Energetics and dynamics of a light-driven sodium-pumping rhodopsin.

Abstract:

:The conversion of light energy into ion gradients across biological membranes is one of the most fundamental reactions in primary biological energy transduction. Recently, the structure of the first light-activated Na+ pump, Krokinobacter eikastus rhodopsin 2 (KR2), was resolved at atomic resolution [Kato HE, et al. (2015) Nature 521:48-53]. To elucidate its molecular mechanism for Na+ pumping, we perform here extensive classical and quantum molecular dynamics (MD) simulations of transient photocycle states. Our simulations show how the dynamics of key residues regulate water and ion access between the bulk and the buried light-triggered retinal site. We identify putative Na+ binding sites and show how protonation and conformational changes gate the ion through these sites toward the extracellular side. We further show by correlated ab initio quantum chemical calculations that the obtained putative photocycle intermediates are in close agreement with experimental transient optical spectroscopic data. The combined results of the ion translocation and gating mechanisms in KR2 may provide a basis for the rational design of novel light-driven ion pumps with optogenetic applications.

authors

Suomivuori CM,Gamiz-Hernandez AP,Sundholm D,Kaila VRI

doi

10.1073/pnas.1703625114

subject

Has Abstract

pub_date

2017-07-03 00:00:00

pages

7043-7048

issue

27

eissn

0027-8424

issn

1091-6490

pii

1703625114

journal_volume

114

pub_type

杂志文章
  • Membrane potential changes caused by thyrotropin-releasing hormone in the clonal GH3 cell and their relationship to secretion of pituitary hormone.

    abstract::Effects of thyrotropin-releasing hormone (TRH; thyroliberin) on membrane electrical properties were studied in the clonal rat anterior pituitary cell (GH3) by continuous recording of the intracellular potential. Application of TRH, which stimulates the release of prolactin and growth hormone from the GH3 cell, elicite...

    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.76.11.6017

    authors: Ozawa S,Kimura N

    更新日期:1979-11-01 00:00:00

  • Selective manipulation of the human T-cell receptor repertoire expressed by thymocytes in organ culture.

    abstract::A recently described organ culture system for human thymocytes is shown to support the generation of a diverse T-cell receptor repertoire in vitro: thymocytes of the alpha beta lineage, including representatives of the V beta families 5.2/5.3, 6.7, and 8, accounted for the majority of T-cell receptor-positive cells th...

    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.89.10.4255

    authors: Merkenschlager M,Fisher AG

    更新日期:1992-05-15 00:00:00

  • An attempt to locate the non-helical and permissively helical sequences of proteins: application to the variable regions of immunoglobulin light and heavy chains.

    abstract::From a consideration of (varphi, Psi) values of the amino acids of myoglobin, lysozyme, the alpha and beta chains of horse oxyhemoglobin, tosyl-alpha-chymotrypsin, and carboxypeptidase A, an empirical procedure of predicting whether amino-acid residues in proteins are in a non-helical or may be in a helical conformati...

    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.68.7.1501

    authors: Wu TT,Kabat EA

    更新日期:1971-07-01 00:00:00

  • Changes in the composition of plasma membrane proteins during differentiation of embryonic chick erythroid cell.

    abstract::Erythroid cells which are homogeneous with regard to stage of maturation are naturally available from the circulation of chick embryos at various times of development. This provides a convenient system for examining the changes in plasma membrane protein composition during red cell maturation. Plasma membranes are iso...

    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.74.3.1062

    authors: Chan LL

    更新日期:1977-03-01 00:00:00

  • To qualify as a social partner, humans hide severe punishment, although their observed cooperativeness is decisive.

    abstract::Conflicts of interest between the community and its members are at the core of human social dilemmas. If observed selfishness has future costs, individuals may hide selfish acts but display altruistic ones, and peers aim at identifying the most selfish persons to avoid them as future social partners. An interaction 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.1108996108

    authors: Rockenbach B,Milinski M

    更新日期:2011-11-08 00:00:00

  • Histone code pathway involving H3 S28 phosphorylation and K27 acetylation activates transcription and antagonizes polycomb silencing.

    abstract::Histone H3 phosphorylation is a critical step that couples signal transduction pathways to gene regulation. To specifically assess the transcriptional regulatory functions of H3 phosphorylation, we developed an in vivo targeting approach and found that the H3 kinase MSK1 is a direct and potent transcriptional activato...

