Time-resolved FTIR studies of sensory rhodopsin II (NpSRII) from Natronobacterium pharaonis: implications for proton transport and receptor activation.

Abstract:

:The photocycle of the photophobic receptor from Natronobacterium pharaonis, NpSRII, is studied by static and time-resolved step-scan Fourier transform infrared spectroscopy. Both low-temperature static and time-resolved spectra resolve a K-like intermediate, and the corresponding spectra show little difference within the noise of the time-resolved data. As compared to intermediate K of bacteriorhodopsin, relatively large amide I bands indicate correspondingly larger distortions of the protein backbone. The time-resolved spectra identify an intermediate L-like state with surprisingly small additional molecular alterations. With the formation of intermediate M, the Schiff-base proton is transferred to the counterion Asp-75. This state is characterized by larger amide bands indicating larger distortions of the protein. We can identify a second M state that differs only in small-protein bands. Reisomerization of the chromophore to all-trans occurs with the formation of intermediate O. The accelerated decay of intermediate M caused by azide results in another red-shifted intermediate with a protonated Schiff base. The chromophore in this state, however, still has 13-cis geometry. Nevertheless, the reisomerization is still as slow as under the conditions without azide. The results are discussed with respect to mechanisms of the observed proton pumping and the possible roles of the intermediates in receptor activation.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Hein M,Wegener AA,Engelhard M,Siebert F

doi

10.1016/S0006-3495(03)74935-2

subject

Has Abstract

pub_date

2003-02-01 00:00:00

pages

1208-17

issue

2 Pt 1

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(03)74935-2

journal_volume

84

pub_type

杂志文章
  • Surface charge movements of purple membrane during light-dark adaptation.

    abstract::The difference in the surface charge distribution between light-adapted and dark-adapted purple membranes was investigated with electric dichroism measurements from approximately pH 5 to pH 11. Purple membrane sheets in solution are oriented in a weak electric field by their permanent dipole moment, which is due to th...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(86)83454-3

    authors: Otomo J,Ohno K,Takeuchi Y,Ikegami A

    更新日期:1986-08-01 00:00:00

  • SAXS study of crotapotin at low pH.

    abstract::The structure of crotapotin, a protein extracted, from the venom of the Crotalus durissus terrificus, in solution at pH = 1.5, was studied by SAXS. The experimental results yield structural parameter values of the molecular radius of gyration Rg = 13.6 A, volume v = 16.2 x 10(3) A3 A3 and maximal dimension Dmax = 46 A...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(93)81395-X

    authors: Abrego JR,Craievich AF,Mascarenhas YP,Laure CJ

    更新日期:1993-02-01 00:00:00

  • Determining the Spatial Relationship of Membrane-Bound Aquaporin-4 Autoantibodies by STED Nanoscopy.

    abstract::Determining the spatial relationship of individual proteins in dense assemblies remains a challenge for superresolution nanoscopy. The organization of aquaporin-4 (AQP4) into large plasma membrane assemblies provides an opportunity to image membrane-bound AQP4 antibodies (AQP4-IgG) and evaluate changes in their spatia...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2017.03.012

    authors: Soltys JN,Meyer SA,Schumann H,Gibson EA,Restrepo D,Bennett JL

    更新日期:2017-04-25 00:00:00

  • Free energy cost of stretching mRNA hairpin loops inhibits small RNA binding.

    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

    authors: Meng Y,Aalberts DP

    更新日期:2013-01-22 00:00:00

  • The role of membrane stiffness and actin turnover on the force exerted by DRG lamellipodia.

    abstract::We used optical tweezers to analyze the effect of jasplakinolide and cyclodextrin on the force exerted by lamellipodia from developing growth cones (GCs) of isolated dorsal root ganglia (DRG) neurons. We found that 25 nM of jasplakinolide, which is known to inhibit actin filament turnover, reduced both the maximal exe...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2012.04.036

    authors: Amin L,Ercolini E,Shahapure R,Migliorini E,Torre V

    更新日期:2012-06-06 00:00:00

  • Equilibrium dynamics of spermine-induced plasmid DNA condensation revealed by fluorescence lifetime correlation spectroscopy.

