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Journal Issue - Volume 10 Issue 4 (April 2001)

Abstract A high resolution NMR structure of hen lysozyme has been determined using 209 residual 1H–15N dipolar coupling restraints from measurements made in two different dilute liquid crystalline phases (bicelles) in conjunction with a data set of 1632 NOE distance restraints, 110 torsion angle restraints, and 60 hydrogen bond restraints. The ensemble of 50 low‐energy calculated structures has an average backbone RMSD of 0.50±0.13Å to the mean...

Abstract 2,3‐didehydro‐2‐deoxy‐N‐acetylneuraminic acid (DANA) is a transition state analog inhibitor of influenza virus neuraminidase (NA). Replacement of the hydroxyl at the C9 position in DANA and 4‐amino‐DANA with an amine group, with the intention of taking advantage of an increased electrostatic interaction with a conserved acidic group in the active site to improve inhibitor binding, significantly reduces the inhibitor ...

Abstract In contrast with other animal species, humans possess three distinct genes for class I alcohol dehydrogenase and show polymorphic variation in the ADH1B and ADH1C genes. The three class I alcohol dehydrogenase isoenzymes share ∼93% sequence identity but differ in their substrate specificity and their developmental expression. We report here the first three‐dimensional structures for the ADH1A and ADH1C*2 gene products at 2.5 and 2.0 Å,...

Abstract The catalytic center of an archaeal Type 2 RNase H has been identified by a combination of X‐ray crystallographic and mutational analyses. The crystal structure of the Type 2 RNase H from Thermococcus kodakaraensis KOD1 has revealed that the N‐terminal major domain adopts the RNase H fold, despite the poor sequence similarity to the Type 1 RNase H. Mutational analyses showed that the catalytic reaction requires four acidic residues,...

Abstract It is widely accepted that solvent‐exposed sites in proteins play only a neglible role in determining protein energetics. In this paper we show that amino acid substitutions at the fully exposed Lys15 in bovine pancreatic trypsin inhibitor (BPTI) influenced the CD‐ and DSC‐monitored stability: The Tden difference between the least (P1 Trp) and the most stable (P1 His) mutant is 11.2°C at pH 2.0. The ΔHden versus Tden plot for all the...

Abstract FTIR spectroscopy was used to characterize and compare the temperature‐ and pressure‐induced unfolding of ribonuclease A and a set of its variants engineered in a hydrophobic region of the C‐terminal part of the molecule postulated as a CFIS. The results show for all the ribonucleases investigated, a cooperative, two‐state, reversible unfolding transition using both pressure and temperature. The relative stabilities, among...

Abstract Tyrosine residues of neuroendocrine peptides are frequently the targets of oxidation reactions, one of which involves hydroxylation to peptidyl‐3, 4‐dihydroxy‐phenyl‐L‐alanine (DOPA). The reactivity in vitro of peptidyl‐DOPA in two neuroendocrine peptides, a neurotensin fragment (pELYENK) and proctolin (RYLPT), was investigated using ultraviolet‐visible scanning spectrophotometry and matrix‐assisted laser desorption...

Abstract Equilibrium and kinetic analyses have been performed to elucidate the roles of dimerization in folding and stability of KSI from Pseudomonas putida biotype B. Folding was reversible in secondary and tertiary structures as well as in activity. Equilibrium unfolding transition, as monitored by fluorescence and ellipticity measurements, could be modeled by a two‐state mechanism without thermodynamically stable intermediates....

Abstract The Erythrina corallodendron lectin (EcorL) crystallizes in monoclinic and hexagonal crystal forms. Comparison of the newly determined hexagonal form (PDB code 1fyu) with the monoclinic form shows that the dimeric structure of EcorL reflects the inherent biological structure of the protein and is not an artifact of the crystal packing. To further understand the factors determining the dimerization modes of legume lectins,...

Abstract Nonspecific lipid transfer protein from wheat is studied by liquid‐state NMR in the presence of xenon. The gas–protein interaction is indicated by the dependence of the protein proton chemical shifts on the xenon pressure and formally confirmed by the first observation of magnetization transfer from laser‐polarized xenon to the protein protons. Twenty‐six heteronuclear nOes have allowed the characterization of four...

Abstract Muscle of amphioxus contains large amounts of a four EF‐hand Ca2+‐binding protein, CaVP, and its target, CaVPT. To study the domain structure of CaVP and assess the structurally important determinants for its interaction with CaVPT, we expressed CaVP and its amino (N‐CaVP) and carboxy‐terminal halves (C‐CaVP). The interactive properties of recombinant and wild‐type CaVP are very similar, despite three post‐translational modifications ...

Abstract A method based on neural networks is trained and tested on a nonredundant set of β‐barrel membrane proteins known at atomic resolution with a jackknife procedure. The method predicts the topography of transmembrane β strands with residue accuracy as high as 78% when evolutionary information is used as input to the network. Of the transmembrane β‐strands included in the training set, 93% are correctly assigned. The predictor...

Abstract Molecular modeling of proteins is confronted with the problem of finding homologous proteins, especially when few identities remain after the process of molecular evolution. Using even the most recent methods based on sequence identity detection, structural relationships are still difficult to establish with high reliability. As protein structures are more conserved than sequences, we investigated the possibility of using...

Abstract Plasminogen activator inhibitor type 1 (PAI‐1) is an inhibitor of plasminogen activators such as tissue‐type plasminogen activator or urokinase‐type plasminogen activator. For this molecule, different conformations are known. The inhibiting form that interacts with the proteinases is called the active form. The noninhibitory, noncleavable form is called the latent form. X‐ray and modeling studies have revealed a large...

Abstract We have used a structure energy‐based computer program developed for protein design, Perla, to provide theoretical estimates of all specific side chain–side chain interaction energies occurring in α helices. The computed side chain–side chain interaction energies were used as substitutes for the corresponding values used by the helix/coil transition algorithm, AGADIR. Predictions of peptide helical contents were nearly as...

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