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Journal Issue - Volume 14 Issue 10 (October 2005)

Abstract The Src homology 3 (SH3) domain of the Src family kinase Lyn binds to the herpesviral tyrosine kinase interacting protein (Tip) more than one order of magnitude stronger than other closely related members of the Src family. In order to identify the molecular basis for high‐affinity binding, the structure of free and Tip‐bound Lyn‐SH3 was determined by NMR spectroscopy. Tip forms additional contacts outside its classical...

Abstract We study forced unbinding of fluorescein from the wild type (WT) and a mutant [H(H58)A] of the single‐chain variable‐fragment (scFv) anti‐fluorescein antibody FITC‐E2 by molecular dynamics simulations using various pulling techniques. A large number of long simulations were needed to obtain statistically meaningful results as both the wild type and the H(H58)A mutant unbinding occurs through multiple pathways, often with...

Abstract Eukaryotic low‐molecular‐weight protein tyrosine phosphatases (LMW PTPs) contain a conserved serine, a histidine with an elevated pKa, and an active site asparagine that together form a highly conserved hydrogen bonding network. This network stabilizes the active site phosphate binding loop for optimal substrate binding and catalysis. In the phosphatase from the bovine parasite Tritrichomonas foetus (TPTP), both the...

Abstract Glutathione S‐transferases catalyze the conjugation of glutathione with endogenous and exogenous xenobiotics. Hu and Colman (1995) proposed that there are two distinct substrate sites in rat GST M1‐1, a 1‐chloro‐2,4‐dintrobenzene (CDNB) substrate site located in the vicinity of tyrosine‐115, and a monobromobimane (mBBr) substrate site. To determine whether the mBBr substrate site is distinguishable from the CDNB substrate...

Abstract The structure of the scFv fragment FITC‐E2, obtained from a naive phage antibody scFv library derived from human donors, was determined at 2.1 Å resolution in the free form and at 3.0 Å in the complexed form. The wild‐type (wt) scFv binds fluorescein with a KD of 0.75 nM. The free scFv readily crystallizes by compacting its 18 amino acid‐long CDR‐H3, partially occluding the binding site and further blocking access by...

Abstract The staphylococcal α‐hemolysin (αHL) and leukocidin (Luk) polypeptides are members of a family of related β‐barrel pore‐forming toxins. Upon binding to susceptible cells, αHL forms water‐filled homoheptameric transmembrane pores. By contrast, Luk pores are formed by two classes of subunit, F and S, rendering a heptameric structure displeasing on symmetry grounds at least. Both the subunit stoichiometry and arrangement...

Abstract Nucleoside diphosphate (NDP) kinases are ubiquitous enzymes that transfer γ‐phosphates from nucleoside triphosphates to nucleoside diphosphates via a ping‐pong mechanism. The important role of this large family of enzymes in controlling cellular functions and developmental processes along with their crystallizability has made them good candidates for structural studies. We recently determined the structure of an evolved...

Abstract We have identified two new lysozyme‐like protein families by using a combination of sequence similarity searches, domain architecture analysis, and structural predictions. First, the P5 protein from bacteriophage ϕ8, which belongs to COG3926 and Pfam family DUF847, is predicted to have a new lysozyme‐like domain. This assignment is consistent with the lytic function of P5 proteins observed in several related double‐stranded...

Abstract The molecular mechanism by which HFIP stabilizes the α‐helical structure of peptides is not well understood. In the present study, we use melittin as a model to gain insight into the details of the atomistic interactions of HFIP with the peptide. We have performed extensive comparative molecular dynamics simulations (up to 100 nsec) in the absence and in the presence of HFIP. In agreement with recent NMR experiments, the...

Abstract The crystal structure of the Type IIP restriction endonuclease MspI bound to DNA containing its cognate recognition sequence has been determined in both monoclinic and orthorhombic space groups. Significantly, these two independent crystal forms present an identical structure of a novel monomer–DNA complex, suggesting a functional role for this novel enzyme–DNA complex. In both crystals, MspI interacts with the CCGG DNA...

Abstract We report the three‐dimensional structure of a late embryogenesis abundant (LEA) protein from Arabidopsis thaliana gene At1g01470.1. This protein is a member of Pfam cluster PF03168, and has been classified as a LEA14 protein. LEA proteins are expressed under conditions of cellular stress, such as desiccation, cold, osmotic stress, and heat. The structure, which was determined by NMR spectroscopy, revealed that the At1g01470.1 protein...

Abstract Mammalian thioredoxin 2 is a mitochondrial isoform of highly evolutionary conserved thioredoxins. Thioredoxins are small ubiquitous protein–disulfide oxidoreductases implicated in a large variety of biological functions. In mammals, thioredoxin 2 is encoded by a nuclear gene and is targeted to mitochondria by a N‐terminal mitochondrial presequence. Recently, mitochondrial thioredoxin 2 was shown to interact with components...

Abstract Structural investigation of GABAA receptors has been limited by difficulties imposed by its trans‐membrane‐complex nature. In the present study, the topology of a membrane‐proximal β‐rich (MPB) domain in the C139–L269 segment of the receptor α1 subunit was probed by mapping the benzodiazepine (BZ)‐binding and epitopic sites, as well as fluorescence resonance energy transfer (FRET) analysis. Ala‐scanning and semiconservative...

Abstract Human peripheral‐type cannabinoid receptor (CB2) was expressed in Escherichia coli as a fusion with the maltose‐binding protein, thioredoxin, and a deca‐histidine tag. Functional activity and structural integrity of the receptor in bacterial protoplast membranes was confirmed by extensive binding studies with a variety of natural and synthetic cannabinoid ligands. E. coli membranes expressing CB2 also activated cognate G‐proteins in an...

  • Evidence from Bombyx mori silk fiber

  • Tetsuo Asakura, Yasumoto Nakazawa, Erika Ohnishi, Fumika Moro
  • Published in Wiley Interscience on Jan 01, 2009
  • DOI: 10.1110/ps.051525505 (p 2654-2657)

Abstract 13C high‐resolution solid‐state NMR coupled with selective 13C isotope‐labeling of different Ala one methyl carbons was used to clarify the structure of (AG)15 peptide in the silk II structure as a model for the crystalline domain of Bombyx mori silk fiber. At the inner part of the peptide, the fraction of the peak at 16.6 ppm of the Ala Cβ resonance assigned to β‐turn structure increased at 11th and 19th positions. These data indicate the...

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