Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography.

Abstract:

:Activation of G protein-coupled receptors (GPCRs) is triggered and regulated by structural rearrangement of the transmembrane heptahelical bundle containing a number of highly conserved residues. In rhodopsin, a prototypical GPCR, the helical bundle accommodates an intrinsic inverse-agonist 11-cis-retinal, which undergoes photo-isomerization to the all-trans form upon light absorption. Such a trigger by the chromophore corresponds to binding of a diffusible ligand to other GPCRs. Here we have explored the functional role of water molecules in the transmembrane region of bovine rhodopsin by using x-ray diffraction to 2.6 A. The structural model suggests that water molecules, which were observed in the vicinity of highly conserved residues and in the retinal pocket, regulate the activity of rhodopsin-like GPCRs and spectral tuning in visual pigments, respectively. To confirm the physiological relevance of the structural findings, we conducted single-crystal microspectrophotometry on rhodopsin packed in our three-dimensional crystals and show that its spectroscopic properties are similar to those previously found by using bovine rhodopsin in suspension or membrane environment.

authors

Okada T,Fujiyoshi Y,Silow M,Navarro J,Landau EM,Shichida Y

doi

10.1073/pnas.082666399

keywords:

subject

Has Abstract

pub_date

2002-04-30 00:00:00

pages

5982-7

issue

9

eissn

0027-8424

issn

1091-6490

pii

082666399

journal_volume

99

pub_type

杂志文章
  • A strategy to capture and characterize the synaptic transcriptome.

    abstract::Here we describe a strategy designed to identify RNAs that are actively transported to synapses during learning. Our approach is based on the characterization of RNA transport complexes carried by molecular motor kinesin. Using this strategy in Aplysia, we have identified 5,657 unique sequences consisting of both codi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1304422110

    authors: Puthanveettil SV,Antonov I,Kalachikov S,Rajasethupathy P,Choi YB,Kohn AB,Citarella M,Yu F,Karl KA,Kinet M,Morozova I,Russo JJ,Ju J,Moroz LL,Kandel ER

    更新日期:2013-04-30 00:00:00

  • Homeotic effects, somitogenesis and the evolution of vertebral numbers in recent and fossil amniotes.

    abstract::The development of distinct regions in the amniote vertebral column results from somite formation and Hox gene expression, with the adult morphology displaying remarkable variation among lineages. Mammalian regionalization is reportedly very conservative or even constrained, but there has been no study investigating v...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0912622107

    authors: Müller J,Scheyer TM,Head JJ,Barrett PM,Werneburg I,Ericson PG,Pol D,Sánchez-Villagra MR

    更新日期:2010-02-02 00:00:00

  • Frequent fusion and fission of plant mitochondria with unequal nucleoid distribution.

    abstract::The balance between mitochondrial fusion and fission influences the reticular shape of mitochondria in yeasts. Little is known about whether mitochondria fusion occurs in plants. Plant mitochondria are usually more numerous and more grain-shaped than animal mitochondria. BLAST searches of the nuclear and mitochondrial...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0401077101

    authors: Arimura S,Yamamoto J,Aida GP,Nakazono M,Tsutsumi N

    更新日期:2004-05-18 00:00:00

  • Partial diversion of a mutant proinsulin (B10 aspartic acid) from the regulated to the constitutive secretory pathway in transfected AtT-20 cells.

    abstract::A patient with type II diabetes associated with hyperproinsulinemia has been shown to have a point mutation in one insulin gene allele, resulting in replacement of histidine with aspartic acid at position 10 of the B-chain. To investigate the basis of the proinsulin processing defect, we introduced an identical mutati...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.11.4107

    authors: Gross DJ,Halban PA,Kahn CR,Weir GC,Villa-Komaroff L

    更新日期:1989-06-01 00:00:00

  • Probable precursors of [Leu]enkephalin and [Met]enkephalin in adrenal medulla: peptides of 3-5 kilodaltons.

    abstract::Adrenal chromaffin granules contain at least 10 peptides, ranging in size from 3 to 5 kilodaltons, that yield, upon digestion with trypsin, peptides that show specific binding to opiate receptors. All are distinctly different from beta-endorphin. Two of these peptides have been purified to homogeneity and subjected to...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.3.1681

    authors: Kimura S,Lewis RV,Stern AS,Rossier J,Stein S,Udenfriend S

    更新日期:1980-03-01 00:00:00

  • Mutational analysis of the structural organization of polyglutamine aggregates.

