Insufficiently dehydrated hydrogen bonds as determinants of protein interactions.

Abstract:

:The prediction of binding sites and the understanding of interfaces associated with protein complexation remains an open problem in molecular biophysics. This work shows that a crucial factor in predicting and rationalizing protein-protein interfaces can be inferred by assessing the extent of intramolecular desolvation of backbone hydrogen bonds in monomeric structures. Our statistical analysis of native structures shows that, in the majority of soluble proteins, most backbone hydrogen bonds are thoroughly wrapped intramolecularly by nonpolar groups except for a few ones. These latter underwrapped hydrogen bonds may be dramatically stabilized by removal of water. This fact implies that packing defects are "sticky" in a way that decisively contributes to determining the binding sites for proteins, as an examination of numerous complexes demonstrates.

authors

Fernández A,Scheraga HA

doi

10.1073/pnas.0136888100

keywords:

subject

Has Abstract

pub_date

2003-01-07 00:00:00

pages

113-8

issue

1

eissn

0027-8424

issn

1091-6490

pii

0136888100

journal_volume

100

pub_type

杂志文章
  • Observing the 1H NMR signal of the myoglobin Val-E11 in myocardium: an index of cellular oxygenation.

    abstract::The 1H NMR signal from oxymyoglobin, a low-concentration diamagnetic protein, is visible in myocardial tissue. The methyl group of the Val-E11 resonates in a clear spectral region at -2.76 ppm and responds to dynamic changes in cellular oxygenation. With CO, the signal shifts to -2.4 ppm. The Val-E11 peak assignment 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.89.10.4731

    authors: Kreutzer U,Wang DS,Jue T

    更新日期:1992-05-15 00:00:00

  • Cloning and complete nucleotide sequence of human 5'-alpha-globin gene.

    abstract::We have cloned one of the two human alpha-globin genes and report its complete nucleotide sequence. The gene is 832 base pairs (bp) long from the 5'-cap site to the 3'-polyadenylylation site. The amino acid coding sequences are separated into three segments (exons) by two short (117 and 140 bp) intervening sequences. ...

    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.77.12.7054

    authors: Liebhaber SA,Goossens MJ,Kan YW

    更新日期:1980-12-01 00:00:00

  • Cloning and characterization of a cell surface receptor for xenotropic and polytropic murine leukemia viruses.

    abstract::Xenotropic and polytropic murine leukemia viruses (X-MLVs and P-MLVs) cross-interfere to various extents in non-mouse species and in wild Asian mice, suggesting that they might use a common receptor for infection. Consistent with this hypothesis, the susceptibility of some wild mice to X-MLVs has been mapped to the 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.96.3.927

    authors: Tailor CS,Nouri A,Lee CG,Kozak C,Kabat D

    更新日期:1999-02-02 00:00:00

  • Mature T cells of autoimmune lpr/lpr mice have a defect in antigen-stimulated suicide.

    abstract::Antigen receptor-stimulated cell death of developing, immature T cells plays an important role in shaping the repertoire of antigens to which mature T cells will respond, but a role for receptor-stimulated death in controlling responses of mature T cells is controversial. Mutant lpr/lpr mice exhibit an autoimmune synd...

    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.90.10.4409

    authors: Russell JH,Rush B,Weaver C,Wang R

    更新日期:1993-05-15 00:00:00

  • Tertiary structure of an amyloid immunoglobulin light chain protein: a proposed model for amyloid fibril formation.

    abstract::An immunoglobulin light chain protein was isolated from the urine of an individual (BRE) with systemic amyloidosis. Complete amino acid sequence of the variable region of the light chain (VL) protein established it as a kappa I, which when compared with other kappa I amyloid associated proteins had unique residues, 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.92.21.9490

    authors: Schormann N,Murrell JR,Liepnieks JJ,Benson MD

    更新日期:1995-10-10 00:00:00

  • The p53-dependent effects of macrophage migration inhibitory factor revealed by gene targeting.

    abstract::Macrophage migration inhibitory factor (MIF) is a mediator of host immunity and functions as a high, upstream activator of cells within the innate and the adaptive immunological systems. Recent studies have suggested a potentially broader role for MIF in growth regulation because of its ability to antagonize p53-media...

