A designed protein with packing between left-handed and right-handed helices.

Abstract:

:A common motif in protein structures is the assembly of alpha-helices. Natural alpha-helical assemblies, such as helical bundles and coiled coils, consist of multiple right-handed alpha-helices. Here we design a protein complex containing both left-handed and right-handed helices, with peptides of D- and L-amino acids, respectively. The two peptides, D-Acid and L-Base, feature hydrophobic heptad repeats and are designed to pack against each other in a "knobs-into-holes" manner. In solution, the peptides form a stable, helical heterotetramer with tight packing in the most solvent-protected core. This motif may be useful for designing protease-resistant, helical D-peptide ligands against biological protein targets.

journal_name

Biochemistry

journal_title

Biochemistry

authors

Sia SK,Kim PS

doi

10.1021/bi010725v

subject

Has Abstract

pub_date

2001-07-31 00:00:00

pages

8981-9

issue

30

eissn

0006-2960

issn

1520-4995

pii

bi010725v

journal_volume

40

pub_type

杂志文章
  • Thermodynamics of bovine spleen galectin-1 binding to disaccharides: correlation with structure and its effect on oligomerization at the denaturation temperature.

    abstract::Isothermal titration calorimetry (ITC) measurements of the binding 1-beta carbohydrate-substituted galactopyranoside derivatives to galectin-1 from bovine spleen, a dimer with one binding site per subunit, were performed at 283-285 and 298 K. The disaccharides were lactose, methyl beta-lactoside, lactulose, 4-O-beta-D...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi9716478

    authors: Schwarz FP,Ahmed H,Bianchet MA,Amzel LM,Vasta GR

    更新日期:1998-04-28 00:00:00

  • Prion protein peptides induce alpha-helix to beta-sheet conformational transitions.

    abstract::The structures of synthetic peptides corresponding to regions of putative secondary structure in the cellular prion protein PrPC were studied as models for the conformational transition that features in the formation of the pathogenic isoform, PrPSc. Transgenetic studies argue that these PrP isoforms interact during t...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00013a006

    authors: Nguyen J,Baldwin MA,Cohen FE,Prusiner SB

    更新日期:1995-04-04 00:00:00

  • Delineation of the Cdc42/Rac-binding domain of p21-activated kinase.

    abstract::p21-activated kinases (PAKs) serve as effector proteins for the GTP-binding proteins Cdc42 and Rac. They are serine/threonine kinases containing the Cdc42/Rac interactive binding (CRIB) motif. The main aim of this study was to define the minimal domain of alphaPAK required for Cdc42/Rac binding. Eight stable PAK fragm...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi980140+

    authors: Thompson G,Owen D,Chalk PA,Lowe PN

    更新日期:1998-05-26 00:00:00

  • Purification of human S-adenosylmethionine decarboxylase expressed in Escherichia coli and use of this protein to investigate the mechanism of inhibition by the irreversible inhibitors, 5'-deoxy-5'-[(3-hydrazinopropyl)methylamino]adenosine and 5'-([(Z)-4-

    abstract::Human S-adenosylmethionine decarboxylase (AdoMetDC) was expressed in high yield in Escherichia coli using the pIN-III(lppP-5) expression vector and purified to apparent homogeneity using affinity chromatography on methylglyoxal bis(guanylhydrazone)-Sepharose. The inactivation of the purified enzyme by 5'-deoxy-5'-[(3-...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00144a027

    authors: Shantz LM,Stanley BA,Secrist JA 3rd,Pegg AE

    更新日期:1992-07-28 00:00:00

  • The 2.7 A crystal structure of the activated FERM domain of moesin: an analysis of structural changes on activation.

    abstract::Moesin binds to a large range of proteins through its N terminal FERM (band 4.1, ezrin, radixin, moesin) domain. In full-length moesin isolated from cells, this binding is masked by binding to the C-terminal domain of moesin (C-ERMAD). Activation takes place by phosphorylation of Thr 558 in the C-ERMAD, which releases...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi010419h

    authors: Edwards SD,Keep NH

    更新日期:2001-06-19 00:00:00

  • Serine protease of hepatitis C virus expressed in insect cells as the NS3/4A complex.

    abstract::Hepatitis C virus (HCV) protease NS3 and its protein activator NS4A participate in the processing of the viral polyprotein into its constituent nonstructural proteins. The NS3/4A complex is thus an attractive target for antiviral therapy against HCV. We expressed the full-length NS3 and NS4A in insect cells as a solub...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi972010r

    authors: Sali DL,Ingram R,Wendel M,Gupta D,McNemar C,Tsarbopoulos A,Chen JW,Hong Z,Chase R,Risano C,Zhang R,Yao N,Kwong AD,Ramanathan L,Le HV,Weber PC

