Inhibition of human pancreatic ribonuclease by the human ribonuclease inhibitor protein.

Abstract:

:The ribonuclease inhibitor protein (RI) binds to members of the bovine pancreatic ribonuclease (RNase A) superfamily with an affinity in the femtomolar range. Here, we report on structural and energetic aspects of the interaction between human RI (hRI) and human pancreatic ribonuclease (RNase 1). The structure of the crystalline hRI x RNase 1 complex was determined at a resolution of 1.95 A, revealing the formation of 19 intermolecular hydrogen bonds involving 13 residues of RNase 1. In contrast, only nine such hydrogen bonds are apparent in the structure of the complex between porcine RI and RNase A. hRI, which is anionic, also appears to use its horseshoe-shaped structure to engender long-range Coulombic interactions with RNase 1, which is cationic. In accordance with the structural data, the hRI.RNase 1 complex was found to be extremely stable (t(1/2)=81 days; K(d)=2.9 x 10(-16) M). Site-directed mutagenesis experiments enabled the identification of two cationic residues in RNase 1, Arg39 and Arg91, that are especially important for both the formation and stability of the complex, and are thus termed "electrostatic targeting residues". Disturbing the electrostatic attraction between hRI and RNase 1 yielded a variant of RNase 1 that maintained ribonucleolytic activity and conformational stability but had a 2.8 x 10(3)-fold lower association rate for complex formation and 5.9 x 10(9)-fold lower affinity for hRI. This variant of RNase 1, which exhibits the largest decrease in RI affinity of any engineered ribonuclease, is also toxic to human erythroleukemia cells. Together, these results provide new insight into an unusual and important protein-protein interaction, and could expedite the development of human ribonucleases as chemotherapeutic agents.

journal_name

J Mol Biol

authors

Johnson RJ,McCoy JG,Bingman CA,Phillips GN Jr,Raines RT

doi

10.1016/j.jmb.2007.02.005

subject

Has Abstract

pub_date

2007-04-27 00:00:00

pages

434-49

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(07)00168-4

journal_volume

368

pub_type

杂志文章
  • Shape-specific nucleotide binding of single-stranded RNA by the GLD-1 STAR domain.

    abstract::Proteins containing the STAR RNA-binding domain fulfill vital roles in RNA biogenesis, yet a detailed understanding of STAR domain RNA binding specificity is lacking. In Caenorhabditis elegans, the STAR protein GLD-1 directly binds the 28 nucleotide recognition element TGE within the 3' untranslated region of tra-2 mR...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.11.049

    authors: Lehmann-Blount KA,Williamson JR

    更新日期:2005-02-11 00:00:00

  • Are the molten globule and the unfolded states of apo-alpha-lactalbumin enthalpically equivalent?

    abstract::Recently, the absence of a thermally induced transition has been offered as proof that the unfolded and the molten globule states of apo-alpha-lactalbumin are enthalpically equivalent. In this paper we demonstrate that that argument is thermodynamically incorrect. In addition, it is shown that the absence of a thermal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1364

    authors: Xie D,Bhakuni V,Freire E

    更新日期:1993-07-05 00:00:00

  • Activity, stability and flexibility in glycosidases adapted to extreme thermal environments.

    abstract::To elucidate the strategy of low temperature adaptation for a cold-adapted family 8 xylanase, the thermal and chemical stabilities, thermal inactivation, thermodependence of activity and conformational flexibility, as well as the thermodynamic basis of these processes, were compared with those of a thermophilic homolo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00287-0

    authors: Collins T,Meuwis MA,Gerday C,Feller G

    更新日期:2003-04-25 00:00:00

  • A conserved unfoldase activity for the p97 AAA-ATPase in proteasomal degradation.

    abstract::The multifunctional AAA-ATPase p97 is one of the most abundant and conserved proteins in eukaryotic cells. The p97/Npl4/Ufd1 complex dislocates proteins that fail the protein quality control in the endoplasmic reticulum to the cytosol where they are subject to degradation by the ubiquitin/proteasome system. Substrate ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.09.050

    authors: Beskow A,Grimberg KB,Bott LC,Salomons FA,Dantuma NP,Young P

    更新日期:2009-12-11 00:00:00

  • Functional interactions of Mycobacterium leprae RuvA with Escherichia coli RuvB and RuvC on holliday junctions.