    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.1533295100

    authors: Fingerle-Rowson G,Petrenko O,Metz CN,Forsthuber TG,Mitchell R,Huss R,Moll U,Müller W,Bucala R

    更新日期:2003-08-05 00:00:00

  • The origin of the eukaryotic cell: a genomic investigation.

    abstract::We have collected a set of 347 proteins that are found in eukaryotic cells but have no significant homology to proteins in Archaea and Bacteria. We call these proteins eukaryotic signature proteins (ESPs). The dominant hypothesis for the formation of the eukaryotic cell is that it is a fusion of an archaeon with a bac...

    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.032658599

    authors: Hartman H,Fedorov A

    更新日期:2002-02-05 00:00:00

  • Enhancing the antitumor efficacy of a cell-surface death ligand by covalent membrane display.

    abstract::TNF superfamily death ligands are expressed on the surface of immune cells and can trigger apoptosis in susceptible cancer cells by engaging cognate death receptors. A recombinant soluble protein comprising the ectodomain of Apo2 ligand/TNF-related apoptosis-inducing ligand (Apo2L/TRAIL) has shown remarkable preclinic...

    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.1418962112

    authors: Nair PM,Flores H,Gogineni A,Marsters S,Lawrence DA,Kelley RF,Ngu H,Sagolla M,Komuves L,Bourgon R,Settleman J,Ashkenazi A

    更新日期:2015-05-05 00:00:00

  • DNA double-strand break repair proteins are required to cap the ends of mammalian chromosomes.

    abstract::Recent findings intriguingly place DNA double-strand break repair proteins at chromosome ends in yeast, where they help maintain normal telomere length and structure. In the present study, an essential telomere function, the ability to cap and thereby protect chromosomes from end-to-end fusions, was assessed in repair...

    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.96.26.14899

    authors: Bailey SM,Meyne J,Chen DJ,Kurimasa A,Li GC,Lehnert BE,Goodwin EH

    更新日期:1999-12-21 00:00:00

  • Mortality invariants and their genetic implications.

    abstract::Old noninbred fly mortality decreases according to the inverse linear law and reduces to a single suborder-specific age. Relative child mortality (the mortality at a given age related to the mortality at 10 years) from 1 mo to 11 years is the same with 8% mean accuracy for all humans, independent of race, country, sex...

    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.95.15.9037

    authors: Azbel' MY

    更新日期:1998-07-21 00:00:00

  • Disruption of the M80-Fe ligation stimulates the translocation of cytochrome c to the cytoplasm and nucleus in nonapoptotic cells.

    abstract::Native cytochrome c (cyt c) has a compact tertiary structure with a hexacoordinated heme iron and functions in electron transport in mitochondria and apoptosis in the cytoplasm. However, the possibility that protein modifications confer additional functions to cyt c has not been explored. Disruption of methionine 80 (...

    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.0809279106

    authors: Godoy LC,Muñoz-Pinedo C,Castro L,Cardaci S,Schonhoff CM,King M,Tórtora V,Marín M,Miao Q,Jiang JF,Kapralov A,Jemmerson R,Silkstone GG,Patel JN,Evans JE,Wilson MT,Green DR,Kagan VE,Radi R,Mannick JB

    更新日期:2009-02-24 00:00:00

  • T-cell receptor usage by melanoma-specific clonal and highly oligoclonal tumor-infiltrating lymphocyte lines.

    abstract::Tumor-infiltrating lymphocytes (TIL) obtained from human melanomas can specifically lyse autologous tumor in vitro and mediate tumor regression in vivo. To develop more effective therapeutic reagents and to further understand the T-cell response to tumors, the diversity of T-cell receptors (TCRs) involved in melanoma ...

    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.91.7.2829

    authors: Shilyansky J,Nishimura MI,Yannelli JR,Kawakami Y,Jacknin LS,Charmley P,Rosenberg SA

    更新日期:1994-03-29 00:00:00

  • Poly(A) binding protein abundance regulates eukaryotic translation initiation factor 4F assembly in human cytomegalovirus-infected cells.

    abstract::By commandeering cellular translation initiation factors, or destroying those dispensable for viral mRNA translation, viruses often suppress host protein synthesis. In contrast, cellular protein synthesis proceeds in human cytomegalovirus (HCMV)-infected cells, forcing viral and cellular mRNAs to compete for limiting ...

