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Journal Issue - Volume 6 Issue 12 (December 1997)

Abstract Mutans streptococci glucosyltransferases catalyze glucosyl transfer from sucrose to a glucan chain. We previously identified an aspartyl residue that participates in stabilizing the glucosyl transition state. The sequence surrounding the aspartate was found to have substantial sequence similarity with members of α‐amylase family. Because little is known of the protein structure beyond the amino acid sequence, we used a...

Abstract The calcium‐binding protein S100B binds to several potential target proteins, but there is no detailed information showing the location of the binding site for any target protein on S100B. We have made backbone assignments of the calcium‐bound form of S100B and used chemical‐shift changes in spectra of 15N‐labeled protein to locate the site that binds a peptide corresponding to residues 265‐276 from CapZα, the actin capping ...

Abstract Thymidylate synthase (TS) is a long‐standing target for anticancer drugs and is of interest for its rich mechanistic features. The enzyme catalyzes the conversion of dUMP to dTMP using the co‐enzyme methylenetetrahydrofolate, and is perhaps the best studied of enzymes that catalyze carbon‐carbon bond formation. Arg 126 is found in all TSs but forms only 1 of 13 hydrogen bonds to dUMP during catalysis, and just one of seven...

  • De novo heme proteins from designed combinatorial libraries

  • Michael H. Hecht, Kathleen M. Vogel, Thomas G. Spiro, Nina R. L. Rojas, Satwik Kamtekar, Cyrena T. Simons, Jeremy E. Mclean, Ramy S. Farid
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560061204 (p 2512-2524)

Abstract We previously reported the design of a library of de novo amino acid sequences targeted to fold into four‐helix bundles. The design of these sequences was based on a “binary code” strategy, in which the patterning of polar and non‐polar amino acids is specified explicitly, but the exact identities of the side chains is varied extensively (Kamtekar S, Schiffer JM, Xiong H, Babik JM, Hecht MH, 1993, Science262:1680‐1685)....

Abstract In Escherichia coli, flavodoxin is the physiological electron donor for the reductive activation of the enzymes pyruvate formate‐lyase, anaerobic ribonucleotide reductase, and B12‐dependent methionine synthase. As a basis for studies of the interactions of flavodoxin with methionine synthase, crystal structures of orthorhombic and trigonal forms of oxidized recombinant flavodoxin from E. coli have been determined. The orthorhombic form...

Abstract Linkers that connect repeating secondary structures fall into conformational classes based on distance and main‐chain torsion clustering. A data set of 300 unique protein chains with low pairwise sequence identity was clustered into only a few groups representing the preferred motifs. The linkers of two to eight residues for the nonredundant data set are designated H‐Ln‐H, H‐Ln‐E, E‐Ln‐H, E‐Ln‐E, where n is the length, H stands for...

Abstract A series of designed peptides has been analyzed by 1H‐NMR spectroscopy in order to investigate the influence of cross‐strand side‐chain interactions in β‐hairpin formation. The peptides differ in the N‐terminal residues of a previously designed linear decapeptide that folds in aqueous solution into two interconverting β‐hairpin conformations, one with a type I turn (β‐hairpin 4:4) and the other with a type I + G1 β‐bulge ...

Abstract The temperature factors obtained from X‐ray refinement of proteins at high resolution show large variations from one structure to another. However, the B‐values expressed in units of standard deviation about their mean value (B'‐factor) at the Cα atoms show remarkably characteristic frequency distribution. In all of the 110 proteins examined in this study, the frequency distribution exhibited a bimodal distribution. The peaks in the...

Abstract Diaspirin crosslinked hemoglobin (DCLHb) was analyzed by mass spectrometric‐based techniques to identify the protein modifications effected by the crosslinking reaction with bis(3,5‐dibromosalicyl) fumarate. DCLHb consists of two principal components. These components were isolated by size‐exclusion chromatography and identified by measurement of their molecular weight using electrospray mass spectrometry and subsequent...

Abstract The isolated, 101‐residue long C‐terminal (so called F2) fragment of the β chain from Escherichia coli tryptophan synthase was shown previously to fold into an ensemble of conformations that are condensed, to contain large amounts of highly dynamic secondary structures, and to behave as a good model of structured intermediates that form at the very early stages of protein folding. Here, solvent perturbations were used to investigate...

Abstract Molecular dynamics simulations in solution are performed for a rubredoxin from the hyperthermophilic archaeon Pyrococcus furiosus (RdPf) and one from the mesophilic organism Desulfovibrio vulgaris (RdDv). The two proteins are simulated at four temperatures: 300 K, 373 K, 473 K (two sets), and 500 K; the various simulations extended from 200 ps to 1,020 ps. At room temperature, the two proteins are stable, remain close to the crystal structure, ...

Abstract To investigate the nature of hydrophobic collapse considered to be the driving force in protein folding, we have simulated aqueous solutions of two model hydrophobic solutes, methane and isobutylene. Using a novel methodology for determining contacts, we can precisely follow hydrophobic aggregation as it proceeds through three stages: dispersed, transition, and collapsed. Theoretical modeling of the cluster formation...

Abstract Thermal unfolding of dodecameric manganese glutamine synthetase (622,000 Mr) at pH 7 and ∼0.02 ionic strength occurs in two observable steps: a small reversible transition (Tm ∼ 42°C; ΔH ≅ 0.9 J/g) followed by a large irreversible transition (Tm ∼ 81°C; ΔH≅ 23.4 J/g) in which secondary structure is lost and soluble aggregates form. Secondary structure, hydrophobicity, and oligomeric structure of the equilibrium intermediate are the same as for the...

Abstract Chemical shift mapping is becoming a popular method for studying protein‐protein interactions in solution. The technique is used to identify putative sites of interaction on a protein surface by detecting chemical shift perturbations in simple (1H, 15N )‐HSQC NMR spectra of a uniformly labeled protein as a function of added (unlabeled) target protein. The high concentrations required for these experiments raise questions concerning the...

Abstract In cases where the structure of a single protein is represented by an ensemble of conformations, there is often a need to determine the common features and to choose a “representative” conformation. This occurs, for example, with structures determined by NMR spectroscopy, analysis of the trajectory from a molecular dynamics simulation, or an ensemble of structures produced by comparative modeling. We reported previously...

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