Refined crystal structure of DsRed, a red fluorescent protein from coral, at 2.0-A resolution.

Abstract:

:The crystal structure of DsRed, a red fluorescent protein from a corallimorpharian, has been determined at 2.0-A resolution by multiple-wavelength anomalous dispersion and crystallographic refinement. Crystals of the selenomethionine-substituted protein have space group P2(1) and contain a tetramer with 222 noncrystallographic symmetry in the asymmetric unit. The refined model has satisfactory stereochemistry and a final crystallographic R factor of 0.162. The protein, which forms an obligatory tetramer in solution and in the crystal, is a squat rectangular prism comprising four protomers whose fold is extremely similar to that of the Aequorea victoria green fluorescent protein despite low ( approximately 23%) amino acid sequence homology. The monomer consists of an 11-stranded beta barrel with a coaxial helix. The chromophores, formed from the primary sequence -Gln-Tyr-Gly- (residues 66-68), are arranged in a approximately 27 x 34-A rectangular array in two approximately antiparallel pairs. The geometry at the alpha carbon of Gln-66 (refined without stereochemical restraints) is consistent with an sp(2) hybridized center, in accord with the proposal that red fluorescence is because of an additional oxidation step that forms an acylimine extension to the chromophore [Gross, L. A., Baird, G. S., Hoffman, R. C., Baldridge, K. K. & Tsien, R. Y. (2000) Proc. Natl. Acad. Sci. USA 87, 11990-11995]. The carbonyl oxygen of Phe-65 is almost 90 degrees out of the plane of the chromophore, consistent with theoretical calculations suggesting that this is the minimum energy conformation of this moiety despite the conjugation of this group with the rest of the chromophore.

authors

Yarbrough D,Wachter RM,Kallio K,Matz MV,Remington SJ

doi

10.1073/pnas.98.2.462

keywords:

subject

Has Abstract

pub_date

2001-01-16 00:00:00

pages

462-7

issue

2

eissn

0027-8424

issn

1091-6490

pii

98/2/462

journal_volume

98

pub_type

杂志文章
  • Localization of a poliovirus type 1 neutralization epitope in viral capsid polypeptide VP1.

    abstract::Poliovirus type 1 cDNA sequences coding for viral capsid polypeptide VP1 were inserted into the beta-lactamase sequence of Escherichia coli plasmid pBR322. Resulting recombinant plasmid pSW119 expressed in Escherichia coli a VP1-beta-lactamase fusion protein that reacted with antibodies raised against poliovirus capsi...

    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.80.16.5080

    authors: van der Werf S,Wychowski C,Bruneau P,Blondel B,Crainic R,Horodniceanu F,Girard M

    更新日期:1983-08-01 00:00:00

  • Rat cardiac ventricle has two Na+,K+-ATPases with different affinities for ouabain: developmental changes in immunologically different catalytic subunits.

    abstract::The mechanism of the inotropic effect of cardiac glycosides on the heart has long been controversial. Inotropic effects at low concentrations of cardiac glycosides indicate more than one class of receptor or more than one cellular mechanism. In the brain of the rat, high- and low-affinity cardiac glycoside receptors h...

    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.84.23.8404

    authors: Sweadner KJ,Farshi SK

    更新日期:1987-12-01 00:00:00

  • Resting and activated subsets of mouse multipotent hematopoietic stem cells.

    abstract::The fluorescent vital dye rhodamine 123 (Rh-123), which preferentially accumulates in mitochondrial membranes, can be used as a probe to indicate mitochondrial and hence cellular activity. In this study, mouse bone marrow hematopoietic stem cells were subdivided into Rh-123lo, Rh-123med, and Rh-123hi populations. The ...

    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.87.19.7433

    authors: Spangrude GJ,Johnson GR

    更新日期:1990-10-01 00:00:00

  • Structure of the gene V protein of bacteriophage f1 determined by multiwavelength x-ray diffraction on the selenomethionyl protein.

    abstract::The crystal structure of the dimeric gene V protein of bacteriophage f1 was determined using multiwavelength anomalous diffraction on the selenomethionine-containing wild-type and isoleucine-47-->methionine mutant proteins with x-ray diffraction data phased to 2.5 A resolution. The structure of the wild-type protein h...

    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.91.6.2071

    authors: Skinner MM,Zhang H,Leschnitzer DH,Guan Y,Bellamy H,Sweet RM,Gray CW,Konings RN,Wang AH,Terwilliger TC

    更新日期:1994-03-15 00:00:00

  • On a fundamental structure of gene networks in living cells.

    abstract::Computers are organized into hardware and software. Using a theoretical approach to identify patterns in gene expression in a variety of species, organs, and cell types, we found that biological systems similarly are comprised of a relatively unchanging hardware-like gene pattern. Orthogonal patterns of software-like ...