    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.1202829109

    authors: McKinney C,Perez C,Mohr I

    更新日期:2012-04-10 00:00:00

  • Growth of a pure population of mouse mast cells in vitro with conditioned medium derived from concanavalin A-stimulated splenocytes.

    abstract::A pure population of mast cells was obtained after 14 days of culturing mouse bone marrow cells in the presence of medium derived from concanavalin A-stimulated mouse spleen cells. The cells were characterized as mast cells by their morphologic appearance and histologic staining, by their histamine content (450 ng per...

    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.78.4.2559

    authors: Razin E,Cordon-Cardo C,Good RA

    更新日期:1981-04-01 00:00:00

  • Enhanced optical properties of chemical vapor deposited single crystal diamond by low-pressure/high-temperature annealing.

    abstract::Single crystal diamond produced by chemical vapor deposition (CVD) at very high growth rates (up to 150 microm/h) has been successfully annealed without graphitization at temperatures up to 2200 degrees C and pressures <300 torr. Crystals were annealed in a hydrogen environment by using microwave plasma techniques 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.0808230105

    authors: Meng YF,Yan CS,Lai J,Krasnicki S,Shu H,Yu T,Liang Q,Mao HK,Hemley RJ

    更新日期:2008-11-18 00:00:00

  • Phototropin perceives temperature based on the lifetime of its photoactivated state.

    abstract::Living organisms detect changes in temperature using thermosensory molecules. However, these molecules and/or their mechanisms for sensing temperature differ among organisms. To identify thermosensory molecules in plants, we investigated chloroplast positioning in response to temperature changes and identified a blue-...

    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.1704462114

    authors: Fujii Y,Tanaka H,Konno N,Ogasawara Y,Hamashima N,Tamura S,Hasegawa S,Hayasaki Y,Okajima K,Kodama Y

    更新日期:2017-08-22 00:00:00

  • Stress impairs cognitive flexibility in infants.

    abstract::In human adults, learning and memory under acute stress are characterized by an increased use of rigid habitual response strategies at the cost of flexible cognitive strategies. The immediate effects of stress on cognitive functioning early in life are not well understood. Here we show experimentally that acute stress...

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

    pub_type: 临床试验,杂志文章

    doi:10.1073/pnas.1508345112

    authors: Seehagen S,Schneider S,Rudolph J,Ernst S,Zmyj N

    更新日期:2015-10-13 00:00:00

  • Dual regulation of NR2B and NR2C expression by NMDA receptor activation in mouse cerebellar granule cell cultures.

    abstract::In the developing cerebellum, switching of the subunit composition of NMDA receptors occurs in granule cells from NR2B-containing receptors to NR2C-containing ones. We investigated the mechanisms underlying switching of NR2B and NR2C subunit composition in primary cultures of mouse granule cells at the physiological 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.0805574105

    authors: Iijima K,Abe H,Okazawa M,Moriyoshi K,Nakanishi S

    更新日期:2008-08-19 00:00:00

  • Spontaneous wettability patterning via creasing instability.

    abstract::Surfaces with patterned wettability contrast are important in industrial applications such as heat transfer, water collection, and particle separation. Traditional methods of fabricating such surfaces rely on microfabrication technologies, which are only applicable to certain substrates and are difficult to scale up 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.1522700113

    authors: Chen D,McKinley GH,Cohen RE

    更新日期:2016-07-19 00:00:00

  • Secretion and autoproteolytic maturation of subtilisin.

    abstract::The sequence of the cloned Bacillus amyloliquefaciens subtilisin gene suggested that this secreted serine protease is produced as a larger precursor, designated preprosubtilisin [Wells, J. A., Ferrari, E., Henner, D. J., Estell, D. A. & Chen, E. Y. (1983) Nucleic Acids Res. 11, 7911-7925]. Biochemical evidence present...

    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.83.10.3096

    authors: Power SD,Adams RM,Wells JA

    更新日期:1986-05-01 00:00:00

  • Primary structure of an extracellular matrix proteoglycan core protein deduced from cloned cDNA.

    abstract::The core protein of a small chondroitin/dermatan sulfate proteoglycan expressed by human fibroblasts and present in extracellular matrices in association with collagen has been cloned from a lambda gt11 fibroblast cDNA library. cDNA clones were isolated by use of antibodies specific for the intact proteoglycan and ant...

