Reconstruction of a kinetic model of the chromatophore vesicles from Rhodobacter sphaeroides.

Abstract:

:We present a molecular model of a chromatophore vesicle from Rhodobacter sphaeroides. These vesicles are ideal benchmark systems for molecular and systemic simulations, because they have been well studied, they are small, and they are naturally separated from their cellular environment. To set up a photosynthetic chain working under steady-state conditions, we compiled from the experimental literature the specific activities and geometries that have been determined for their constituents. This data then allowed defining the stoichiometries for all membrane proteins. This article contains the kinetic part of the reconstructed model, while the spatial reconstruction is presented in a companion article. By considering the transport properties of the Cytochrome c(2) and ubiquinone pools, we show that their size and oxidation states allow for an efficient buffering of the statistical fluctuations that arise from the small size of the vesicles. Stoichiometric and kinetic considerations indicate that a typical chromatophore vesicle of Rb. sphaeroides with a diameter of 45 nm should contain approximately five bc(1) monomers.

journal_name

Biophys J

journal_title

Biophysical journal

authors

Geyer T,Helms V

doi

10.1529/biophysj.105.067561

subject

Has Abstract

pub_date

2006-08-01 00:00:00

pages

927-37

issue

3

eissn

0006-3495

issn

1542-0086

pii

S0006-3495(06)71805-7

journal_volume

91

pub_type

杂志文章
  • Reversible surface aggregation in pore formation by pardaxin.

    abstract::The mechanism of leakage induced by surface active peptides is not yet fully understood. To gain insight into the molecular events underlying this process, the leakage induced by the peptide pardaxin from phosphatidylcholine/ phosphatidylserine/cholesterol large unilamellar vesicles was studied by monitoring the rate ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(96)79822-3

    authors: Rapaport D,Peled R,Nir S,Shai Y

    更新日期:1996-06-01 00:00:00

  • Stability and folding rates of domains spanning the large A-band super-repeat of titin.

    abstract::Titin is a very large (>3 MDa) protein found in striated muscle where it is believed to participate in myogenesis and passive tension. A prominent feature in the A-band portion of titin is the presence of an 11-domain super-repeat of immunoglobulin superfamily and fibronectin-type-III-like domains. Seven overlapping c...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/s0006-3495(01)75811-0

    authors: Head JG,Houmeida A,Knight PJ,Clarke AR,Trinick J,Brady RL

    更新日期:2001-09-01 00:00:00

  • Interfacial Binding Sites for Cholesterol on TRP Ion Channels.

    abstract::Transient receptor potential (TRP) channels are members of a large family of ion channels located in membranes rich in cholesterol, some of whose functions are affected by the cholesterol content of the membrane. Here, cholesterol binding to TRPs is studied using a docking procedure that allows the transmembrane surfa...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2019.10.011

    authors: Lee AG

    更新日期:2019-11-19 00:00:00

  • Measuring actin flow in 3D cell protrusions.

    abstract::Actin dynamics is important in determining cell shape, tension, and migration. Methods such as fluorescent speckle microscopy and spatial temporal image correlation spectroscopy have been used to capture high-resolution actin turnover dynamics within cells in two dimensions. However, these methods are not directly app...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2013.07.057

    authors: Chiu CL,Digman MA,Gratton E

    更新日期:2013-10-15 00:00:00

  • A liquid crystalline phase in spermidine-condensed DNA.

    abstract::Over a large range of salt and spermidine concentrations, short DNA fragments precipitated by spermidine (a polyamine) sediment in a pellet from a dilute isotropic supernatant. We report here that the DNA-condensed phase consists of a cholesteric liquid crystal in equilibrium with a more concentrated phase. These resu...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(94)80640-X

    authors: Sikorav JL,Pelta J,Livolant F

    更新日期:1994-10-01 00:00:00

  • Competition between primary nucleation and autocatalysis in amyloid fibril self-assembly.

