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Journal Issue - Volume 6 Issue 3 (March 1997)

Abstract Subtilases are members of the clan (or superfamily) of subtilisin‐like serine proteases. Over 200 subtilases are presently known, more than 170 of which with their complete amino acid sequence. In this update of our previous overview (Siezen RJ, de Vos WM, Leunissen JAM, Dijkstra BW, 1991, Protein Eng 4:719–731), details of more than 100 new subtilases discovered in the past five years are summarized, and amino acid...

Abstract Molecular (locking is a popular way to screen for novel drug compounds. The method involves aligning small molecules to a protein structure and estimating their binding affinity. To do this rapidly for tens of thousands of molecules requires an effective representation of the binding region of the target protein. This paper presents an algorithm for representing a protein's binding site in a way that is specifically suited...

Abstract We have used 15N NMR relaxation experiments to probe, for the glycosylated human CD2 adhesion domain, the overall molecular motion, as well as very fast nanosecond‐picosecond (ns‐ps) and slow millisecond‐microsecond (ms‐/xs) internal motions. Using a novel analysis method that considers all residues, we obtained a correlation time for the overall motion of 9.5 ± 0.3 ns. Surprisingly, we found a large contiguous patch of...

Abstract The expression of genes transcribed by the RNA polymerase with the alternative sigma factor <r54 (Ecr54) is absolutely dependent on activator proteins that bind to enhancer‐like sites, located far upstream from the promoter. These unique prokaryotic proteins, known as enhancer‐binding proteins (EBP), mediate open promoter complex formation in a reaction dependent on NTP hydrolysis. The best characterized proteins of this...

Abstract Methane monooxygenase (MMO), found in aerobic methanotrophic bacteria, catalyzes the 02‐dependent conversion of methane to methanol. The soluble form of the enzyme (sMMO) consists of three components: a reductase, a regulatory “B” component (MMOB), and a hydroxylase component (MMOH), which contains a hydroxo‐bridged dinuclear iron cluster. Two genera of methanotrophs, termed Type X and Type II, which differ markedly in...

Abstract All eukaryotic protein kinases share a conserved catalytic core. In the catalytic (C) subunit of cAMP‐dependent protein kinase (cAPK) this core is preceded by a myristylation motif followed by a long helix with Tip 30 at the end of this A‐helix filling a hydrophobic cavity between the two lobes of the core. To understand the importance of the A‐helix, the myristylation motif (A 1‐14) as well as the entire N‐terminal segment...

Abstract The peptide group between residues B24 and B25 of insulin was replaced by an ester bond. This modification only in the backbone was meant to eliminate a structurally important H‐bond between the amide proton of B25 and the carbonyl oxygen of A19. and consequently to enhance detachment of the C‐terminal B‐chain from the body of the molecule, exposing the underlying A‐chain. According to a model derived from the effects of...

Abstract The two terminal complement control protein (CCP) modules of the CD46 glycoprotein mediate measles virus binding. Three‐dimensional models for these two domains were derived based on the NMR structures of two CCP modules of factor H. Both CD46 CCP modules are about 35 A long, and form a five‐stranded antiparallel /3‐barrel structure. Monte Carlo simulations, sampling the backbone torsion angles of the linker peptide and...

Abstract IL‐8 dimers have been observed in NMR and X‐ray structures of the protein. We have engineered IL‐8 monomers by mutations of residues throughout the dimer interface, which introduce hindrance determinants to dimerization. These IL‐8 variants are shown by NMR to have wild‐type monomer folding, but by ultracentrifugation to have a range of dimerization constants from /xM to mM, as compared with a dimerization constant of about...

Abstract Covalent single‐chain dimers of the chemokine interleukin‐8 (IL‐8) have been designed to mimic the dimeric form of IL‐8 in solution and facilitate the production of heterodimer variants of IL‐8. Physical studies indicated that use of a simple peptide linker to join two subunits, while allowing receptor binding and activation, led to self‐association of the tethered dimers. However, addition of a single disulfide crosslink...

  • Fast folding of cytochrome c

  • Michael M. Pierce, Barry T. Nall
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560060311 (p 618-627)

Abstract Native iso‐2 cytochrome c contains two residues (His 18, Met 80) coordinated to the covalently attached heme. On unfolding of iso‐2, the His 18 ligand remains coordinated to the heme iron, whereas Met 80 is displaced by a non‐native heme ligand, His 33 or His 39. To test whether non‐native His‐heme ligation slows folding, we have constructed a double mutant protein in which the non‐native ligands are replaced by asparagine...

Abstract The periplasmic maltose binding protein, MalE, is a major element in maltose transport and in chemotaxis towards this sugar. Previous genetic analysis of the MalE protein revealed functional domains involved in transport and chemotactic functions. Among them the surface located a helix 7, which is part of the C‐lobe, one of the two lobes forming the three dimensional structure of MalE. Small deletions in this...

Abstract The high molecular weight (HMW) proteins from wheat contain a repetitive domain that forms 60‐80% of their sequence. The consensus peptides PGQGQQ and GYYPTSPQQ form more than 90% of the domain; both are predicted to adopt /3‐turn structure. This paper describes the structural characterization of these consensus peptides and forms the basis for the structural characterization of the repetitive HMW domain, described in the...

Abstract The structure of the central repetitive domain of high molecular weight (HMW) wheat gluten proteins was characterized in solution and in the dry state using HMW proteins Bx6 and Bx7 and a subcloned, bacterially expressed part of the repetitive domain of HMW Dx5. Model studies of the HMW consensus peptides PGQGQQ and GYYPTSPQQ formed the basis for the data analysis (van Dijk AA et al., 1997, Protein Sci 6:637‐648). In...

Abstract Thermal denaturation studies as a function of pH were carried out on wild‐type iso‐1‐cytochrome c and three variants of this protein at the solvent‐exposed position 73 of the sequence. By examining the enthalpy and Tm at various pH values, the heat capacity increment (ACP), which is dominated by the degree of change in nonpolar hydration upon protein unfolding, was found for the wild type where lysine 73 is normally present...

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