    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.1200790109

    authors: Kravchenko-Balasha N,Levitzki A,Goldstein A,Rotter V,Gross A,Remacle F,Levine RD

    更新日期:2012-03-20 00:00:00

  • Formation of termination-resistant transcription complex at phage lambda nut locus: effects of altered translation and a ribosomal mutation.

    abstract::Transcription antitermination by lambda N gene product is affected in a mutant Escherichia coli with altered ribosomal protein S10, caused by the nusE71 mutation. To study the role of translation in antitermination, we have fused the phage nutR locus, the site of action of N, with the lac regulatory region. We have mo...

    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.81.12.3612

    authors: Warren F,Das A

    更新日期:1984-06-01 00:00:00

  • Setting the bar: Standards for ecosystem services.

    abstract::Progress in ecosystem service science has been rapid, and there is now a healthy appetite among key public and private sector decision makers for this science. However, changing policy and management is a long-term project, one that raises a number of specific practical challenges. One impediment to broad adoption 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.1406490112

    authors: Polasky S,Tallis H,Reyers B

    更新日期:2015-06-16 00:00:00

  • Global trends in nature's contributions to people.

    abstract::Declining biodiversity and ecosystem functions put many of nature's contributions to people at risk. We review and synthesize the scientific literature to assess 50-y global trends across a broad range of nature's contributions. We distinguish among trends in potential and realized contributions of nature, as well as ...

    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.2010473117

    authors: Brauman KA,Garibaldi LA,Polasky S,Aumeeruddy-Thomas Y,Brancalion PHS,DeClerck F,Jacob U,Mastrangelo ME,Nkongolo NV,Palang H,Pérez-Méndez N,Shannon LJ,Shrestha UB,Strombom E,Verma M

    更新日期:2020-12-22 00:00:00

  • Membrane orientation of the FMO antenna protein from Chlorobaculum tepidum as determined by mass spectrometry-based footprinting.

    abstract::The high excitation energy-transfer efficiency demanded in photosynthetic organisms relies on the optimal pigment-protein binding orientation in the individual protein complexes and also on the overall architecture of the photosystem. In green sulfur bacteria, the membrane-attached Fenna-Matthews-Olson (FMO) antenna 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.0901691106

    authors: Wen J,Zhang H,Gross ML,Blankenship RE

    更新日期:2009-04-14 00:00:00

  • Local sources of retinoic acid coincide with retinoid-mediated transgene activity during embryonic development.

    abstract::We have assessed whether retinoic acid (RA) comes from local sources or is available widely to activate gene expression in embryos. We used an RA-responsive indicator cell line, L-C2A5, to localize RA sources. In these cells, an RA-sensitive promoter/lacZ reporter construct used previously by us to produce indicator 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.90.14.6572

    authors: Colbert MC,Linney E,LaMantia AS

    更新日期:1993-07-15 00:00:00

  • Library preparation methodology can influence genomic and functional predictions in human microbiome research.

    abstract::Observations from human microbiome studies are often conflicting or inconclusive. Many factors likely contribute to these issues including small cohort sizes, sample collection, and handling and processing differences. The field of microbiome research is moving from 16S rDNA gene sequencing to a more comprehensive gen...

    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.1519288112

    authors: Jones MB,Highlander SK,Anderson EL,Li W,Dayrit M,Klitgord N,Fabani MM,Seguritan V,Green J,Pride DT,Yooseph S,Biggs W,Nelson KE,Venter JC

    更新日期:2015-11-10 00:00:00

  • A single dose of doxorubicin-functionalized bow-tie dendrimer cures mice bearing C-26 colon carcinomas.

    abstract::The antitumor effect of doxorubicin (DOX) conjugated to a biodegradable dendrimer was evaluated in mice bearing C-26 colon carcinomas. An asymmetric biodegradable polyester dendrimer containing 8-10 wt % DOX was prepared. The design of the dendrimer carrier optimized blood circulation time through size and molecular 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.0607705103

    authors: Lee CC,Gillies ER,Fox ME,Guillaudeu SJ,Fréchet JM,Dy EE,Szoka FC

    更新日期:2006-11-07 00:00:00

  • A thermodynamic framework for Mg2+ binding to RNA.

    abstract::We present a model describing how Mg(2+) binds and stabilizes specific RNA structures. In this model, RNA stabilization arises from two energetically distinct modes of Mg(2+) binding: diffuse- and site-binding. Diffusely bound Mg(2+) are electrostatically attracted to the strong anionic field around the RNA and are ac...

