The retinal chromophore/chloride ion pair: structure of the photoisomerization path and interplay of charge transfer and covalent states.

Abstract:

:Ab initio multi-reference second-order perturbation theory computations are used to explore the photochemical behavior of two ion pairs constituted by a chloride counterion interacting with either a rhodopsin or bacteriorhodopsin chromophore model (i.e., the 4-cis-gamma-methylnona-2,4,6,8-tetraeniminium and all-trans-nona-2,4,6,8-tetraeniminium cations, respectively). Significant counterion effects on the structure of the photoisomerization paths are unveiled by comparison with the paths of the same chromophores in vacuo. Indeed, we demonstrate that the counterion (i) modulates the relative stability of the S0, S1, and S2 energy surfaces leading to an S1 isomerization energy profile where the S1 and S2 states are substantially degenerate; (ii) leads to the emergence of significant S1 energy barriers along all of the isomerization paths except the one mimicking the 11-cis --> all-trans isomerization of the rhodopsin chromophore model; and (iii) changes the nature of the S1 --> S0 decay funnel that becomes a stable excited state minimum when the isomerizing double bond is located at the center of the chromophore moiety. We show that these (apparently very different) counterion effects can be rationalized on the basis of a simple qualitative electrostatic model, which also provides a crude basis for understanding the behavior of retinal protonated Schiff bases in solution.

authors

Cembran A,Bernardi F,Olivucci M,Garavelli M

doi

10.1073/pnas.0408723102

keywords:

subject

Has Abstract

pub_date

2005-05-03 00:00:00

pages

6255-60

issue

18

eissn

0027-8424

issn

1091-6490

pii

0408723102

journal_volume

102

pub_type

杂志文章
  • Significance analysis of xMap cytokine bead arrays.

    abstract::Highly multiplexed assays using antibody coated, fluorescent (xMap) beads are widely used to measure quantities of soluble analytes, such as cytokines and antibodies in clinical and other studies. Current analyses of these assays use methods based on standard curves that have limitations in detecting low or high abund...

    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.1112599109

    authors: Won JH,Goldberger O,Shen-Orr SS,Davis MM,Olshen RA

    更新日期:2012-02-21 00:00:00

  • Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB.

    abstract::PdxB (erythronate 4-phosphate dehydrogenase) is expected to be required for synthesis of the essential cofactor pyridoxal 5'-phosphate (PLP) in Escherichia coli Surprisingly, incubation of the ∆pdxB strain in medium containing glucose as a sole carbon source for 10 d resulted in visible turbidity, suggesting that PLP ...

    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.1915569116

    authors: Kim J,Flood JJ,Kristofich MR,Gidfar C,Morgenthaler AB,Fuhrer T,Sauer U,Snyder D,Cooper VS,Ebmeier CC,Old WM,Copley SD

    更新日期:2019-11-26 00:00:00

  • Retinal counterion switch in the photoactivation of the G protein-coupled receptor rhodopsin.

    abstract::The biological function of Glu-181 in the photoactivation process of rhodopsin is explored through spectroscopic studies of site-specific mutants. Preresonance Raman vibrational spectra of the unphotolyzed E181Q mutant are nearly identical to spectra of the native pigment, supporting the view that Glu-181 is uncharged...

    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.1531970100

    authors: Yan EC,Kazmi MA,Ganim Z,Hou JM,Pan D,Chang BS,Sakmar TP,Mathies RA

    更新日期:2003-08-05 00:00:00

  • Adaptive coding of reward prediction errors is gated by striatal coupling.

    abstract::To efficiently represent all of the possible rewards in the world, dopaminergic midbrain neurons dynamically adapt their coding range to the momentarily available rewards. Specifically, these neurons increase their activity for an outcome that is better than expected and decrease it for an outcome worse than expected,...

    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.1119969109

    authors: Park SQ,Kahnt T,Talmi D,Rieskamp J,Dolan RJ,Heekeren HR

    更新日期:2012-03-13 00:00:00

  • A reinvestigation of a synthetic peptide (TrPepz) designed to mimic trypsin.

    abstract::Recently, a 29-residue cyclic peptide was synthesized (TrPepz) that was reported to possess nearly the same catalytic activity and specificity as the pancreatic serine protease, trypsin, for hydrolysis of a small ester substrate, N-tosyl-L-arginine methyl ester (TAME), and small and large peptides [Atassi, M. Z. & Man...

