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F Jurnak

Publications and source records attributed to F Jurnak.

47 records · Page 3Linked to original sources
PubMed1984

Relative affinities of all Escherichia coli aminoacyl-tRNAs for elongation factor Tu-GTP.

The relative affinities of all Escherichia coli amino-acyl-tRNAs for E. coli elongation factor (EF) Tu-GTP have been measured by two independent applications of the competition form of the ribonuclease resistance assay. The set of aminoacyl-tRNAs includes at least one tRNA for each of the 20 amino acids as well as purified isoacceptor tRNA species for arginine, glycine, leucine, lysine, and tyrosine. In the first competition study, [3H]Phe-tRNA was used as the competing aminoacyl-tRNA against [14C]aminoacyl-tRNA in the set of all tRNAs; in the second study, [3H]Leu-tRNALeu4 was used as the competing aminoacyl-tRNA. The relative order of aminoacyl-tRNA affinities for EF-Tu-GTP was the same in each study. The results indicate that the affinity of EF-Tu-GTP at 4 degrees C, pH 7.4, is strongest for Gln-tRNA and weakest for Val-tRNA. Both Gly-tRNA and Pro-tRNA bind very strongly to EF-Tu-GTP relative to other aminoacyl-tRNAs. Various models of ternary complex interactions are discussed in light of the new data. Although the properties of the amino acid substituent are primarily responsible for the differences in relative affinities among the noninitiator aminoacyl-tRNAs, the results for the four isoacceptor species of Leu-tRNALeu indicate that the secondary structural features of the tRNA are also influential.

Escherichia coli↗
PubMed1984

An improved bulk purification method for Escherichia coli elongation factor, Ts.

A bulk purification procedure has been designed to maximize the yield of Escherichia coli elongation factor, Ts, with a minimum of effort and time. The enzyme purification is achieved by DEAE-Sepharose and elongation factor Tu-affinity chromatographies. The typical yield is 150 mg/kg of E. coli (B) cells.

Chromatography, Affinity↗
PubMed1984

Affinity purification of aminoacyl-tRNA.

A procedure for separating Escherichia coli aminoacyl-tRNA from unacylated tRNA or components of the aminoacylation reaction, thereby achieving an aminoacyl-tRNA product with a very high specific activity, is described. The method utilizes the specific recognition of aminoacyl-tRNA for E. coli protein synthesis elongation factor Tu which has been immobilized on an affinity matrix. The application of the affinity procedure as a means of purifying a single aminoacyl-tRNA from an unfractionated mixture of tRNAs is also discussed.

Chemical Phenomena↗
PubMed1980

Biochemical and structural studies of the tetragonal crystalline modification of the Escherichia coli elongation factor Tu.

The tetragonal crystalline form of the trypsin-treated Escherichia coli protein elongation factor Tu has been analyzed by biochemical and x-ray crystallographic techniques. The crystals contain two tightly associated polypeptide fragments of molecular weight 36,000 and 6,500 which represent 97% of the native enzyme. The crystals do not contain a short internal polypeptide fragment of 14 amino acids which dissociates from the native enzyme following mild trypsin digestion. The short fragment has been implicated in the aminoacyl-tRNA binding function and its location has been determined. The structure of the modified enzyme in the P4(3)2(1)2 crystal form has been determined to 5 A resolution by x-ray diffraction methods. The protein consists of two domains: the larger domain exhibits considerable alpha helical characteristics and the smaller domain has no identifiable secondary structural features. The relationship between the double domain structure of the enzyme and its biochemical properties is discussed.

Bacterial Proteins↗
PubMed1980

The structure of a DNA unwinding protein and its complexes with oligodeoxynucleotides by x-ray diffraction.

The structure of the gene 5 DNA unwinding protein from bacteriophage fd has been solved to 2.3 A resolution by x-ray diffraction techniques. The molecule contains an extensive cleft region that we have identified as the DNA binding site on the basis of the residues that comprise its surface. The interior of the groove has a rather large number of basic amino acid residues that serve to draw the polynucleotide backbone into the cleft. Arrayed along the external edges of the groove are a number of aromatic amino acid side groups that are in position to stack upon the bases of the DNA and fix it in place. The cleft then acts as an elongated pair of jaws that draws the DNA between them by charge interactions involving the phosphates with the interior lysines and arginines. The jaws then close on the DNA strand through small conformation changes and the rotation of aromatic side-chains into position to stack upon the purines and pyrimidines. Complexes of the gene 5 protein with a variety of oligodeoxynucleotides have been formed and crystallized for x-ray diffraction analysis. The crystallographic parameters of four different unit cells indicate that the fundamental unit of the complex is composed of six gene 5 protein dimers. We believe this aggregate has 622 point group symmetry and is a ring formed by end to end closure of a linear array of six dimers. From our results we have proposed a double helical model for the gene 5 protein-DNA complex in which the protein forms a spindle or core around which the DNA is spooled. 5.0-A x-ray diffraction data from one of the crystalline complexes is currently being analyzed by molecular replacement techniques to obtain what we believe will be the first direct visualization of a protein-deoxyribonucleic acid complex approaching atomic resolution.

Coliphages↗
PubMed1979

Structure of the DNA binding cleft of the gene 5 protein from bacteriophage fd.

The structure of the gene 5 DNA unwinding protein from bacteriophage fd has been solved to 2.3-A resolution by X-ray diffraction techniques. The molecule contains an extensive cleft region that we have identified as the DNA binding site on the basis of the residues that comprise its surface. The interior of the groove has a rather large number of basic amino acid residues that serve to draw the polynucleotide backbone into the cleft. Arrayed along the external edges of the groove are a number of aromatic amino acid side groups that are in position to stack upon the bases of the DNA and fix it in place. The structure and binding mechanism as we visualize it appear to be fully consistent with evidence provided by physical-chemical studies of the protein in solution.

Binding Sites↗
PubMedDate not supplied

Structure-based multiple alignment of extracellular pectate lyase sequences.

Pectate lyases are secreted virulence factors which degrade the pectate component of plant cell walls. The evolutionary-based multiple alignment of extracellular pectate lyases has been corrected using three-dimensional structural information derived from Erwinia chyrsanthemi pectate lyases C and E. The new multiple alignment reveals invariant amino acids likely to be involved in two different enzymatic functions.

Amino Acid Sequence↗