tRNA topography during translocation: steady-state and kinetic fluorescence energy-transfer studies.

Abstract:

:The distances between the anticodon loops of fluorescent tRNAPhe bound to the E site and to either the A or the P site of poly(U)-programmed Escherichia coli ribosomes were measured by fluorescence energy transfer. Donor and acceptor molecules were wybutine and proflavin, respectively, both located 3' to the anticodon of tRNAPhe. The anticodon loops were found to be separated by 42 +/- 10 A (A to E site) and 34 +/- 8 A (P to E site). The latter distance is much larger than the one measured between the anticodon loops of A and P site bound tRNAs [24 +/- 4 A; Paulsen, H., Robertson, J. M., & Wintermeyer, W. (1983) J. Mol. Biol. 167, 411-426], rendering unlikely simultaneous codon-anticodon interaction in the P and E sites. In kinetic stopped-flow measurements, the energy transfer between the anticodon loops of the tRNA molecules was followed during translocation. The transfer efficiency decreases in three steps with apparent rate constants on the order of 1, 0.1, and 0.01 s-1. The fast step is ascribed to the simultaneous displacement of the deacylated tRNAPhe out of the P site and of the N-AcPhe-tRNAPhe from the A site to the P site. The distance between the anticodon loops does not change appreciably during this reaction. A significant separation of the two tRNAs occurs during the intermediate and the slow steps. The latter most likely represents a rearrangement of the posttranslocation complex containing both tRNA molecules.(ABSTRACT TRUNCATED AT 250 WORDS)

journal_name

Biochemistry

journal_title

Biochemistry

authors

Paulsen H,Wintermeyer W

doi

10.1021/bi00358a002

subject

Has Abstract

pub_date

1986-05-20 00:00:00

pages

2749-56

issue

10

eissn

0006-2960

issn

1520-4995

journal_volume

25

pub_type

杂志文章
  • Aminoacyl-tRNA synthetases from yeast: generality of chemical proofreading in the prevention of misaminoacylation of tRNA.

    abstract::The specificity of valyl-, phenylalanyl-, and tyrosyl-tRNA synthetases from yeast has been examined by a series of stringent tests designed to eliminate the possibility of artefactual interference. Valyl-tRNA synthetase, as well as activating a number of amino acid analogues, will accept alanine, cysteine, isoleucine,...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00610a006

    authors: Igloi GL,von der Haar F,Cramer F

    更新日期:1978-08-22 00:00:00

  • Neuronal Synapses: Microscale Signal Processing Machineries Formed by Phase Separation?

    abstract::The organization principles underlying non-membrane-bound organelles have started to unravel in the past 10 years. A new biophysical model known as biomolecular condensates has been proposed to explain many aspects of membraneless organelle assembly and regulation. Neurons are extremely complex, and each neuron can co...

    journal_title:Biochemistry

    pub_type: 杂志文章,评审

    doi:10.1021/acs.biochem.8b00313

    authors: Feng Z,Zeng M,Chen X,Zhang M

    更新日期:2018-05-01 00:00:00

  • Isolation, purification, and reconstitution of a proline carrier protein from Mycobacterium phlei.

    abstract::Membrane vesicles from Mycobacterium phlei contain carrier proteins for proline, glutamine, and glutamic acid. The transport of proline is Na+ dependent and required substrate oxidation. A proline carrier protein was solubilized from the membrane vesicles by treatment with cholate and Triton X-100. Electron microscopi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00578a015

    authors: Lee SH,Cohen NS,Jacobs AJ,Brodie AF

    更新日期:1979-05-29 00:00:00

  • Time-resolved resonance Raman and time-resolved step-scan FTIR studies of nitric oxide reductase from Paracoccus denitrificans: comparison of the heme b3-FeB site to that of the heme-CuB in oxidases.