    abstract::The formation of amyloid-like aggregates by expanded polyglutamine (polyGln) sequences is suspected to play a critical role in the neuropathology of Huntington's disease and other expanded CAG-repeat diseases. To probe the folding of the polyGln sequence in the aggregate, we replaced Gln-Gln pairs at different sequenc...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.252523899

    authors: Thakur AK,Wetzel R

    更新日期:2002-12-24 00:00:00

  • Equitable decision making is associated with neural markers of intrinsic value.

    abstract::Standard economic and evolutionary models assume that humans are fundamentally selfish. On this view, any acts of prosociality--such as cooperation, giving, and other forms of altruism--result from covert attempts to avoid social injunctions against selfishness. However, even in the absence of social pressure, individ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章,随机对照试验

    doi:10.1073/pnas.1112324108

    authors: Zaki J,Mitchell JP

    更新日期:2011-12-06 00:00:00

  • Engineering graded tissue interfaces.

    abstract::Interfacial zones between tissues provide specialized, transitional junctions central to normal tissue function. Regenerative medicine strategies focused on multiple cell types and/or bi/tri-layered scaffolds do not provide continuously graded interfaces, severely limiting the integration and biological performance of...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0801988105

    authors: Phillips JE,Burns KL,Le Doux JM,Guldberg RE,García AJ

    更新日期:2008-08-26 00:00:00

  • E2F1 and E1A(12S) have a homologous activation domain regulated by RB and CBP.

    abstract::The E2F1 transcription factor has a well-characterized activation domain at its C terminus and the E1A protein has a recently defined activation domain at its N terminus. Here we show that these activation domains are highly related in sequence. The sequence homology reflects, at least partly, the conservation of comm...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.4.1439

    authors: Trouche D,Kouzarides T

    更新日期:1996-02-20 00:00:00

  • Activation of human beta-globin genes from nonerythroid cells by fusion with murine erythroleukemia cells.

    abstract::A human beta-globin gene derived from an established human lymphoblast cell line was introduced into murine erythroleukemia (MEL) cells by cell fusion. The globin genes in MEL cells are inducible by dimethyl sulfoxide (Me2SO); induction leads to the accumulation of mouse globin mRNA and hemoglobin. Globin mRNA was not...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.6.3435

    authors: Pyati J,Kucherlapati RS,Skoultchi AI

    更新日期:1980-06-01 00:00:00

  • Detection of atomic spin labels in a lipid bilayer using a single-spin nanodiamond probe.

    abstract::Magnetic field fluctuations arising from fundamental spins are ubiquitous in nanoscale biology, and are a rich source of information about the processes that generate them. However, the ability to detect the few spins involved without averaging over large ensembles has remained elusive. Here, we demonstrate the detect...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1300640110

    authors: Kaufmann S,Simpson DA,Hall LT,Perunicic V,Senn P,Steinert S,McGuinness LP,Johnson BC,Ohshima T,Caruso F,Wrachtrup J,Scholten RE,Mulvaney P,Hollenberg L

    更新日期:2013-07-02 00:00:00

  • Kras mutant genetically engineered mouse models of human cancers are genomically heterogeneous.

    abstract::KRAS mutant tumors are largely recalcitrant to targeted therapies. Genetically engineered mouse models (GEMMs) of Kras mutant cancer recapitulate critical aspects of this disease and are widely used for preclinical validation of targets and therapies. Through comprehensive profiling of exomes and matched transcriptome...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1708391114

    authors: Chung WJ,Daemen A,Cheng JH,Long JE,Cooper JE,Wang BE,Tran C,Singh M,Gnad F,Modrusan Z,Foreman O,Junttila MR

    更新日期:2017-12-19 00:00:00

  • Feedback-inducible nuclear-receptor-driven reporter gene expression in transgenic mice.

    abstract::Understanding nuclear receptor signaling in vivo would be facilitated by an efficient methodology to determine where a nuclear receptor is active. Herein, we present a feedback-inducible expression system in transgenic mice to detect activated nuclear receptor effector proteins by using an inducible reporter gene. Wit...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.23.13270

    authors: Mata De Urquiza A,Solomin L,Perlmann T

    更新日期:1999-11-09 00:00:00

  • Arsenic-induced PML targeting onto nuclear bodies: implications for the treatment of acute promyelocytic leukemia.

    abstract::Acute promyelocytic leukemia (APL) is associated with the t(15;17) translocation, which generates a PML/RAR alpha fusion protein between PML, a growth suppressor localized on nuclear matrix-associated bodies, and RAR alpha, a nuclear receptor for retinoic acid (RA). PML/RAR alpha was proposed to block myeloid differen...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.8.3978

    authors: Zhu J,Koken MH,Quignon F,Chelbi-Alix MK,Degos L,Wang ZY,Chen Z,de Thé H

    更新日期:1997-04-15 00:00:00

  • Isoflurane inhibits synaptic vesicle exocytosis through reduced Ca2+ influx, not Ca2+-exocytosis coupling.