    更新日期:1998-03-10 00:00:00

  • Transthyretin aggregation under partially denaturing conditions is a downhill polymerization.

    abstract::The deposition of fibrils and amorphous aggregates of transthyretin (TTR) in patient tissues is a hallmark of TTR amyloid disease, but the molecular details of amyloidogenesis are poorly understood. Tetramer dissociation is typically rate-limiting for TTR amyloid fibril formation, so we have used a monomeric variant o...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi049621l

    authors: Hurshman AR,White JT,Powers ET,Kelly JW

    更新日期:2004-06-15 00:00:00

  • SNX-325, a novel calcium antagonist from the spider Segestria florentina.

    abstract::A novel selective calcium channel antagonist peptide, SNX-325, has been isolated from the venom of the spider Segestria florentina. The peptide was isolated using as bioassays the displacement of radioiodinated omega-conopeptide SNX-230 (MVIIC) from rat brain synaptosomal membranes, as well as the inhibition of the ba...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00026a015

    authors: Newcomb R,Palma A,Fox J,Gaur S,Lau K,Chung D,Cong R,Bell JR,Horne B,Nadasdi L

    更新日期:1995-07-04 00:00:00

  • On the charge regulation of proteins.

    abstract::It is known that the overall charge of a protein can change as the molecule approaches a charged object like another protein or a cell membrane. We have formalized this mechanism using a statistical mechanical framework and show how this rather overlooked interaction increases the attraction between protein molecules....

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi047630o

    authors: Lund M,Jönsson B

    更新日期:2005-04-19 00:00:00

  • Dissection of porphyrin-induced conformational dynamics in the heme biosynthesis enzyme ferrochelatase.

    abstract::Human ferrochelatase (EC 4.99.1.1) catalyzes the insertion ferrous iron into protoporphyrin IX as the last step in heme biosynthesis, an essential process to most organisms given the vast intracellular functions of heme. Even with multiple ferrochelatase structures available, the exact mechanism for iron insertion int...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi300704c

    authors: Asuru AP,An M,Busenlehner LS

    更新日期:2012-09-11 00:00:00

  • Coherent dynamics during the primary electron-transfer reaction in membrane-bound reaction centers of Rhodobacter sphaeroides.

    abstract::The temporal evolution of the near-infrared stimulated emission band of the special pair excited state (P*) in the reaction center of Rhodobacter sphaeroides has been studied in intracytoplasmic membranes of the antenna-deficient RCO1 mutant at 10 K with a resolution of 30 fs. On the 100-fs time scale the emission ban...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00188a002

    authors: Vos MH,Jones MR,Hunter CN,Breton J,Lambry JC,Martin JL

    更新日期:1994-06-07 00:00:00

  • Bound Compound, Interfacial Water, and Phenyl Ring Rotation Dynamics of a Compound in the DNA Minor Groove.

    abstract::DB2277, a heterocyclic diamidine, is a successful design for mixed base pair (bp) DNA sequence recognition. The compound has a central aza-benzimidazole group that forms two H-bonds with a GC bp that has flanking AT bps. The nuclear magnetic resonance structure of the DB2277-DNA complex with an AAGATA recognition site...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/acs.biochem.8b00647

    authors: Harika NK,Wilson WD

    更新日期:2018-08-21 00:00:00

  • Calvarial cells synthesize 1 alpha,25-dihydroxyvitamin D3 from 25-hydroxyvitamin D3.

    abstract::A metabolite of vitamin D has been isolated in pure form from incubation of 25-hydroxyvitamin D3 with embryonic chick calvarial cells that had been grown on Cytodex 1 microcarrier beads. The isolation involved dichloromethane extraction of the cells and incubation medium, followed by Sephadex LH-20 column chromatograp...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00274a012

    authors: Turner RT,Howard GA,Puzas JE,Baylink DJ,Knapp DR

    更新日期:1983-03-01 00:00:00

  • Studies on the irreversible step of pepsinogen activation.

    abstract::The bond cleavage step of pepsinogen activation has been investigated in a kinetic study in which the denatured products of short-term acidifications were separated on SDS-polyacrylamide gels and the peptide products were quantitated by densitometry. Although several peptide products were observed, under the condition...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00432a040

    authors: Glick DM,Shalitin Y,Hilt CR

    更新日期:1989-03-21 00:00:00

  • Optimization of alternate-strand triple helix formation at the 5'CpG3' and 5'GpC3' junction steps.