    abstract::Time-resolved resonance Raman (TR(3)) and time-resolved step-scan (TRS(2)) FTIR spectroscopies have been used to probe the structural dynamics at the heme b(3) proximal and distal sites after carbon monoxide photolysis from fully reduced CO-bound nitric oxide reductase. The Raman spectra of the transient species exhib...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi035289m

    authors: Pinakoulaki E,Varotsis C

    更新日期:2003-12-23 00:00:00

  • Presence of divalent cation is not mandatory for the formation of intramolecular purine-motif triplex containing human c-jun protooncogene target.

    abstract::Modulation of endogenous gene function, through sequence-specific recognition of double helical DNA via oligonucleotide-directed triplex formation, is a promising approach. Compared to the formation of pyrimidine motif triplexes, which require relatively low pH, purine motif appears to be the most gifted for their sta...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi1012589

    authors: Kaushik S,Kaushik M,Svinarchuk F,Malvy C,Fermandjian S,Kukreti S

    更新日期:2011-05-17 00:00:00

  • Exchange mechanisms for hydrogen bonding protons of cytidylic and guanylic acids.

    abstract::The pH dependence of buffer catalysis of exchange of the C-4 amino protons of cyclic cytosine 2',3'-monophosphate (cCMP) and the N-1 proton of cyclic guanosine 2',3'-monophosphate (cGMP) conforms to an exchange mechanism, in which protonation of the nucleobases at C(N-3) AND G(N-7) establishes the important intermedia...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00608a035

    authors: McConnell B

    更新日期:1978-07-25 00:00:00

  • A coupled dinuclear iron cluster that is perturbed by substrate binding in myo-inositol oxygenase.

    abstract::myo-Inositol oxygenase (MIOX) uses iron as its cofactor and dioxygen as its cosubstrate to effect the unique, ring-cleaving, four-electron oxidation of its cyclohexan-(1,2,3,4,5,6-hexa)-ol substrate to d-glucuronate. The nature of the iron cofactor and its interaction with the substrate, myo-inositol (MI), have been p...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0519607

    authors: Xing G,Hoffart LM,Diao Y,Prabhu KS,Arner RJ,Reddy CC,Krebs C,Bollinger JM Jr

    更新日期:2006-05-02 00:00:00

  • Identification of amino acids important for binding of Clostridium perfringens epsilon toxin to host cells and to HAVCR1.

    abstract::Clostridium perfringens epsilon toxin belongs to the aerolysin-like family of pore-forming toxins and is one of the most potent bacterial toxins known. The epsilon toxin causes fatal enterotoxemia in sheep, goats, and possibly humans. Evidence indicates that the toxin binds to protein receptors including hepatitis A v...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi300690a

    authors: Ivie SE,McClain MS

    更新日期:2012-09-25 00:00:00

  • A theory of phase transitions and phase diagrams for one- and two-component phospholipid bilayers.

    abstract::A statistical mechanical partition function for phospholipid bilayers is constructed to obtain a theoretical description of the chain melting phase transition in lipid bilayer membranes and of the phase diagrams for two-component bilayers. In addition to providing an accurate representation of the transition temperatu...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00639a004

    authors: Jacobs RE,Hudson BS,Andersen HC

    更新日期:1977-10-04 00:00:00

  • Interaction of human immunodeficiency virus type 1 Tat-derived peptides with TAR RNA.

    abstract::Basic peptides from the carboxy terminus of the human immunodeficiency virus type 1 (HIV-1) Tat protein bind to the stem-loop region of TAR RNA, spanning a trinucleotide bulge, with high affinity and moderate specificity. Previous studies have demonstrated that TAR RNA contains a specific arginine binding pocket. A se...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00027a041

    authors: Long KS,Crothers DM

    更新日期:1995-07-11 00:00:00

  • Kinetic characterization of recombinant human acidic mammalian chitinase.

    abstract::Human acidic mammalian chitinase (AMCase), a member of the family 18 glycosyl hydrolases, is one of the important proteins involved in Th2-mediated inflammation and has been implicated in asthma and allergic diseases. Inhibition of AMCase results in decreased airway inflammation and airway hyper-responsiveness in a mo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0525977

    authors: Chou YT,Yao S,Czerwinski R,Fleming M,Krykbaev R,Xuan D,Zhou H,Brooks J,Fitz L,Strand J,Presman E,Lin L,Aulabaugh A,Huang X