    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.91.10.4110

    authors: Wells JA,Fairbrother WJ,Otlewski J,Laskowski M Jr,Burnier J

    更新日期:1994-05-10 00:00:00

  • Human eosinophils regulate human lung- and skin-derived fibroblast properties in vitro: a role for transforming growth factor beta (TGF-beta).

    abstract::Eosinophils have been associated with fibrosis. To investigate their direct role in fibrosis, human peripheral blood eosinophil sonicate was added to human lung or dermal fibroblasts, and proliferation ([(3)H]thymidine) and collagen synthesis ([(3)H]proline) were evaluated. Proliferation was enhanced significantly 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.96.17.9660

    authors: Levi-Schaffer F,Garbuzenko E,Rubin A,Reich R,Pickholz D,Gillery P,Emonard H,Nagler A,Maquart FA

    更新日期:1999-08-17 00:00:00

  • CUB-domain-containing protein 1 (CDCP1) activates Src to promote melanoma metastasis.

    abstract::We report the application of quantitative mass spectrometry to identify plasma membrane proteins differentially expressed in melanoma cells with high vs. low metastatic abilities. Using stable isotope labeling with amino acids in culture (SILAC) coupled with nanospray tandem mass spectrometry, we identified CUB-domain...

    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.1017228108

    authors: Liu H,Ong SE,Badu-Nkansah K,Schindler J,White FM,Hynes RO

    更新日期:2011-01-25 00:00:00

  • Papillomavirus sequences integrate near cellular oncogenes in some cervical carcinomas.

    abstract::The chromosomal locations of cellular sequences flanking integrated papillomavirus DNA in four cervical carcinoma cell lines and a primary cervical carcinoma have been determined. The two human papillomavirus (HPV) 16 flanking sequences derived from the tumor were localized to chromosome regions 20pter----20q13 and 3p...

    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.84.4.1070

    authors: Dürst M,Croce CM,Gissmann L,Schwarz E,Huebner K

    更新日期:1987-02-01 00:00:00

  • Direct observation of hydrogen atom dynamics and interactions by ultrahigh resolution neutron protein crystallography.

    abstract::The 1.1 Å, ultrahigh resolution neutron structure of hydrogen/deuterium (H/D) exchanged crambin is reported. Two hundred ninety-nine out of 315, or 94.9%, of the hydrogen atom positions in the protein have been experimentally derived and resolved through nuclear density maps. A number of unconventional interactions ar...

    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.1208341109

    authors: Chen JC,Hanson BL,Fisher SZ,Langan P,Kovalevsky AY

    更新日期:2012-09-18 00:00:00

  • Mitogen-activated protein kinase kinase 3 is a pivotal pathway regulating p38 activation in inflammatory arthritis.

    abstract::p38 mitogen-activated protein kinase (MAPK) regulates cytokines in arthritis and is, in turn, regulated by MAPK kinase (MKK) 3 and MKK6. To modulate p38 function but potentially minimize toxicity, we evaluated the utility of targeting MKK3 by using MKK3(-/-) mice. These studies showed that TNF-alpha increased phosphor...

    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.0509188103

    authors: Inoue T,Boyle DL,Corr M,Hammaker D,Davis RJ,Flavell RA,Firestein GS

    更新日期:2006-04-04 00:00:00

  • Visual representations during saccadic eye movements.

    abstract::In normal vision, shifts of attention are usually followed by saccadic eye movements. Neurons in extrastriate area V4 are modulated by focal attention when eye movements are withheld, but they also respond in advance of visually guided saccadic eye movements. We have examined the visual selectivity of saccade-related ...

    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.95.15.8981

    authors: Moore T,Tolias AS,Schiller PH

    更新日期:1998-07-21 00:00:00

  • Modified recombination and transmission of mitochondrial genetic markers in rho minus mutants of Saccharomyces cerevisiae.

    abstract::A large number of primary petite (rho-) clones were isolated after ethidium bromide mutagenesis of various grande (rho+) strains of S. cerevisiae that contained the mitochondrial genetic markers, CR, ER, OIR (or OIIR), and PR. From the frequency of coretention of markers in the petites, we have deduced a probable circ...

    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.73.12.4608

    authors: Boltin-Fukuhara M,Fukuhara H

    更新日期:1976-12-01 00:00:00

  • Erratic overdispersion of three molecular clocks: GPDH, SOD, and XDH.

    abstract::The neutrality theory predicts that the rate of neutral molecular evolution is constant over time, and thus that there is a molecular clock for timing evolutionary events. It has been observed that the variance of the rate of evolution is generally larger than expected according to the neutrality theory, which has rai...

    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.201392198

    authors: Rodríguez-Trelles F,Tarrío R,Ayala FJ

    更新日期:2001-09-25 00:00:00

  • Shear waves in the diamond-anvil cell reveal pressure-induced instability in (Mg,Fe)O.

    abstract::The emerging picture of Earth's deep interior from seismic tomography indicates more complexity than previously thought. The presence of lateral anisotropy and heterogeneity in Earth's mantle highlights the need for fully anisotropic elasticity data from mineral physics. A breakthrough in high-frequency (gigahertz) ul...