    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.221234598

    authors: Misra VK,Draper DE

    更新日期:2001-10-23 00:00:00

  • Temperature and manganese as determining factors in the presence of diatom or blue-green algal floras in streams.

    abstract::Diatoms are usually the major component of the algal flora in many streams, although green and blue-green algae may be present. These experiments were designed to determine if high temperature or a shift in the chemical composition of the water might bring about a dominance of blue-green algae and/or green algae rathe...

    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.64.2.472

    authors: Patrick R,Crum B,Coles J

    更新日期:1969-10-01 00:00:00

  • A transmembrane formin nucleates subapical actin assembly and controls tip-focused growth in pollen tubes.

    abstract::Pollen tubes are highly polarized plant cells specialized in delivering sperm for fertilization. Pollen tube growth is rapid, occurs exclusively at the tip, and can reach distances thousands of times the diameter of the pollen grain without cell division, thus representing an excellent model system for studying asymme...

    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.1008527107

    authors: Cheung AY,Niroomand S,Zou Y,Wu HM

    更新日期:2010-09-14 00:00:00

  • X-linked H3K27me3 demethylase Utx is required for embryonic development in a sex-specific manner.

    abstract::Embryogenesis requires the timely and coordinated activation of developmental regulators. It has been suggested that the recently discovered class of histone demethylases (UTX and JMJD3) that specifically target the repressive H3K27me3 modification play an important role in the activation of "bivalent" genes in respon...

    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.1210787109

    authors: Welstead GG,Creyghton MP,Bilodeau S,Cheng AW,Markoulaki S,Young RA,Jaenisch R

    更新日期:2012-08-07 00:00:00

  • Topological basis for the robust distribution of blood to rodent neocortex.

    abstract::The maintenance of robust blood flow to the brain is crucial to the health of brain tissue. We examined the pial network of the middle cerebral artery, which distributes blood from the cerebral arteries to the penetrating arterioles that source neocortical microvasculature, to characterize how vascular topology may su...

    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.1007239107

    authors: Blinder P,Shih AY,Rafie C,Kleinfeld D

    更新日期:2010-07-13 00:00:00

  • Genetic analysis of the metabolome exemplified using a rice population.

    abstract::Plant metabolites are crucial for both plant life and human nutrition. Despite recent advance in metabolomics, the genetic control of plant metabolome remains largely unknown. Here, we performed a genetic analysis of the rice metabolome that provided over 2,800 highly resolved metabolic quantitative trait loci for 900...

    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.1319681110

    authors: Gong L,Chen W,Gao Y,Liu X,Zhang H,Xu C,Yu S,Zhang Q,Luo J

    更新日期:2013-12-10 00:00:00

  • Illuminating cell-cycle progression in the developing zebrafish embryo.

    abstract::By exploiting the cell-cycle-dependent proteolysis of two ubiquitination oscillators, human Cdt1 and geminin, which are the direct substrates of SCF(Skp2) and APC(Cdh1) complexes, respectively, Fucci technique labels mammalian cell nuclei in G(1) and S/G(2)/M phases with different colors. Transgenic mice expressing 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.0906464106

    authors: Sugiyama M,Sakaue-Sawano A,Iimura T,Fukami K,Kitaguchi T,Kawakami K,Okamoto H,Higashijima S,Miyawaki A

    更新日期:2009-12-08 00:00:00

  • Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins.

    abstract::Peptidoglycan recognition proteins (PGRPs) are highly conserved pattern-recognition molecules of the innate immune system that bind bacterial peptidoglycans (PGNs), which are polymers of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) cross-linked by short peptide stems. Human PRGPs are bactericid...

    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.0701453104

    authors: Cho S,Wang Q,Swaminathan CP,Hesek D,Lee M,Boons GJ,Mobashery S,Mariuzza RA

    更新日期:2007-05-22 00:00:00

  • Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2.

    abstract::DNA methylation at CpG dinucleotides is an important epigenetic regulator common to virtually all mammalian cell types, but recent evidence indicates that during early postnatal development neuronal genomes also accumulate uniquely high levels of two alternative forms of methylation, non-CpG methylation and hydroxymet...

    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.1411269112

    authors: Kinde B,Gabel HW,Gilbert CS,Griffith EC,Greenberg ME

    更新日期:2015-06-02 00:00:00

  • Expression of a complete soybean leghemoglobin gene in root nodules of transgenic Lotus corniculatus.

    abstract::The complete soybean leghemoglobin lbc(3) gene was transferred into the legume Lotus corniculatus using an Agrobacterium rhizogenes vector system. Organ-specific expression of the soybean gene was observed in root nodules formed on regenerated transgenic plants after infection with Rhizobium loti. The primary transcri...

