Evidence for the amphipathic nature and tilted topology of helices 4 and 5 in the closed state of the colicin E1 channel.

Abstract:

:The membrane-bound closed channel structure of helices 4 and 5 (Lys-406-Asp-446) of the colicin E1 channel domain was investigated by using a site-directed fluorescence labeling technique. A bimane probe was covalently attached to a cysteine residue in a series of single-cysteine mutant proteins to scan each helix in a residue-by-residue fashion. A variety of fluorescence properties of the bimane fluorophore were measured for both the soluble and membrane-bound states of the channel peptide, including the fluorescence emission maximum, fluorescence anisotropy, and membrane bilayer penetration depth. The fluorescence properties were collated for construction of a membrane-bound topology model of helices 4 and 5 of the channel domain. Finally, the data reveal that both helices 4 and 5 are two separate amphipathic alpha-helices that are situated parallel to the membrane surface. Dual fluorescence quencher analysis shows that helix 4 adopts a tilted topology in which its C-terminus is more buried than its N-terminus within the bilayer. In contrast, helix 5 is relatively solvent-exposed and located parallel to the interfacial region of the membrane surface. However, the loop region of both helices 4 and 5 was shown to be relatively buried within the bilayer. In addition, a least-squares fit of the data to a harmonic wave function indicated that both periodicity and frequency are typical for an amphipathic alpha-helix (3.75 +/- 0.1 residues per turn for helix 4 and 3.70 +/- 0.1 residues per turn for helix 5). Squared residual plots of the harmonic wave function also reveal that the N-terminus of helix 4 is elongated by two residues from Lys-406 to Phe-404, while the C-terminus of helix 5 is elongated by three residues from Tyr-434 to Ile-437 upon membrane association.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Ho D,Merrill AR

doi

10.1021/bi801906v

subject

Has Abstract

pub_date

2009-02-17 00:00:00

pages

1369-80

issue

6

eissn

0006-2960

issn

1520-4995

pii

10.1021/bi801906v

journal_volume

48

pub_type

杂志文章
  • Deamidation Slows Curli Amyloid-Protein Aggregation.

    abstract::Nonenzymatic deamidation of asparagine and glutamine in peptides and proteins is a frequent modification both in vivo and in vitro. The biological effect is not completely understood, but it is often associated with protein degradation and loss of biological function. Here we describe the deamidation of CsgA, the majo...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00241

    authors: Wang H,Shu Q,Frieden C,Gross ML

    更新日期:2017-06-13 00:00:00

  • Directed evolution of the suicide protein O⁶-alkylguanine-DNA alkyltransferase for increased reactivity results in an alkylated protein with exceptional stability.

    abstract::Here we present a biophysical, structural, and computational analysis of the directed evolution of the human DNA repair protein O(6)-alkylguanine-DNA alkyltransferase (hAGT) into SNAP-tag, a self-labeling protein tag. Evolution of hAGT led not only to increased protein activity but also to higher stability, especially...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi2016537

    authors: Mollwitz B,Brunk E,Schmitt S,Pojer F,Bannwarth M,Schiltz M,Rothlisberger U,Johnsson K

    更新日期:2012-02-07 00:00:00

  • Kinetic mechanism for the model reaction of NADPH-cytochrome P450 oxidoreductase with cytochrome c.

    abstract::The kinetic mechanism of NADPH-cytochrome P450 oxidoreductase (P450R) has been determined for the model reaction with cytochrome c3+. Although initial velocity studies show parallel patterns, consistent with a classical (one-site) ping-pong mechanism that precludes the formation of a ternary NADPH-P450R-cytochrome c3+...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00206a002

    authors: Sem DS,Kasper CB

    更新日期:1994-10-11 00:00:00

  • Cysteine pKa depression by a protonated glutamic acid in human DJ-1.