    abstract::Identifying presynaptic mechanisms of general anesthetics is critical to understanding their effects on synaptic transmission. We show that the volatile anesthetic isoflurane inhibits synaptic vesicle (SV) exocytosis at nerve terminals in dissociated rat hippocampal neurons through inhibition of presynaptic Ca(2+) inf...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1500525112

    authors: Baumgart JP,Zhou ZY,Hara M,Cook DC,Hoppa MB,Ryan TA,Hemmings HC Jr

    更新日期:2015-09-22 00:00:00

  • A B lymphocyte mitogen is a Brucella abortus virulence factor required for persistent infection.

    abstract::Microbial pathogens with the ability to establish chronic infections have evolved strategies to actively modulate the host immune response. Brucellosis is a disease caused by a Gram-negative intracellular pathogen that if not treated during the initial phase of the infection becomes chronic as the bacteria persist for...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0603362103

    authors: Spera JM,Ugalde JE,Mucci J,Comerci DJ,Ugalde RA

    更新日期:2006-10-31 00:00:00

  • The LIM-domain binding protein Ldb1 and its partner LMO2 act as negative regulators of erythroid differentiation.

    abstract::The nuclear LIM domain protein LMO2, a T cell oncoprotein, is essential for embryonic erythropoiesis. LIM-only proteins are presumed to act primarily through protein-protein interactions. We, and others, have identified a widely expressed protein, Ldb1, whose C-terminal 76-residues are sufficient to mediate interactio...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.25.13707

    authors: Visvader JE,Mao X,Fujiwara Y,Hahm K,Orkin SH

    更新日期:1997-12-09 00:00:00

  • NK cytotoxicity against CD4+ T cells during HIV-1 infection: a gp41 peptide induces the expression of an NKp44 ligand.

    abstract::HIV infection leads to a state of chronic immune activation and progressive deterioration in immune function, manifested most recognizably by the progressive depletion of CD4+ T cells. A substantial percentage of natural killer (NK) cells from patients with HIV infection are activated and express the natural cytotoxic...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0504315102

    authors: Vieillard V,Strominger JL,Debré P

    更新日期:2005-08-02 00:00:00

  • X inactivation and somatic cell selection rescue female mice carrying a Piga-null mutation.

    abstract::A somatic mutation in the X linked PIGA gene is responsible for the deficiency of glycosyl phosphatidylinositol (GPI)-anchored proteins on blood cells from patients with paroxysmal nocturnal hemoglobinuria. No inherited form of GPI-anchor deficiency has been described. Because conventional Piga gene knockout is associ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.13.7479

    authors: Keller P,Tremml G,Rosti V,Bessler M

    更新日期:1999-06-22 00:00:00

  • Varicella-zoster virus infection of human dorsal root ganglia in vivo.

    abstract::Varicella-zoster virus (VZV) causes varicella and establishes latency in sensory ganglia. VZV reactivation results in herpes zoster. We developed a model using human dorsal root ganglion (DRG) xenografts in severe combined immunodeficient (SCID) mice to investigate VZV infection of differentiated neurons and satellite...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0501045102

    authors: Zerboni L,Ku CC,Jones CD,Zehnder JL,Arvin AM

    更新日期:2005-05-03 00:00:00

  • Specific release of the thioesterase component of the fatty acid synthetase multienzyme complex by limited trypsinization.

    abstract::Limited trypsinization of the fatty acid synthetase multienzyme complex from rat mammary gland results in the release of a protein, molecular weight 32,000, with thioesterase activity. The other components of the multienzyme complex--the acyl carrier protein, acetyl and malonyl transferases, condensing enzyme, keto re...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.73.4.1184

    authors: Smith S,Agradi E,Libertini L,Dileepan KN

    更新日期:1976-04-01 00:00:00

  • A gene encoding the tryptophan synthase beta subunit of Arabidopsis thaliana.

    abstract::The DNA sequence of a tryptophan synthase gene and the flanking 5' and 3' regions has been determined for Arabidopsis thaliana. The sequence encodes only the beta subunit domain, indicating that alpha and beta subunits are specified by separate genes. The gene contains four introns and encodes 470 amino acid residues....