    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.1012798108

    authors: Lau PN,Cheung P

    更新日期:2011-02-15 00:00:00

  • Repeat associated small RNAs vary among parents and following hybridization in maize.

    abstract::Small RNAs (sRNAs) are hypothesized to contribute to hybrid vigor because they maintain genome integrity, contribute to genetic diversity, and control gene expression. We used Illumina sequencing to assess how sRNA populations vary between two maize inbred lines (B73 and Mo17) and their hybrid. We sampled sRNAs from 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.1202073109

    authors: Barber WT,Zhang W,Win H,Varala KK,Dorweiler JE,Hudson ME,Moose SP

    更新日期:2012-06-26 00:00:00

  • Site-specific genome editing for correction of induced pluripotent stem cells derived from dominant dystrophic epidermolysis bullosa.

    abstract::Genome editing with engineered site-specific endonucleases involves nonhomologous end-joining, leading to reading frame disruption. The approach is applicable to dominant negative disorders, which can be treated simply by knocking out the mutant allele, while leaving the normal allele intact. We applied this strategy ...

    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.1512028113

    authors: Shinkuma S,Guo Z,Christiano AM

    更新日期:2016-05-17 00:00:00

  • Retrograde transfer RNA nuclear import provides a new level of tRNA quality control in Saccharomyces cerevisiae.

    abstract::In eukaryotes, transfer RNAs (tRNAs) are transcribed in the nucleus yet function in the cytoplasm; thus, tRNA movement within the cell was believed to be unidirectional--from the nucleus to the cytoplasm. It is now known that mature tRNAs also move in a retrograde direction from the cytoplasm to the nucleus via retrog...

    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.1316579110

    authors: Kramer EB,Hopper AK

    更新日期:2013-12-24 00:00:00

  • Syndecan-4 proteoliposomes enhance fibroblast growth factor-2 (FGF-2)-induced proliferation, migration, and neovascularization of ischemic muscle.

    abstract::Ischemia of the myocardium and lower limbs is a common consequence of arterial disease and a major source of morbidity and mortality in modernized countries. Inducing neovascularization for the treatment of ischemia is an appealing therapeutic strategy for patients for whom traditional treatment modalities cannot be p...

    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.1117885109

    authors: Jang E,Albadawi H,Watkins MT,Edelman ER,Baker AB

    更新日期:2012-01-31 00:00:00

  • Genetic rescue models refute nonautonomous rod cell death in retinitis pigmentosa.

    abstract::Retinitis pigmentosa (RP) is an inherited neurodegenerative disease, in which the death of mutant rod photoreceptors leads secondarily to the non-cell autonomous death of cone photoreceptors. Gene therapy is a promising treatment strategy. Unfortunately, current methods of gene delivery treat only a fraction of diseas...

    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.1615394114

    authors: Koch SF,Duong JK,Hsu CW,Tsai YT,Lin CS,Wahl-Schott CA,Tsang SH

    更新日期:2017-05-16 00:00:00

  • Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells.

    abstract::Aire is a transcriptional regulator that induces expression of peripheral tissue antigens (PTA) in thymic medullary epithelial cells (MECs), driving immunological self-tolerance in differentiating T cells. To elucidate its mechanistic pathways, we examined its transcriptional impact in MECs in vivo by microarray analy...

    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.1119351109

    authors: Giraud M,Yoshida H,Abramson J,Rahl PB,Young RA,Mathis D,Benoist C

    更新日期:2012-01-10 00:00:00

  • Direct interaction of the major light-harvesting complex II and PsbS in nonphotochemical quenching.

    abstract::The photosystem II (PSII) subunit S (PsbS) plays a key role in nonphotochemical quenching, a photoprotective mechanism for dissipation of excess excitation energy in plants. The precise function of PsbS in nonphotochemical quenching is unknown. By reconstituting PsbS together with the major light-harvesting complex 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.1205561110

    authors: Wilk L,Grunwald M,Liao PN,Walla PJ,Kühlbrandt W

    更新日期:2013-04-02 00:00:00

  • Collective evolution and the genetic code.

    abstract::A dynamical theory for the evolution of the genetic code is presented, which accounts for its universality and optimality. The central concept is that a variety of collective, but non-Darwinian, mechanisms likely to be present in early communal life generically lead to refinement and selection of innovation-sharing pr...

    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.0603780103

    authors: Vetsigian K,Woese C,Goldenfeld N

    更新日期:2006-07-11 00:00:00

  • Cloning and comparison of repeated DNA sequences from the human filarial parasite Brugia malayi and the animal parasite Brugia pahangi.

    abstract::A 320-base-pair repeated sequence was observed when DNA samples from the filarial parasites Brugia malayi and Brugia pahangi were digested with the restriction endonuclease Hha I. A 640-base-pair dimer of the repeated sequence from B. malayi was inserted into the plasmid pBR322. When dot hybridization was used, the co...

