ABSTRACT
The targets of the Structural GenomiX (SGX) bacterial genomics project were proteins conserved in multiple prokaryotic organisms with no obvious sequence homolog in the Protein Data Bank of known structures. The outcome of this work was 80 structures, covering 60 unique sequences and 49 different genes. Experimental phase determination from proteins incorporating Se-Met was carried out for 45 structures with most of the remainder solved by molecular replacement using members of the experimentally phased set as search models. An automated tool was developed to deposit these structures in the Protein Data Bank, along with the associated X-ray diffraction data (including refined experimental phases) and experimentally confirmed sequences. BLAST comparisons of the SGX structures with structures that had appeared in the Protein Data Bank over the intervening 3.5 years since the SGX target list had been compiled identified homologs for 49 of the 60 unique sequences represented by the SGX structures. This result indicates that, for bacterial structures that are relatively easy to express, purify, and crystallize, the structural coverage of gene space is proceeding rapidly. More distant sequence-structure relationships between the SGX and PDB structures were investigated using PDB-BLAST and Combinatorial Extension (CE). Only one structure, SufD, has a truly unique topology compared to all folds in the PDB.
Subject(s)
Escherichia coli Proteins/chemistry , Escherichia coli/genetics , Genome, Bacterial , Genomics , Databases, Protein , Enzymes/chemistry , Enzymes/genetics , Escherichia coli Proteins/genetics , Models, Molecular , Protein Conformation , Regression Analysis , X-Ray DiffractionABSTRACT
An analysis of 12 peptide fragment insertions into the major coat protein (protein pVIII) of bacteriophages M13, f1 and fd has been done. To elucidate the relations between protein structural characteristics and viability of mutant phages, we used the program Pro-Anal. Correlations were found between phage viability and different physicochemical and structural characteristics of protein N-termini. Thus peptide insertions in nonviable phages have high indexes of alpha-helicity, volumes, and polarity as well as high moments (alpha-helical and beta-structural) of isoelectric point. On the other hand, high beta-turn indexes are correlated with viability. The most important factor which determines phage viability is the lack of positively charged amino acid residues on the C-terminal ends of peptide insertions. The correlations found hold for the pVIII proteins of four related phages-M13, IKe, If1 and I2-2. Based on these results, the rule of obtaining viable mutant phages with insertions in the major coat protein is suggested. A new site is described for peptide insertions--upstream of the first amino acid residue of the mature protein sequence.
Subject(s)
Bacteriophage M13/chemistry , Bacteriophages/chemistry , Capsid/chemistry , Mutation , Peptide Fragments/chemistry , Amino Acid Sequence , Bacteriophage M13/genetics , Bacteriophages/genetics , Molecular Sequence Data , Protein ConformationABSTRACT
While applying amniotic fluid of cow embryos, as one of the components of nutrition medium, the tumor-producing ability of cells is manifested in later period of cultivation. Less malignancy of the transformed cultures was noted, that is supported by a more slow tumor development, by nearly complete absence of metastases, and longer survival of tumor-bearing animals. On the other hand, amniotic fluid renders a somewhat accelerating (2--3 times greater than in the control) effect on the impairment of cultures diploidy. Heteroploidization of the cultures proceeds largely on account of chromosome number shifts from diploid to near-tetraploid amount. Thus, amniotic liquor inhibits the process of "spontaneous" malignant transformation of embryonal cells in prolonged cultivation, simultaneously accelerating the impairment of culture diploidy.
