Cold-adaptation in sea-water-borne signal proteins: sequence and NMR structure of the pheromone En-6 from the Antarctic ciliate Euplotes nobilii.

Abstract:

:Ciliates of Euplotes species constitutively secrete pleiotropic protein pheromones, which are capable to function as prototypic autocrine growth factors as well as paracrine inducers of mating processes. This paper reports the amino acid sequence and the NMR structure of the pheromone En-6 isolated from the antarctic species Euplotes nobilii. The 63-residue En-6 polypeptide chain forms three alpha-helices in positions 18-25, 36-40 and 46-56, which are arranged in an up-down-up three-helix bundle forming the edges of a distorted trigonal pyramid. The base of the pyramid is covered by the N-terminal heptadecapeptide segment, which includes a 3(10)-turn of residues 3-6. This topology is covalently anchored by four long-range disulfide bonds. Comparison with the smaller pheromones of E. raikovi, a closely related species living in temperate waters, shows that the two-pheromone families have the same three-helix bundle architecture. It then appears that cold-adaptation of the En proteins is primarily related to increased lengths of the chain-terminal peptide segments and the surface-exposed loops connecting the regular secondary structures, and to the presence of solvent-exposed clusters of negatively charged side-chains.

journal_name

J Mol Biol

authors

Pedrini B,Placzek WJ,Koculi E,Alimenti C,LaTerza A,Luporini P,Wüthrich K

doi

10.1016/j.jmb.2007.06.046

subject

Has Abstract

pub_date

2007-09-14 00:00:00

pages

277-86

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(07)00841-8

journal_volume

372

pub_type

杂志文章
  • Exploring conformational space with a simple lattice model for protein structure.

    abstract::We present a low resolution lattice model for which we can exhaustively generate all possible compact backbone conformations for small proteins. Using simple structural and energetic criteria, for a variety of proteins, we can select for lattice structures that have significant similarities with their known native str...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(94)90040-x

    authors: Hinds DA,Levitt M

    更新日期:1994-11-04 00:00:00

  • In a staphylococcal nuclease mutant the side-chain of a lysine replacing valine 66 is fully buried in the hydrophobic core.

    abstract::The crystal structure of the staphylococcal nuclease mutant V66K, in which valine 66 is replaced by lysine, has been solved at 1.97 A resolution. Unlike lysine residues in previously reported protein structures, this residue appears to bury its side-chain in the hydrophobic core without salt bridging, hydrogen bonding...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)80195-z

    authors: Stites WE,Gittis AG,Lattman EE,Shortle D

    更新日期:1991-09-05 00:00:00

  • Molecular crowding limits the role of fetal hemoglobin in therapy for sickle cell disease.

    abstract::The dominant assumption central to most treatments for sickle cell anemia has been that replacement of sickle hemoglobin (HbS) by fetal hemoglobin (HbF) would have major clinical benefit. Using laser photolysis, we have measured polymerization kinetics including rates of homogeneous and heterogeneous nucleation on mix...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.02.006

    authors: Rotter M,Aprelev A,Adachi K,Ferrone FA

    更新日期:2005-04-15 00:00:00

  • Knowledge-based scoring function to predict protein-ligand interactions.

    abstract::The development and validation of a new knowledge-based scoring function (DrugScore) to describe the binding geometry of ligands in proteins is presented. It discriminates efficiently between well-docked ligand binding modes (root-mean-square deviation <2.0 A with respect to a crystallographically determined reference...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3371

    authors: Gohlke H,Hendlich M,Klebe G

    更新日期:2000-01-14 00:00:00

  • Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI.

    abstract::The SgrAI endonuclease displays its maximal activity on DNA with two copies of its recognition sequence, cleaving both sites concertedly. While most restriction enzymes that act concurrently at two sites are tetramers, SgrAI is a dimer in solution. Its reaction at two cognate sites involves the association of two DNA-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.04.053

    authors: Wood KM,Daniels LE,Halford SE

    更新日期:2005-07-08 00:00:00

  • Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming.

    abstract::A protein is defined as an indexed string of elements at each level in the hierarchy of protein structure: sequence, secondary structure, super-secondary structure, etc. The elements, for example, residues or secondary structure segments such as helices or beta-strands, are associated with a series of properties and c...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90134-8

    authors: Sali A,Blundell TL

    更新日期:1990-03-20 00:00:00

  • Structure determination of the three disulfide bond isomers of alpha-conotoxin GI: a model for the role of disulfide bonds in structural stability.

