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Journal Issue - Volume 5 Issue 1 (January 1996)

Abstract The reaction mechanism of protein tyrosine phosphatases (PTPases) and dual‐specificity protein phosphatases is thought to involve a catalytic aspartic acid residue. This residue was recently identified by site‐directed mutagenesis in Yersinia PTPase, VHR protein phosphatase, and bovine low molecular weight protein phosphatase. Herein we identify aspartic acid 383 as a potential candidate for the catalytic acid in human Cdc25A protein...

Abstract Because of the low solubility of lipids in water, intercellular and intracellular pathways of lipid transfer are necessary, e.g., for membrane formation. The mechanism by which lipids in vivo are transported from their site of biogenesis (endoplasmatic reticulum and the chloroplasts) to their place of action is unknown. Several small plant proteins with the ability to mediate transfer of radiolabeled phospholipids in vitro...

Abstract The Serratia endonuclease is an extracellularly secreted enzyme capable of cleaving both single‐ and double‐stranded forms of DNA and RNA. It is the first member of a large class of related and usually dimeric endonucleases for which a structure is known. Using X‐ray crystallography, the structure of monomer of this enzyme was reported by us previously (Miller MD et al., 1994, Nature Struct Biol 1:461–468). We now confirm...

Abstract Escherichia coli D‐3‐phosphoglycerate dehydrogenase (ePGDH) is a tetramer of identical subunits that is alloste‐rically inhibited by L‐serine, the end product of its metabolic pathway. Because serine binding affects the velocity of the reaction and not the binding of substrate or cofactor, the enzyme is classified as of the Vmax type. Inhibition by a variety of amino acids and analogues of L‐serine indicate that all three functional...

Abstract A water‐soluble dimeric form of acetylcholinesterase from electric organ tissue of Torpedo californica was obtained by solubilization with phosphatidylinositol‐specific phospholipase C of the glycophosphatidylinositol‐anchored species, followed by purification by affinity chromatography. The water‐soluble species, in its catalytically active native conformation, did not interact with unilamellar vesicles of...

Abstract Trypanothione reductase (TR) is an NADPH‐dependent flavoprotein unique to protozoan parasites from the genera Trypanosoma and Leishmania and is an important target for the design of improved trypanocidal drugs. We present details of the structure of TR from the human pathogen Trypanosoma cruzi, the agent responsible for Chagas' disease or South American trypanosomiasis. The structure has been solved by molecular replacement, using as...

Abstract The CRP:cAMP complex functions as a transcription factor that facilitates RNA polymerase recognition of several bacterial promoters. Detailed crystal structure information is available for CRP:(cAMP)2 and for CRP:(cAMP)2 complexed with DNA. In the crystalline environment, CRP:(cAMP)2 subunits are asymmetrically related; one subunit has a closed conformation and the other has an open conformation. The CRP:(cAMP)2 complexed with DNA shows both...

Abstract We present a method based on hierarchical self‐organizing maps (SOMs) for recognizing patterns in protein sequences. The method is fully automatic, does not require prealigned sequences, is insensitive to redundancy in the training set, and works surprisingly well even with small learning sets. Because it uses unsupervised neural networks, it is able to extract patterns that are not present in all of the unaligned sequences...

Abstract Molecular modeling showed that the enantiomers of heptyl 2‐methyldecanoate are productively bound to the active site of Candida rugosa lipase in quite different conformations. The fast‐reacting S‐enantiomer may well occupy the previously identified acyl‐binding tunnel in the active site of the lipase. By contrast, the slow‐reacting R‐enantiomer must be bound to the active site, leaving the tunnel empty to allow the formation of two catalytically...

Abstract A series of recombinant peptides, each including the sequence proposed to be the first nucleotide‐binding fold of cystic fibrosis transmembrane conductance regulator (CFTR), has been produced in an attempt to find a model peptide that would autologously fold into a soluble structure with native‐like properties. The peptide NBD1F, which contains the 267‐amino acid sequence of CFTR from 384 to 650, meets these requirements. The peptide...

Abstract Protoporphyrinogen oxidase (E.C.1.3.3.4) catalyzes the oxygen‐dependent oxidation of protoporphyrinogen IX to protoporphyrin IX. The enzyme from human placenta has been cloned, sequenced, expressed in Escherichia coli, purified to homogeneity, and characterized. Northern blot analysis of eight different human tissues show evidence for only a single transcript in all tissue types and the size of this transcript is approximately 1.8 kb....

Abstract Most recent protein secondary structure prediction methods use sequence alignments to improve the prediction quality. We investigate the relationship between the location of secondary structural elements, gaps, and variable residue positions in multiple sequence alignments. We further investigate how these relationships compare with those found in structurally aligned protein families. We show how such associations may be...

Abstract Based on the properties of two low oxygen affinity mutated hemoglobins (Hb), we have engineered a double mutant Hb (rHb βYD) in which the βF41Y substitution is associated with K82D. Functional studies have shown that the Hb α2/β2(C7)F41Y exhibits a decreased oxygen affinity relative to Hb A, without a significantly increased auto‐oxidation rate. The oxygen affinity of the natural mutant βK82D (Hb Providence‐Asp) is decreased due to the...

Abstract The pressure dependence of the flexibility of the 8‐anilino‐1‐naphthalene sulfonate (ANS)‐apomyoglobin complex was investigated in the range between atmospheric pressure and 2.4 kbar by frequency domain fluorometry. We examined two structural states: native and acidic compact. The conformational dynamics of the ANS‐apomyoglobin complex were deduced by studying the emission decay of ANS, which can form a noncovalent complex...

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