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Journal Issue - Volume 10 Issue 10 (October 2001)

  • Thank you Ralph Bradshaw!

  • Mark Hermodson
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.101925 (p 1925-1925)

Abstract The role of the channels and cavities present in the catalase from Proteus mirabilis (PMC) was investigated using molecular dynamics (MD) simulations. The reactant and products of the reaction, H2O2 →1/2 O2 + H2O, catalyzed by the enzyme were allowed to diffuse to and from the active site. Dynamic fluctuations in the structure are found necessary for the opening of the major channel, ideied in the X‐ray model, which allows access to the active...

Abstract One of the difficulties that can impede structural work on a molecule of interest is limited solubility. Although functionally similar to the human immunodeficiency virus type‐1 reverse transcriptase (HIV‐1 RT), the Moloney murine leukemia virus reverse transcriptase (MMLV RT) differs both in architecture and solubility properties. Reverse transcriptase is an essential retroviral enzyme that replicates the single‐stranded...

Abstract Transesterification of (±)‐menthol using propionic acid anhydride and Candida rugosa lipase was performed in chloroform and water at different pressures (1, 10, 50, and 100 bar) to study the pressure dependence of enantioselectivity E. As a result, E significantly decreased with increasing pressure from E = 55 (1 bar) to E = 47 (10 bar), E = 37 (50 bar), and E = 9 (100 bar). To rationalize the experimental findings, molecular dynamics...

Abstract The nature of the dynamical coupling between a protein and its surrounding solvent is an important, yet open issue. Here we used temperature‐dependent protein crystallography to study structural alterations that arise in the enzyme acetylcholinesterase upon X‐ray irradiation at two temperatures: below and above the glass transition of the crystal solvent. A buried disulfide bond, a buried cysteine, and solvent exposed...

Abstract Outer membrane phospholipase A (OMPLA) from Escherichia coli is an integral‐membrane enzyme with a unique His–Ser–Asn catalytic triad. In serine proteases and serine esterases usually an Asp occurs in the catalytic triad; its role has been the subject of much debate. Here the role of the uncharged asparagine in the active site of OMPLA is investigated by structural characterization of the Asn156Ala mutant. Asparagine 156 is not ...

Abstract More than 30 organisms have been sequenced entirely. Here, we applied a variety of simple bioinformatics tools to analyze 29 proteomes for representatives from all three kingdoms: eukaryotes, prokaryotes, and archaebacteria. We confirmed that eukaryotes have relatively more long proteins than prokaryotes and archaes, and that the overall amino acid composition is similar among the three. We predicted that ∼15%–30% of all...

Abstract Although it is commonly accepted that binding of mitochondrial transcription factor sc‐mtTFB to the mitochondrial RNA polymerase is required for specific transcription initiation in Saccharomyces cerevisiae, its precise role has remained undefined. In the present work, the crystal structure of sc‐mtTFB has been determined to 2.6 Å resolution. The protein consists of two domains, an N‐terminal α/β‐domain and a smaller domain made up of...

Abstract Protein–nucleic acid complexes are commonly studied by photochemical cross‐linking. UV‐induced cross‐linking of protein to nucleic acid may be followed by structural analysis of the conjugated protein to localize the cross‐linked amino acids and thereby idey the nucleic acid binding site. Mass spectrometry is becoming increasingly popular for characterization of purified peptide–nucleic acid heteroconjugates derived from UV...

Abstract Eukaryotic histone proteins condense DNA into compact structures called nucleosomes. Nucleosomes were viewed as a distinguishing feature of eukaryotes prior to ideication of histone orthologs in methanogens. Although evolutionarily distinct from methanogens, the methane‐producing hyperthermophile Methanopyrus kandleri produces a novel, 154‐residue histone (HMk). Amino acid sequence comparisons show that HMk differs from both...

Abstract SB‐219383 and its analogues are a class of potent and specific inhibitors of bacterial tyrosyl‐tRNA synthetases. Crystal structures of these inhibitors have been solved in complex with the tyrosyl‐tRNA synthetase from Staphylococcus aureus, the bacterium that is largely responsible for hospital‐acquired infections. The full‐length enzyme yielded crystals that diffracted to 2.8 Å resolution, but a truncated version of the enzyme allowed...

Abstract Ribonuclease A aggregates (dimers, trimers, tetramers, pentamers) can be obtained by lyophilization from 40% acetic acid solutions. Each aggregate forms two conformational isomers distinguishable by different basic net charge. The crystal structure of the two dimers has recently been determined; the structure of the higher oligomers is unknown. The results of the study of the two trimeric and tetrameric conformers can be...

Abstract Escherichia coli cold shock protein, CspA, folds very rapidly (time constant, τ = 4 msec) by an apparent two‐state mechanism. However, recent time‐resolved infrared (IR) temperature‐jump experiments indicate that the folding trajectory of CspA may be more complicated. The sole tryptophan of wild‐type CspA (Trp11), which is used to monitor the folding process by fluorescence spectroscopy, is located in an unusual aromatic...

Abstract The conformational dynamics of wild‐type Escherichia coli thioredoxin reductase (TrxR) and the mutant enzyme C138S were studied by ultrafast time‐resolved fluorescence of the flavin cofactor in combination with circular dichroism (both in the flavin fingerprint and far‐UV regions) and steady‐state fluorescence and absorption spectroscopy. The spectroscopic data show two conformational states of the enzyme (named FO and FR), of which ...

Abstract Rat corticotropin‐releasing factor receptor 1 (rCRFR1) was produced either in transfected HEK 293 cells as a complex glycosylated protein or in the presence of the mannosidase I inhibitor kifunensine as a high mannose glycosylated protein. The altered glycosylation did not influence the biological function of rCRFR1 as demonstrated by competitive binding of rat urocortin (rUcn) or human/rat corticotropin‐releasing factor...

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