    abstract::The Mycobacterium leprae RuvA homologue (MlRuvA) was over-expressed in Escherichia coli and purified to homogeneity. The DNA-binding specificity and the functional interactions of MlRuvA with E. coli RuvB and RuvC (EcRuvB and EcRuvC) were examined using synthetic Holliday junctions. MlRuvA bound specifically to Hollid...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4009

    authors: Arenas-Licea J,van Gool AJ,Keeley AJ,Davies A,West SC,Tsaneva IR

    更新日期:2000-08-25 00:00:00

  • A zinc site in the C-terminal domain of RAG1 is essential for DNA cleavage activity.

    abstract::The recombination-activating protein, RAG1, a key component of the V(D)J recombinase, binds multiple Zn(2+) ions in its catalytically required core region. However, the role of zinc in the DNA cleavage activity of RAG1 is not well resolved. To address this issue, we determined the stoichiometry of Zn(2+) ions bound to...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.05.076

    authors: Gwyn LM,Peak MM,De P,Rahman NS,Rodgers KK

    更新日期:2009-07-31 00:00:00

  • A structural-informatics approach for mining beta-sheets: locating sheets in intermediate-resolution density maps.

    abstract::Here, we report a new computational method, called sheetminer, for mining beta-sheets in the density maps at intermediate resolutions of 6 to 10A. The method employs a multi-step ad hoc morphological analysis of density maps to identify the unique characteristics of beta-sheets. It was tested on density maps from 12 p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00859-3

    authors: Kong Y,Ma J

    更新日期:2003-09-12 00:00:00

  • Predictive QM/MM Modeling of Modulations in Protein-Protein Binding by Lysine Methylation.

    abstract::Lysine methylation is a key regulator of protein-protein binding. The amine group of lysine can accept up to three methyl groups, and experiments show that protein-protein binding free energies are sensitive to the extent of methylation. These sensitivities have been rationalized in terms of chemical and structural fe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.166745

    authors: Rahman S,Wineman-Fisher V,Al-Hamdani Y,Tkatchenko A,Varma S

    更新日期:2021-02-05 00:00:00

  • Peroxisome proliferator-activated receptor alpha controls hepatic heme biosynthesis through ALAS1.

    abstract::Heme is an essential prosthetic group of proteins involved in oxygen transport, energy metabolism and nitric oxide production. ALAS1 (5-aminolevulinate synthase) is the rate-limiting enzyme in heme synthesis in the liver and is highly regulated to adapt to the metabolic demand of the hepatocyte. In the present study, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,收录出版

    doi:10.1016/j.jmb.2009.03.024

    authors: Degenhardt T,Väisänen S,Rakhshandehroo M,Kersten S,Carlberg C

    更新日期:2009-05-01 00:00:00

  • From dusk till dawn: one-plasmid systems for light-regulated gene expression.

    abstract::Signaling photoreceptors mediate diverse organismal adaptations in response to light. As light-gated protein switches, signaling photoreceptors provide the basis for optogenetics, a term that refers to the control of organismal physiology and behavior by light. We establish as novel optogenetic tools the plasmids pDus...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.01.001

    authors: Ohlendorf R,Vidavski RR,Eldar A,Moffat K,Möglich A

    更新日期:2012-03-02 00:00:00

  • Enhanced specificity of mint geranyl pyrophosphate synthase by modifying the R-loop interactions.

    abstract::Isoprenoids, most of them synthesized by prenyltransferases (PTSs), are a class of important biologically active compounds with diverse functions. The mint geranyl pyrophosphate synthase (GPPS) is a heterotetramer composed of two LSU·SSU (large/small subunit) dimers. In addition to C(10)-GPP, the enzyme also produces ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.10.011

    authors: Hsieh FL,Chang TH,Ko TP,Wang AH

    更新日期:2010-12-17 00:00:00

  • Crystallization and preliminary X-ray diffraction study of the ligand-binding domain of the bacterial chemotaxis-mediating aspartate receptor of Salmonella typhimurium.

    abstract::The periplasmic domain of the aspartate chemotaxis receptor from Salmonella typhimurium has been crystallized in the presence and absence of bound aspartate. Both crystal forms were grown by precipitation with lithium sulfate and diffract to 1.8 A resolution. The aspartate receptor structure is believed to be prototyp...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)80198-4

    authors: Jancarik J,Scott WG,Milligan DL,Koshland DE Jr,Kim SH

    更新日期:1991-09-05 00:00:00

  • An ecdysterone-responsive puff site in Drosophila contains a cluster of seven differentially regulated genes.

    abstract::We have determined the molecular organization of an ecdysterone-responsive puff site in Drosophila melanogaster. The 71E puff site contains a tightly linked cluster of at least seven genes within a neighborhood of 10 X 10(3) base-pairs. All the genes are expressed in a tissue-specific manner in either the larval or th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(86)80002-x

    authors: Restifo LL,Guild GM

    更新日期:1986-04-20 00:00:00

  • Carbohydrate specificity and quaternary association in basic winged bean lectin: X-ray analysis of the lectin at 2.5 A resolution.

