Test of the contribution of an amino-aromatic hydrogen bond to protein function.

Abstract:

:Hydrogen bonds which form between a hydrogen bond donor and an aromatic ring as acceptor are thought to contribute to the stability and function of proteins. We have tested the function of such an interaction in a highly homologous pair of proteins, cellular retinol-binding protein (CRBP) and cellular retinol-binding protein, type II [CRBP(II)]. Both proteins bind the ligand all-trans-retinal with comparable affinities, but CRBP has an approximately 100-fold higher affinity for all-trans retinal. The greater affinity of CRBP for all-trans-retinol has been attributed to the presence of an amino-aromatic hydrogen bond, which is absent in CRBP(II). We have generated a pair of mutant proteins, in which the amino-aromatic interaction was removed from CRBP and introduced into CRBP(II). Spectral analyses of retinol when bound to the wild-type and mutant CRBP suggested that it adopted an identical conformation within both proteins, a conformation that was distinct from that of retinol bound to CRBP(II), both wild-type and mutant. Unexpectedly, the affinities of the mutant binding proteins for all-trans-retinol were indistinguishable from those of their corresponding wild-type proteins. Further, in ligand competition experiments, there were no observable differences between mutant and wild-type CRBP, or between mutant and wild-type CRBP(II), in their preferences for binding all-trans-retinol versus all-trans-retinal. The results of this direct test of the proposed function of an amino-aromatic hydrogen bond did not support a functional role for such bonds, at least in this system.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Jamison RS,Kakkad B,Ebert DH,Newcomer ME,Ong DE

doi

10.1021/bi00035a018

subject

Has Abstract

pub_date

1995-09-05 00:00:00

pages

11128-32

issue

35

eissn

0006-2960

issn

1520-4995

journal_volume

34

pub_type

杂志文章
  • Complete amino acid sequence of the 4Fe-4S, thermostable ferredoxin from Clostridium thermoaceticum.

    abstract::The complete amino acid sequence of the 4Fe-4S ferredoxin from the thermophilic bacterium Clostridium thermoaceticum has been determined. The protein is extremely thermostable and is the only known clostridial ferredoxin to contain a single [4Fe-4S] cluster. The sequence totals 63 residues and includes the first trypt...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00257a007

    authors: Elliott JI,Yang SS,Ljungdahl LG,Travis J,Reilly CF

    更新日期:1982-07-06 00:00:00

  • Studies on transcription of 3'-extended templates by mammalian RNA polymerase II. Parameters that affect the initiation and elongation reactions.

    abstract::Addition of short sequences of dCMP residues to the 3'-OH end of duplex linear DNAs allows rapid and efficient transcription to be initiated at these sites by purified mammalian RNA polymerase II [Kadesch, T. R., & Chamberlin, M. J. (1982) J. Biol. Chem. 257, 5286-5295]. The use of such tailed DNA templates should all...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00330a019

    authors: Dedrick RL,Chamberlin MJ

    更新日期:1985-04-23 00:00:00

  • Dihydrofolate reductase from Escherichia coli: probing the role of aspartate-27 and phenylalanine-137 in enzyme conformation and the binding of NADPH.

    abstract::In the absence of ligands, dihydrofolate reductase from Escherichia coli exists in at least two interconvertible conformations, only one of which binds NADPH with high affinity. This equilibrium is pH dependent, involving an ionizable group of the enzyme (pK approximately 5.5), and the proportion of the NADPH-binding ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00489a010

    authors: Dunn SM,Lanigan TM,Howell EE

    更新日期:1990-09-18 00:00:00

  • Dihydroorotase from the hyperthermophile Aquifex aeolicus is activated by stoichiometric association with aspartate transcarbamoylase and forms a one-pot reactor for pyrimidine biosynthesis.

    abstract::In prokaryotes, the first three enzymes in pyrimidine biosynthesis, carbamoyl phosphate synthetase (CPS), aspartate transcarbamoylase (ATC), and dihydroorotase (DHO), are commonly expressed separately and either function independently (Escherichia coli) or associate into multifunctional complexes (Aquifex aeolicus). I...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi801831r

    authors: Zhang P,Martin PD,Purcarea C,Vaishnav A,Brunzelle JS,Fernando R,Guy-Evans HI,Evans DR,Edwards BF

    更新日期:2009-02-03 00:00:00

  • Purification and characterization of a novel growth factor from human breast cancer cells.

    abstract::We have purified and characterized a novel 30-kDa glycoprotein (gp30) with TGF alpha-like properties secreted from the estrogen receptor negative breast cancer cell line MDA-MB-231. This factor was immunoprecipitated by an anti-TGF alpha polyclonal antibody and also had TGF alpha-like biological activity, as assayed b...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00147a018

    authors: Lupu R,Wellstein A,Sheridan J,Ennis BW,Zugmaier G,Katz D,Lippman ME,Dickson RB

