当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Energy-optimized structure of antifreeze protein and its binding mechanism.

Energy-optimized structure of antifreeze protein and its binding mechanism.

Abstract：

:A combination of Monte Carlo simulated annealing and energy minimization was utilized to determine the conformation of the antifreeze protein from the fish winter flounder. It was found from the energy-optimized structure that the hydroxyl groups of its four threonine residues, i.e. Thr2, Thr13, Thr24, Thr35, are aligned on almost the same line parallel to the helix axis and separated successively by 16.1, 16.0 and 16.2 A, respectively, very close to the 16.6 A repeat spacing along [0112] in ice. Based on such a space match, a zipper-like model is proposed to elucidate the binding mechanism of the antifreeze protein to ice crystals. According to the current model, the antifreeze protein may bind to an ice nucleation structure in a zipper-like fashion through hydrogen bonding of the hydroxyl groups of these four Thr residues to the oxygen atoms along the [0112] direction in ice lattice, subsequently stopping or retarding the growth of ice pyramidal planes so as to depress the freeze point. The calculated results and the binding mechanism thus derived accord with recent experimental observations. The mechanistic implications derived from such a special antifreeze molecule might be generally applied to elucidate the structure-function relationship of other antifreeze proteins with the following two common features: (1) recurrence of a Thr residue (or any other polar amino acid residue whose side-chain can form a hydrogen bond with water) in an 11-amino-acid period along the sequence concerned; and (2) a high percentage of Ala residue component therein. Further experiments are suggested to test the ice binding model.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Chou KC

doi

10.1016/0022-2836(92)90666-8

subject

Has Abstract

pub_date

1992-01-20 00:00:00

pages

509-17

issue

2

eissn

0022-2836

issn

1089-8638

pii

0022-2836(92)90666-8

journal_volume

223

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase.

    abstract：:The Escherichia coli T4 bacteriophage uses two glycosyltransferases to glucosylate and thus protect its DNA: the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). They glucosylate 5-hydroxymethyl cytosine (5-HMC) bases of duplex DNA using UDP-glucose as the sugar donor to form...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.07.007

    authors： Larivière L,Sommer N,Moréra S

    更新日期：2005-09-09 00:00:00

  • Crystal structure of human ribosomal protein L10 core domain reveals eukaryote-specific motifs in addition to the conserved fold.

    abstract：:A phylogenetically conserved ribosomal protein L16p/L10e organizes the architecture of the aminoacyl tRNA binding site on the large ribosomal subunit. Eukaryotic L10 also exhibits a variety of cellular activities, and, in particular, human L10 is known as a putative tumor suppressor, QM. We have determined the 2.5-A c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.01.003

    authors： Nishimura M,Kaminishi T,Takemoto C,Kawazoe M,Yoshida T,Tanaka A,Sugano S,Shirouzu M,Ohkubo T,Yokoyama S,Kobayashi Y

    更新日期：2008-03-21 00:00:00

  • Evolution of an interloop disulfide bond in high-affinity antibody mimics based on fibronectin type III domain and selected by yeast surface display: molecular convergence with single-domain camelid and shark antibodies.

    abstract：:The 10th human fibronectin type III domain ((10)Fn3) is one of several protein scaffolds used to design and select families of proteins that bind with high affinity and specificity to macromolecular targets. To date, the highest affinity (10)Fn3 variants have been selected by mRNA display of libraries generated by ran...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.02.029

    authors： Lipovsek D,Lippow SM,Hackel BJ,Gregson MW,Cheng P,Kapila A,Wittrup KD

    更新日期：2007-05-11 00:00:00

  • Structural Principles Governing Disease-Causing Germline Mutations.

    abstract：:Advancements in sequencing in the past decades enabled not only the determination of the human proteome but also the identification of a large number of genetic variations in the human population. The phenotypic effects of these mutations range from neutral for polymorphisms to severe for some somatic mutations. Disea...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2018.10.005

    authors： Dobson L,Mészáros B,Tusnády GE

    更新日期：2018-12-07 00:00:00

  • Autogenous regulation of transcription termination factor Rho.

    abstract：:We present evidence that the transcription termination factor Rho is autogenously regulated in Escherichia coli. The steady-state level of Rho is increased approximately tenfold in rho mutant cells. In the rho+ revertants, the content of Rho is similar to the wild-type level. A rho-/rho+ merodiploid produces equimolar...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90236-0

    authors： Barik S,Bhattacharya P,Das A

    更新日期：1985-04-20 00:00:00

  • Bacteriophage P2 late promoters. II. Comparison of the four late promoter sequences.