    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.0401564101

    authors: Jacobsen SD,Spetzler H,Reichmann HJ,Smyth JR

    更新日期:2004-04-20 00:00:00

  • p70S6 kinase signals cell survival as well as growth, inactivating the pro-apoptotic molecule BAD.

    abstract::Cytokines often deliver simultaneous, yet distinct, cell growth and cell survival signals. The 70-kDa ribosomal protein S6 kinase (p70S6K) is known to regulate cell growth by inducing protein synthesis components. We purified membrane-based p70S6K as a kinase responsible for site-specific phosphorylation of BAD, which...

    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.171301998

    authors: Harada H,Andersen JS,Mann M,Terada N,Korsmeyer SJ

    更新日期:2001-08-14 00:00:00

  • S-adenosyl methionine is necessary for inhibition of the methyltransferase G9a by the lysine 9 to methionine mutation on histone H3.

    abstract::Lysine to methionine (K-to-M) mutations in genes encoding histone H3 are thought to drive a subset of pediatric brain and bone cancers. These high-frequency K-to-M mutations occur at sites of methylation on histone H3, and tumors containing the mutant histones exhibit a global loss of specific histone methylation mark...

    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.1605523113

    authors: Jayaram H,Hoelper D,Jain SU,Cantone N,Lundgren SM,Poy F,Allis CD,Cummings R,Bellon S,Lewis PW

    更新日期:2016-05-31 00:00:00

  • The AML1/ETO fusion protein activates transcription of BCL-2.

    abstract::The AML1 gene, located on chromosome 21, is involved in several distinct chromosomal translocations in human leukemia. In t(8;21) acute myelogenous leukemia (AML), the AML1 gene is juxtaposed to the ETO gene located on chromosome 8, generating an AML1/ETO fusion protein. Both AML1/ETO and the AML1 proteins recognize t...

    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.93.24.14059

    authors: Klampfer L,Zhang J,Zelenetz AO,Uchida H,Nimer SD

    更新日期:1996-11-26 00:00:00

  • Elastic free energy of anisotropic helical ribbons as metastable intermediates in the crystallization of cholesterol.

    abstract::We report measurements of the geometrical structure and temporal evolution of metastable helical intermediates in the pathway for cholesterol crystallization in native and model biles. We find that the lecithin component in the bile can dramatically affect the kinetics along this pathway. We also present a theoretical...

    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.90.23.11341

    authors: Chung DS,Benedek GB,Konikoff FM,Donovan JM

    更新日期:1993-12-01 00:00:00

  • Population declines in North American birds that migrate to the neotropics.

    abstract::Using data from the North American Breeding Bird Survey, we determined that most neotropical migrant bird species that breed in forests of the eastern United States and Canada have recently (1978-1987) declined in abundance after a period of stable or increasing populations. Most permanent residents and temperate-zone...

    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.86.19.7658

    authors: Robbins CS,Sauer JR,Greenberg RS,Droege S

    更新日期:1989-10-01 00:00:00

  • Transcriptional and translational control of cytoplasmic proteins after serum stimulation of quiescent Swiss 3T3 cells.

    abstract::The synthesis of cytoplasmic proteins from quiescent and serum-stimulated Swiss 3T3 cells was compared by two-dimensional polyacrylamide gel electrophoresis. Four new proteins of Mrs 26,000, 28,000, 45,000, and 47,000 designated N26, N28, N45, and N47, which were not detectable in quiescent cells, appeared 60 min afte...

    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.78.9.5712

    authors: Thomas G,Thomas G,Luther H

    更新日期:1981-09-01 00:00:00

  • Characterization of individual polynucleotide molecules using a membrane channel.

    abstract::We show that an electric field can drive single-stranded RNA and DNA molecules through a 2.6-nm diameter ion channel in a lipid bilayer membrane. Because the channel diameter can accommodate only a single strand of RNA or DNA, each polymer traverses the membrane as an extended chain that partially blocks the channel. ...

    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.93.24.13770

    authors: Kasianowicz JJ,Brandin E,Branton D,Deamer DW

    更新日期:1996-11-26 00:00:00

  • Cleavage of replicating forms of mitochondrial DNA by EcoRI endonuclease.

    abstract::Digestion of mouse L cell mitochondrial DNA with EcoRI restriction endonuclease produces two linear duplex fragments comprising 86.3 +/- 2.0% and 14.2 +/- 1.0% of the circular genome length (16,000 +/- 470 nucleotide pairs). Digestion of human HeLa cell mitochondrial DNA with EcoRI produces three linear duplex fragmen...