    abstract::The three possible disulfide bonded isomers of alpha-conotoxin GI have been selectively synthesised and their structures determined by 1H NMR spectroscopy. alpha-Conotoxin GI derives from the venom of Conus geographus and is a useful neuropharmacological tool as it selectively binds to the nicotinic acetylcholine rece...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1998.1701

    authors: Gehrmann J,Alewood PF,Craik DJ

    更新日期:1998-05-01 00:00:00

  • On the connection between inherent DNA flexure and preferred binding of hydroxymethyluracil-containing DNA by the type II DNA-binding protein TF1.

    abstract::TF1 is a member of the family of type II DNA-binding proteins, which also includes the bacterial HU proteins and the Escherichia coli integration host factor (IHF). Distinctive to TF1, which is encoded by the Bacillus subtilis bacteriophage SPO1, is its preferential binding to DNA in which thymine is replaced by 5-hyd...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0392

    authors: Grove A,Galeone A,Mayol L,Geiduschek EP

    更新日期:1996-07-12 00:00:00

  • Sequence-dependent upstream DNA-RNA polymerase interactions in the open complex with lambdaPR and lambdaPRM promoters and implications for the mechanism of promoter interference.

    abstract::Upstream interactions of Escherichia coli RNA polymerase (RNAP) in an open promoter complex (RPo) formed at the P(R) and P(RM) promoters of bacteriophage lambda have been studied by atomic force microscopy. We demonstrate that the previously described 30-nm DNA compaction observed upon RPo formation at P(R) [Rivetti, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.11.019

    authors: Mangiarotti L,Cellai S,Ross W,Bustamante C,Rivetti C

    更新日期:2009-01-23 00:00:00

  • Thermodynamic dissection of the polymerizing and editing modes of a DNA polymerase.

    abstract::DNA polymerases with intrinsic proofreading activity interact with DNA primer/templates in two distinct modes, corresponding to the complexes formed during the 5'-3' polymerization or 3'-5' editing of a nascent DNA chain. Thermodynamic measurements designed to quantify the energetic contributions of individual DNA-pro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.11.023

    authors: Bailey MF,van der Schans EJ,Millar DP

    更新日期:2004-02-20 00:00:00

  • Conserved C-terminal region of global repressor KorA of broad-host-range plasmid RK2 is required for co-operativity between KorA and a second RK2 global regulator, KorB.

    abstract::KorA and KorB proteins of IncP1 plasmid RK2 are encoded in the central control region (ccr) of the plasmid and act as global regulators of plasmid genes for replication, transfer and stable inheritance. KorA represses seven promoters on RK2, by binding to a defined operator site, OA, which always occurs in promoter re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2761

    authors: Kostelidou K,Jones AC,Thomas CM

    更新日期:1999-06-04 00:00:00

  • Amino acid acceptor identity switch of Escherichia coli tmRNA from alanine to histidine in vitro.

    abstract::According to a trans -translation model, tmRNA facilitates the resumption of translation that has been stalled on the ribosome with the 3' end of a terminator-less mRNA, to produce a chimera polypeptide of the nascent peptide and the tmRNA-encoding 11 amino acid-tag. The first alanine residue of the tag-sequence is en...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2754

    authors: Nameki N,Tadaki T,Muto A,Himeno H

    更新日期:1999-05-28 00:00:00

  • NMR structure of activated CheY.

    abstract::The CheY protein is the response regulator in bacterial chemotaxis. Phosphorylation of a conserved aspartyl residue induces structural changes that convert the protein from an inactive to an active state. The short half-life of the aspartyl-phosphate has precluded detailed structural analysis of the active protein. Pe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3595

    authors: Cho HS,Lee SY,Yan D,Pan X,Parkinson JS,Kustu S,Wemmer DE,Pelton JG

    更新日期:2000-03-31 00:00:00

  • One is not enough.

    abstract::In both prokaryotic and eukaryotic organisms, repressors and activators are responsible for regulating gene expression. The lac operon is a paradigm for understanding how metabolites function as signaling molecules and modulate transcription. These metabolites or allosteric effector molecules bind to the repressor and...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.07.050

    authors: Daber R,Sharp K,Lewis M

    更新日期:2009-10-09 00:00:00

  • Efficient Catalysis of Protein Folding by GroEL/ES of the Obligate Chaperonin Substrate MetF.

