Halogen bonds in biological molecules.

Abstract:

:Short oxygen-halogen interactions have been known in organic chemistry since the 1950s and recently have been exploited in the design of supramolecular assemblies. The present survey of protein and nucleic acid structures reveals similar halogen bonds as potentially stabilizing inter- and intramolecular interactions that can affect ligand binding and molecular folding. A halogen bond in biomolecules can be defined as a short C-X...O-Y interaction (C-X is a carbon-bonded chlorine, bromine, or iodine, and O-Y is a carbonyl, hydroxyl, charged carboxylate, or phosphate group), where the X...O distance is less than or equal to the sums of the respective van der Waals radii (3.27 A for Cl...O, 3.37 A for Br...O, and 3.50 A for I...O) and can conform to the geometry seen in small molecules, with the C-X...O angle approximately 165 degrees (consistent with a strong directional polarization of the halogen) and the X...O-Y angle approximately 120 degrees . Alternative geometries can be imposed by the more complex environment found in biomolecules, depending on which of the two types of donor systems are involved in the interaction: (i) the lone pair electrons of oxygen (and, to a lesser extent, nitrogen and sulfur) atoms or (ii) the delocalized pi -electrons of peptide bonds or carboxylate or amide groups. Thus, the specific geometry and diversity of the interacting partners of halogen bonds offer new and versatile tools for the design of ligands as drugs and materials in nanotechnology.

authors

Auffinger P,Hays FA,Westhof E,Ho PS

doi

10.1073/pnas.0407607101

keywords:

subject

Has Abstract

pub_date

2004-11-30 00:00:00

pages

16789-94

issue

48

eissn

0027-8424

issn

1091-6490

pii

0407607101

journal_volume

101

pub_type

杂志文章
  • Modern origin of numerous alternatively spliced human introns from tandem arrays.

    abstract::Despite the widespread occurrence of spliceosomal introns in the genomes of higher eukaryotes, their origin remains controversial. One model proposes that the duplication of small genomic portions could have provided the boundaries for new introns. If this mechanism has occurred recently, the 5' and 3' boundaries of e...

    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.0604777104

    authors: Zhuo D,Madden R,Elela SA,Chabot B

    更新日期:2007-01-16 00:00:00

  • Sucrose biosynthesis in a prokaryotic organism: Presence of two sucrose-phosphate synthases in Anabaena with remarkable differences compared with the plant enzymes.

    abstract::Biosynthesis of sucrose-6-P catalyzed by sucrose-phosphate synthase (SPS), and the presence of sucrose-phosphate phosphatase (SPP) leading to the formation of sucrose, have both been ascertained in a prokaryotic organism: Anabaena 7119, a filamentous heterocystic cyanobacterium. Two SPS activities (SPS-I and SPS-II) 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.93.24.13600

    authors: Porchia AC,Salerno GL

    更新日期:1996-11-26 00:00:00

  • Master curve of boosted diffusion for 10 catalytic enzymes.

    abstract::Molecular agitation more rapid than thermal Brownian motion is reported for cellular environments, motor proteins, synthetic molecular motors, enzymes, and common chemical reactions, yet that chemical activity coupled to molecular motion contrasts with generations of accumulated knowledge about diffusion at equilibriu...

    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.2019810117

    authors: Jee AY,Tlusty T,Granick S

    更新日期:2020-11-24 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

  • Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing.

    abstract::Bar-coded multiplexed sequencing approaches based on new-generation sequencing technologies provide capacity to sequence a mapping population in a single sequencing run. However, such approaches usually generate low-coverage and error-prone sequences for each line in a population. Thus, it is a significant challenge 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.1005931107

    authors: Xie W,Feng Q,Yu H,Huang X,Zhao Q,Xing Y,Yu S,Han B,Zhang Q

    更新日期:2010-06-08 00:00:00

  • Class I MHC molecules on hematopoietic cells can support intrathymic positive selection of T cell receptor transgenic T cells.

    abstract::The identity of cells that mediate positive selection of CD8(+) T cells was investigated in two T cell receptor (TCR) transgenic systems. Irradiated beta(2)-microglobulin mutant mice or mice with mutations in both the K(b) and D(b) genes were repopulated with fetal liver cells from class I(+) TCR transgenic mice. In 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.96.20.11470

    authors: Zerrahn J,Volkmann A,Coles MC,Held W,Lemonnier FA,Raulet DH

    更新日期:1999-09-28 00:00:00

  • A predictive, size-dependent continuum model for dense granular flows.

    abstract::Dense granular materials display a complicated set of flow properties, which differentiate them from ordinary fluids. Despite their ubiquity, no model has been developed that captures or predicts the complexities of granular flow, posing an obstacle in industrial and geophysical applications. Here we propose a 3D cons...