    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.83.3.797

    authors: McReynolds LA,DeSimone SM,Williams SA

    更新日期:1986-02-01 00:00:00

  • Activation of human immunodeficiency virus by herpesvirus infection: identification of a region within the long terminal repeat that responds to a trans-acting factor encoded by herpes simplex virus 1.

    abstract::Herpes simplex virus 1 (HSV-1) infection induces transcription of the chloramphenicol acetyltransferase (CAT) gene directed by the long terminal repeat (LTR) of human immunodeficiency virus (HIV) in both transiently and permanently transfected cells containing the HIV-LTR/CAT hybrid gene. To define the mechanism by wh...

    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.84.21.7408

    authors: Mosca JD,Bednarik DP,Raj NB,Rosen CA,Sodroski JG,Haseltine WA,Hayward GS,Pitha PM

    更新日期:1987-11-01 00:00:00

  • The Great Recession, genetic sensitivity, and maternal harsh parenting.

    abstract::Using data from the Fragile Families and Child Wellbeing Study, this study examined the effects of the Great Recession on maternal harsh parenting. We found that changes in macroeconomic conditions, rather than current conditions, affected harsh parenting, that declines in macroeconomic conditions had a stronger impac...

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

    pub_type: 历史文章,杂志文章

    doi:10.1073/pnas.1312398110

    authors: Lee D,Brooks-Gunn J,McLanahan SS,Notterman D,Garfinkel I

    更新日期:2013-08-20 00:00:00

  • NOD2 contributes to cutaneous defense against Staphylococcus aureus through alpha-toxin-dependent innate immune activation.

    abstract::Staphylococcus aureus is a major cause of community-acquired and nosocomial infections including the life-threatening conditions endocarditis, necrotizing pneumonia, necrotizing fasciitis, and septicemia. Toll-like receptor (TLR)-2, a membrane-bound microbial sensor, detects staphylococcal components, but macrophages ...

    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.0904958106

    authors: Hruz P,Zinkernagel AS,Jenikova G,Botwin GJ,Hugot JP,Karin M,Nizet V,Eckmann L

    更新日期:2009-08-04 00:00:00

  • Development and persistence of kindling epilepsy are impaired in mice lacking glial cell line-derived neurotrophic factor family receptor alpha 2.

    abstract::Seizure activity regulates gene expression for glial cell line-derived neurotrophic factor (GDNF) and neurturin (NRTN), and their receptor components, the transmembrane c-Ret tyrosine kinase and the glycosylphosphatidylinositol-anchored GDNF family receptor (GFR) alpha 1 and alpha 2 in limbic structures. We demonstrat...

    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.97.22.12312

    authors: Nanobashvili A,Airaksinen MS,Kokaia M,Rossi J,Asztély F,Olofsdotter K,Mohapel P,Saarma M,Lindvall O,Kokaia Z

    更新日期:2000-10-24 00:00:00

  • DNA recognition code of transcription factors in the helix-turn-helix, probe helix, hormone receptor, and zinc finger families.

    abstract::We have previously reported that in four transcription factor families the DNA-recognition rules can be described as (i) chemical rules, which list possible pairings between the 20 amino acid residues and the four DNA bases, and (ii) stereochemical rules, which describe the base and amino acid positions in contact. We...

    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.91.26.12357

    authors: Suzuki M,Yagi N

    更新日期:1994-12-20 00:00:00

  • Imaging burst kinetics and spatial coordination during serial killing by single natural killer cells.

    abstract::Cytotoxic lymphocytes eliminate virus-infected and cancerous cells by immune recognition and killing through the perforin-granzyme pathway. Traditional killing assays measure average target cell lysis at fixed times and high effector:target ratios. Such assays obscure kinetic details that might reveal novel physiology...

    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.1221312110

    authors: Choi PJ,Mitchison TJ

    更新日期:2013-04-16 00:00:00

  • The cytoplasmic component of the bacterial flagellar motor.

    abstract::We have used electron microscopy to examine freshly isolated Salmonella typhimurium and Escherichia coli basal flagellar fragments, purified without resort to extremes of pH or ionic strength. Such fragments contain the large bell-like basal structures visualized recently in freeze-substituted or fixed preparations. W...