    abstract::The spermine-induced DNA condensation is a first-order phase transition. Here, we apply a novel technique fluorescence lifetime correlation spectroscopy to analyze this transition in a greater detail. We show that the method allows for the observation of the condensed and uncondensed molecules simultaneously based sol...

    journal_title:Biophysical journal

    pub_type: 信件

    doi:10.1529/biophysj.107.122408

    authors: Humpolícková J,Benda A,Sýkora J,Machán R,Kral T,Gasinska B,Enderlein J,Hof M

    更新日期:2008-02-01 00:00:00

  • Long-time dynamics of Met-enkephalin: comparison of theory with Brownian dynamics simulations.

    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

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(99)77185-7

    authors: Kostov KS,Freed KF

    更新日期:1999-01-01 00:00:00

  • Sodium channels: ionic model of slow inactivation and state-dependent drug binding.

    abstract::Inactivation is a fundamental property of voltage-gated ion channels. Fast inactivation of Na(+) channels involves channel block by the III-IV cytoplasmic interdomain linker. The mechanisms of nonfast types of inactivation (intermediate, slow, and ultraslow) are unclear, although the ionic environment and P-loops rear...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.106.100248

    authors: Tikhonov DB,Zhorov BS

    更新日期:2007-09-01 00:00:00

  • Structure of membrane-embedded M13 major coat protein is insensitive to hydrophobic stress.

    abstract::The structure of a membrane-embedded alpha-helical reference protein, the M13 major coat protein, is characterized under different conditions of hydrophobic mismatch using fluorescence resonance energy transfer in combination with high-throughput mutagenesis. We show that the structure is similar in both thin (14:1) a...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.112698

    authors: Vos WL,Schor M,Nazarov PV,Koehorst RB,Spruijt RB,Hemminga MA

    更新日期:2007-11-15 00:00:00

  • Improved resolution of tertiary structure elasticity in muscle protein.

    abstract::Rearrangement of tertiary structure in response to mechanical force (termed tertiary structure elasticity) in the tandem Ig chain is the first mode of elastic response for muscle protein titin. Tertiary structure elasticity occurs at low stretching forces (few tens of pN), and was described at atomic resolution in a r...

    journal_title:Biophysical journal

    pub_type: 信件

    doi:10.1016/j.bpj.2011.01.019

    authors: Hsin J,Schulten K

    更新日期:2011-02-16 00:00:00

  • Conformation of reconstituted mononucleosomes and effect of linker histone H1 binding studied by scanning force microscopy.

    abstract::The conformation of mononucleosome complexes reconstituted with recombinant core histones on a 614-basepair-long DNA fragment containing the Xenopus borealis 5S rRNA nucleosome positioning sequence was studied by scanning/atomic force microscopy in the absence or presence of linker histone H1. Imaging without prior fi...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(03)74815-2

    authors: Kepert JF,Tóth KF,Caudron M,Mücke N,Langowski J,Rippe K

    更新日期:2003-12-01 00:00:00

  • Loss of rotational mobility of band 3 proteins in human erythrocyte membranes induced by antibodies to glycophorin A.

    abstract::The effect of antibodies to glycophorin A on the rotational diffusion of band 3 in human erythrocyte membranes was investigated by transient dichrosim. Three antibodies that recognize different epitopes on the exofacial domain of glycophorin A all strongly reduce the rotational mobility of band 3. The effect is at mos...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(95)80365-6

    authors: Che A,Cherry RJ

    更新日期:1995-05-01 00:00:00

  • Thermodynamic Modeling of the Statistics of Cell Spreading on Ligand-Coated Elastic Substrates.

    abstract::Biological spread cells exist in a perpetually fluctuating state and therefore cannot be described in terms of a unique deterministic system. For modeling approaches to provide novel insight and uncover new mechanisms that drive cell behavior, a framework is required that progresses from traditional deterministic meth...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2018.11.007

    authors: McEvoy E,Shishvan SS,Deshpande VS,McGarry JP

    更新日期:2018-12-18 00:00:00

  • Prediction of Thylakoid Lipid Binding Sites on Photosystem II.

    abstract::The thylakoid membrane has a unique lipid composition, consisting mostly of galactolipids. These thylakoid lipids have important roles in photosynthesis. Here, we investigate to what extent these lipids bind specifically to the Photosystem II complex. To this end, we performed coarse-grain MD simulations of the Photos...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2017.09.039

    authors: Van Eerden FJ,Melo MN,Frederix PWJM,Marrink SJ

    更新日期:2017-12-19 00:00:00

  • A phenomenological theory of muscular contraction. I. Rate equations at a given length based on irreversible thermodynamics.