    abstract::The structure of basic Winged Bean Agglutinin (WBAI) with two dimeric molecules complexed with methyl-alpha-D-galactopyranoside in the asymmetric unit, has been determined by the molecular replacement method and refined with 2.5 A X-ray intensity data. The polypeptide chain of each monomer has the characteristic legum...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1568

    authors: Prabu MM,Sankaranarayanan R,Puri KD,Sharma V,Surolia A,Vijayan M,Suguna K

    更新日期:1998-03-06 00:00:00

  • Titration calculations of foot-and-mouth disease virus capsids and their stabilities as a function of pH.

    abstract::Foot-and-mouth disease virus (FMDV), a non-enveloped picornavirus, is sensitive to acidic conditions. At pH values below 7 the icosahedral virus capsid, formed from 60 copies of a protomer containing four polypeptides (VP1 to 4), dissociates into 12 pentamers, releasing the viral RNA. Evidence suggests that this acid ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1418

    authors: van Vlijmen HW,Curry S,Schaefer M,Karplus M

    更新日期:1998-01-16 00:00:00

  • The crystal structure of ZapA and its modulation of FtsZ polymerisation.

    abstract::FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. The widely conserved ZapA has been shown to interact with FtsZ, to drive its polymerisation and to promote FtsZ filament bundling thereby contributing to the spati...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.05.031

    authors: Low HH,Moncrieffe MC,Löwe J

    更新日期:2004-08-13 00:00:00

  • The reliability of in vivo structure-function analysis of tRNA aminoacylation.

    abstract::The G.U wobble base-pair in the acceptor helix of Escherichia coli tRNAAlais critical for aminoacylation by the alanine synthetase. Previous work by several groups probed the mechanism of enzyme recognition of G.U by a structure-function analysis of mutant tRNAs using either a cell assay (amber suppressor tRNA) or a t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2884

    authors: McClain WH,Jou YY,Bhattacharya S,Gabriel K,Schneider J

    更新日期:1999-07-09 00:00:00

  • Mutations in beta-myosin S2 that cause familial hypertrophic cardiomyopathy (FHC) abolish the interaction with the regulatory domain of myosin-binding protein-C.

    abstract::The myosin filaments of striated muscle contain a family of enigmatic myosin-binding proteins (MyBP), MyBP-C and MyBP-H. These modular proteins of the intracellular immunoglobulin superfamily contain unique domains near their N termini. The N-terminal domain of cardiac MyBP-C, the MyBP-C motif, contains additional pho...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.2522

    authors: Gruen M,Gautel M

    更新日期:1999-02-26 00:00:00

  • Highly cooperative recruitment of Ets-1 and release of autoinhibition by Pax5.

    abstract::Pax5 (paired box binding factor 5) is a critical regulator of transcription and lineage commitment in B lymphocytes. In B cells, mb-1 (Ig-alpha/immunoglobulin-associated alpha) promoter transcription is activated by Pax5 through its recruitment of E74-like transforming sequence (Ets) family proteins to a composite sit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.07.028

    authors: Fitzsimmons D,Lukin K,Lutz R,Garvie CW,Wolberger C,Hagman J

    更新日期:2009-09-18 00:00:00

  • Crystal structure of the antitoxin-toxin protein complex RelB-RelE from Methanococcus jannaschii.

    abstract::Here we present the crystal structure of the Methanococcus jannaschii RelE-RelB (RelBE) toxin-antitoxin (TA) protein complex determined by the MIRAS (multiple isomorphous replacement with anomalous signal) method. The genes encoding this TA system are located in the chromosome of this archaeon and involved in stress r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.08.048

    authors: Francuski D,Saenger W

    更新日期:2009-11-06 00:00:00

  • Mutational analysis of the pseudoknot in the tRNA-like structure of turnip yellow mosaic virus RNA. Aminoacylation efficiency and RNA pseudoknot stability.

    abstract::Site-directed mutations were introduced in the connecting loops and one of the two stem regions of the RNA pseudoknot in the tRNA-like structure of turnip yellow mosaic virus RNA. The kinetic parameters of valylation for each mutated RNA were determined in a cell-free extract from wheat germ. Structure mapping was per...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90727-2

    authors: Mans RM,Van Steeg MH,Verlaan PW,Pleij CW,Bosch L

    更新日期:1992-01-05 00:00:00

  • A group of repetitive human DNA families that is characterized by extrachromosomal oligomers and restriction-fragment length polymorphism.

