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Journal Issue - Volume 2 Issue 7 (July 1993)

Abstract Combinatorial mutagenesis with an alphabet limited to alanine, glutamic acid, lysine, and threonine was used to probe the role of interactions involving surface residues in stabilizing a short α‐helical coiled coil. The residues at eight e and g positions in the leucine zipper of the Saccharomyces cerevisiae transcription factor GCN4 were randomized to these four residues in a λ repressor–leucine zipper fusion protein, resulting in 65,...

Abstract An important goal in the de novo design of enzymes is the control of molecular geometry. To this end, an analog of the protease from human immunodeficiency virus 1 (HIV‐1 protease) was prepared by total chemical synthesis, containing a constrained, nonpeptidic type II' β‐turn mimic of predetermined three‐dimensional structure. The mimic β‐turn replaced residues Gly16, 17 in each subunit of the homodimeric molecule. These residues...

Abstract Coproporphyrinogen oxidase (EC 1.3.3.3), protoporphyrinogen oxidase (EC 1.3.3.4), and ferrochelatase (EC 4.99.1.1) catalyze the terminal three steps of the heme biosynthetic pathway. All three are either bound to or associated with the inner mitochondrial membrane in higher eukaryotic cells. A current model proposes that these three enzymes may participate in some form of multienzyme complex with attendant substrate...

Abstract The peptide backbones in folded native proteins contain distinctive secondary structures, α‐helices, β‐sheets, and turns, with significant frequency. One question that arises in folding is how the stability of this secondary structure relates to that of the protein as a whole. To address this question, we substituted the α‐helix‐stabilizing alanine side chain at 16 selected sites in the sequence of sperm whale myoglobin, 12 at helical sites on ...

Abstract The atomic structure of an antibody antigen‐binding fragment (Fab) at 2.45Åresolution shows that polysaccharide antigen conformation and Fab structure dictated by combinatorial diversity and domain association are responsible for the fine specificity of the Brucella‐specific antibody, YsT9.1. It discriminates the Brucella abortus A antigen from the nearly identical Brucella melitensis M antigen by forming a groove‐type binding site,...

Abstract The complete amino acid sequence of the 125‐residue photoactive yellow protein (PYP) from Ectothiorhodospira halophila has been determined to be MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKEVIGKNFFKDVAP CTDSPEFYGKFKEGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV. This is the first sequence to be reported for this class of proteins. There is no obvious sequence homology to any other protein, ...

Abstract The small, soluble, (2Fe‐2S)‐containing protein ferredoxin (Fd) mediates electron transfer from the chloroplast photosystem I to ferredoxin:NADP+ oxidoreductase (FNR), a flavoenzyme located on the stromal side of the thylakoid membrane. Ferredoxin and FNR form a 1:1 complex, which is stabilized by electrostatic interactions between acidic residues of Fd and basic residues of FNR. We have used differential chemical...

Abstract The crystal structure of activated tobacco rubisco, complexed with the reaction‐intermediate analogue 2‐carboxy‐arabinitol 1, 5‐bisphosphate (CABP) has been determined by molecular replacement, using the structure of activated spinach rubisco (Knight, S., Andersson, I., &Brändén, C.‐I., 1990, J. Mol. Biol. 215, 113‐160) as a model. The R‐factor after refinement is 21.0% for 57, 855 reflections between 9.0 and 2.7Åresolution. ...

Abstract The role of Leu 332 in ribulose‐1, 5‐bisphosphate carboxylase/oxygenase from the cyanobacterium Anacystis nidulans was investigated by site‐directed mutagenesis. Substitutions of this residue with Met, Ile, Val, Thr, or Ala decreased the CO2/O2 specificity factor by as much as 67% and 96% for the Ile mutant in the presence of Mg2+ and Mn2+, respectively. For the Met, Ile, and Ala mutants in the presence of Mg2+, no loss of oxygenase activity was...

Abstract Titration of a salt‐free solution of native staphylococcal nuclease by HC1 leads to an unfolding transition in the vicinity of pH 4, as determined by near‐ and far‐UV circular dichroism. At pH 2‐3, the protein is substantially unfolded. The addition of further HC1 results in a second transition, this one to a more structured species (the A state) with the properties of an expanded molten globule, namely substantial...

Abstract Bacteriorhodopsin (BR), from the purple membrane (PM) of Halobacterium halobium, was chemically modified with methoxypolyethylene glycol (m‐PEG; molecular weight = 5, 000 Da) succinimidyl carbonate. The polyethylene glycol‐bacteriorhodopsin (m‐PEG‐SC‐BR33) conjugate, containing one polyethylene glycol chain, was water soluble. The secondary structure of the conjugate in water appeared partially denatured, but was shown to contain...

Abstract We present an approach to predicting protein structural class that uses amino acid composition and hydrophobic pattern frequency information as input to two types of neural networks: (1) a three‐layer back‐propagation network and (2) a learning vector quantization network. The results of these methods are compared to those obtained from a modified Euclidean statistical clustering algorithm. The protein sequence data used to...

  • Polarity of disulfide bonds

  • Aleister J. Saunders, Gregory B. Young, Gary J. Pielak
  • Published in Wiley Interscience on Dec 31, 2008
  • DOI: 10.1002/pro.5560020713 (p 1183-1184)

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