    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

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(70)86290-7

    authors: Bornhorst WJ,Minardi JE

    更新日期:1970-02-01 00:00:00

  • Cytoplasmic polyamines as permeant blockers and modulators of the voltage-gated sodium channel.

    abstract::We report that voltage-gated Na+ channels (Na(V)) from rat muscle (mu1) expressed in HEK293 cells exhibit anomalous rectification of whole-cell outward current under conditions of symmetrical Na+. This behavior gradually fades with time after membrane break-in, as if a diffusible blocking substance in the cytoplasm is...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(01)76102-4

    authors: Huang CJ,Moczydlowski E

    更新日期:2001-03-01 00:00:00

  • Site-specific dichroism analysis utilizing transmission FTIR.

    abstract::Infrared spectroscopy has long been used to examine the average secondary structure and orientation of membrane proteins. With the recent utilization of site-specific isotope labeling (e.g., peptidic 1-(13)C = (18)O) it is now possible to examine localized properties, rather than global averages. The technique of site...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(03)74670-0

    authors: Arbely E,Kass I,Arkin IT

    更新日期:2003-10-01 00:00:00

  • Physical model for self-organization of actin cytoskeleton and adhesion complexes at the cell front.

    abstract::Cell motion is driven by interplay between the actin cytoskeleton and the cell adhesions in the front part of the cell. The actin network segregates into lamellipodium and lamellum, whereas the adhesion complexes are characteristically distributed underneath the actin system. Here, we suggest a computational model for...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2012.03.006

    authors: Shemesh T,Bershadsky AD,Kozlov MM

    更新日期:2012-04-18 00:00:00

  • Scanning near-field fluorescence resonance energy transfer microscopy.

    abstract::A new microscopic technique is demonstrated that combines attributes from both near-field scanning optical microscopy (NSOM) and fluorescence resonance energy transfer (FRET). The method relies on attaching the acceptor dye of a FRET pair to the end of a near-field fiber optic probe. Light exiting the NSOM probe, whic...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(99)77341-8

    authors: Vickery SA,Dunn RC

    更新日期:1999-04-01 00:00:00

  • Sacrificial bonds in polymer brushes from rat tail tendon functioning as nanoscale velcro.

    abstract::Polymers play an important role in many biological systems, so a fundamental understanding of their cross-links is crucial not only for the development of medicines but also for the development of biomimetic materials. The biomechanical movements of all mammals are aided by tendon fibrils. The self-organization and bi...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.104.056747

    authors: Gutsmann T,Hassenkam T,Cutroni JA,Hansma PK

    更新日期:2005-07-01 00:00:00

  • A delayed rectifier potassium current in Xenopus oocytes.

    abstract::A delayed voltage-dependent K+ current endogenous to Xenopus oocytes has been investigated by the voltage-clamp technique. Both activation and inactivation of the K+ current are voltage-dependent processes. The K+ currents were activated when membrane potential was depolarized from a holding potential of -90 to -50 mV...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(90)82632-1

    authors: Lu L,Montrose-Rafizadeh C,Hwang TC,Guggino WB

    更新日期:1990-06-01 00:00:00

  • The donnan equilibrium: a theoretical study of the effects of interionic forces.

    abstract::We investigate the conditions under which nonideality in solution influences the Donnan equilibrium. Of the various parameters that characterize this equilibrium, the osmotic pressure established across the Donnan membrane is found to be particularly sensitive to intermolecular interactions between the diffusible and ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(86)83526-3

    authors: Stell G,Joslin CG

    更新日期:1986-11-01 00:00:00

  • Lipid bilayer deformation and the free energy of interaction of a Kv channel gating-modifier toxin.