    abstract：:The late genes of bacteriophage P2 are clustered into four transcription units. We have reported the transcription initiation sites for two of the late messenger RNAs, encoding genes QP and ONMLKRS. We have now located the 5' ends of the two remaining late mRNAs. The first gene in the VJHG transcription unit has been ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90226-8

    authors： Christie GE,Calendar R

    更新日期：1985-02-05 00:00:00

  • CTL recognition of a protective immunodominant influenza A virus nucleoprotein epitope utilizes a highly restricted Vbeta but diverse Valpha repertoire: functional and structural implications.

    abstract：:To investigate protective immunity conferred by CTL against viral pathogens, we have analyzed CD8(+) T cell responses to the immunodominant nucleoprotein epitope (NP(366-374)) of influenza A virus in B6 mice during primary and secondary infections in vivo. Unlike the highly biased TCR Vbeta repertoire, the associated ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.06.057

    authors： Zhong W,Dixit SB,Mallis RJ,Arthanari H,Lugovskoy AA,Beveridge DL,Wagner G,Reinherz EL

    更新日期：2007-09-14 00:00:00

  • Construction of a microphage variant of filamentous bacteriophage.

    abstract：:The intergenic region in the genome of the Ff class of filamentous phage (comprising strains fl, fd and M13) genome constitutes 8% of the viral genome, and has essential functions in DNA replication and phage morphogenesis. The functional domains of this region may be inserted into separate sites of a plasmid to funct...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90858-h

    authors： Specthrie L,Bullitt E,Horiuchi K,Model P,Russel M,Makowski L

    更新日期：1992-12-05 00:00:00

  • A novel calmodulin-like gene from the nematode Caenorhabditis elegans.

    abstract：:A novel gene from the nematode Caenorhabditis elegans was isolated by hybridization with a human calmodulin complementary DNA probe. This gene, cal-1, is present at one copy per haploid genome. In-situ hybridization of the cloned gene to metaphase chromosomes allowed us to assign it to the nematode linkage group IV. T...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90002-1

    authors： Salvato M,Sulston J,Albertson D,Brenner S

    更新日期：1986-08-05 00:00:00

  • Intact ribonucleic acid from defective particles of bacteriophage R17.

    abstract：:The growth of one group of amber mutants of R17 (class A) in non-permissive hosts results in a burst of bacteriophage-like particles, which are defective in that they are non-infectious. Here studies of particles produced by the growth of wild-type R17 and four class A mutants on AB301, a non-permissive Hfr Escherichi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(66)90016-7

    authors： Argetsinger JE,Gussin GN

    更新日期：1966-11-28 00:00:00

  • The crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase II from Sulfolobus solfataricus, a thermophilic enzyme stabilized by intramolecular disulfide bonds.

    abstract：:The crystal structure of Sulfolobus solfataricus 5'-deoxy-5'-methylthioadenosine phosphorylase II (SsMTAPII) in complex with 5'-deoxy-5'-methylthioadenosine (MTA) and sulfate was determined to 1.45A resolution. The hexameric structure of SsMTAPII is a dimer-of-trimers with one active site per monomer. The oligomeric a...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.12.040

    authors： Zhang Y,Porcelli M,Cacciapuoti G,Ealick SE

    更新日期：2006-03-17 00:00:00

  • The crystal structure of C2a, the catalytic fragment of classical pathway C3 and C5 convertase of human complement.

    abstract：:The multi-domain serine protease C2 provides the catalytic activity for the C3 and C5- convertases of the classical and lectin pathways of complement activation. Formation of these convertases requires the Mg(2+)-dependent binding of C2 to C4b, and the subsequent cleavage of C2 by C1s or MASP2, respectively. The C-ter...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.12.039

    authors： Krishnan V,Xu Y,Macon K,Volanakis JE,Narayana SV

    更新日期：2007-03-16 00:00:00

  • Structural analysis of yeast HSF by site-specific crosslinking.

    abstract：:We have introduced cysteine substitutions into the yeast HSF1 gene at a variety of locations. Most have no phenotypic effect, and therefore provide site-specific probes for thiol-specific reagents. Crosslinking of single mutants identifies locations where equivalent regions of individual monomers can approach each oth...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4096

    authors： Bonner JJ,Chen D,Storey K,Tushan M,Lea K

    更新日期：2000-09-22 00:00:00

  • Coupling of protein assembly and DNA binding: biotin repressor dimerization precedes biotin operator binding.