    更新日期:1992-08-18 00:00:00

  • High-resolution crystal structures of the lectin-like xylan binding domain from Streptomyces lividans xylanase 10A with bound substrates reveal a novel mode of xylan binding.

    abstract::Carbohydrate-binding module (CBM) family 13 includes the "R-type" or "ricin superfamily" beta-trefoil lectins. The C-terminal CBM, CBM13, of xylanase 10A from Streptomyces lividans is a family 13 CBM that is not only structurally similar to the "R-type" lectins but also somewhat functionally similar. The primary funct...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi015865j

    authors: Notenboom V,Boraston AB,Williams SJ,Kilburn DG,Rose DR

    更新日期:2002-04-02 00:00:00

  • Hydrogen-deuterium exchange and mass spectrometry reveal the pH-dependent conformational changes of diphtheria toxin T domain.

    abstract::The translocation (T) domain of diphtheria toxin plays a critical role in moving the catalytic domain across the endosomal membrane. Translocation/insertion is triggered by a decrease in pH in the endosome where conformational changes of T domain occur through several kinetic intermediates to yield a final trans-membr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi500893y

    authors: Li J,Rodnin MV,Ladokhin AS,Gross ML

    更新日期:2014-11-04 00:00:00

  • Dehydroquinate synthase from Escherichia coli: purification, cloning, and construction of overproducers of the enzyme.

    abstract::Dehydroquinate synthase has been purified 9000-fold from Escherichia coli K-12 (strain MM294). The synthase is encoded by the aroB gene, which is carried by plasmid pLC29-47 from the Carbon-Clarke library. Construction of an appropriate host bearing pLC29-47 results in a strain that produces 20 times more enzyme than ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00314a036

    authors: Frost JW,Bender JL,Kadonaga JT,Knowles JR

    更新日期:1984-09-11 00:00:00

  • Substrate-dependent unfolding of the energy coupling motif of a membrane transport protein determined by double electron-electron resonance.

    abstract::BtuB is a TonB-dependent transport protein that binds and carries vitamin B(12) across the outer membrane of Gram negative bacteria such as Escherichia coli. Previous work has demonstrated that the Ton box, a highly conserved segment near the N-terminus of the protein, undergoes an order-to-disorder transition upon th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi061051x

    authors: Xu Q,Ellena JF,Kim M,Cafiso DS

    更新日期:2006-09-12 00:00:00

  • Evidence for rapid inter- and intramolecular chlorine transfer reactions of histamine and carnosine chloramines: implications for the prevention of hypochlorous-acid-mediated damage.

    abstract::Hypochlorous acid (HOCl) is a powerful oxidant generated from H(2)O(2) and Cl(-) by the heme enzyme myeloperoxidase, which is released from activated leukocytes. HOCl possesses potent antibacterial properties, but excessive production can lead to host tissue damage that is implicated in a wide range of human diseases ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi060348s

    authors: Pattison DI,Davies MJ

    更新日期:2006-07-04 00:00:00

  • A dynamic model for the structure of acyl carrier protein in solution.

    abstract::The determination of solution structures of proteins using two-dimensional NMR data is commonly based on the assumption that the structure can be represented by a single rigid conformer. We present here a procedure whereby this assumption can be relaxed and illustrate its application to acyl carrier protein from Esche...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00448a017

    authors: Kim Y,Prestegard JH

    更新日期:1989-10-31 00:00:00

  • Interactions between model proteins and deoxyribonucleic acids.

    abstract::Interactions between DNA and model proteins, poly(L-Lys(m)L-Ala(n)), where m + n = 100%, have been investigated using thermal denaturation and circular dichroism (CD). All complexes of DNA with these proteins precipitate in a small range of input ratios, protein to DNA, with the midpoints of all precipitation curves c...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00653a014

    authors: Pinkston MF,Ritter AH,Li HJ

    更新日期:1976-04-20 00:00:00

  • [FeFe]-hydrogenase maturation.

    abstract::Hydrogenases are metalloenzymes that catalyze the reversible reduction of protons at unusual metal centers. This Current Topic discusses recent advances in elucidating the steps involved in the biosynthesis of the complex metal cluster at the [FeFe]-hydrogenase (HydA) active site, known as the H-cluster. The H-cluster...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi500210x

    authors: Shepard EM,Mus F,Betz JN,Byer AS,Duffus BR,Peters JW,Broderick JB

    更新日期:2014-07-01 00:00:00

  • Characterization of the nuclease activity of Drosophila Rrp1 on phosphoglycolate- and phosphate-modified DNA 3'-termini.