    abstract::Oligonucleotide-directed triple helix formation normally requires a long tract of oligopyrimidine.oligopurine sequence. This limitation can be partially overcome by alternate-strand triple helix (or switch triple helix) formation which enables recognition of alternating oligopurine/oligopyrimidine sequences. The prese...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi980618+

    authors: Marchand C,Sun JS,Bailly C,Waring MJ,Garestier T,Hélène C

    更新日期:1998-09-22 00:00:00

  • Poly(dA).poly(dT) exists in an unusual conformation under physiological conditions: propidium binding to poly(dA).poly(dT) and poly[d(A-T)].poly[d(A-T)].

    abstract::The binding of propidium to poly(dA).poly(dT) [poly(dA.dT)] and to poly[d(A-T)].poly[d(A-T)] [poly[d(A-T)2]] has been compared under a variety of solution conditions by viscometric titrations, binding studies, and kinetic experiments. The binding of propidium to poly[d(A-T)2] is quite similar to its binding to calf th...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00336a029

    authors: Wilson WD,Wang YH,Krishnamoorthy CR,Smith JC

    更新日期:1985-07-16 00:00:00

  • Site-directed mutagenesis of highly conserved residues in helix VIII of subunit I of the cytochrome bo ubiquinol oxidase from Escherichia coli: an amphipathic transmembrane helix that may be important in conveying protons to the binuclear center.

    abstract::Cytochrome bo from Escherichia coli is a ubiquinol oxidase which is a member of the superfamily of heme-copper respiratory oxidases. This superfamily, which includes the eukaryotic cytochrome c oxidases, has in common a bimetallic center consisting of a high-spin heme component and a copper atom (CuB) which is the sit...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00092a029

    authors: Thomas JW,Lemieux LJ,Alben JO,Gennis RB

    更新日期:1993-10-19 00:00:00

  • KappaM-conotoxin RIIIK, structural and functional novelty in a K+ channel antagonist.

    abstract::Venomous organisms have evolved a variety of structurally diverse peptide neurotoxins that target ion channels. Despite the lack of any obvious structural homology, unrelated toxins that interact with voltage-activated K(+) channels share a dyad motif composed of a lysine and a hydrophobic amino acid residue, usually ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0495681

    authors: Al-Sabi A,Lennartz D,Ferber M,Gulyas J,Rivier JE,Olivera BM,Carlomagno T,Terlau H

    更新日期:2004-07-13 00:00:00

  • Conformational fluctuations in deoxy hemoglobin revealed as a major contributor to anionic modulation of function through studies of the oxygenation and oxidation of hemoglobins A0 and Deer Lodge beta2(NA2)His --> Arg.

    abstract::Organisms rely on regulation at the molecular level, such as the allosteric regulation of hemoglobin (Hb) function by anions, to meet challenges presented by changing environmental and physiological conditions. A comparison of the effects of anions on oxygenation, oxidation, and sulfhydryl reactivity of Hb leads us to...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi971574s

    authors: Bonaventura C,Tesh S,Faulkner KM,Kraiter D,Crumbliss AL

    更新日期:1998-01-13 00:00:00

  • Proximity between nucleotide/dinucleotide and metal ion binding sites in DNA-dependent RNA polymerase from Escherichia coli.

    abstract::In order to understand translocation in transcription, it is important to develop a continuous functional assay for RNA polymerase (RNAP) activity in vitro. Fluorescent derivatives of ATP, UTP, UpA, and CpA with aminonaphthalene-5-sulfonic acid (AmNS) attached to the nucleotide triphosphates via a gamma-phosphoramidat...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00143a013

    authors: Tyagi SC,Wu FY

    更新日期:1992-07-21 00:00:00

  • DNA damage levels and biochemical repair capacities associated with XRCC1 deficiency.

    abstract::Base excision repair (BER) is the major corrective pathway for most spontaneous, oxidative, and alkylation DNA base and sugar damage. X-ray cross-complementing 1 (XRCC1) has been suggested to function at nearly every step of this repair process, primarily through direct protein-protein interactions. Using whole cell e...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi051161o

    authors: Wong HK,Kim D,Hogue BA,McNeill DR,Wilson DM 3rd

    更新日期:2005-11-01 00:00:00

  • Polymorphism at residue 129 modulates the conformational conversion of the D178N variant of human prion protein 90-231.

    abstract::One of the arguments in favor of the protein-only hypothesis of transmissible spongiform encephalopathies is the link between inherited prion diseases and specific mutations in the PRNP gene. One such mutation (Asp178 --> Asn) is associated with two distinct disorders: fatal familial insomnia or familial Creutzfeldt-J...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi051455+

    authors: Apetri AC,Vanik DL,Surewicz WK

    更新日期:2005-12-06 00:00:00

  • Kinetic mechanism of deoxyadenosine kinase from Mycoplasma determined by surface plasmon resonance technology.