    abstract::Human DJ-1, a disease-associated protein that protects cells from oxidative stress, contains an oxidation-sensitive cysteine (C106) that is essential for its cytoprotective activity. The origin of C106 reactivity is obscure, due in part to the absence of an experimentally determined p K a value for this residue. We ha...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi800282d

    authors: Witt AC,Lakshminarasimhan M,Remington BC,Hasim S,Pozharski E,Wilson MA

    更新日期:2008-07-15 00:00:00

  • Effects of the DNA intercalators 4'-(9-acridinylamino)methanesulfon-m-anisidide and 2-methyl-9-hydroxyellipticinium on topoisomerase II mediated DNA strand cleavage and strand passage.

    abstract::DNA topoisomerase II is believed to be the enzyme that produces the protein-associated DNA strand breaks observed in mammalian cell nuclei treated with various intercalating agents. Two intercalators--4'-(9-acridinylamino)methanesulfon-m-anisidide (m-AMSA, amsacrine) and 2-methyl-9-hydroxyellipticinium (2-Me-9-OH-E+)-...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00344a015

    authors: Pommier Y,Minford JK,Schwartz RE,Zwelling LA,Kohn KW

    更新日期:1985-11-05 00:00:00

  • Interpretation of the doublet at 850 and 830 cm-1 in the Raman spectra of tyrosyl residues in proteins and certain model compounds.

    abstract::The doublet at 850 and 830 cm-1 in the Raman spectra of proteins containing tyrosyl residues has been examined as to its origin and the relation of its components to the environment of the phenyl ring, the state of the phenolic hydroxyl group, and the conformation of the amino acid backbone. Raman spectral studies on ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00693a014

    authors: Siamwiza MN,Lord RC,Chen MC,Takamatsu T,Harada I,Matsuura H,Shimanouchi T

    更新日期:1975-11-04 00:00:00

  • ADP-ribosylation and functional effects of Pseudomonas exoenzyme S on cellular RalA.

    abstract::Exoenzyme S (ExoS) is a bifunctional virulence factor directly translocated into eukaryotic cells by the type III secretory process of Pseudomonas aeruginosa. Bacterial translocation of ExoS into epithelial cells is associated with diverse effects on cell function, including inhibition of growth, alterations in cell m...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi025826n

    authors: Fraylick JE,Riese MJ,Vincent TS,Barbieri JT,Olson JC

    更新日期:2002-07-30 00:00:00

  • Fluorescence-detected circular dichroism of ethidium in vivo and bound to deoxyribonucleic acid in vitro.

    abstract::Fluorescence-detected circular dichroism (FDCD) spectra are reported for ethidium in Escherichia coli cells and bound to E. coli DNA in vitro. FDCD bands are observed at 325 and 385 nm. These bands change amplitude as the ethidium to DNA ratio changes. Spectra are similar for in vivo and in vitro measurements. However...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00333a001

    authors: Lamos ML,Turner DH

    更新日期:1985-06-04 00:00:00

  • Structural and Biochemical Investigation of PglF from Campylobacter jejuni Reveals a New Mechanism for a Member of the Short Chain Dehydrogenase/Reductase Superfamily.

    abstract::Within recent years it has become apparent that protein glycosylation is not limited to eukaryotes. Indeed, in Campylobacter jejuni, a Gram-negative bacterium, more than 60 of its proteins are known to be glycosylated. One of the sugars found in such glycosylated proteins is 2,4-diacetamido-2,4,6-trideoxy-α-d-glucopyr...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.7b00910

    authors: Riegert AS,Thoden JB,Schoenhofen IC,Watson DC,Young NM,Tipton PA,Holden HM

    更新日期:2017-11-14 00:00:00

  • Stereochemistry of phospho group transfer catalyzed by a mutant alkaline phosphatase.