    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.83.20.7683

    authors: Krusius T,Ruoslahti E

    更新日期:1986-10-01 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

  • Squid Pax-6 and eye development.

    abstract::Pax-6 in vertebrates and its homolog eyeless in Drosophila are known to be essential for eye development. Here we investigate the role of Pax-6 in eye development in another major systematic group, molluscs. We demonstrate that alternatively spliced RNAs derived from a single Pax-6 gene in the squid (Loligo opalescens...

    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.94.6.2421

    authors: Tomarev SI,Callaerts P,Kos L,Zinovieva R,Halder G,Gehring W,Piatigorsky J

    更新日期:1997-03-18 00:00:00

  • Identification of a nuclear domain with deacetylase activity.

    abstract::Here, we describe the identification and characterization of a nuclear body (matrix-associated deacetylase body) whose formation and integrity depend on deacetylase activity. Typically, there are 20-40 0.5-microM bodies per nucleus, although the size and number can vary substantially. The structure appears to contain ...

    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.97.19.10330

    authors: Downes M,Ordentlich P,Kao HY,Alvarez JG,Evans RM

    更新日期:2000-09-12 00:00:00

  • The human sex-reversing ATRX gene has a homologue on the marsupial Y chromosome, ATRY: implications for the evolution of mammalian sex determination.

    abstract::Mutations in the ATRX gene on the human X chromosome cause X-linked alpha-thalassemia and mental retardation. XY patients with deletions or mutations in this gene display varying degrees of sex reversal, implicating ATRX in the development of the human testis. To explore further the role of ATRX in mammalian sex diffe...

    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.230424497

    authors: Pask A,Renfree MB,Marshall Graves JA

    更新日期:2000-11-21 00:00:00

  • Geographically varying associations between personality and life satisfaction in the London metropolitan area.

    abstract::Residential location is thought to influence people's well-being, but different individuals may value residential areas differently. We examined how life satisfaction and personality traits are geographically distributed within the UK London metropolitan area, and how the strength of associations between personality 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.1415800112

    authors: Jokela M,Bleidorn W,Lamb ME,Gosling SD,Rentfrow PJ

    更新日期:2015-01-20 00:00:00

  • Calcium-dependent oligomerization of CAR proteins at cell membrane modulates ABA signaling.

    abstract::Regulation of ion transport in plants is essential for cell function. Abiotic stress unbalances cell ion homeostasis, and plants tend to readjust it, regulating membrane transporters and channels. The plant hormone abscisic acid (ABA) and the second messenger Ca(2+) are central in such processes, as they are involved ...

    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.1512779113

    authors: Diaz M,Sanchez-Barrena MJ,Gonzalez-Rubio JM,Rodriguez L,Fernandez D,Antoni R,Yunta C,Belda-Palazon B,Gonzalez-Guzman M,Peirats-Llobet M,Menendez M,Boskovic J,Marquez JA,Rodriguez PL,Albert A

    更新日期:2016-01-19 00:00:00

  • Specificity and robustness of long-distance connections in weighted, interareal connectomes.

    abstract::Brain areas' functional repertoires are shaped by their incoming and outgoing structural connections. In empirically measured networks, most connections are short, reflecting spatial and energetic constraints. Nonetheless, a small number of connections span long distances, consistent with the notion that the functiona...

    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.1720186115

    authors: Betzel RF,Bassett DS

    更新日期:2018-05-22 00:00:00

  • An empirical basis for Mach bands.

    abstract::Mach bands, the illusory brightness maxima and minima perceived at the initiation and termination of luminance gradients, respectively, are generally considered a direct perceptual manifestation of lateral inhibitory interactions among retinal or other lower order visual neurons. Here we examine an alternative explana...

    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.96.9.5239

    authors: Lotto RB,Williams SM,Purves D

    更新日期:1999-04-27 00:00:00

  • cDNA cloning reveals that the major group rhinovirus receptor on HeLa cells is intercellular adhesion molecule 1.

    abstract::A 90-kDa surface glycoprotein was previously isolated and shown to be required for infection by the "major" group of human rhinovirus (HRV) serotypes. In the present work, the amino acid sequence of the receptor protein was obtained from CNBr and tryptic peptides. Using degenerate oligonucleotides predicted from the 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.86.13.4907

    authors: Tomassini JE,Graham D,DeWitt CM,Lineberger DW,Rodkey JA,Colonno RJ

    更新日期:1989-07-01 00:00:00