    更新日期:2006-04-11 00:00:00

  • Delta-elimination by T4 endonuclease V at a thymine dimer site requires a secondary binding event and amino acid Glu-23.

    abstract::Endonuclease V from bacteriophage T4 is a well characterized enzyme that initiates the repair of ultraviolet light induced pyrimidine dimers. Scission of the phosphodiester backbone between the pyrimidines within a dimer, or 3' to an abasic (AP) site, occurs by a beta-elimination mechanism. In addition, high concentra...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00027a031

    authors: Latham KA,Lloyd RS

    更新日期:1995-07-11 00:00:00

  • Allosteric changes in solvent accessibility observed in thrombin upon active site occupation.

    abstract::The solvent accessibility of thrombin in its substrate-free and substrate-bound forms has been compared by amide hydrogen/deuterium (H/(2)H) exchange. The optimized inhibitor peptide dPhe-Pro-Arg chloromethyl ketone (PPACK) was used to simulate the substrate-bound form of thrombin. These studies were motivated by the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0499718

    authors: Croy CH,Koeppe JR,Bergqvist S,Komives EA

    更新日期:2004-05-11 00:00:00

  • Photo-cross-linking of CRP to nonspecific DNA in the absence of cAMP. DNA interacts with both the N- and C-terminal parts of the protein.

    abstract::Adenosine cyclic 3',5'-phosphate receptor protein (CRP or CAP) is a regulatory protein involved in the transcription of several operons in Escherichia coli. cAMP-independent, nonspecific complexes of CRP and DNA were investigated by photochemical cross-linking of the protein to nonspecific DNA, whose thymines are subs...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00058a010

    authors: Katouzian-Safadi M,Blazy B,Cremet JY,Le Caer JP,Rossier J,Charlier M

    更新日期:1993-02-23 00:00:00

  • Thioesterase portability and peptidyl carrier protein swapping in yersiniabactin synthetase from Yersinia pestis.

    abstract::Multimodular enzymes, including polyketide synthases (PKSs), nonribosomal peptide synthetases (NRPSs), and mixed PKS/NRPS systems, contain functional domains with similar functions. Domain swapping and module fusion are potential powerful strategies for creating hybrid enzymes to synthesize modified natural products. ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi047538s

    authors: Suo Z

    更新日期:2005-03-29 00:00:00

  • Catalytic significance of the specificity of divalent cations as KS* and kcat* cofactors for secreted phospholipase A2.

    abstract::Calcium is required for the substrate binding and for the chemical step of the interfacial catalytic turnover cycle of pancreatic phospholipase A2 (PLA2), but not for the binding of the enzyme to the interface. The role of calcium and other divalent cations (C) is analyzed for the effect on the substrate binding and k...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9728607

    authors: Yu BZ,Rogers J,Nicol GR,Theopold KH,Seshadri K,Vishweshwara S,Jain MK

    更新日期:1998-09-08 00:00:00

  • Water structural changes in lumirhodopsin, metarhodopsin I, and metarhodopsin II upon photolysis of bovine rhodopsin: analysis by Fourier transform infrared spectroscopy.

    abstract::Difference Fourier transform infrared spectra of lumirhodopsin, metarhodopsin I, and metarhodopsin II versus rhodopsin were recorded with hydrated films of bovine rod outer segments at 200, 240, and 270 K. In the region between 3700 and 3450 cm-1, the O-H stretching vibrational bands of water were identified by H(2)18...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00096a013

    authors: Maeda A,Ohkita YJ,Sasaki J,Shichida Y,Yoshizawa T

    更新日期:1993-11-16 00:00:00

  • The Structure of the Bimolecular Complex between Amphotericin B and Ergosterol in Membranes Is Stabilized by Face-to-Face van der Waals Interaction with Their Rigid Cyclic Cores.