    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.84.16.5754

    authors: Stougaard J,Petersen TE,Marcker KA

    更新日期:1987-08-01 00:00:00

  • Searching for missing heritability: designing rare variant association studies.

    abstract::Genetic studies have revealed thousands of loci predisposing to hundreds of human diseases and traits, revealing important biological pathways and defining novel therapeutic hypotheses. However, the genes discovered to date typically explain less than half of the apparent heritability. Because efforts have largely foc...

    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.1322563111

    authors: Zuk O,Schaffner SF,Samocha K,Do R,Hechter E,Kathiresan S,Daly MJ,Neale BM,Sunyaev SR,Lander ES

    更新日期:2014-01-28 00:00:00

  • A mutant of Escherichia coli defective in DNA polymerase II activity.

    abstract::A mutant of E. coli defective in DNA polymerase II activity was isolated. Extracts had about 0.1% of the normal activity of the DNA polymerase. The effect of the mutation on the ability of cells to replicate DNA of various sources was analyzed. Mutant bacteria grow normally, at 41 degrees as well as at 30 degrees . Al...

    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.69.11.3238

    authors: Hirota Y,Gefter M,Mindich L

    更新日期:1972-11-01 00:00:00

  • Transcriptional collision between convergent genes in budding yeast.

    abstract::Transcriptional interference between genes and the regulatory elements of simple eukaryotes such as Saccharomyces cerevisiae is an unavoidable consequence of their compressed genetic arrangement. We have shown previously that with the tandem arranged genes GAL10 and GAL7, inefficient transcriptional termination of the...

    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.132270899

    authors: Prescott EM,Proudfoot NJ

    更新日期:2002-06-25 00:00:00

  • Elevation of intracellular calcium by muscarinic receptor activation induces a block of voltage-activated rat ether-à-go-go channels in a stably transfected cell line.

    abstract::We have studied the properties of r-eag voltage-activated potassium channels in a stably transfected human embryonic kidney cell line. It was found that r-eag channels are rapidly and reversibly inhibited by a rise in intracellular calcium from 30 to 300 nM. The inhibition does not appear to depend on the activity 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.93.18.9910

    authors: Stansfeld CE,Röper J,Ludwig J,Weseloh RM,Marsh SJ,Brown DA,Pongs O

    更新日期:1996-09-03 00:00:00

  • Borrowed alleles and convergence in serpentine adaptation.

    abstract::Serpentine barrens represent extreme hazards for plant colonists. These sites are characterized by high porosity leading to drought, lack of essential mineral nutrients, and phytotoxic levels of metals. Nevertheless, nature forged populations adapted to these challenges. Here, we use a population-based evolutionary ge...

    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.1600405113

    authors: Arnold BJ,Lahner B,DaCosta JM,Weisman CM,Hollister JD,Salt DE,Bomblies K,Yant L

    更新日期:2016-07-19 00:00:00

  • Escherichia coli genes regulated by cell-to-cell signaling.

    abstract::Utilizing the bicistronic reporter transposon mini-Tn5 lacZ-tet/1, we have identified lacZ fusions to four Escherichia coli genes/operons that are strongly activated by the accumulation of self-produced extracellular signals. These fusions were designated cma9, cma48, cma113, and cma114 for conditioned medium activate...

    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.96.8.4610

    authors: Baca-DeLancey RR,South MM,Ding X,Rather PN

    更新日期:1999-04-13 00:00:00

  • Host cell recognition by the henipaviruses: crystal structures of the Nipah G attachment glycoprotein and its complex with ephrin-B3.

    abstract::Nipah virus (NiV) and Hendra virus are the type species of the highly pathogenic paramyxovirus genus Henipavirus, which can cause severe respiratory disease and fatal encephalitis infections in humans, with case fatality rates approaching 75%. NiV contains two envelope glycoproteins, the receptor-binding G glycoprotei...

    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.0804797105

    authors: Xu K,Rajashankar KR,Chan YP,Himanen JP,Broder CC,Nikolov DB

    更新日期:2008-07-22 00:00:00

  • Cultural implications of late Holocene climate change in the Cuenca Oriental, Mexico.

    abstract::There is currently no consensus on the importance of climate change in Mesoamerican prehistory. Some invoke drought as a causal factor in major cultural transitions, including the abandonment of many sites at 900 CE, while others conclude that cultural factors were more important. This lack of agreement reflects the f...

    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.1405653112

    authors: Bhattacharya T,Byrne R,Böhnel H,Wogau K,Kienel U,Ingram BL,Zimmerman S

    更新日期:2015-02-10 00:00:00