    abstract：:The kinetics of coupling of protein dimerization and DNA binding have been investigated in the biotin repressor system. Two repressor monomers bind to the 40 base-pair biotin operator sequence. In previous analyses of equilibrium-binding data the weak dimerization of the repressor has justified using a model in which ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)01308-6

    authors： Streaker ED,Beckett D

    更新日期：2003-01-31 00:00:00

  • Protein secondary structure prediction using nearest-neighbor methods.

    abstract：:We have studied the use of nearest-neighbor classifiers to predict the secondary structure of proteins. The nearest-neighbor rule states that a test instance is classified according to the classifications of "nearby" training examples from a database of known structures. In the context of secondary structure predictio...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1464

    authors： Yi TM,Lander ES

    更新日期：1993-08-20 00:00:00

  • Interior and surface of monomeric proteins.

    abstract：:The solvent-accessible surface area (As) of 46 monomeric proteins is calculated using atomic co-ordinates from high-resolution and well-refined crystal structures. The As of these proteins can be determined to within 1 to 2% and that of their individual residues to within 10 to 20%. The As values of proteins are corre...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90038-6

    authors： Miller S,Janin J,Lesk AM,Chothia C

    更新日期：1987-08-05 00:00:00

  • Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex.

    abstract：:The mechanism of inhibition of the transcriptional activator nuclear factor kappaB (NF-kappaB) by the inhibitor IkappaB* is central to the understanding of the control of transcriptional activity via this widely employed pathway. Previous studies suggested that IkappaB* , a modular protein with an NF-kappaB binding do...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.05.048

    authors： Sue SC,Cervantes C,Komives EA,Dyson HJ

    更新日期：2008-07-25 00:00:00

  • Roles of the Hydrophobic Gate and Exit Channel in Vigna radiata Pyrophosphatase Ion Translocation.

    abstract：:Membrane-embedded pyrophosphatase (M-PPase) hydrolyzes pyrophosphate to drive ion (H+ and/or Na+) translocation. We determined crystal structures and functions of Vigna radiata M-PPase (VrH+-PPase), the VrH+-PPase-2Pi complex and mutants at hydrophobic gate (residue L555) and exit channel (residues T228 and E225). Ion...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2019.03.009

    authors： Tsai JY,Tang KZ,Li KM,Hsu BL,Chiang YW,Goldman A,Sun YJ

    更新日期：2019-04-05 00:00:00

  • Relationship of DNA structure to internal dynamics: correlation of helical parameters from NOE-based NMR solution structures of d(GCGTACGC)(2) and d(CGCTAGCG)(2) with (13)C order parameters implies conformational coupling in dinucleotide units.

    abstract：:The coupling between the conformational properties of double-stranded DNA and its internal dynamics has been examined. The solution structures of the isomeric DNA oligomers d(GCGTACGC)(2) (UM) and d(CGCTAGCG)(2) (CTSYM) were determined with (1)H NMR spectroscopy by utilizing distance restraints from total relaxation m...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4498

    authors： Isaacs RJ,Spielmann HP

    更新日期：2001-03-23 00:00:00

  • Structural insights into transcriptional repression by noncoding RNAs that bind to human Pol II.

    abstract：:Gene transcription is regulated in response to environmental changes and developmental cues. In mammalian cells subjected to stress conditions such as heat shock, transcription of most protein-coding genes decreases, while the transcription of heat shock protein genes increases. Repression involves direct binding to R...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.08.024

    authors： Kassube SA,Fang J,Grob P,Yakovchuk P,Goodrich JA,Nogales E

    更新日期：2013-10-09 00:00:00

  • RNA-dependent folding and stabilization of C5 protein during assembly of the E. coli RNase P holoenzyme.

    abstract：:The pre-tRNA processing enzyme ribonuclease P is a ribonucleoprotein. In Escherichia coli assembly of the holoenzyme involves binding of the small (119 amino acid residue) C5 protein to the much larger (377 nucleotide) P RNA subunit. The RNA subunit makes the majority of contacts to the pre-tRNA substrate and contains...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.05.001

    authors： Guo X,Campbell FE,Sun L,Christian EL,Anderson VE,Harris ME

    更新日期：2006-06-30 00:00:00

  • Initiation of DNA replication in a eukaryotic rolling-circle replicon: identification of multiple DNA-protein complexes at the geminivirus origin.

