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Journal Issue - Volume 14 Issue 11 (November 2005)

Abstract Water from the solvent very strongly absorbs light in the frequency range of interest for studying protein structure by infrared (IR) spectroscopy. This renders handling of the observation cells painstaking and time consuming, and limits the reproducibility of the measurements when IR spectroscopy is applied to proteins in aqueous solutions. These difficulties are circumvented by the use of an Attenuated Total Reflectance...

Abstract The precise regulation of epidermal growth factor receptor (EGFR) signaling is crucial to its function in cellular growth control. Various studies have suggested that the C‐terminal phosphorylation domain, itself a substrate for the EGFR kinase activity, exerts a regulatory influence upon it, although the molecular mechanism for this regulation is unknown. The fluorescence resonance energy transfer (FRET) technique was...

Abstract As the number of complete genomes rapidly increases, accurate methods to automatically predict the subcellular location of proteins are increasingly useful to help their functional annotation. In order to improve the predictive accuracy of the many prediction methods developed to date, a novel representation of protein sequences is proposed. This representation involves local compositions of amino acids and twin amino...

  • Misfolding of a bacterial autotransporter

  • Jesper E. Mogensen, Jörg H. Kleinschmidt, M. Alexander Schmidt, Daniel E. Otzen
  • Published in Wiley Interscience on Jan 01, 2009
  • DOI: 10.1110/ps.051628705 (p 2814-2827)

Abstract The adhesin involved in diffuse adherence (AIDA) is an autotransporter protein that confers the diffuse adherence phenotype to certain diarrheagenic Escherichia coli strains. It consists of a 49 amino acid signal peptide, a 797 amino acid passenger domain, and a 440 amino acid β‐domain integrated into the outer membrane. The β‐domain consists of two parts: the β1‐domain, which is predicted to form two β‐strands on the bacterial cell...

Abstract Methionine sulfoxide reductases B (MsrBs) catalyze the reduction of methionine‐R‐sulfoxide via a three‐step chemical mechanism including a reductase step, formation of an intradisulfide bond followed by a thioredoxin recycling process. Fifty percent of the MsrBs, including the Escherichia coli enzyme, possess a metal binding site composed of two CXXC motifs of unknown function. It is located on the opposite side of the active site. The...

Abstract The tenth fibronectin type III (FN3) domain of human fibronectin (FNfn10), a prototype of the ubiquitous FN3 domain, is a small, monomeric β‐sandwich protein. In this study, we have bisected FNfn10 in each loop to generate a total of six fragment pairs. We found that fragment pairs bisected at multiple loops of FNfn10 show complementation in vivo as tested with a yeast two‐hybrid system. The dissociation constant of these...

Abstract The solution structure of protein AF2095 from the thermophilic archaea Archaeglobus fulgidis, a 123‐residue (13.6‐kDa) protein, has been determined by NMR methods. The structure of AF2095 is comprised of four α‐helices and a mixed β‐sheet consisting of four parallel and anti‐parallel β‐strands, where the α‐helices sandwich the β‐sheet. Sequence and structural comparison of AF2095 with proteins from Homo sapiens, Methanocaldococcus...

Abstract Replacement of a cis‐proline by glycine at position 114 in ribonuclease A leads to a large decrease in thermal stability and simplifies the refolding kinetics. A crystallographic approach was used to determine whether the decrease in thermal stability results from the presence of a cis glycine peptide bond, or from a localized structural rearrangement caused by the isomerization of the mutated cis 114 peptide bond. The structure was...

Abstract Glu230, one of the acidic residues that cluster around the active site of the catalytic subunit of cAMP‐dependent protein kinase, plays an important role in substrate recognition. Specifically, its side chain forms a direct salt‐bridge interaction with the substrate's P‐2 Arg. Previous studies showed that mutation of Glu230 to Gln (E230Q) caused significant decreases not only in substrate binding but also in the rate of...

Abstract The NMR structure of the conserved hypothetical protein TM0487 from Thermotoga maritima represents an α/β‐topology formed by the regular secondary structures α1–β1–β2–α2–β3–β4–α3– β5–310–α4, with a small anti‐parallel β‐sheet of β‐strands 1 and 2, and a mixed parallel/anti‐parallel β‐sheet of β‐strands 3–5. Similar folds have previously been observed in other proteins, with amino acid sequence identity as low as 3% and a variety of...

Abstract We report here the first crystal structure of the N‐terminal domain of an A‐type Lon protease. Lon proteases are ubiquitous, multidomain, ATP‐dependent enzymes with both highly specific and non‐specific protein binding, unfolding, and degrading activities. We expressed and purified a stable, monomeric 119‐amino acid N‐terminal subdomain of the Escherichia coli A‐type Lon protease and determined its crystal structure at 2.03 Å (Protein...

Abstract The new antigen receptor (IgNAR) antibodies from sharks are disulphide bonded dimers of two protein chains, each containing one variable and five constant domains. Three types of IgNAR variable domains have been discovered, with Type 3 appearing early in shark development and being overtaken by the antigen‐driven affinity‐matured Type 1 and 2 response. Here, we have determined the first structure of a naturally occurring...

Abstract β‐Turns are sites at which proteins change their overall chain direction, and they occur with high frequency in globular proteins. The Protein Data Bank has many instances of conformations that resemble β‐turns but lack the characteristic N–H(i) → O=C(i − 3) hydrogen bond of an authentic β‐turn. Here, we identify potential hydrogen‐bonded β‐turns in the coil library, a Web‐accessible database utility comprised of all...

Abstract We have determined the critical concentrations of a set of 18 variants of Alzheimer's Aβ(1–40) peptide, each carrying a different residue at position 18. We find that the critical concentrations depend on the hydrophobicity and β‐sheet propensity of residue 18, and therefore on properties that we identified previously to affect also the kinetics by which these peptides aggregate. Since the critical concentrations can be...

Abstract NMR spectroscopy of encapsulated proteins dissolved in low‐viscosity fluids is emerging as a tool for biophysical studies of proteins in atomic detail in a variety of otherwise inaccessible contexts. The central element of the approach is the encapsulation of the protein of interest within the aqueous core of a reverse micelle with high structural fidelity. The process of encapsulation is highly dependent upon the nature of...

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