    abstract::Drosophila Rrp1 includes a carboxy-terminal region homologous to Escherichia coli exonuclease III which is sufficient to repair both oxidative and alkylation damage to DNA. An apurinic/apyrimidinic endonuclease activity intrinsic to Rrp1 was characterized previously. In this work, the 3'-phosphodiesterase and 3'-phosp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00004a021

    authors: Sander M,Huang SM

    更新日期:1995-01-31 00:00:00

  • Biochemical characterization of the multidrug regulator QacR distinguishes residues that are crucial to multidrug binding and induction of qacA transcription.

    abstract::Staphylococcus aureus transcription factor QacR regulates expression of the qacA multidrug efflux determinant. In response to binding cationic lipophilic compounds, including ethidium and rhodamine 6G, QacR dissociates from the qacA operator alleviating repression. Such ligand binding uniformly induces a coil-to-helix...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi901102h

    authors: Peters KM,Sharbeen G,Theis T,Skurray RA,Brown MH

    更新日期:2009-10-20 00:00:00

  • Deamidation of triosephosphate isomerase in reverse micelles: effects of water on catalysis and molecular wear and tear.

    abstract::The specific deamidation of asparagine-71 of triosephosphate isomerase increases upon substrate binding and catalysis. This deamidation at the dimer interface initiates subunit dissociation, unfolding, and protein degradation. The apparent connection between catalysis and terminal marking supports the concept of "mole...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00188a027

    authors: Garza-Ramos G,Tuena de Gomez-Puyou M,Gomez-Puyou A,Yüksel KU,Gracy RW

    更新日期:1994-06-07 00:00:00

  • Mechanism of inhibition of the class C beta-lactamase of Enterobacter cloacae P99 by phosphonate monoesters.

    abstract::The class C serine beta-lactamase of Enterobacter cloacae P99 was inhibited by a series of aryl methylphosphonate monoester monoanions. The effectiveness of these inhibitors was promoted by an acylamido substituent on the methyl group and a good leaving group at phosphorus. The former preference suggests that noncoval...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00140a024

    authors: Rahil J,Pratt RF

    更新日期:1992-06-30 00:00:00

  • Cholesterol decreases the interfacial elasticity and detergent solubility of sphingomyelins.

    abstract::The interfacial interactions of cholesterol with sphingomyelins (SMs) containing various homogeneous acyl chains have been investigated by Langmuir film balance approaches. Low in-plane elasticity among the packed lipids was identified as an important physical feature of the cholesterol-sphingomyelin liquid-ordered ph...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi002791n

    authors: Li XM,Momsen MM,Smaby JM,Brockman HL,Brown RE

    更新日期:2001-05-22 00:00:00

  • Importance of phosphatidylethanolamine for association of protein kinase C and other cytoplasmic proteins with membranes.

    abstract::Biological membranes exhibit an asymmetric distribution of phospholipids. Phosphatidylserine (PS) is an acidic phospholipid that is found almost entirely on the interior of the cell where it is important for interaction with many cellular components. A less well understood phenomenon is the asymmetry of the neutral ph...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00119a022

    authors: Bazzi MD,Youakim MA,Nelsestuen GL

    更新日期:1992-02-04 00:00:00

  • Kinetic, crystallographic, and mechanistic characterization of TomN: elucidation of a function for a 4-oxalocrotonate tautomerase homologue in the tomaymycin biosynthetic pathway.

    abstract::The biosynthesis of the C ring of the antitumor antibiotic agent, tomaymycin, is proposed to proceed through five enzyme-catalyzed steps from l-tyrosine. The genes encoding these enzymes have recently been cloned and their functions tentatively assigned, but there is limited biochemical evidence supporting the assignm...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200947w

    authors: Burks EA,Yan W,Johnson WH Jr,Li W,Schroeder GK,Min C,Gerratana B,Zhang Y,Whitman CP

    更新日期:2011-09-06 00:00:00

  • Preparation and Application of 13C-Labeled myo-Inositol to Identify New Catabolic Products in Inositol Metabolism in Lactobacillus casei.

    abstract::myo-Inositol (mI) is widely distributed in all domains of life and is important for several cellular functions, including bacterial survival. The enzymes responsible for the bacterial catabolism of mI, encoded in the iol operon, can vary from one organism to another, and these pathways have yet to be fully characteriz...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.0c00539

    authors: Ramos-Figueroa JS,Aamudalapalli HB,Jagdhane RC,Smith J,Palmer DRJ

    更新日期:2020-08-18 00:00:00

  • Characterization of amyloid formation by glucagon-like peptides: role of basic residues in heparin-mediated aggregation.

    abstract::Glycosaminoglycans (GAGs) have been reported to play a significant role in amyloid formation of a wide range of proteins/peptides either associated with diseases or native biological functions. The exact mechanism by which GAGs influence amyloid formation is not clearly understood. Here, we studied two closely related...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi401398k

    authors: Jha NN,Anoop A,Ranganathan S,Mohite GM,Padinhateeri R,Maji SK

    更新日期:2013-12-10 00:00:00

  • Nuclear Overhauser effect studies of the conformation of Co(NH3)4ATP bound to kidney Na,K-ATPase.