    abstract：:The mechanism of initiation of DNA replication in eukaryotic rolling- circle replicons is still poorly understood in molecular terms. Geminiviruses, a family of plant DNA viruses, which use this strategy during part of their replicative cycle, replicate in the nucleus and are amenable to molecular studies. Except for ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.2916

    authors： Castellano MM,Sanz-Burgos AP,Gutiérrez C

    更新日期：1999-07-16 00:00:00

  • Discrete RNA libraries from pseudo-torsional space.

    abstract：:The discovery that RNA molecules can fold into complex structures and carry out diverse cellular roles has led to interest in developing tools for modeling RNA tertiary structure. While significant progress has been made in establishing that the RNA backbone is rotameric, few libraries of discrete conformations specif...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2012.03.002

    authors： Humphris-Narayanan E,Pyle AM

    更新日期：2012-08-03 00:00:00

  • Structure of an enclosed dimer formed by the Drosophila period protein.

    abstract：:Period (PER) is the major transcription inhibitor in metazoan circadian clocks and lies at the center of several feedback loops that regulate gene expression. Dimerization of Drosophila PER influences nuclear translocation, repressor activity, and behavioral rhythms. The structure of a central, 346-residue PER fragmen...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2011.08.048

    authors： King HA,Hoelz A,Crane BR,Young MW

    更新日期：2011-10-28 00:00:00

  • Dissecting the Conformational Dynamics of the Bile Acid Transporter Homologue ASBTNM.

    abstract：:Apical sodium-dependent bile acid transporter (ASBT) catalyses uphill transport of bile acids using the electrochemical gradient of Na+ as the driving force. The crystal structures of two bacterial homologues ASBTNM and ASBTYf have previously been determined, with the former showing an inward-facing conformation, and ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2020.166764

    authors： Lu PH,Li CC,Chiang YW,Liu JH,Chiang WT,Chao YH,Li GS,Weng SE,Lin SY,Hu NJ

    更新日期：2021-01-13 00:00:00

  • phi29 DNA polymerase active site: role of residue Val250 as metal-dNTP complex ligand and in protein-primed initiation.

    abstract：:DNA polymerases require two acidic residues to coordinate metal ions A and B at their polymerisation active site during catalysis of nucleotide incorporation. Crystallographic resolution of varphi29 DNA polymerase ternary complex showed that metal B coordination also depends on the carbonyl group of Val250 that belong...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.10.061

    authors： Pérez-Arnaiz P,Lázaro JM,Salas M,de Vega M

    更新日期：2010-01-15 00:00:00

  • Active site trapping of nucleotide by smooth and non-muscle myosins.

    abstract：:The folded 10 S monomer conformation of smooth muscle myosin traps the hydrolysis products ADP and Pi in its active sites. To test the significance of this, we have searched for equivalent trapping in other conformational and assembly states of avian gizzard and brush border myosins, using formycin triphosphate (FTP) ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90100-3

    authors： Cross RA,Jackson AP,Citi S,Kendrick-Jones J,Bagshaw CR

    更新日期：1988-09-05 00:00:00

  • Atomic force microscopy of cholera toxin B-oligomers bound to bilayers of biologically relevant lipids.

    abstract：:Cholera toxin B-oligomer was imaged by atomic force microscopy (AFM) on biologically relevant model membranes, such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine and egg yolk phosphatidylcholine at room temperature in solution at a resolution in the range of 1 to 2 nm. In addition, two-dimensional arrays we...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0238

    authors： Mou J,Yang J,Shao Z

    更新日期：1995-05-05 00:00:00

  • Aurora Kinase B Phosphorylates Histone H3.3 at Serine 31 during Mitosis in Mammalian Cells.

    abstract：:Serine 31 of histone H3.3 is phosphorylated during mitosis in mammalian cells and has been shown to influence chromosome segregation. We established a screening system to identify candidate kinase(s) phosphorylating H3.3S31 by using siRNA library targeting 720 human kinases, and we confirmed the results with an indepe...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2017.01.016

    authors： Li M,Dong Q,Zhu B

    更新日期：2017-06-30 00:00:00

  • Structural comparisons of some small spherical plant viruses.

    abstract：:The structures of tomato bushy stunt virus, southern bean mosaic virus and satellite tobacco necrosis virus have been compared quantitatively. The organization of the shell domains of tomato bushy stunt virus and southern bean mosaic virus within the icosahedral envelope is identical. The wedge-shaped end of the subun...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(83)80276-9

    authors： Rossmann MG,Abad-Zapatero C,Murthy MR,Liljas L,Jones TA,Strandberg B

    更新日期：1983-04-25 00:00:00