    abstract::The cylindrical chaperonin GroEL and its cofactor GroES mediate ATP-dependent protein folding in Escherichia coli by transiently encapsulating non-native substrate in a nano-cage formed by the GroEL ring cavity and the lid-shaped GroES. Mechanistic studies of GroEL/ES with heterologous protein substrates suggested tha...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.02.031

    authors: Singh AK,Balchin D,Imamoglu R,Hayer-Hartl M,Hartl FU

    更新日期:2020-03-27 00:00:00

  • An on-pathway hidden intermediate and the early rate-limiting transition state of Rd-apocytochrome b562 characterized by protein engineering.

    abstract::The folding pathway of Rd-apocytochrome b562, a four-helix bundle protein, was characterized using Trp and Ala/Gly pair mutations. We found that the Trp mutants (F65W) of both the fully folded Rd-apocytochrome b562 and a partially unfolded intermediate with the N-terminal helix (helix I) unfolded, fold with identical ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.07.057

    authors: Zhou Z,Huang Y,Bai Y

    更新日期:2005-09-30 00:00:00

  • Folding studies on a knotted protein.

    abstract::YibK is a 160 residue homodimeric protein belonging to the SPOUT class of methyltransferases. Proteins in this group all display a unique topological feature; the backbone polypeptide chain folds to form a deep trefoil knot. Such knotted structures were completely unpredicted, it being thought impossible for a protein...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.12.055

    authors: Mallam AL,Jackson SE

    更新日期:2005-03-11 00:00:00

  • An in-the-groove view of DNA structures in complexes with proteins.

    abstract::DNA structures bound to transcription factors are studied by using the crystal coordinates of complexes. Structural characteristics which are found at the sites where a protein secondary structure, an alpha-helix or a beta-sheet binds, can be understood in terms of fitting of the concave surface of the DNA major groov...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0055

    authors: Suzuki M,Yagi N

    更新日期:1996-02-09 00:00:00

  • Adaptation of protein surfaces to subcellular location.

    abstract::In vivo, proteins occur in widely different physio-chemical environments, and, from in vitro studies, we know that protein structure can be very sensitive to environment. However, theoretical studies of protein structure have tended to ignore this complexity. In this paper, we have approached this problem by grouping ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1498

    authors: Andrade MA,O'Donoghue SI,Rost B

    更新日期:1998-02-20 00:00:00

  • Defining the molecular basis of Arf and Hdm2 interactions.

    abstract::Understanding the interaction of Arf and Hdm2 has recently become a central issue in cancer biology. In response to hyperproliferative signals, p14(Arf) stabilizes p53 by binding to Hdm2 and inhibits the ubiquitination and subsequent proteosome-dependent degradation of p53. The medical importance of the Arf-Hdm2-p53 r...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.5110

    authors: Bothner B,Lewis WS,DiGiammarino EL,Weber JD,Bothner SJ,Kriwacki RW

    更新日期:2001-11-23 00:00:00

  • Solution structures of the YAP65 WW domain and the variant L30 K in complex with the peptides GTPPPPYTVG, N-(n-octyl)-GPPPY and PLPPY and the application of peptide libraries reveal a minimal binding epitope.

    abstract::The single mutation L30 K in the Hu-Yap65 WW domain increased the stability of the complex with the peptide GTPPPPYTVG (K(d)=40(+/-5) microM). Here we report the refined solution structure of this complex by NMR spectroscopy and further derived structure-activity relationships by using ligand peptide libraries with tr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.5199

    authors: Pires JR,Taha-Nejad F,Toepert F,Ast T,Hoffmüller U,Schneider-Mergener J,Kühne R,Macias MJ,Oschkinat H

    更新日期:2001-12-14 00:00:00

  • The crystal structure of a sulfurtransferase from Azotobacter vinelandii highlights the evolutionary relationship between the rhodanese and phosphatase enzyme families.

    abstract::Rhodanese is an ubiquitous enzyme that in vitro catalyses the transfer of a sulfur atom from suitable donors to nucleophilic acceptors by way of a double displacement mechanism. During the catalytic process the enzyme cycles between a sulfur-free and a persulfide-containing form, via formation of a persulfide linkage ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3651

    authors: Bordo D,Deriu D,Colnaghi R,Carpen A,Pagani S,Bolognesi M

    更新日期:2000-05-12 00:00:00

  • DNA topology and geometry in Flp and Cre recombination.