    abstract::The stereochemical course of the phospho group transfer catalyzed by mutant (S102C) alkaline phosphatase from Escherichia coli was investigated by using 31P nuclear magnetic resonance spectroscopy. Transphosphorylation from 4-nitrophenyl (Rp)-[16O, 17O, 18O]phosphate to (S)-propane-1,2-diol occurs with overall retenti...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00413a029

    authors: Butler-Ransohoff JE,Kendall DA,Freeman S,Knowles JR,Kaiser ET

    更新日期:1988-06-28 00:00:00

  • Reconstitution of a defunct glycolytic pathway via recruitment of ambiguous sugar kinases.

    abstract::During a recent investigation of the persistence of substrate ambiguity in contemporary enzymes, we identified three distinct ambiguous sugar kinases embedded within the modern Escherichia coli genome [Miller, B. G., and Raines, R. T. (2004) Biochemistry 43, 6387-6392]. These catalysts are the YajF, YcfX, and NanK pol...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0506268

    authors: Miller BG,Raines RT

    更新日期:2005-08-16 00:00:00

  • Evolutionary coadaptation of the motif 2--acceptor stem interaction in the class II prolyl-tRNA synthetase system.

    abstract::Known crystal structures of class II aminoacyl-tRNA synthetases complexed to their cognate tRNAs reveal that critical acceptor stem contacts are made by the variable loop connecting the beta-strands of motif 2 located within the catalytic core of class II synthetases. To identify potential acceptor stem contacts made ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi001835p

    authors: Burke B,Yang F,Chen F,Stehlin C,Chan B,Musier-Forsyth K

    更新日期:2000-12-19 00:00:00

  • Identification of effector binding sites on S100 beta: studies with guanylate cyclase and p80, a retinal phosphoprotein.

    abstract::S100 beta is a calcium-binding protein, which regulates the activities of several enzymes and inhibits the phosphorylation of a variety of protein kinase C substrates in a calcium-dependent manner. The protein was recently found to activate a retinal membrane guanylate cyclase, and in this paper, we report that it inh...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9802115

    authors: Pozdnyakov N,Margulis A,Sitaramayya A

    更新日期:1998-07-28 00:00:00

  • Refinement of the solution structure of the DNA dodecamer 5'd(CGCGPATTCGCG)2 containing a stable purine-thymine base pair: combined use of nuclear magnetic resonance and restrained molecular dynamics.

    abstract::The solution structure of the self-complementary dodecamer 5'd(CGCGPATTCGCG)2, containing a purine-thymine base pair within the hexameric canonical recognition site GAATTC for the restriction endonuclease EcoRI, is investigated by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Nonexchangeab...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00411a042

    authors: Clore GM,Oschkinat H,McLaughlin LW,Benseler F,Happ CS,Happ E,Gronenborn AM

    更新日期:1988-05-31 00:00:00

  • Structures of gangliosides from bovine adrenal medulla.

    abstract::Five gangliosides, accounting for over 95% of the total ganglioside fraction, were isolated from bovine adrenal medulla by preparative thin-layer chromatography and the carbohydrate structures determined by a combination of periodate oxidation and permethylation techniques. Partially methylated alditol acetates were g...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00678a026

    authors: Price H,Kundu S,Ledeen R

    更新日期:1975-04-08 00:00:00

  • Inhibition of the gastric H,K-ATPase by clotrimazole.

    abstract::The antimycotic drug clotrimazole inhibits the function of the gastric H,K-ATPase in a manner similar to that observed for the Na,K-ATPase. Because of the high hydrophobicity of the compound, the interaction between clotrimazole and the ion pump occurs at the membrane domain in the apolar core of the membrane. The enz...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi1004014

    authors: Witzke A,Lindner K,Munson K,Apell HJ

    更新日期:2010-06-01 00:00:00

  • Purification, characterization, and fibrinogen cleavage sites of three fibrinolytic enzymes from the venom of Crotalus basiliscus basiliscus.

