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Journal Issue - Volume 4 Issue 12 (December 1995)

Abstract 3D domain swapping is a mechanism for forming oligomeric proteins from their monomers. In 3D domain swapping, one domain of a monomeric protein is replaced by the same domain from an identical protein chain. The result is an intertwined dimer or higher oligomer, with one domain of each subunit replaced by the identical domain from another subunit. The swapped “domain” can be as large as an entire tertiary globular domain,...

  • N‐acetyl‐ α ‐D‐glucose

  • N. G. Oikonomakos, M. Kontou, S. E. Zographos, K. A. Watson, L. N. Johnson, C. J. F. Bichard, G. W. J. Fleet, K. R. Acharya
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560041203 (p 2469-2477)

Abstract Structure‐based drug design has led to the discovery of a number of glucose analogue inhibitors of glycogen phosphorylase that have an increased affinity compared to α‐D‐glucose (Ki = 1.7 mM). The best inhibitor in the class of N‐acyl derivatives of β‐D‐glucopyranosylamine, N‐acetyl‐β‐D‐glucopyranosylamine (1‐GlcNAc), has been characterized by kinetic, ultracentrifugation, and crystallographic studies. 1‐GlcNAc acts as a competitive...

Abstract The serine‐phosphorylated form of histidine‐containing protein (HPr), a component of the phosphoenol‐pyruvate:sugar phosphotransferase system from Bacillus subtilis, has been characterized by NMR spectroscopy and solvent denaturation studies. The results indicate that phosphorylation of Ser 46, the N‐cap of α‐helix‐B, does not cause a conformational change but rather stabilizes the helix. Amide proton exchange rates in helix‐B are ...

Abstract Stromelysin, a representative matrix metalloproteinase and target of drug development efforts, plays a prominent role in the pathological proteolysis associated with arthritis and secondarily in that of cancer metastasis and invasion. To provide a structural template to aid the development of therapeutic inhibitors, we have determined a medium‐resolution structure of a 20‐kDa complex of human stromelysin's catalytic domain...

Abstract Atomic solvation parameters (ASP) are widely used to estimate the solvation contribution to the thermodynamic stability of proteins as well as the free energy of association for protein‐ligand complexes. They are also included in several molecular mechanics computer programs. In this work, a total of eight atomic solvation parametric sets has been employed to calculate the solvation contribution to the free energy of...

Abstract The internal residue Phe 25 in Rhodobacter sphaeroides thioredoxin was changed to five amino acids (Ala, Val, Leu, IIe, Tyr) by site‐directed mutagenesis, and the mutant proteins were characterized in vitro and in vivo using the mutant trxA genes in an Escherichia coli TrxA− background. The substitution F25A severely impaired the functional properties of the enzyme. Strains expressing all other mutations can grow on methionine...

Abstract To improve secondary structure predictions in protein sequences, the information residing in multiple sequence alignments of substituted but structurally related proteins is exploited. A database comprised of 70 protein families and a total of 2, 500 sequences, some of which were aligned by tertiary structural superpositions, was used to calculate residue exchange weight matrices within α‐helical, β‐strand, and coil...

Abstract Recently, protease 2A of human rhinovirus 2 (HRV2 2A) was shown to require a zinc ion for the formation of an active enzyme although zinc is not involved mechanistically. The data presented clearly show that the zinc ion bound to a picornaviral‐specific motif represents an essential component of the native structure, probably representing a new Zn‐binding motif. This structure, containing mostly β‐strand elements as shown...

Abstract A new method is presented for measuring sensitively the interactions between ligands and their membrane‐bound receptors in situ using integrated optics, thus avoiding the need for additional labels. Phospholipid bilayers were attached covalently to waveguides by a novel protocol, which can in principle be used with any glass‐like surface. In a first step, phospholipids carrying head‐group thiols were covalently immobilized...

Abstract Nine single substitution cysteine mutants of staphylococcal nuclease (nuclease) were preferentially crosslinked at the introduced cysteine residues using three different bifunctional crosslinking reagents; 1, 6‐bismaleimidohexane (BMH), 1, 3‐dibromo‐2‐propanol (DBP), and the chemical warfare agent, mustard gas (bis(2‐chloroethyl)sulfide; mustard). BMH and mustard gas are highly specific reagents for cysteine residues, whereas DBP is...

Abstract Isothermal calorimetric titration of 18‐crown‐6 ether with BaCl2 in pure aqueous solution over the temperature range 7‐40 °C gives precise binding constants and enthalpy changes. Nonlinear least‐squares fitting of the binding constants to the integrated van't Hoff equation, including a temperature‐independent change in heat capacity, leads to van't Hoff enthalpies that differ significantly from the observed calorimetric enthalpies. ...

Abstract Conserved tyrosine‐12 of Ectothiorhodospira halophila high‐potential iron sulphur protein (HiPIP) iso‐I was substituted with phenylalanine (Y12F), histidine (Y12H), tryptophan (Y12W), isoleucine (Y12I), and alanine (Y12A). Variants Y12A and Y12I were expressed to reasonable levels in cells grown at lower temperatures, but decomposed during purification. Variants Y12F, Y12H, and Y12W were substantially destabilized with ...

Abstract Filtration effects of turkey egg white lysozyme solution (TEWL) prior to subjecting it to crystallization conditions are investigated. Filtering TEWL solution and crystallizing it in ungelled media significantly decreased the number of conditions yielding crystals. This decrease depended on the membrane cut‐off used for filtration. From this, the postulated factors aiding in nucleation are estimated to be 0.17 μm in...

Abstract Of the major amino acid side chains that anchor pyridoxal 5′‐phosphate at the coenzyme binding site of bacterial D‐amino acid transaminase, two have been substituted using site‐directed mutagenesis. Thus, Ser‐180 was changed to an Ala (S180A) with little effect on enzyme activity, but replacement of Tyr‐31 by Gln (Y31Q) led to 99% loss of activity. Titration of SH groups of the native Y31Q enzyme with DTNB proceeded much...

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