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Journal Issue - Volume 4 Issue 1 (January 1995)

Abstract Interleukin‐1β converting enzyme is the first member of a new class of cysteine proteases. The most distinguishing feature of this family is a nearly absolute specificity for cleavage at aspartic acid. This enzyme has been the subject of intense research because of its role in the production of IL‐1β, a key mediator of inflammation. These studies have culminated in the design of potent inhibitors and determination of its...

Abstract Activated epidermal growth factor receptor (EGFR) undergoes autophosphorylation on several cytoplasmic tyrosine residues, which may then associate with the src homology‐2 (SH2) domains of effector proteins such as phospholipase Cγ‐1 (PLCγ‐1). Specific phosphotyrosine (pTyr)‐modified EGFR fragment peptides can inhibit this intermolecular binding between activated EGFR and a tandem amino‐ and carboxy‐terminal (N/C) SH2...

Abstract A recombinant (r) mutant hemoglobin (Hb) with Asn‐102(β) replaced by an Ala (N102A(β)) has been prepared by PCR amplification of a mutagenic DNA fragment and expression of the recombinant protein in yeast. The side chain of Asn‐102(β) is part of an important region of the α1β2 interface that undergoes large structural changes in the transition between the deoxy and oxy conformations. Three natural mutant Hbs with neutral...

Abstract Hemopexin is a serum glycoprotein that binds heme with high affinity and delivers heme to the liver cells via receptor‐mediated endocytosis. A hinge region connects the two non‐disulfide‐linked domains of hemopexin, a 35‐kDa N‐terminal domain (domain I) that binds heme, and a 25‐kDa C‐terminal domain (domain II). Although domain II does not bind heme, it assumes one structural state in apo‐hemopexin and another in...

Abstract The conformational stability of the histidine‐containing phosphocarrier protein (HPr) from Bacillus subtilis has been determined using a combination of thermal unfolding and solvent denaturation experiments. The urea‐induced denaturation of HPr was monitored spectroscopically at fixed temperatures and thermal unfolding was performed in the presence of fixed concentrations of urea. These data were analyzed in several different ways to...

Abstract Colipase (Mr 10 kDa) confers catalytic activity to pancreatic lipase under physiological conditions (high bile salt concentrations). Previously determined 3‐Å‐resolution X‐ray structures of lipase‐colipase complexes have shown that, in the absence of substrate, colipase binds to the noncatalytic C‐terminal domain of pancreatic lipase (van Tilbeurgh H, Sarda L, Verger R, Cambillau C, 1992, Nature 559:159–162; van Tilbeurgh et al.,...

Abstract The stability properties of oxidized wild‐type (wt) and site‐directed mutants in surface residues of vegetative (Vfd) and heterocyst (Hfd) ferredoxins from Anabaena 7120 have been characterized by guanidine hydrochloride (Gdn‐HCl) denaturation. For Vfd it was found that mutants E95K, E94Q, F65Y, F65W, and T48A are quite similar to wt in stability. E94K is somewhat less stable, whereas E94D, F65A, F65I, R42A, and R42H are...

Abstract The modes of hydrogen bonding of arginine, asparagine, and glutamine side chains and of urea have been examined in small‐molecule crystal structures in the Cambridge Structural Database and in crystal structures of protein‐nucleic acid and protein‐protein complexes. Analysis of the hydrogen bonding patterns of each by graph‐set theory shows three patterns of rings (R) with one or two hydrogen bond acceptors and two donors...

Abstract Direct comparisons between the recently solved X‐ray and NMR structures of human endothelin‐1 with respect to secondary structure, RMS deviations, surface accessibilities, and side‐chain conformers indicate important differences in conformation, especially in the C‐terminus, but also in the central loop region, that are important for defining the specificity of binding. These differences are larger than seen for other X‐ray...

Abstract The Thermus thermophilus 3‐isopropylmalate dehydrogenase (IPMDH) and Escherichia coli isocitrate dehydrogenase (ICDH) are two functionally and evolutionarily related enzymes with distinct substrate specificities. To understand the determinants of substrate specificities of the two proteins, the substrate and coenzyme in IPMDH were docked into their respective binding sites based on the published structure for apo IPMDH and its sequence...

Abstract An algorithm is described for automatically detecting hydrophobic cores in proteins of known structure. Three pieces of information are considered in order to achieve this goal. These are: secondary structure, side‐chain accessibility, and side‐chain‐side‐chain contacts. Residues are considered to contribute to a core when they occur in regular secondary structure and have buried side chains that form predominantly nonpolar...

Abstract A procedure is described for detecting domains in proteins of known structure. The method is based on the intuitively simple idea that each domain should contain an identifiable hydrophobic core. By applying the algorithm described in the companion paper (Swindells MB, 1995, Protein Sci 4:93–102) to identify distinct cores in multi‐domain proteins, one can use this information to determine both the number and the location...

Abstract We describe a simple, fast, sensitive, and nonisotopic bioanalytical technique for the detection of tyrosine‐phosphorylated peptides and the determination of sites of protein tyrosine phosphorylation. The technique employs a protein tyrosine phosphatase micro enzyme reactor coupled on‐line to either capillary electrophoresis or liquid chromatography and electrospray ionization mass spectrometry instruments. ...

Abstract Primary sequence patterns based on known conserved sites in eukaryotic protein kinases were used to search for eukaryotic‐like protein kinase sequences in a six‐frame translation of the bacterial subsection of GenBank. This search identified a previously unrecognized eukaryotic‐like protein kinase gene in three related methanogenic archaebacteria, Methanococcus vannielii, M. voltae, and M. thermolithotrophicus. The proposed coding...

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