    abstract::Kinetic measurements of the self-assembly of proteins into amyloid fibrils are often used to make inferences about molecular mechanisms. In particular, the lag time--the quiescent period before aggregates are detected--is often found to scale with the protein concentration as a power law, whose exponent has been used ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2014.11.3465

    authors: Eden K,Morris R,Gillam J,MacPhee CE,Allen RJ

    更新日期:2015-02-03 00:00:00

  • Pulsed interleaved excitation.

    abstract::In this article, we demonstrate the new method of pulsed interleaved excitation (PIE), which can be used to extend the capabilities of multiple-color fluorescence imaging, fluorescence cross-correlation spectroscopy (FCCS), and single-pair fluorescence resonance energy transfer (spFRET) measurements. In PIE, multiple ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.105.064766

    authors: Müller BK,Zaychikov E,Bräuchle C,Lamb DC

    更新日期:2005-11-01 00:00:00

  • Effect of pore structure on energy barriers and applied voltage profiles. II. Unsymmetrical channels.

    abstract::This paper examines "realistic" pores, i.e., ones that are neither symmetric nor of uniform diameter. Methods are described that permit estimation of the image potential for an ion in an aqueous pore spanning a lipid membrane and for the electric field produced in such a pore when a transmembrane potential is applied....

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/s0006-3495(84)84258-7

    authors: Jordan PC

    更新日期:1984-06-01 00:00:00

  • Thermodynamics of long supercoiled molecules: insights from highly efficient Monte Carlo simulations.

    abstract::Supercoiled DNA polymer models for which the torsional energy depends on the total twist of molecules (Tw) are a priori well suited for thermodynamic analysis of long molecules. So far, nevertheless, the exact determination of Tw in these models has been based on a computation of the writhe of the molecules (Wr) by ex...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2015.06.005

    authors: Lepage T,Képès F,Junier I

    更新日期:2015-07-07 00:00:00

  • Electrostatic and hydrodynamic orientational steering effects in enzyme-substrate association.

    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

    authors: Antosiewicz J,McCammon JA

    更新日期:1995-07-01 00:00:00

  • Dynamics in a protein-lipid complex: nuclear magnetic resonance measurements on the headgroup of cardiolipin when bound to cytochrome c.

    abstract::Deuterium and phosphorus nuclear magnetic resonance (NMR) has been used to investigate the dynamics of slow motional processes induced in bilayer cardiolipin upon binding with cytochrome c. 31P NMR line shapes suggest that protein binding induces less restricted, isotropic-like motions in the lipid phosphates within t...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(93)81048-8

    authors: Spooner PJ,Duralski AA,Rankin SE,Pinheiro TJ,Watts A

    更新日期:1993-07-01 00:00:00

  • Small angle X-ray scattering studies and modeling of Eudistylia vancouverii chlorocruorin and Macrobdella decora hemoglobin.

    abstract::Annelids possess giant extracellular oxygen carriers that exhibit a hexagonal bilayer appearance and have molecular masses of approximately 3.5 MDa. By small angle x-ray scattering (SAXS), Eudistylia vancouverii chlorocruorin and Macrobdella decora hemoglobin were investigated in solution. On the basis of the experime...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.103.037929

    authors: Krebs A,Durchschlag H,Zipper P

    更新日期:2004-08-01 00:00:00

  • Surface rheology and adsorption kinetics reveal the relative amphiphilicity, interfacial activity, and stability of human exchangeable apolipoproteins.

    abstract::Exchangeable apolipoproteins are located in the surface of lipoprotein particles and regulate lipid metabolism through direct protein-protein and protein-lipid interactions. These proteins are characterized by the presence of tandem repeats of amphiphatic alpha-helix segments and a high surface activity in monolayers ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.115220

    authors: Bolanos-Garcia VM,Renault A,Beaufils S

    更新日期:2008-03-01 00:00:00

  • Tetraethylammonium block of the BNC1 channel.

    abstract::The brain Na+ channel-1 (BNC1, also known as MDEG1 or ASIC2) is a member of the DEG/ENaC cation channel family. Mutation of a specific residue (Gly430) that lies N-terminal to the second membrane-spanning domain activates BNC1 and converts it from a Na+-selective channel to one permeable to both Na+ and K+. Because al...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(99)77299-1

    authors: Adams CM,Price MP,Snyder PM,Welsh MJ

    更新日期:1999-03-01 00:00:00

  • Quantitative intensity-based FRET approaches--a comparative snapshot.

