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Journal Issue - Volume 8 Issue 5 (1999)

Abstract The amino acid sequence of the small copper protein auracyanin A isolated from the thermophilic photosynthetic green bacterium Chloroflexus aurantiacus has been determined to be a polypeptide of 139 residues. His58, Cys123, His128, and Met132 are spaced in a way to be expected if they are the evolutionary conserved metal ligands as in the known small copper proteins plastocyanin and azurin. Secondary structure prediction...

Abstract Alanine scanning mutagenesis of the HyHEL‐10 paratope of the HyHEL‐10/HEWL complexdemonstrates that the energetically important side chains (hot spots) of both partners are in contact.A plot of ΔΔGHyHEL‐10_mutant vs.ΔΔGhewl_mutant for the five of six interacting side‐chain hydrogen bonds is linear (Slope = 1).Only 3 of the 13 residues in the HEWL epitope contribute >4 kcal/mol to the free energy of formation of the complexwhen...

Abstract The accumulation of hundreds of olfactory receptor (OR) sequences, along with the recent availability of detailed models of other G‐protein‐coupled receptors, allows us to analyze the OR amino acid variability patterns in a structural context. A Fourier analysis of 197 multiply aligned olfactory receptor sequences showed an α‐helical periodicity in the variability profile. This was particularly pronounced in the more...

Abstract We present a neural network based method (ChloroP) for identifying chloroplast transit peptides and their cleavage sites. Using cross‐validation, 88% of the sequences in our homology reduced training set were correctly classified as transit peptides or nontransit peptides. This performance level is well above that of the publicly available chloroplast localization predictor PSORT. Cleavage sites are predicted using a...

Abstract Following hints from X‐ray data (Ostermeier C et al., 1997, Proc Natl Acad Sci USA 94:10547–10553; Yoshikawa S et al., 1998, Science 280:1723–1729), chemical evidence is presented from four distantly related cytochrome‐c oxidases for the existence of a copperB‐coordinated His240–Tyr244) cross‐link at the O2‐activating Heme Fea3–CuB center in the catalytic subunit I of the enzyme. The early evolutionary invention of this unusual structure may have prevented ...

Abstract An expanded, highly dynamic denatured state of staphylococcal nuclease exhibits a native‐like topology in the apparent absence of tight packing and fixed hydrogen bonds (Gillespie JR, Shortle D, 1997, J Mol Biol 268:158–169, 170–184). To address the physical basis of the long‐range spatial ordering of this molecule, we probe the effects of perturbations of the sequence and solution conditions on the local chain dynamics of a denatured...

Abstract Methods for protein structure (3D)–sequence (1D) compatibility evaluation (threading) have been developed during the past decade. The protocol in which a sequence can recognize its compatible structure in the structural library (i.e., the fold recognition or the forward‐folding search) is available for the structure prediction of new proteins. However, the reverse protocol, in which a structure recognizes its homologous...

Abstract Human growth hormone (hGH) binds to its receptor (hGHr) in a three‐body interaction: one molecule of the hormone and two identical monomers of the receptor form a trimer. Curiously, the hormone‐receptor interactions in the trimer are not equivalent and the formation of the complex occurs in a specific kinetic order (Cunningham BC, Ultsch M, De Vos AM, Mulkerrin MG, Clauser KR, Wells JA, 1991, Science 254:821–825). In this...

Abstract Site‐directed mutagenesis was used to replace Lys68 of the human hypoxanthine phosphoribosyltransferase (HGPRTase) with alanine to exploit this less reactive form of the enzyme to gain additional insights into the structure activity relationship of HGPRTase. Although this substitution resulted in only a minimal (one‐to threefold) increase in the Km values for binding pyrophosphate or phosphoribosylpyrophosphate, the catalytic...

Abstract At least four mRNAs for oat phytochrome A (phyA) are present in etiolated oat tissue. The complete amino acid sequences of two phyA isoforms (A3 and A4) and the N‐terminal amino acid sequence of a third isoform (A5) were deduced from cDNA sequencing (Hershey et al., 1985). In the present study, heterogeneity of phyA on a protein level was studied by tryptic mapping using electrospray ionization mass‐spectrometry (ESIMS)....

Abstract A neural network has been used to predict both the location and the type of β‐turns in a set of 300 nonhomologous protein domains. A substantial improvement in prediction accuracy compared with previous methods has been achieved by incorporating secondary structure information in the input data. The total percentage of residues correctly classified as β‐turn or not‐β‐turn is around 75% with predicted secondary structure...

Abstract In this paper, elevated pressures up to 750 atm (1 atm = 101 kPa) were found to have a strong stabilizing effect on two extremely thermophilic glutamate dehydrogenases (GDHs): the native enzyme from the hyperthermophile Pyrococcus furiosus (Pf), and a recombinant GDH mutant containing an extra tetrapeptide at the C‐terminus (rGDHt). The presence of the tetrapeptide greatly destabilized the recombinant mutant at ambient pressure; however, the...

Abstract The “calorimetric criterion” is one of the important experimental approaches for determining whether protein folding is an “all‐or‐none” two‐state transition (i.e., whether intermediates are present at equilibrium). The calorimetric criterion states that the equivalence of the “measured” calorimetric enthalpy change and the effective two‐state van't Hoff enthalpy change demonstrates that there is a two‐state transition....

Abstract We have made a comparative structure based analysis of the thermodynamics of lectin‐carbohydrate (L‐C) binding and protein folding. Examination of the total change in accessible surface area in those processes revealed a much larger decrease in free energy per unit of area buried in the case of L‐C associations. According to our analysis, this larger stabilization of L‐C interactions arises from a more favorable enthalpy of...

Abstract Evidence already available is used to demonstrate that although prostaglandin G/H synthase hydroxylates arachidonic acid through radical intermediates, it effects cyclizations through a carbocation center at C‐10. This is produced following migration of H to the initial radical at C‐13 and a 1 oxidation. Under orbital symmetry control, the cyclizations can give only the ring size and trans stereochemistry actually observed....

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