    abstract::The Flp recombinase of yeast and the Cre recombinase of bacteriophage P1 both belong to the lambda-integrase (Int) family of site-specific recombinases. These recombination systems recognize recombination-target sequences that consist of two 13bp inverted repeats flanking a 6 or 8bp spacer sequence. Recombination reac...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.01.037

    authors: Vetcher AA,Lushnikov AY,Navarra-Madsen J,Scharein RG,Lyubchenko YL,Darcy IK,Levene SD

    更新日期:2006-04-07 00:00:00

  • RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box.

    abstract::We have used a hidden Markov model (HMM) to identify the consensus sequence of the RpoD promoters in the genome of Campylobacter jejuni. The identified promoter consensus sequence is unusual compared to other bacteria, in that the region upstream of the TATA-box does not contain a conserved -35 region, but shows a ver...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00034-2

    authors: Petersen L,Larsen TS,Ussery DW,On SL,Krogh A

    更新日期:2003-03-07 00:00:00

  • DRoP: a water analysis program identifies Ras-GTP-specific pathway of communication between membrane-interacting regions and the active site.

    abstract::Ras GTPase mediates several cellular signal transduction pathways and is found mutated in a large number of cancers. It is active in the GTP-bound state, where it interacts with effector proteins, and at rest in the GDP-bound state. The catalytic domain is tethered to the membrane, with which it interacts in a nucleot...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.10.036

    authors: Kearney BM,Johnson CW,Roberts DM,Swartz P,Mattos C

    更新日期:2014-02-06 00:00:00

  • Recombinant DNA approach for defining the primary structure of monoclonal antibody epitopes. The analysis of a conformation-specific antibody to myosin light chain 2.

    abstract::A monoclonal antibody (MF5), capable of recognizing a divalent cation-induced conformational change in myosin light chain 2 (LC2f), has been used to screen a cDNA library constructed in the expression vector lambda gt11. A clone has been isolated that contains the whole coding sequence of this myosin subunit. The ligh...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90229-3

    authors: Reinach FC,Fischman DA

    更新日期:1985-02-05 00:00:00

  • Translation elongation factor EF-Tu modulates filament formation of actin-like MreB protein in vitro.

    abstract::EF-Tu has been shown to interact with actin-like protein MreB and to affect its localization in Escherichia coli and in Bacillus subtilis cells. We have purified YFP-MreB in an active form, which forms filaments on glass slides in vitro and was active in dynamic light-scattering assays, polymerizing in milliseconds af...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.01.025

    authors: Defeu Soufo HJ,Reimold C,Breddermann H,Mannherz HG,Graumann PL

    更新日期:2015-04-24 00:00:00

  • Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI.

    abstract::The restriction enzyme R.BbvCI cleaves duplex DNA within a seven base-pair asymmetric recognition sequence, thus: CCTCAGC/GCTGAGG-->CC--TCAGC/GC--TGAGG. We show that R.BbvCI comprises two different subunits, R(1) and R(2); that each subunit contains a catalytic site for DNA strand hydrolysis; and that these sites act ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.02.034

    authors: Heiter DF,Lunnen KD,Wilson GG

    更新日期:2005-05-06 00:00:00

  • Structural characterization of intramolecular Hg(2+) transfer between flexibly linked domains of mercuric ion reductase.

    abstract::The enzyme mercuric ion reductase MerA is the central component of bacterial mercury resistance encoded by the mer operon. Many MerA proteins possess metallochaperone-like N-terminal domains (NmerA) that can transfer Hg(2+) to the catalytic core domain (Core) for reduction to Hg(0). These domains are tethered to the h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.08.042

    authors: Johs A,Harwood IM,Parks JM,Nauss RE,Smith JC,Liang L,Miller SM

    更新日期:2011-10-28 00:00:00

  • Molecular extensibility of mini-dystrophins and a dystrophin rod construct.

    abstract::Muscular dystrophies arise with various mutations in dystrophin, implicating this protein in force transmission in normal muscle. With 24 three-helix, spectrin repeats interspersed with proline-rich hinges, dystrophin's large size is an impediment to gene therapy, prompting the construction of mini-dystrophins. Result...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.07.064

    authors: Bhasin N,Law R,Liao G,Safer D,Ellmer J,Discher BM,Sweeney HL,Discher DE

    更新日期:2005-09-30 00:00:00