    abstract::Förster resonance energy transfer (FRET) has become an important tool for analyzing different aspects of interactions among biological macromolecules in their native environments. FRET analysis has also been successfully applied to study the spatiotemporal regulation of various cellular processes using genetically enc...

    journal_title:Biophysical journal

    pub_type: 杂志文章,评审

    doi:10.1016/j.bpj.2012.09.031

    authors: Zeug A,Woehler A,Neher E,Ponimaskin EG

    更新日期:2012-11-07 00:00:00

  • Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient.

    abstract::Interactions between proteins are often sufficiently weak that their study through the use of conventional structural techniques becomes problematic. Of the few techniques capable of providing experimental measures of weak protein-protein interactions, perhaps the most useful is the second virial coefficient, B(22), w...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(01)76042-0

    authors: Elcock AH,McCammon JA

    更新日期:2001-02-01 00:00:00

  • Properties of palmitoyl phosphatidylcholine, sphingomyelin, and dihydrosphingomyelin bilayer membranes as reported by different fluorescent reporter molecules.

    abstract::The properties of vesicle membranes prepared from 16:0-SM, 16:0-DHSM, or DPPC were characterized using steady-state and time-resolved fluorescence spectroscopy and different fluorescent reporter molecules. The acyl-chain region was probed using free and phospholipid-bound 1,6-diphenyl-1,3,5-hexatriene. 16:0-DHSM was f...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(03)74915-7

    authors: Nyholm T,Nylund M,Söderholm A,Slotte JP

    更新日期:2003-02-01 00:00:00

  • A model of alpha-helical distribution in proteins.

    abstract::It is shown that alpha-helical content of eleven proteins is well correlated with alanine plus leucine content. These residues, taken singly or together, are to a first approximation randomly distributed in the four proteins whose tertiary structures have been determined (i.e., myoglobin, lysozyme, ribonuclease, alpha...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(68)86553-1

    authors: Prothero JW

    更新日期:1968-11-01 00:00:00

  • Characterization of the azide-dependent bacteriorhodopsin-like photocycle of salinarum halorhodopsin.

    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

    authors: Lakatos M,Groma GI,Ganea C,Lanyi JK,Váró G

    更新日期:2002-04-01 00:00:00

  • Prediction of protein solubility from calculation of transfer free energy.

    abstract::Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a d...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1529/biophysj.107.127746

    authors: Tjong H,Zhou HX

    更新日期:2008-09-15 00:00:00

  • High gradient magnetic separation of erythrocytes.

    abstract::The high gradient magnetic separation technique has been applied to separate paramagnetic erythrocytes from a cell suspension that also contained diamagnetic cells. Paramagnetism was induced in the red blood cells by oxidizing the iron atoms in the cell hemoglobin to the ferric state (methemoglobin). Diamagnetic cells...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(78)85482-4

    authors: Owen CS

    更新日期:1978-05-01 00:00:00

  • Probing the energetics of dissociation of carbonic anhydrase-ligand complexes in the gas phase.

    abstract::This paper describes the use of electrospray ionization-Fourier transform ion cyclotron mass spectrometry (ESI-FTICR-MS) to study the relative stabilities of noncovalent complexes of carbonic anhydrase II (CAII, EC 4.2.1.1) and benzenesulfonamide inhibitors in the gas phase. Sustained off-resonance irradiation collisi...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/s0006-3495(99)77477-1

    authors: Gao J,Wu Q,Carbeck J,Lei QP,Smith RD,Whitesides GM

    更新日期:1999-06-01 00:00:00

  • Kinetics and thermodynamics of association of a phospholipid derivative with lipid bilayers in liquid-disordered and liquid-ordered phases.