    abstract::Amphotericin B (AmB) is a polyene macrolide antibiotic isolated from Streptomyces nodosus. The antifungal activity of AmB can be attributed to the formation of an ion-channel assembly in the presence of ergosterol (Erg), in which there are two different AmB-Erg orientations, parallel and antiparallel, as reported prev...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00193

    authors: Nakagawa Y,Umegawa Y,Matsushita N,Yamamoto T,Tsuchikawa H,Hanashima S,Oishi T,Matsumori N,Murata M

    更新日期:2016-06-21 00:00:00

  • Nuclear magnetic resonance solution structure of an undecanucleotide duplex with a complementary thymidine base opposite a 10R adduct derived from trans addition of a deoxyadenosine N6-amino group to (-)-(7R,8S,9R,10S)-7,8-dihydroxy- 9,10-epoxy-7,8,9,10-t

    abstract::The solution structure of a modified undecamer duplex containing (-)-(7R,8S,9R,10S)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-tetrahydrobenzo[a] pyrene covalently bonded through trans ring opening at C10 of the epoxide by the N6-amino group of deoxyadenosine (dA) was studied. This diol epoxide 1 diastereomer has the benzylic ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00028a009

    authors: Schurter EJ,Sayer JM,Oh-hara T,Yeh HJ,Yagi H,Luxon BA,Jerina DM,Gorenstein DG

    更新日期:1995-07-18 00:00:00

  • Proteolysis of the cytochrome d complex with trypsin and chymotrypsin localizes a quinol oxidase domain.

    abstract::The cytochrome d complex is a two-subunit, membrane-bound terminal oxidase in the aerobic respiratory chain of Escherichia coli. The enzyme catalyzes the two-electron oxidation of ubiquinol and the four-electron reduction of oxygen to water. Previous work demonstrated that the site for ubiquinol oxidation was selectiv...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00228a007

    authors: Dueweke TJ,Gennis RB

    更新日期:1991-04-09 00:00:00

  • Linkage and sequence analysis of mannose-rich glycoprotein core oligosaccharides by proton nuclear magnetic resonance spectroscopy.

    abstract::The anomeric proton (H-1) chemical shifts of D-mannopyranosides in aqueous solution are affected both by the aglycon and by substitution of the ring [Lee, Y. C., & Ballou, C. E. (1965) Biochemistry 4, 257]. We have examined the 1H NMR spectra for a variety of linear and branched mannooligosaccharides and have assigned...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00559a031

    authors: Cohen RE,Ballou CE

    更新日期:1980-09-02 00:00:00

  • Conformational Dynamics and Protein-Substrate Interaction of ABC Transporter BtuCD at the Occluded State Revealed by Molecular Dynamics Simulations.

    abstract::ATP-binding cassette (ABC) transporters are ubiquitous in all three kingdoms of life and are implicated in many clinically relevant physiological processes. They couple the energy released by ATP hydrolysis to facilitate substrate translocation across cell membranes. The crystal structures of type II ABC importers hav...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.6b00386

    authors: Pan C,Weng J,Wang W

    更新日期:2016-12-13 00:00:00

  • Enantiomeric free radicals and enzymatic control of stereochemistry in a radical mechanism: the case of lysine 2,3-aminomutases.

    abstract::The product of yjeK in Escherichia coli is a homologue of lysine 2,3-aminomutase (LAM) from Clostridium subterminale SB4, and both enzymes catalyze the isomerization of (S)- but not (R)-alpha-lysine by radical mechanisms. The turnover number for LAM from E. coli is 5.0 min(-1), 0.1% of the value for clostridial LAM. T...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi061328t

    authors: Behshad E,Ruzicka FJ,Mansoorabadi SO,Chen D,Reed GH,Frey PA

    更新日期:2006-10-24 00:00:00

  • Probing the acyl-binding pocket of aminoacylase-1.