    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.1219153110

    authors: Henann DL,Kamrin K

    更新日期:2013-04-23 00:00:00

  • Genetic absolute dating based on microsatellites and the origin of modern humans.

    abstract::We introduce a new genetic distance for microsatellite loci, incorporating features of the stepwise mutation model, and test its performance on microsatellite polymorphisms in humans, chimpanzees, and gorillas. We find that it performs well in determining the relations among the primates, but less well than other dist...

    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.92.15.6723

    authors: Goldstein DB,Ruiz Linares A,Cavalli-Sforza LL,Feldman MW

    更新日期:1995-07-18 00:00:00

  • Regulation of binding properties of the nicotinic receptor protein by cholinergic ligands in membrane fragments from Torpedo marmorata.

    abstract::Exposure of receptor-rich membrane fragments from Torpedo marmorata to carbamylcholine causes a slow (half-time of 5--10 min) and reversible change of properties of the cholinergic receptor protein manifested by a decrease of the initial rate of Naja nigricollis alpha-[3H]toxin binding in the presence of carbamylcholi...

    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.72.9.3443

    authors: Weber M,David-Pfeuty T,Changeux JP

    更新日期:1975-09-01 00:00:00

  • Fusogenic segments of bovine leukemia virus and simian immunodeficiency virus are interchangeable and mediate fusion by means of oblique insertion in the lipid bilayer of their target cells.

    abstract::Modified bovine leukemia virus (BLV) glycoproteins were expressed by using vaccinia virus recombinants, and their fusogenic capacities were examined by a syncytia-formation assay. This analysis indicates that (i) both BLV envelope glycoproteins gp51 and gp30 are necessary for cell fusion; (ii) insertion of the N-termi...

    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.89.9.3810

    authors: Vonèche V,Portetelle D,Kettmann R,Willems L,Limbach K,Paoletti E,Ruysschaert JM,Burny A,Brasseur R

    更新日期:1992-05-01 00:00:00

  • Dominant-negative cyclin-selective ubiquitin carrier protein E2-C/UbcH10 blocks cells in metaphase.

    abstract::Destruction of mitotic cyclins by ubiquitin-dependent proteolysis is required for cells to complete mitosis and enter interphase of the next cell cycle. In clam eggs, this process is catalyzed by a cyclin-selective ubiquitin carrier protein, E2-C, and the cyclosome/anaphase promoting complex (APC), a 20S particle cont...

    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.94.6.2362

    authors: Townsley FM,Aristarkhov A,Beck S,Hershko A,Ruderman JV

    更新日期:1997-03-18 00:00:00

  • Contribution of phenotypic heterogeneity to adaptive antibiotic resistance.

    abstract::Antibiotic-resistant isolates of Salmonella enterica were selected on plates containing lethal concentrations of rifampicin, kanamycin, and nalidixic acid. The stability of the resistance phenotype was scored after nonselective growth. Rifampicin-resistant (Rif(r)) isolates were stable, suggesting that they had arisen...

    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.1316084111

    authors: Sánchez-Romero MA,Casadesús J

    更新日期:2014-01-07 00:00:00

  • Termination of transcription by Escherichia coli RNA polymerase: influence of secondary structure of RNA transcripts on rho-independent and rho-dependent termination.

    abstract::The effect of RNA secondary structure on rho-independent and rho-dependent termination of transcription of T3 DNA by Escherichia coli RNA polymerase has been studied by incorporating, into nascent transcripts, base analogs that lead to altered base-pairing properties. A guanine --> hypoxanthine substitution, with atte...

    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.76.4.1613

    authors: Adhya S,Sarkar P,Valenzuela D,Maitra U

    更新日期:1979-04-01 00:00:00

  • p47 licenses activation of the immune deficiency pathway in the tick Ixodes scapularis.

    abstract::The E3 ubiquitin ligase X-linked inhibitor of apoptosis (XIAP) acts as a molecular rheostat for the immune deficiency (IMD) pathway of the tick Ixodes scapularis How XIAP activates the IMD pathway in response to microbial infection remains ill defined. Here, we identified the XIAP enzymatic substrate p47 as a positive...