    abstract::Three distinct fibrinolytic enzymes have been purified from the venom of Crotalus basiliscus basiliscus (the Mexican west coast rattlesnake). The high-performance liquid chromatography-based purification comprised the following steps: (a) hydrophobic interaction chromatography; (b) hydroxylapatite chromatography; (c) ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00134a003

    authors: Retzios AD,Markland FS Jr

    更新日期:1992-05-19 00:00:00

  • Hypoxanthine in deoxyribonucleic acid: generation by heat-induced hydrolysis of adenine residues and release in free form by a deoxyribonucleic acid glycosylase from calf thymus.

    abstract::A slow conversion of adenine residues to hypoxanthine occurs in single-stranded DNA when heated in neutral aqueous buffers. The rate of this reaction at pH 7.6 and 110 degrees C is k = 4 x 10(-8) s-1, as determined by base analysis of heat-treated DNA that contains radioactively labeled adenine residues. It is propose...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00567a010

    authors: Karran P,Lindahl T

    更新日期:1980-12-23 00:00:00

  • Amino acid and sequence analysis of the cytochrome and flavoprotein subunits of p-cresol methylhydroxylase.

    abstract::The flavocytochrome p-cresol methylhydroxylase from Pseudomonas putida has been reported to have a Mr of 114,000 and to consist of two subunits, a flavoprotein and a cytochrome c, each with a Mr of 58,000. Recent X-ray crystallographic data from our laboratories [Shamala, N., Lim, L. W., Mathews, F. S., McIntire, W., ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00368a021

    authors: McIntire W,Singer TP,Smith AJ,Mathews FS

    更新日期:1986-10-07 00:00:00

  • Molecular characterization of the AP180 coated vesicle assembly protein.

    abstract::Recently, a new clathrin assembly protein (AP180) has been purified from coated vesicles of bovine brain (Ahle & Ungewickell, 1986). This protein has been shown to promote polymerization of clathrin into a homogeneous population of baskets under conditions where pure clathrin does not polymerize by itself. We have pur...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00416a040

    authors: Prasad K,Lippoldt RE

    更新日期:1988-08-09 00:00:00

  • Specific inhibition of expression of a human collagen gene (COL1A1) with modified antisense oligonucleotides. The most effective target sites are clustered in double-stranded regions of the predicted secondary structure for the mRNA.

    abstract::A series of antisense oligonucleotides (ASOs) were synthesized and tested to define the best target sites within an RNA transcript of collagen for effective inhibition of expression. The test system consisted of mouse NIH 3T3 fibroblasts that were stably transfected with a human minigene for procollagen I so that the ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00202a024

    authors: Laptev AV,Lu Z,Colige A,Prockop DJ

    更新日期:1994-09-13 00:00:00

  • Simultaneous binding of drugs with different chemical structures to Ca2+-calmodulin: crystallographic and spectroscopic studies.

    abstract::The modulatory action of Ca2+-calmodulin on multiple targets is inhibited by trifluoperazine, which competes with target proteins for calmodulin binding. The structure of calmodulin crystallized with two trifluoperazine molecules is determined by X-ray crystallography at 2.74 A resolution. The X-ray data together with...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi980795a

    authors: Vertessy BG,Harmat V,Böcskei Z,Náray-Szabó G,Orosz F,Ovádi J

    更新日期:1998-11-03 00:00:00

  • Calcium-induced structural transition in the regulatory domain of human cardiac troponin C.

    abstract::While calcium binding to troponin C (TnC) triggers the contraction of both skeletal and cardiac muscle, there is clear evidence that different mechanisms may be involved. For example, activation of heart myofilaments occurs with binding to a single regulatory site on TnC, whereas activation of fast skeletal myofilamen...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971223d

    authors: Spyracopoulos L,Li MX,Sia SK,Gagné SM,Chandra M,Solaro RJ,Sykes BD

    更新日期:1997-10-07 00:00:00

  • Thermodynamic characterization of ligand-induced conformational changes in UDP-N-acetylglucosamine enolpyruvyl transferase.