    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

    authors: Abreu MS,Moreno MJ,Vaz WL

    更新日期:2004-07-01 00:00:00

  • The transmembrane domain peptide of vesicular stomatitis virus promotes both intermediate and pore formation during PEG-mediated vesicle fusion.

    abstract::We propose mechanisms by which the transmembrane domain of vesicular stomatitis virus (VSV-TMD) promotes both initiation of fusion and formation of a fusion pore. Time courses of polyethyleneglycol (PEG)-mediated fusion of 25 nm small unilamellar vesicles composed of dioleoylphosphatidylcholine, dioleoylphosphatidylet...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2014.03.053

    authors: Sengupta T,Chakraborty H,Lentz BR

    更新日期:2014-09-16 00:00:00

  • Abeta oligomers and fibrillar aggregates induce different apoptotic pathways in LAN5 neuroblastoma cell cultures.

    abstract::Fibril deposit formation of amyloid beta-protein (Abeta) in the brain is a hallmark of Alzheimer's disease (AD). Increasing evidence suggests that toxicity is linked to diffusible Abeta oligomers, which have been found in soluble brain extracts of AD patients, rather than to insoluble fibers. Here we report a study of...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2008.11.056

    authors: Picone P,Carrotta R,Montana G,Nobile MR,San Biagio PL,Di Carlo M

    更新日期:2009-05-20 00:00:00

  • How to make tubular crystals by reconstitution of detergent-solubilized Ca2(+)-ATPase.

    abstract::In an attempt to better define the parameters governing reconstitution and two-dimensional crystallization of membrane proteins, we have studied Ca2(+)-ATPase from rabbit sarcoplasmic reticulum. This ion pump forms vanadate-induced crystals in its native membrane and has previously been reconstituted at high lipid-to-...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(97)78898-2

    authors: Young HS,Rigaud JL,Lacapère JJ,Reddy LG,Stokes DL

    更新日期:1997-06-01 00:00:00

  • Quick shear-flow alignment of biological filaments for X-ray fiber diffraction facilitated by methylcellulose.

    abstract::X-ray fiber diffraction is one of the most useful methods for examining the structural details of live biological filaments under physiological conditions. To investigate biologically active or labile materials, it is crucial to finish fiber alignment within seconds before diffraction analysis. However, the convention...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2009.09.041

    authors: Sugiyama T,Miyashiro D,Takao D,Iwamoto H,Sugimoto Y,Wakabayashi K,Kamimura S

    更新日期:2009-12-16 00:00:00

  • Structural study of poly(beta-benzyl-L-aspartate) monolayers at air-liquid interfaces.

    abstract::As normally studied, in the solid state or in solution, poly(beta-benzyl-L-aspartate) (PBLA) differs from the other helical polyamino acids in that its alpha-helical conformation is most stable in the left-handed rather than in the right-handed form. The slightly lower energy per residue for the left-handed form in PB...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/S0006-3495(98)77689-1

    authors: Riou SA,Hsu SL,Stidham HD

    更新日期:1998-11-01 00:00:00

  • Patch-Clamp Study of Hepatitis C p7 Channels Reveals Genotype-Specific Sensitivity to Inhibitors.

    abstract::Hepatitis C is a major worldwide disease and health hazard, affecting ∼3% of the world population. The p7 protein of hepatitis C virus (HCV) is an intracellular ion channel and pH regulator that is involved in the viral replication cycle. It is targeted by various classical ion channel blockers. Here, we generated p7 ...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2016.04.018

    authors: Breitinger U,Farag NS,Ali NKM,Breitinger HA

    更新日期:2016-06-07 00:00:00

  • Partition of Repeat-Induced Point Mutations Reveals Structural Aspects of Homologous DNA-DNA Pairing.

    abstract::In some fungi, a premeiotic process known as repeat-induced point mutation (RIP) can accurately identify and mutate nearly all gene-sized DNA repeats present in the haploid germline nuclei. Studies in Neurospora crassa have suggested that RIP detects sequence homology directly between intact DNA double helices, withou...

    journal_title:Biophysical journal

    pub_type: 杂志文章

    doi:10.1016/j.bpj.2018.06.030

    authors: Mazur AK,Gladyshev E

    更新日期:2018-08-21 00:00:00