    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.1808905116

    authors: McClure Carroll EE,Wang X,Shaw DK,O'Neal AJ,Oliva Chávez AS,Brown LJ,Boradia VM,Hammond HL,Pedra JHF

    更新日期:2019-01-02 00:00:00

  • The Ndc80 kinetochore complex directly modulates microtubule dynamics.

    abstract::The conserved Ndc80 complex is an essential microtubule-binding component of the kinetochore. Recent findings suggest that the Ndc80 complex influences microtubule dynamics at kinetochores in vivo. However, it was unclear if the Ndc80 complex mediates these effects directly, or by affecting other factors localized at ...

    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.1209615109

    authors: Umbreit NT,Gestaut DR,Tien JF,Vollmar BS,Gonen T,Asbury CL,Davis TN

    更新日期:2012-10-02 00:00:00

  • Effects of in vivo adventitial expression of recombinant endothelial nitric oxide synthase gene in cerebral arteries.

    abstract::Nitric oxide (NO), synthesized from L-arginine by NO synthases (NOS), plays an essential role in the regulation of cerebrovascular tone. Adenoviral vectors have been widely used to transfer recombinant genes to different vascular beds. To determine whether the recombinant endothelial NOS (eNOS) gene can be delivered i...

    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.94.23.12568

    authors: Chen AF,Jiang SW,Crotty TB,Tsutsui M,Smith LA,O'Brien T,Katusic ZS

    更新日期:1997-11-11 00:00:00

  • Ecological character displacement in Plethodon: biomechanical differences found from a geometric morphometric study.

    abstract::Ecological character displacement describes a pattern where morphological differences between sympatric species are enhanced through interspecific competition. Although widely considered a pervasive force in evolutionary ecology, few clear-cut examples have been documented. Here we report a case of ecological characte...

    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.97.8.4106

    authors: Adams DC,Rohlf FJ

    更新日期:2000-04-11 00:00:00

  • Pineal control of aging: effect of melatonin and pineal grafting on aging mice.

    abstract::Dark-cycle, night administration of the pineal hormone melatonin in drinking water to aging mice (15 months of age) prolongs survival of BALB/c females from 23.8 to 28.1 months and preserves aspects of their youthful state. Similar results were seen in New Zealand Black females beginning at 5 months and C57BL/6 males ...

    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.91.2.787

    authors: Pierpaoli W,Regelson W

    更新日期:1994-01-18 00:00:00

  • Two forms of yeast glycogen synthetase and their role in glycogen accumulation.

    abstract::The glycogen content of yeast rises dramatically just before the onset of the stationary phase of growth. Concomitantly, a rapid increase was found in the glucose 6-phosphate-independent (I) activity of glycogen synthetase, as well as in the total amount of enzyme. A mutant (GS 1-36) was obtained, which did not accumu...

    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.66.3.967

    authors: Rothman-Denes LB,Cabib E

    更新日期:1970-07-01 00:00:00

  • Photochromic activators of the acetylcholine receptor.

    abstract::Two photochromic activators of the electrogenic membrane of the electroplax of Electrophorus electricus are described. Trans-3,3'-bis[alpha-(trimethylammonium)methyl]azobenzene dibromide (Bis-Q), one of the most potent ever reported, is active at concentrations of less than 10(-7) M. Its cis isomer, which is obtained ...

    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.68.8.1820

    authors: Bartels E,Wassermann NH,Erlanger BF

    更新日期:1971-08-01 00:00:00

  • Shear stress regulates the endothelial Kir2.1 ion channel.

    abstract::Endothelial cells (ECs) line the mammalian vascular system and respond to the hemodynamic stimulus of fluid shear stress, the frictional force produced by blood flow. When ECs are exposed to shear stress, one of the fastest responses is an increase of K(+) conductance, which suggests that ion channels are involved 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.102184999

    authors: Hoger JH,Ilyin VI,Forsyth S,Hoger A

    更新日期:2002-05-28 00:00:00

  • Population genetic structure of Plasmodium falciparum in the two main African vectors, Anopheles gambiae and Anopheles funestus.

    abstract::We investigated patterns of genetic diversity of Plasmodium falciparum associated with its two main African vectors: Anopheles gambiae and Anopheles funestus. We dissected 10,296 wild-caught mosquitoes from three tropical sites, two in Cameroon (Simbock and Tibati, separated by 320 km) and one in Kenya (Rota, >2,000 k...