    abstract::A number of membrane proteins act via binding at the water/lipid bilayer interface. An important example of such proteins is provided by the gating-modifier toxins that act on voltage-gated potassium (Kv) channels. They are thought to partition to the headgroup region of lipid bilayers, and so provide a good system fo...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.108.130971

    authors: Wee CL,Gavaghan D,Sansom MS

    更新日期:2008-10-01 00:00:00

  • Response kinetics of tethered Rhodobacter sphaeroides to changes in light intensity.

    abstract::Rhodobacter sphaeroides can swim toward a wide range of attractants (a process known as taxis), propelled by a single rotating flagellum. The reversals of motor direction that cause tumbles in Eschericia coli taxis are replaced by brief motor stops, and taxis is controlled by a complex sensory system with multiple hom...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(00)76678-1

    authors: Berry RM,Armitage JP

    更新日期:2000-03-01 00:00:00

  • Hydroxide and proton migration in aquaporins.

    abstract::Hypothetical hydroxide and proton migration along the linear water chain in Aquaporin GlpF from Escherichia coli are studied by ab initio Car-Parrinello molecular dynamics simulations. It is found that the protein stabilizes a bipolar single file of water. The single file features a contiguous set of water-water hydro...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.104.058206

    authors: Jensen MØ,Röthlisberger U,Rovira C

    更新日期:2005-09-01 00:00:00

  • Single-molecule analysis of epidermal growth factor signaling that leads to ultrasensitive calcium response.

    abstract::Quantitative relationships between inputs and outputs of signaling systems are fundamental information for the understanding of the mechanism of signal transduction. Here we report the correlation between the number of epidermal growth factor (EGF) bindings and the response probability of intracellular calcium elevati...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.104.053330

    authors: Uyemura T,Takagi H,Yanagida T,Sako Y

    更新日期:2005-05-01 00:00:00

  • Modeling the step of endosomal escape during cell infection by a nonenveloped virus.

    abstract::Widely disparate viruses enter the host cell through an endocytic pathway and travel the cytoplasm inside an endosome. For the viral genetic material to be delivered into the cytoplasm, these viruses have to escape the endosomal compartment, an event triggered by the conformational changes of viral endosomolytic prote...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2011.12.037

    authors: Lagache T,Danos O,Holcman D

    更新日期:2012-03-07 00:00:00

  • Nanog Fluctuations in Embryonic Stem Cells Highlight the Problem of Measurement in Cell Biology.

    abstract::A number of important pluripotency regulators, including the transcription factor Nanog, are observed to fluctuate stochastically in individual embryonic stem cells. By transiently priming cells for commitment to different lineages, these fluctuations are thought to be important to the maintenance of, and exit from, p...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2017.05.005

    authors: Smith RCG,Stumpf PS,Ridden SJ,Sim A,Filippi S,Harrington HA,MacArthur BD

    更新日期:2017-06-20 00:00:00

  • Disentangling Viral Membrane Fusion from Receptor Binding Using Synthetic DNA-Lipid Conjugates.

    abstract::Enveloped viruses must bind to a receptor on the host membrane to initiate infection. Membrane fusion is subsequently initiated by a conformational change in the viral fusion protein, triggered by receptor binding, an environmental change, or both. Here, we present a strategy to disentangle the two processes of recept...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2016.05.048

    authors: Rawle RJ,Boxer SG,Kasson PM

    更新日期:2016-07-12 00:00:00

  • Theoretical models for cooperative steady-state ATPase activity of myosin subfragment-1 on regulated actin.

    abstract::Recent theoretical work on the cooperative equilibrium binding of myosin subfragment-1-ADP to regulated actin, as influenced by Ca2+, is extended here to the cooperative steady-state ATPase activity of myosin subfragment-1 on regulated actin. Exact solution of the general steady-state problem will require Monte Carlo ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(81)84777-7

    authors: Hill TL,Eisenberg E,Chalovich JM

    更新日期:1981-07-01 00:00:00