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.86.12.4604

    authors: Berlyn MB,Last RL,Fink GR

    更新日期:1989-06-01 00:00:00

  • Interleukin-1 deficiency prolongs ovarian lifespan in mice.

    abstract::Oocyte endowment dwindles away during prepubertal and adult life until menopause occurs, and apoptosis has been identified as a central mechanism responsible for oocyte elimination. A few recent reports suggest that uncontrolled inflammation may adversely affect ovarian reserve. We tested the possible role of the proi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1323955111

    authors: Uri-Belapolsky S,Shaish A,Eliyahu E,Grossman H,Levi M,Chuderland D,Ninio-Many L,Hasky N,Shashar D,Almog T,Kandel-Kfir M,Harats D,Shalgi R,Kamari Y

    更新日期:2014-08-26 00:00:00

  • KCNE1 and KCNE3 modulate KCNQ1 channels by affecting different gating transitions.

    abstract::KCNE β-subunits assemble with and modulate the properties of voltage-gated K+ channels. In the heart, KCNE1 associates with the α-subunit KCNQ1 to generate the slowly activating, voltage-dependent potassium current (IKs) in the heart that controls the repolarization phase of cardiac action potentials. By contrast, in ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1710335114

    authors: Barro-Soria R,Ramentol R,Liin SI,Perez ME,Kass RS,Larsson HP

    更新日期:2017-08-29 00:00:00

  • Specific lysine labeling by 18OH- during alkaline cleavage of the alpha-1-antitrypsin-trypsin complex.

    abstract::alpha-1-Antitrypsin is a serum protein that inhibits many proteolytic enzymes. Recently, it was suggested that the alpha-1-antitrypsin-trypsin complex is an acyl ester analogous to the acyl intermediate that forms between trypsin and its substrates. In previous work we showed that the alpha-1-antitrypsin-trypsin compl...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.74.10.4311

    authors: Cohen AB,Gruenke LD,Craig JC,Geczy D

    更新日期:1977-10-01 00:00:00

  • Insights into antibody catalysis: structure of an oxygenation catalyst at 1.9-angstrom resolution.

    abstract::The x-ray crystal structures of the sulfide oxidase antibody 28B4 and of antibody 28B4 complexed with hapten have been solved at 2.2-angstrom and 1.9-angstrom resolution, respectively. To our knowledge, these structures are the highest resolution catalytic antibody structures to date and provide insight into the molec...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.11.5363

    authors: Hsieh-Wilson LC,Schultz PG,Stevens RC

    更新日期:1996-05-28 00:00:00

  • Immunologic evidence that the gene for L-gulono-gamma-lactone oxidase is not expressed in animals subject to scurvy.

    abstract::L-Gulono-gamma-lactone oxidase (L-gulono-gamma-lactone:oxygen 2-oxidoreductase, EC 1.1.3.8) is the enzyme that catalyzes the terminal step of L-ascorbic acid biosynthesis in mammalian liver. The absence of the oxidase activity in primates and guinea pigs is the reason why these animals are subject to scurvy, which mus...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.73.6.2066

    authors: Nishikimi M,Udenfriend S

    更新日期:1976-06-01 00:00:00

  • Structural insights into phosphoinositide 3-kinase activation by the influenza A virus NS1 protein.

    abstract::Seasonal epidemics and periodic worldwide pandemics caused by influenza A viruses are of continuous concern. The viral nonstructural (NS1) protein is a multifunctional virulence factor that antagonizes several host innate immune defenses during infection. NS1 also directly stimulates class IA phosphoinositide 3-kinase...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0910715107

    authors: Hale BG,Kerry PS,Jackson D,Precious BL,Gray A,Killip MJ,Randall RE,Russell RJ

    更新日期:2010-02-02 00:00:00

  • The spectrum of NGC 7027 (367-650 nm).

    abstract::NGC 7027 shows the richest spectrum of any known gaseous nebula. In the region of the spectrum surveyed we have measured lines of ions of H, He, C, N, O, F, Ne, Mg, Si, P, S, Cl, Ar, K, Ca, Mn, and Fe using the new Hamilton Echelle Spectrograph of Lick Observatory with a charge-coupled device (CCD) detector. Since a C...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.8.2417

    authors: Aller LH,Keyes CD

    更新日期:1988-04-01 00:00:00

  • Tropical amphibian populations experience higher disease risk in natural habitats.

    abstract::Habitat loss and disease are main drivers of global amphibian declines, yet the interaction between them remains largely unexplored. Here we show that paradoxically, habitat loss is negatively associated with occurrence, prevalence, and infection intensity of the chytrid fungus Batrachochytrium dendrobatidis (Bd) in a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1014497108

    authors: Becker CG,Zamudio KR

    更新日期:2011-06-14 00:00:00