    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.0702715104

    authors: Annan Z,Durand P,Ayala FJ,Arnathau C,Awono-Ambene P,Simard F,Razakandrainibe FG,Koella JC,Fontenille D,Renaud F

    更新日期:2007-05-08 00:00:00

  • Crystal structure of the antigen-binding fragment of the murine anti-arsonate monoclonal antibody 36-71 at 2.9-A resolution.

    abstract::The structure of the antigen-binding fragment (Fab) of an anti-phenylarsonate monoclonal antibody (36-71) bearing a major crossreacting idiotype of A/J mice has been solved and refined to an R factor of 19.3% at a resolution of 2.9 A. An initial electron density map was obtained with phase information from a total 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.87.1.338

    authors: Rose DR,Strong RK,Margolies MN,Gefter ML,Petsko GA

    更新日期:1990-01-01 00:00:00

  • Single cell sequencing reveals low levels of aneuploidy across mammalian tissues.

    abstract::Whole-chromosome copy number alterations, also known as aneuploidy, are associated with adverse consequences in most cells and organisms. However, high frequencies of aneuploidy have been reported to occur naturally in the mammalian liver and brain, fueling speculation that aneuploidy provides a selective advantage 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.1415287111

    authors: Knouse KA,Wu J,Whittaker CA,Amon A

    更新日期:2014-09-16 00:00:00

  • Oil platforms off California are among the most productive marine fish habitats globally.

    abstract::Secondary (i.e., heterotrophic or animal) production is a main pathway of energy flow through an ecosystem as it makes energy available to consumers, including humans. Its estimation can play a valuable role in the examination of linkages between ecosystem functions and services. We found that oil and gas platforms 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.1411477111

    authors: Claisse JT,Pondella DJ 2nd,Love M,Zahn LA,Williams CM,Williams JP,Bull AS

    更新日期:2014-10-28 00:00:00

  • Strand specificity in the transcriptional targeting of recombination at immunoglobulin switch sequences.

    abstract::B-lymphocyte-specific class switch recombination is known to occur between pairs of 2- to 10-kb switch regions located immediately upstream of the immunoglobulin constant heavy-chain genes. Others have shown that the recombination is temporally correlated with the induction of transcription at the targeted switch regi...

    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.92.12.5625

    authors: Daniels GA,Lieber MR

    更新日期:1995-06-06 00:00:00

  • Sustained effects of brief daily stress (fighting) upon brain and adrenal catecholamines and adrenal spleen, and heart weights of mice.

    abstract::Male white Swiss mice that had previously been made aggressive by several weeks of individual housing were allowed to fight for 5 to 10 minutes each day for 5, 10, or 14 consecutive days; fighting caused a marked enlargement of their adrenals, spleens, and hearts, and a large increase in adrenal catecholamines; brain ...

    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.64.1.100

    authors: Welch BL,Welch AS

    更新日期:1969-09-01 00:00:00

  • Physical interaction between the serotonin transporter and neuronal nitric oxide synthase underlies reciprocal modulation of their activity.

    abstract::The spatiotemporal regulation of neurotransmitter transporters involves proteins that interact with their intracellular domains. Using a proteomic approach, we identified several proteins that interact with the C terminus of the serotonin transporter (SERT). These included neuronal nitric oxide synthase (nNOS), a PSD-...

    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.0610964104

    authors: Chanrion B,Mannoury la Cour C,Bertaso F,Lerner-Natoli M,Freissmuth M,Millan MJ,Bockaert J,Marin P

    更新日期:2007-05-08 00:00:00

  • Identification and origin of some chloroplast aminoacyl-tRNA synthetases and tRNAs.

    abstract::Light-grown, wild type Euglena gracilis contains two aminoacyl-tRNA synthetases for both phenylalanine and isoleucine. Only one of the two synthetases for each amino acid is found in isolated chloroplasts, as are the light-induced phenylalanine and isoleucine tRNAs. In each case the light-induced chloroplast tRNAs can...

    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.67.3.1207

    authors: Reger BJ,Fairfield SA,Epler JL,Barnett WE

    更新日期:1970-11-01 00:00:00

  • IL-33 exacerbates antigen-induced arthritis by activating mast cells.

    abstract::IL-33, a cytokine of the IL-1 family, is closely associated with type II T cell responses. Here, we report an unexpected proinflammatory role of IL-33 in inflammatory arthritis. IL-33 was expressed in synovial fibroblasts from patients with rheumatoid arthritis (RA). Expression was markedly elevated in vitro by inflam...

    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.0801898105

    authors: Xu D,Jiang HR,Kewin P,Li Y,Mu R,Fraser AR,Pitman N,Kurowska-Stolarska M,McKenzie AN,McInnes IB,Liew FY

    更新日期:2008-08-05 00:00:00