    abstract::We have recently reported a novel human repetitive DNA (Sau3A family) that exists both in the chromosomes and in the extrachromosomal fraction. Several more clones that hybridized with the Sau3A family were isolated from the extrachromosomal fraction of HeLa cells. Use of these clones as probes has revealed that at le...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90342-1

    authors: Kiyama R,Matsui H,Okumura K,Oishi M

    更新日期:1987-02-20 00:00:00

  • Crystallization and preliminary crystallographic study of cytochrome cd1 nitrite reductase from Thiosphaera pantotropha.

    abstract::Single crystals of cytochrome cd1 nitrite reductase from Thiosphaera pantotropha have been grown in the presence of ammonium sulphate by vapour diffusion techniques. Crystals are suitable for X-ray analysis and diffract to dmin = 1.5 A. They belong to space group P2(1) with unit cell dimensions of a = 107.8 A, b = 61....

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1473

    authors: Fülöp V,Moir JW,Ferguson SJ,Hajdu J

    更新日期:1993-08-20 00:00:00

  • Active-site determination of a pyrimidine dimer glycosylase.

    abstract::One mechanism for the repair of UV-induced DNA damage is the base excision repair pathway. The initial step in this pathway and the specificity for the type of damage that is to be repaired reside in DNA glycosylase/abasic (AP) lyases. Cleavage of the glycosyl bond of the 5' pyrimidine of a cyclobutane pyrimidine dime...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3369

    authors: Garvish JF,Lloyd RS

    更新日期:2000-01-21 00:00:00

  • Local interactions dominate folding in a simple protein model.

    abstract::Recent computational studies of simple models of protein folding have concluded that a pronounced energy minimum (i.e. large gap in energy between low-energy states of the model) is a necessary and sufficient condition to ensure folding of a sequence to its lowest-energy conformation. Here, we show that this conclusio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0375

    authors: Unger R,Moult J

    更新日期:1996-06-28 00:00:00

  • Diversity of molecular transformations involved in the formation of spider silks.

    abstract::Spiders that spin orb webs secrete seven types of silk. Although the spinning process of the dragline thread is beginning to be understood, the molecular events that occur in spiders' opisthosomal glands, which produce the other fibers, are unknown due to a lack of data regarding their initial and final structures. Ta...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.10.052

    authors: Lefèvre T,Boudreault S,Cloutier C,Pézolet M

    更新日期:2011-01-07 00:00:00

  • Direct visualization of dynamics and co-operative conformational changes within RecA filaments that appear to be associated with the hydrolysis of adenosine 5'-O-(3-thiotriphosphate).

    abstract::Highly co-operative structural transitions and conformational changes can be directly observed in bundles of filaments formed by the RecA protein of Escherichia coli. These filaments have been formed with RecA protein, DNA and the ATP analog adenosine 5'-O-(3-thiotriphosphate) (ATP-gamma-S). We show that while ATP-gam...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)91036-o

    authors: Yu X,Egelman EH

    更新日期:1992-05-05 00:00:00

  • A Two-Component System Acquired by Horizontal Gene Transfer Modulates Gene Transfer and Motility via Cyclic Dimeric GMP.

    abstract::Bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) is an important intracellular signaling molecule that affects diverse physiological processes in bacteria. The intracellular levels of c-di-GMP are controlled by proteins acting as diguanylate cyclase (DGC) and phosphodiesterase (PDE) enzymes that synthesiz...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.07.001

    authors: Pallegar P,Canuti M,Langille E,Peña-Castillo L,Lang AS

    更新日期:2020-08-07 00:00:00

  • Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate.

    abstract::Set8 is the only mammalian monomethyltransferase responsible for H4K20me1, a methyl mark critical for genomic integrity of eukaryotic cells. We present here a structural model for how Set8 uses multivalent interactions to bind and methylate the nucleosome based on crystallographic and solution studies of the Set8/nucl...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.02.025

    authors: Girish TS,McGinty RK,Tan S

    更新日期:2016-04-24 00:00:00

  • Modular structure, local flexibility and cold-activity of a novel chitobiase from a psychrophilic Antarctic bacterium.

    abstract::The gene archb encoding for the cell-bound chitobiase from the Antarctic Gram-positive bacterium Arthrobacter sp. TAD20 was cloned and expressed in Escherichia coli in a soluble form. The mature chitobiase ArChb possesses four functionally independent domains: a catalytic domain stabilized by Ca(2+), a galactose-bindi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4774

    authors: Lonhienne T,Zoidakis J,Vorgias CE,Feller G,Gerday C,Bouriotis V

    更新日期:2001-07-06 00:00:00