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Journal Issue - Volume 3 Issue 5 (May 1994)

Abstract The role of hydrophobicity as a determinant of protein‐protein interactions is examined. Surfaces of apo‐protein targets comprising 9 classes of enzymes, 7 antibody fragments, hirudin, growth hormone, and retinol‐binding protein, and their associated ligands with available X‐ray structures for their complexed forms, are scanned to determine clusters of surface‐accessible amino acids. Clusters of surface residues are ranked...

Abstract The hallmark of the class of proteins called chaperones is the amazing ability to bind tightly to a wide array of polypeptide ligands that have no consensus in sequence; chaperones recognize non‐native structure. As a step in the elucidation of the molecular mechanism of such remarkable binding, we have characterized complexes between the bacterial chaperone SecB and a series of ligands related to maltose‐binding protein....

Abstract Two distinct spontaneous variants of the murine anti‐digoxin hybridoma 26‐10 were isolated by fluorescenceactivated cell sorting for reduced affinity of surface antibody for antigen. Nucleotide and partial amino acid sequencing of the variant antibody variable regions revealed that 1 variant had a single amino acid substitution: Lys for Asn at heavy chain position 35. The second variant antibody had 2 heavy chain...

Abstract Four amatoxin‐binding proteins with KD values in the nanomolar range, 3 monoclonal antibodies and RNA polymerase II, were studied with respect to their affinities to 24 α‐amanitin derivatives with modified side chains. From KD values we estimated the amounts of binding energy that single side chains of the amatoxins contribute to complex formation. Ile6, previously identified by X‐ray analysis to be part of a β‐turn (Kostansek EC,...

Abstract Previous analyses of limited proteolytic sites within native, folded protein structures have shown that a significant conformational change is required in order to facilitate binding into the active site of the attacking proteinase. For the serine proteinases, the optimum conformation to match the proteinase binding‐site geometry has been well characterized crystallographically by the conserved main‐chain geometry of the...

Abstract We have recently developed a fast approach to comparisons of 3‐dimensional structures. Our method is unique, treating protein structures as collections of unconnected points (atoms) in space. It is completely independent of the amino acid sequence order. It is unconstrained by insertions, deletions, and chain directionality. It matches single, isolated amino acids between 2 different structures strictly by their spatial...

Abstract Triosephosphate isomerase (TIM) is a dimeric enzyme consisting of 2 identical subunits. Trypanosomal TIM can be crystallized in 4 different spacegroups: P212121, C2(big cell), C2(small cell), and P1. The P1 crystal form only grows in the presence of 1.4 M DMSO; there are 2 DMSO binding sites per subunit. The structures have been refined at a resolution of 1.83 Å, 2.10 Å, 2.13 Å, and 1.80 Å, respectively. In the 4 different...

Abstract The crystal structures of pheasant and guinea fowl lysozymes have been determined by X‐ray diffraction methods. Guinea fowl lysozyme crystallizes in space group P6122 with cell dimensions a = 89.2 Å and c = 61.7 Å. The structure was refined to a final crystallographic R‐factor of 17.0% for 8,854 observed reflections in the resolution range 6‐1.9 Å. Crystals of pheasant lysozyme are tetragonal, space group P43212, with a = 98.9 Å, c =...

Abstract The crystal structure of the dimeric flavoenzyme glutathione reductase from Escherichia coli was determined and refined to an R‐factor of 16.8% at 1.86 Å resolution. The molecular 2‐fold axis of the dimer is local but very close to a possible crystallographic 2‐fold axis; the slight asymmetry could be rationalized from the packing contacts. The 2 crystallographically independent subunits of the dimer are virtually identical, yielding...

Abstract The crystal structure of recombinant human triosephosphate isomerase (hTIM) has been determined complexed with the transition‐state analogue 2‐phosphoglycolate at a resolution of 2.8 Å. After refinement, the R‐factor is 16.7% with good geometry. The asymmetric unit contains 1 complete dimer of 53,000 Da, with only 1 of the subunits binding the inhibitor. The so‐called flexible loop, comprising residues 168‐174, is in its “closed”...

Abstract The present studies demonstrate that matrix Gla protein (MGP), a 10‐kDa vitamin K‐dependent protein, is phosphorylated at 3 serine residues near its N‐terminus. Phosphoserine was identified at residues 3, 6, and 9 of bovine, human, rat, and lamb MGP by N‐terminal protein sequencing. All 3 modified serines are in tandemly repeated Ser‐X‐Glu sequences. Two of the serines phosphorylated in shark MGP, residues 2 and 5, also...

Abstract To investigate the structural stability of proteins, we analyzed the thermodynamics of an artificially designed 30‐residue peptide. The designed peptide, NH2‐EELLPLAEALAPLLEALLPLAEALAPLLKK‐COOH (PERI COIL‐l), with prolines at i + 7 positions, forms a pentameric α‐helical structure in aqueous solution. The thermal denaturation curves of the CD at 222 nm (pH 7.5) show an unusual cold denaturation occurring well above 0 °C and no thermal...

Abstract Serine endopeptidases of the chymotrypsin family contain a salt bridge situated centrally within the active site, the acidic component of the salt bridge being adjacent to the catalytically essential serine. Serine carboxypeptidases also contain an acidic residue in this position but it interacts through a short hydrogen bond, probably of low‐barrier type, with another acidic residue, hence forming a “glutamic acid bridge.”...

Abstract Helix propensities of the amino acids have been measured in alanine‐based peptides in the absence of helix‐stabilizing side‐chain interactions. Fifty‐eight peptides have been studied. A modified form of the Lifson‐Roig theory for the helix‐coil transition, which includes helix capping (Doig AJ, Chakrabartty A, Klingler TM, Baldwin RL, 1994, Biochemistry 33:3396‐3403), was used to analyze the results. Substitutions were made at various...

Abstract Two families of deaminases, one specific for cytidine, the other for deoxycytidylate, are shown to possess a novel zinc‐binding motif, here designated ZBS. We have (1) identified the protein members of these 2 families, (2) carried out sequence analyses that allow specification of this zinc‐binding motif, and (3) determined signature sequences that will allow identification of additional members of these families as their...

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