    abstract::The aminoacylase-1/metallopeptidase 20 (Acy1/M20) family features several l-aminoacylases useful in biocatalysis. Mammalian Acy1, in particular, has been applied in racemic resolution and reverse hydrolysis. Despite recent advances in our understanding of the active site architecture and functioning, determinants of A...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi702156h

    authors: Lindner HA,Alary A,Wilke M,Sulea T

    更新日期:2008-04-08 00:00:00

  • Structure-function relationships of the Escherichia coli ATP synthase probed by trypsin digestion.

    abstract::Trypsin cleavage has been used to probe structure-function relationships of the Escherichia coli ATP synthase (ECF1F0). Trypsin cleaved all five subunits, alpha, beta, gamma, delta, and epsilon, in isolated ECF1. Cleavage of the alpha subunit involved the removal of the N-terminal 15 residues, the beta subunit was cle...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00402a016

    authors: Gavilanes-Ruiz M,Tommasino M,Capaldi RA

    更新日期:1988-01-26 00:00:00

  • Activation of GlcNAc-P-P-dolichol synthesis by mannosylphosphoryldolichol is stereospecific and requires a saturated alpha-isoprene unit.

    abstract::Exogenous mannosylphosphoryldolichol (Man-P-Dol) has previously been shown to stimulate UDP-GlcNAc:dolichyl phosphate N-acetylglucosamine 1-phosphate transferase (GPT1), the enzyme catalyzing the biosynthesis of N-acetylglucosaminylpyrophosphoryldolichol (GlcNAc-P-P-Dol). To define the structural specificity of the ma...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00200a036

    authors: Kean EL,Rush JS,Waechter CJ

    更新日期:1994-08-30 00:00:00

  • Correlation of beta-amyloid aggregate size and hydrophobicity with decreased bilayer fluidity of model membranes.

    abstract::beta-amyloid peptide (Abeta) is the primary constituent of senile plaques, a defining feature of Alzheimer's disease. Aggregated Abeta is toxic to neurons, but the mechanism of toxicity remains unproven. One proposal is that Abeta toxicity results from relatively nonspecific Abeta-membrane interactions. We hypothesize...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0001980

    authors: Kremer JJ,Pallitto MM,Sklansky DJ,Murphy RM

    更新日期:2000-08-22 00:00:00

  • Metal-ligand vibrations of cyanoferric myeloperoxidase and cyanoferric horseradish peroxidase: evidence for a constrained heme pocket in myeloperoxidase.

    abstract::The low-frequency FeCN vibrations of cyanoferric myeloperoxidase (MPO) and horseradish peroxidase (HRP) have been measured by resonance Raman spectroscopy. The ordering of the frequencies of the predominantly FeC stretching and FeCN bending normal vibrational modes in the two peroxidases differs. These normal mode vib...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00492a012

    authors: López-Garriga JJ,Oertling WA,Kean RT,Hoogland H,Wever R,Babcock GT

    更新日期:1990-10-09 00:00:00

  • Elimination of the hydrolytic water molecule in a class A beta-lactamase mutant: crystal structure and kinetics.

    abstract::Two site-directed mutant enzymes of the class A beta-lactamase from Staphylococcus aureus PC1 were produced with the goal of blocking the site that in the native enzyme is occupied by the proposed hydrolytic water molecule. The crystal structures of these two mutant enzymes, N170Q and N170M, have been determined and r...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi962242a

    authors: Zawadzke LE,Chen CC,Banerjee S,Li Z,Wäsch S,Kapadia G,Moult J,Herzberg O

    更新日期:1996-12-24 00:00:00

  • Circular dichroism studies on the interaction of tryptophan synthase with pyridoxal 5'-phosphate.

    abstract::The interaction between the beta 2 subunit of tryptophan synthase and the coenzyme pyridoxal 5'-phosphate (PLP) is characterized by induced circular dichroism (CD) in the near-UV (260-285 nm) and in the visible region (320-480 nm, extrinsic Cotton effect). Because of its high mean residue ellipticity ([theta] = 56 deg...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00525a017

    authors: Balk H,Merkl I,Bartholmes P

    更新日期:1981-10-27 00:00:00