    abstract::Surface plasmon resonance (SPR) detection technology was employed to investigate the kinetic mechanism of deoxyadenosine kinase from Mycoplasma mycoides ssp. mycoides SC. In our experimental approach, the enzyme was attached to the sensor surface, the reactants were injected in the mobile phase, and the product-enzyme...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0515523

    authors: Pol E,Wang L

    更新日期:2006-01-17 00:00:00

  • Use of cytochrome P-450scc to measure cholesterol-lipid interactions.

    abstract::The interaction of cholesterol with phospholipids has been studied with a variety of techniques; however, the possible consequences of such interactions in vivo have not been demonstrated. In this study, the cholesterol-dependent absorbance spectrum of cytochrome P-450scc was used to monitor cholesterol availability i...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00363a017

    authors: Stevens VL,Lambeth JD,Merrill AH Jr

    更新日期:1986-07-29 00:00:00

  • Catalytic mechanism of enzymes: preorganization, short strong hydrogen bond, and charge buffering.

    abstract::During the past decade, there has been much debate about the enormous catalytic rate enhancement observed in enzymatic reactions involving carbanion intermediates. Our recent theoretical study has demonstrated the importance of the short strong hydrogen bond (SSHB) in the enzymatic reactions. Nevertheless, other recen...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi0255118

    authors: Kim KS,Kim D,Lee JY,Tarakeshwar P,Oh KS

    更新日期:2002-04-23 00:00:00

  • Structural and thermodynamic basis of affinity in anti-dinitrophenyl antibody.

    abstract::The thermodynamic quantities of the anti-dinitrophenyl antibody-hapten interaction are reported for rabbit, goat, and guinea pig antibodies. Rabbit and goat antibodies had similar exothermic enthalpy changes for their reaction with 2,4-dinitrophenyl-L-lysine (-13.9 and -14.8 kcal/mol, respectively). The enthalpy chang...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00694a032

    authors: Halsey JF,Cebra JJ,Biltonen RL

    更新日期:1975-11-18 00:00:00

  • Hydrogen-1 nuclear magnetic resonance study of the complexes of two diastereoisomers of folinic acid with dihydrofolate reductase.

    abstract::The 1H chemical shifts for the formyl and benzoyl protons of the individual diastereoisomeres of folinic acid bound to dihydrofolate reductase have been measured. For the tightly bound biologically active 6S, alpha S isomer, the "bound" signals were assigned by using transfer of saturation methods. In this case, only ...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00510a019

    authors: Feeney J,Birdsall B,Albrand JP,Roberts GC,Burgen AS,Charlton PA,Young DW

    更新日期:1981-03-31 00:00:00

  • Structure of alpha-glycerophosphate oxidase from Streptococcus sp.: a template for the mitochondrial alpha-glycerophosphate dehydrogenase.

    abstract::The FAD-dependent alpha-glycerophosphate oxidase (GlpO) from Enterococcus casseliflavus and Streptococcus sp. was originally studied as a soluble flavoprotein oxidase; surprisingly, the GlpO sequence is 30-43% identical to those of the alpha-glycerophosphate dehydrogenases (GlpDs) from mitochondrial and bacterial sour...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi701685u

    authors: Colussi T,Parsonage D,Boles W,Matsuoka T,Mallett TC,Karplus PA,Claiborne A

    更新日期:2008-01-22 00:00:00

  • Kinetics of hepatic cytochrome P-450 reduction: correlation with spin state of the ferric heme.

    abstract::The reduction kinetics of cytochrome P-450 are known to be biphasic, with a rapid initial phase and a slower subsequent phase, both of which appear linear in semilogarithmic plots. The present report demonstrates that these biphasic reduction kinetics can be described in terms of a preequilibrium between high- and low...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00535a034

    authors: Backes WL,Sligar SG,Schenkman JB

    更新日期:1982-03-16 00:00:00

  • Binding of initiation factor 2 and initiator tRNA to the Escherichia coli 30S ribosomal subunit induces allosteric transitions in 16S rRNA.

    abstract::The specific effect of the binding of IF2 and initiator fMET-tRNA(fMet) on Escherichia coli 16S rRNA has been probed by phosphate alkylation with ethylnitrosourea. The results show that IF2 does not significantly shield portions of 16S rRNA but induces both reductions and enhancements of reactivity scattered in the en...

    journal_title:Biochemistry

    pub_type: 杂志文章

    doi:10.1021/bi00487a023

    authors: Wakao H,Romby P,Laalami S,Ebel JP,Ehresmann C,Ehresmann B

    更新日期:1990-09-04 00:00:00