    abstract::Transferred nuclear Overhauser effect measurements (in the two-dimensional mode) have been used to determine the three-dimensional conformation of an ATP analogue, Co(NH3)4ATP, at the active site of sheep kidney Na,K-ATPase. Previous studies have shown that Co(NH3)4ATP is a competitive inhibitor with respect to MnATP ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00437a028

    authors: Stewart JM,Jørgensen PL,Grisham CM

    更新日期:1989-05-30 00:00:00

  • Insights into the mechanism of flavoprotein-catalyzed amine oxidation from nitrogen isotope effects on the reaction of N-methyltryptophan oxidase.

    abstract::The mechanism of N-methyltryptophan oxidase, a flavin-dependent amine oxidase from Escherichia coli, was studied using a combination of kinetic isotope effects and theoretical calculations. The 15(kcat/Km) kinetic isotope effect for sarcosine oxidation is pH-dependent with a limiting value of 0.994-0.995 at high pH. D...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi700482h

    authors: Ralph EC,Hirschi JS,Anderson MA,Cleland WW,Singleton DA,Fitzpatrick PF

    更新日期:2007-06-26 00:00:00

  • Binding of calcium, magnesium, and target peptides to Cdc31, the centrin of yeast Saccharomyces cerevisiae.

    abstract::Cdc31, the Saccharomyces cerevisiae centrin, is an EF-hand calcium-binding protein essential for the cell division and mRNA nuclear export. We used biophysical techniques to investigate its calcium, magnesium, and protein target binding properties as well as their conformations in solution. We show here that Cdc31 dis...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi200518d

    authors: Miron S,Durand D,Chilom C,Pérez J,Craescu CT

    更新日期:2011-07-26 00:00:00

  • Probing the binding of coumarins and cyclothialidines to DNA gyrase.

    abstract::DNA gyrase is the target of a number of antibacterial agents, including the coumarins and the cyclothialidines. To extend our understanding of the mechanism of action of these compounds, we have examined the previously published crystal structures of the complexes between the 24 kDa fragment of GyrB and coumarin and c...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi982320p

    authors: Kampranis SC,Gormley NA,Tranter R,Orphanides G,Maxwell A

    更新日期:1999-02-16 00:00:00

  • Bovine enterokinase. Purification, specificity, and some molecular properties.

    abstract::Enterokinase has been isolated from the contents of bovine duodena and purified 1200-fold in 41% yield. The isolation procedure employed DEAE chromatography, affinity chromatography on immobilized p-aminobenzamidine, and gel filtration. The resultant pure enzyme exhibits a single band on sodium dodecyl sulfate gel ele...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00634a011

    authors: Anderson LE,Walsh KA,Neurath H

    更新日期:1977-07-26 00:00:00

  • Conformational Closure of the Catalytic Site of Human CD38 Induced by Calcium.

    abstract::First identified on the surface of lymphoids as a type II transmembrane protein, CD38 has now been established to have dual functions not only as a receptor but also as a multifunctional enzyme,catalyzing the synthesis of and hydrolysis of a general calcium messenger molecule, cyclic ADP-ribose(cADPR). The receptorial...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:

    authors: Liu Q,Graeff R,Kriksunov IA,Lam CM,Lee HC,Hao Q

    更新日期:2008-12-30 00:00:00

  • Kinetic analyses of mutations in the glycine-rich loop of cAMP-dependent protein kinase.

    abstract::The conserved glycines in the glycine-rich loop (Leu-Gly50-Thr-Gly52-Ser-Phe-Gly55-Arg-Val) of the catalytic (C) subunit of cAMP-dependent protein kinase were each mutated to Ser (G50S, G52S, and G55S). The effects of these mutations were assessed here using both steady-state and pre-steady-state kinetic methods. Whil...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi972987w

    authors: Grant BD,Hemmer W,Tsigelny I,Adams JA,Taylor SS

    更新日期:1998-05-26 00:00:00

  • Structural polymorphism and dynamism in the DNA segment GATCTTCCCCCCGGAA: NMR investigations of hairpin, dumbbell, nicked duplex, parallel strands, and i-motif.

    abstract::Structure and dynamism in a DNA segment d-GATCTTCCCCCCGGAA have been investigated by nuclear magnetic resonance (NMR) spectroscopy. At neutral pH, the molecule exists largely as a dumbbell, formed by the association of two hairpins with sticky ends. A small percentage of hairpin is also detectable. The stem of the dum...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi970819y

    authors: Singh S,Patel PK,Hosur RV

    更新日期:1997-10-28 00:00:00