    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.89.13.5956

    authors: Khan IH,Reese TS,Khan S

    更新日期:1992-07-01 00:00:00

  • Functional neuroanatomy of antisaccade eye movements investigated with positron emission tomography.

    abstract::Increasing interest in the role of the frontal lobe in relation to psychiatric and neurologic disorders has popularized tests of frontal function. One of these is the antisaccade task, in which both frontal lobe patients and schizophrenics are impaired despite normal performance on (pro)saccadic tasks. We used positio...

    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.92.3.925

    authors: O'Driscoll GA,Alpert NM,Matthysse SW,Levy DL,Rauch SL,Holzman PS

    更新日期:1995-01-31 00:00:00

  • Neutrophils induce proangiogenic T cells with a regulatory phenotype in pregnancy.

    abstract::Although neutrophils are known to be fundamental in controlling innate immune responses, their role in regulating adaptive immunity is just starting to be appreciated. We report that human neutrophils exposed to pregnancy hormones progesterone and estriol promote the establishment of maternal tolerance through the ind...

    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.1611944114

    authors: Nadkarni S,Smith J,Sferruzzi-Perri AN,Ledwozyw A,Kishore M,Haas R,Mauro C,Williams DJ,Farsky SH,Marelli-Berg FM,Perretti M

    更新日期:2016-12-27 00:00:00

  • Maximum-valence radii of transition metals.

    abstract::In many of their compounds the transition metals have covalence 9, forming nine bonds with use of nine hybrid spd bond orbitals. A set of maximum-valence single-bond radii is formulated for use in these compounds. These radii are in reasonably good agreement with observed bond lengths. Quadruple bonds between two tran...

    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.72.10.3799

    authors: Pauling L

    更新日期:1975-10-01 00:00:00

  • Underdeveloped uterus and reduced estrogen responsiveness in mice with disruption of the estrogen-responsive finger protein gene, which is a direct target of estrogen receptor alpha.

    abstract::The biological roles of estrogen-responsive finger protein (efp) in vivo were evaluated in mice carrying a loss-of-function mutation in efp by gene-targeted mutagenesis. Although efp homozygous mice were viable and fertile in both sexes, the uterus that expressed abundant estrogen receptor alpha exhibited significant ...

    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.96.21.12027

    authors: Orimo A,Inoue S,Minowa O,Tominaga N,Tomioka Y,Sato M,Kuno J,Hiroi H,Shimizu Y,Suzuki M,Noda T,Muramatsu M

    更新日期:1999-10-12 00:00:00

  • Intein-mediated assembly of a functional beta-glucuronidase in transgenic plants.

    abstract::The DnaE intein in Synechocystis sp. strain PCC6803 is the first and only naturally split intein that has been identified so far. It is capable of catalyzing a protein trans-splicing mechanism to assemble a mature protein from two separate precursors. Therefore, it is a powerful tool for protein modification and engin...

    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.0635899100

    authors: Yang J,Fox GC Jr,Henry-Smith TV

    更新日期:2003-03-18 00:00:00

  • RNAi-mediated silencing of estrogen receptor {alpha} in the ventromedial nucleus of hypothalamus abolishes female sexual behaviors.

    abstract::Estrogen receptor alpha (ERalpha) plays a major role in the regulation of neuroendocrine functions and behaviors by estrogens. Although the generation of ERalpha knockout mice advanced our knowledge of ERalpha functions, gene deletion using this method is global and potentially confounded by developmental consequences...

    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.0603045103

    authors: Musatov S,Chen W,Pfaff DW,Kaplitt MG,Ogawa S

    更新日期:2006-07-05 00:00:00

  • Atomic structure of the 75 MDa extremophile Sulfolobus turreted icosahedral virus determined by CryoEM and X-ray crystallography.

    abstract::Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution electron microscopy and X-ray crystallography allowing tracing of structural polypeptide chains and visualization of transm...

    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.1300601110

    authors: Veesler D,Ng TS,Sendamarai AK,Eilers BJ,Lawrence CM,Lok SM,Young MJ,Johnson JE,Fu CY

    更新日期:2013-04-02 00:00:00

  • The axonal attractant Netrin-1 is an angiogenic factor.

    abstract::Blood vessels and nerves often follow parallel trajectories, suggesting that distal targets use common cues that induce vascularization and innervation. Netrins are secreted by the floor plate and attract commissural axons toward the midline of the neural tube. Here, we show that Netrin-1 is also a potent vascular mit...

    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.0405984101

    authors: Park KW,Crouse D,Lee M,Karnik SK,Sorensen LK,Murphy KJ,Kuo CJ,Li DY

    更新日期:2004-11-16 00:00:00