    pub_type: 杂志文章,评审


    authors: Bertoni S,Machness A,Tiboni M,Bártolo R,Santos HA

    更新日期:2020-01-01 00:00:00

  • Molecular dynamics simulations of a winter flounder "antifreeze" polypeptide in aqueous solution.

    abstract::A winter flounder antifreeze polypeptide (HPLC-6) has been studied in vacuo and in aqueous solution using molecular dynamics computer simulation techniques. The helical conformation of this polypeptide was found to be stable both in vacuum and in solution. The major stabilizing interactions were found to be the main-c...


    pub_type: 杂志文章


    authors: McDonald SM,Brady JW,Clancy P

    更新日期:1993-10-01 00:00:00

  • Vibrational CD (VCD) and atomic force microscopy (AFM) study of DNA interaction with Cr3+ ions: VCD and AFM evidence of DNA condensation.

    abstract::The interaction of natural calf thymus DNA with Cr(3+) ions was studied at room temperature by means of vibrational CD (VCD) and infrared absorption (ir) spectroscopy, and atomic force microscopy (AFM). Cr(3+) ion binding mainly to N(7) (G) and to phosphate groups was demonstrated. Psi-type VCD spectra resembling elec...


    pub_type: 杂志文章


    authors: Andrushchenko V,Leonenko Z,Cramb D,van de Sande H,Wieser H

    更新日期:2001-01-01 00:00:00

  • Individual-site binding data and the energetics of protein-DNA interactions.

    abstract::Individual-site isotherms for the binding of bacteriophage lambda repressor to the left and right lambda operators have been determined [D. F. Senear, M. Brenowitz, M. A. Shea, and G. K. Ackers (1986) Biochemistry, Vol. 25, pp. 7344-7354.] using the DNAse protection technique [footprinting; D. J. Galas and A. Schmitz ...


    pub_type: 杂志文章


    authors: Saroff HA

    更新日期:1993-09-01 00:00:00

  • Solvent interactions with the Trp-cage peptide in 35% ethanol-water.

    abstract::Intermolecular NOE experiments have been used to explore interactions of water and ethanol molecules in 35% ethanol/65% water (v/v) with the peptide Trp-cage at temperatures from 5 to 25 degrees C. Magnetic dipole-dipole cross-relaxation terms sigma(HH) (NOE) and sigma(HH) (ROE) for interaction of solvent components w...


    pub_type: 杂志文章


    authors: Neuman RC Jr,Gerig JT

    更新日期:2008-10-01 00:00:00

  • Ultrabright fluorescein-labeled antibodies near silver metallic surfaces.

    abstract::Fluorescein-labeled antibodies are widely used in clinical assays and fluorescence microscopy. The fluorescent signal per labeled antibody is limited by fluorescein self-quenching, which occurs when the antibody is heavily labeled with multiple fluoresceins. We examined immunoglobulin G (IgG) when labeled with 0.7 to ...


    pub_type: 杂志文章


    authors: Lakowicz JR,Malicka J,Huang J,Gryczynski Z,Gryczynski I

    更新日期:2004-08-15 00:00:00

  • Targeting duplex DNA with DNA-PNA chimeras? Physico-chemical characterization of a triplex DNA-PNA/DNA/DNA.

    abstract::Targeting double-stranded DNA with homopyrimidine PNAs results in strand displacement complexes PNA/DNA/PNA rather than PNA/DNA/DNA triplex structures. Not much is known about the binding properties of DNA-PNA chimeras. A 16-mer 5'-DNA-3'-p-(N)PNA(C) has been investigated for its ability to hybridize a complementary d...


    pub_type: 杂志文章


    authors: Petraccone L,Erra E,Messere A,Montesarchio D,Piccialli G,De Napoli L,Barone G,Giancola C

    更新日期:2004-03-01 00:00:00

  • Homo- and heteropolymer self-assembly of recombinant trichocytic keratins.

    abstract::In the past two decades, keratin biomaterials have shown impressive results as scaffolds for tissue engineering, wound healing, and nerve regeneration. In addition to its intrinsic biocompatibility, keratin interacts with specific cell receptors eliciting beneficial biochemical cues. However, during extraction from na...


    pub_type: 杂志文章


    authors: Parker RN,Roth KL,Kim C,McCord JP,Van Dyke ME,Grove TZ

    更新日期:2017-10-01 00:00:00