    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.71.11.4447

    authors: Robberson DL,Clayton DA,Morrow JF

    更新日期:1974-11-01 00:00:00

  • DNA replication meets genetic exchange: chromosomal damage and its repair by homologous recombination.

    abstract::Proceedings of the National Academy of Sciences Colloquium on the roles of homologous recombination in DNA replication are summarized. Current findings in experimental systems ranging from bacteriophages to mammalian cell lines substantiate the idea that homologous recombination is a system supporting DNA replication ...

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

    pub_type: 杂志文章,评审

    doi:10.1073/pnas.151260698

    authors: Kuzminov A

    更新日期:2001-07-17 00:00:00

  • Topographically induced hierarchical assembly and geometrical transformation of focal conic domain arrays in smectic liquid crystals.

    abstract::Controlling topological defects in 3D liquid crystal phases is a crucial element in the development of novel devices, from blue-phase displays to passive biochemical sensors. However, it remains challenging to realize the 3D topological conditions necessary to robustly and arbitrarily direct the formation of defects. ...

    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.1214708109

    authors: Honglawan A,Beller DA,Cavallaro M Jr,Kamien RD,Stebe KJ,Yang S

    更新日期:2013-01-02 00:00:00

  • p53 mutations in human lymphoid malignancies: association with Burkitt lymphoma and chronic lymphocytic leukemia.

    abstract::We have investigated the frequency of p53 mutations in B- and T-cell human lymphoid malignancies, including acute lymphoblastic leukemia, the major subtypes of non-Hodgkin lymphoma, and chronic lymphocytic leukemia. p53 exons 5-9 were studied by using genomic DNA from 197 primary tumors and 27 cell lines by single-str...

    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.88.12.5413

    authors: Gaidano G,Ballerini P,Gong JZ,Inghirami G,Neri A,Newcomb EW,Magrath IT,Knowles DM,Dalla-Favera R

    更新日期:1991-06-15 00:00:00

  • Tubulins from different higher plant species are immunologically nonidentical and bind colchicine differentially.

    abstract::We have initiated immunological and drug-binding studies on the tubulins from different higher plant species. Antibodies were raised against electrophoretically separated rose (Rosa sp.) tubulin alpha- and beta-subunits and characterized by immunoblot autoradiographic assays. Each IgG preparation bound to its antigen ...

    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.81.5.1440

    authors: Morejohn LC,Bureau TE,Tocchi LP,Fosket DE

    更新日期:1984-03-01 00:00:00

  • Cell line-specific differences in the control of cell cycle progression in the absence of mitosis.

    abstract::This paper reports that there are major differences between mammalian cell lines in the propensity to progress into subsequent cell cycles when mitosis is inhibited with agents that disrupt the assembly of the mitotic spindle apparatus (Colcemid, nocodazole, and taxol). Human HeLa S3 cells, which represent one extreme...

    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.87.24.9553

    authors: Kung AL,Sherwood SW,Schimke RT

    更新日期:1990-12-01 00:00:00

  • Basolateral amygdala noradrenergic influence enables enhancement of memory consolidation induced by hippocampal glucocorticoid receptor activation.

    abstract::Previously, we reported that bilateral excitotoxic lesions of the basolateral nucleus of the amygdala (BLA) block the enhancing effects of posttraining systemic or intrahippocampal glucocorticoid administration on memory for inhibitory avoidance training. The present study further examined the basis of this permissive...

    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.96.20.11642

    authors: Roozendaal B,Nguyen BT,Power AE,McGaugh JL

    更新日期:1999-09-28 00:00:00

  • Stigmergy, collective actions, and animal social spacing.

    abstract::Collective animal behavior studies have led the way in developing models that account for a large number of individuals, but mostly have considered situations in which alignment and attraction play a key role, such as in schooling and flocking. By quantifying how animals react to one another's presence, when interacti...

    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.1307071110

    authors: Giuggioli L,Potts JR,Rubenstein DI,Levin SA

    更新日期:2013-10-15 00:00:00

  • Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel.

    abstract::The ecology of microbes in the gut has been shown to play important roles in the health of the host. To better understand microbial growth and population dynamics in the proximal colon, the primary region of bacterial growth in the gut, we built and applied a fluidic channel that we call the "minigut." This is a chann...

    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.1601306113

    authors: Cremer J,Segota I,Yang CY,Arnoldini M,Sauls JT,Zhang Z,Gutierrez E,Groisman A,Hwa T

    更新日期:2016-10-11 00:00:00