    abstract::The binding of UDP-N-acetylglucosamine (UDPNAG) to the enzyme UDP-N-acetylglucosamine enolpyruvyl transferase (MurA) was studied in the absence and presence of the antibiotic fosfomycin by isothermal titration calorimetry. Fosfomycin binds covalently to MurA in the presence of UDPNAG and also in its absence as demonst...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0107041

    authors: Samland AK,Jelesarov I,Kuhn R,Amrhein N,Macheroux P

    更新日期:2001-08-21 00:00:00

  • Polypeptides of nonpolyribosomal messenger ribonucleoprotein complexes of sea urchin eggs.

    abstract::RNA competent in directing protein synthesis is sequestered in unfertilized sea urchin eggs as translationally quiescent, nonpolyribosomal, messenger ribonucleoprotein complexes (mRNPs). Following fertilization, these mRNPs are derepressed and actively translated, presumably due to changes in the mRNA-associated prote...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00553a029

    authors: Moon RT,Moe KD,Hille MB

    更新日期:1980-06-10 00:00:00

  • Interactions of a Bacterial Cu(I)-ATPase with a Complex Lipid Environment.

    abstract::Phospholipids and sterols play multiple roles in cells. In addition to establishing barriers between compartments, they also provide the matrix for assembly and function of a large variety of catalytic processes. Lipid composition is a highly regulated feature of biological membranes, yet its implications for membrane...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b00326

    authors: Autzen HE,Koldsø H,Stansfeld PJ,Gourdon P,Sansom MSP,Nissen P

    更新日期:2018-07-17 00:00:00

  • Investigation of the shape and size of myosin subfragment 1 using small-angle X-ray scattering.

    abstract::Measurement of x-ray scattering at very small angles by solutions of myosin subfragment 1 (S1) yields a radius of gyration of 3.24 nm (mean) +/- 0.03 nm (standard error for N = 9). If S1 is assumed to be ellipsoid of revolution, of uniform electron density, with a molecular weight of 1.15 X 10(5) and a partial specifi...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00605a009

    authors: Kretzschmar KM,Mendelson RA,Morales MF

    更新日期:1978-06-13 00:00:00

  • beta-Lactamase proceeds via an acyl-enzyme intermediate. Interaction of the Escherichia coli RTEM enzyme with cefoxitin.

    abstract::The use of cefoxitin, a poor substrate of the RTEM beta-lactamase, has allowed the kinetic and spectroscopic characterization of a covalent acyl-enzyme intermediate in the enzyme-catalyzed reaction. The rate of reappearance of catalytic activity in an enzyme sample diluted from an incubation with cefoxitin is nearly i...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00554a012

    authors: Fisher J,Belasco JG,Khosla S,Knowles JR

    更新日期:1980-06-24 00:00:00

  • Kinetics and thermodynamics of phalloidin binding to actin filaments from three divergent species.

    abstract::We compared the kinetics and thermodynamics of rhodamine phalloidin binding to actin purified from rabbit skeletal muscle, Acanthamoeba castellanii, and Saccharomyces cerevisiae in 50 mM KCl, 1 mM MgCl2, and pH 7.0 buffer at 22 degrees C. Filaments of S. cerevisiae actin bind rhodamine phalloidin more weakly than Acan...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi961047t

    authors: De La Cruz EM,Pollard TD

    更新日期:1996-11-12 00:00:00

  • Solid state 15N NMR evidence for a complex Schiff base counterion in the visual G-protein-coupled receptor rhodopsin.

    abstract::Using the baculovirus/Sf9 cell expression system, we have incorporated 99% 15N-enriched [alpha,epsilon-15N2]-L-lysine into the rod visual pigment rhodopsin. We have subsequently investigated the protonated Schiff base (pSB) linkage in the [alpha, epsilon-15N2]Lys-rhodopsin with cross-polarization magic angle spinning ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9830157

    authors: Creemers AF,Klaassen CH,Bovee-Geurts PH,Kelle R,Kragl U,Raap J,de Grip WJ,Lugtenburg J,de Groot HJ

    更新日期:1999-06-01 00:00:00