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Journal Issue - Volume 4 Issue 5 (May 1995)

  • Reviews

  • Hans Neurath
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560040501 (p 821-822)

Abstract The three‐dimensional structures of the zinc endopeptidases human neutrophil collagenase, adamalysin II from rattle snake venom, alkaline proteinase from Pseudomonas aeruginosa, and astacin from crayfish are topologically similar, with respect to a five‐stranded β‐sheet and three α‐helices arranged in typical sequential order. The four proteins exhibit the characteristic consensus motif HEXXHXXGXXH, whose three histidine ...

Abstract Cholera is a widespread disease for which there is no efficient vaccine. A better understanding of the conformational rearrangements at the epitope might be very helpful for the development of a good vaccine. Cholera toxin (CT) as well as the closely related heat‐labile toxin from Escherichia coli (LT) are composed of two subunits, A and B, which form an oligomeric assembly AB5. Residues 50–64 on the surface of the B subunits comprise...

Abstract Two of the five domains in the structure of the ornithine decarboxylase (OrnDC) from Lactobacillus 30a share similar structural folds around the pyridoxal‐5′‐phosphate (PLP)‐binding pocket with the aspartate aminotransferases (AspATs). Sequence comparisons focusing on conserved residues of the aligned structures reveal that this structural motif is also present in a number of other PLP‐dependent enzymes including the histidine, dopa,...

Abstract The backbone dynamics of the tetrameric p53 oligomerization domain (residues 319–360) have been investigated by two‐dimensional inverse detected heteronuclear 1H‐15N NMR spectroscopy at 500 and 600 MHz. 15N T1, T2, and heteronuclear NOEs were measured for 39 of 40 non‐proline backbone NH vectors at both field strengths. The overall correlation time for the tetramer, calculated from the T1/T2 ratios, was found to be 14.8 ns at 35 °C....

Abstract A new self‐correcting distance geometry method for predicting the three‐dimensional structure of small globular proteins was assessed with a test set of 8 helical proteins. With the knowledge of the amino acid sequence and the helical segments, our completely automated method calculated the correct backbone topology of six proteins. The accuracy of the predicted structures ranged from 2.3 Å to 3.1 Å for the helical segments...

Abstract An algorithm is presented for the fast and accurate definition of protein structural domains from coordinate data without prior knowledge of the number or type of domains. The algorithm explicitly locates domains that comprise one or two continuous segments of protein chain. Domains that include more than two segments are also located. The algorithm was applied to a nonredundant database of 230 protein...

  • Monte Carlo docking with ubiquitin

  • Maxwell D. Cummings, Trevor N. Hart, Randy J. Read
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560040508 (p 885-899)

Abstract The development of general strategies for the performance of docking simulations is prerequisite to the exploitation of this powerful computational method. Comprehensive strategies can only be derived from docking experiences with a diverse array of biological systems, and we have chosen the ubiquitin/diubiquitin system as a learning tool for this process. Using our multiple‐start Monte Carlo docking method, we have...

Abstract The failure of newly synthesized polypeptide chains to reach the native conformation due to their accumulation as inclusion bodies is a serious problem in biotechnology. The critical intermediate at the junction between the productive folding and the inclusion body pathway has been previously identified for the P22 tailspike endorham‐nosidase. We have been able to trap subsequent intermediates in the in vitro pathway to the...

Abstract Holo and apo adrenodoxin were studied by differential scanning calorimetry, absorption spectroscopy, limited proteolysis, and size‐exclusion chromatography. To determine the conformational stability of adrenodoxin, a method was found that prevents the irreversible destruction of the iron‐sulfur center. The approach makes use of a buffer solution that contains sodium sulfide and mercaptoethanol. The thermal transition of...

Abstract Antibody folding is a complex process comprising folding and association reactions. Although it is usually difficult to characterize kinetic folding intermediates, in the case of the antibody Fab fragment, domain‐domain interactions lead to a rate‐limiting step of folding, thus accumulating folding intermediates at a late step of folding. Here, we analyzed a late folding intermediate of the Fab fragment of the monoclonal...

Abstract Wild‐type flavocytochrome b2 (L‐lactate dehydrogenase) from Saccharotnyces cerevisiae, as well as a number of its point mutants, can be expressed to a reasonable level as recombinant proteins in Escherichia coli (20–25 mg per liter culture) with a full complement of prosthetic groups. At the same expression level, active‐site mutants Y254L and D282N, on the other hand, were obtained with an FMN/heme ratio significantly less than unity, which could...

Abstract Anomalous NMR behavior of the hydroxyl proton resonance for Ser 31 has been reported for histidine‐containing protein (HPr) from two microorganisms: Escherichia coli and Staphylococcus aureus. The unusual slow exchange and chemical shift exhibited by the resonance led to the proposal that the hydroxyl group is involved in a strong hydrogen bond. To test this hypothesis and to characterize the importance of such an interaction, a mutant...

Abstract We constructed a gene encoding rCAS, recombinant constant and subrepeat protein, modeled after tandem repeats found in the major silk proteins synthesized by aquatic larvae of the midge, Chironomus tentans. Bacterially synthesized rCAS was purified to near homogeneity and characterized by several biochemical and biophysical methods including amino‐terminal sequencing, amino acid compositional analysis, sedimentation equilibrium...

Abstract A new large‐scale purification method for benzoylformate decarboxylase from Pseudomonas putida has allowed us to undertake an X‐ray crystallographic study of the enzyme. The previously observed instability of the enzyme was overcome by addition of 100 μM thiamine pyrophosphate to buffers used in the purification. The final enzyme preparation was more than 97% pure, as determined by denaturing gel electrophoresis and densitometry. The...

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