Allosteric regulation of substrate binding and product release in geranylgeranyltransferase type II

GTPases of the Rab family are key components of vesicular transport in eukaryotic cells. Posttranslational attachment of geranylgeranyl moieties is essential for Rab function. Geranylgeranyltransferase type II (GGTase-II) catalyzes the modification of Rab proteins once they are in complex with their escort protein (REP). Upon completion of prenylation, REP and modified Rab leave the enzyme, enabling a new round of catalysis. We have studied the mechanism underlying substrate binding and product release in the geranylgeranylation of Rab proteins. Binding of the Rab7:REP-1 complex to GGTase-II was found to be strongly modulated by geranylgeranyl pyrophosphate (GGpp). The affinity of GGTase-II for the Rab7:REP-1 complex increases from ca. 120 nM to ca. 2 nM in the presence of GGpp. To study the effect of GGpp on interaction of the enzyme with its product, we generated semisynthetic doubly prenylated Rab7 bearing a fluorescent reporter group. Using this novel compound, we demonstrated that the affinity of doubly prenylated Rab7:REP-1 complex for GGTase-II was 2 and 18 nM in the absence and presence of GGpp, respectively. The difference in affinities originates mainly from a difference in the dissociation rates. Thus, binding of the new isoprenoid substrate molecule facilitates the product release by GGTase-II. The affinity of GGpp for the prenylated Rab7:REP-1:GGTase-II was K(d) = 22 nM, with one molecule of GGpp binding per molecule of prenylated ternary complex. We interpreted this finding as an indication that the geranylgeranyl moieties transferred to Rab protein do not occupy the GGpp binding site of the GGTase-II. In summary, these results demonstrate that GGpp acts as an allosteric activator that stabilizes the Rab7:REP-1:GGTase-II complex and triggers product release upon prenylation, preventing product inhibition of the enzyme.     

The net charge of the first 18 residues of the mature sequence affects protein translocation across the cytoplasmic membrane of gram-negative bacteria

This statistical study shows that in proteins of gram-negative bacteria exported by the Sec-dependent pathway, the first 14 to 18 residues of the mature sequences have the highest deviation between the observed and expected net charge distributions. Moreover, almost all sequences have either neutral or negative net charge in this region. This rule is restricted to gram-negative bacteria, since neither eukaryotic nor gram-positive bacterial exported proteins have this charge bias. Subsequent experiments performed with a series of Escherichia coli alkaline phosphatase mutants confirmed that this charge bias is associated with protein translocation across the cytoplasmic membrane. Two consecutive basic residues inhibit translocation effectively when placed within the first 14 residues of the mature protein but not when placed in positions 19 and 20. The sensitivity to arginine partially reappeared again 30 residues away from the signal sequence. These data provide new insight into the mechanism of protein export in gram-negative bacteria and lead to practical recommendations for successful secretion of hybrid proteins.     

System-theoretical (Holistic) approach to the modelling of structural-functional relationships of biomolecules and their evolution: an example of triterpene glycosides from sea cucumbers (Echinodermata, holothurioidea)

Triterpene glycosides from sea cucumbers (Holothurioidea, Echinodermata) are used as a model for studying the biochemical evolution for correlation between the glycoside membranolytic activity and biological functions. Concepts of evolutionary morphology are applied at the molecular level. The concept of Van-der-Klaauve's- Dullemeijer's system-theoretical (holistic) approach is used for the model of structural-functional relationships of the glycosides. Network diagrams of structural-functional relationships have been prepared for many glycosides. The diagrams correlate well with experimental data and show a very complex and flexible action of the natural selection on the structural fragments of the glycosides. The diagrams also show overlapping in the functional components that provide stability to the general structural plan of glycosides during evolution. The method may be applied to other biomolecules.     

Solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli

The solution structure of the ribosome-associated cold shock response protein Yfia of Escherichia coli was determined by nuclear magnetic resonance with a RMSD of 0.6A. Yfia shows a global beta-alpha-beta-beta-beta-alpha folding topology similar to its homologue HI0257 of Haemophilus influenzae and the double-strand-binding domain of Drosophila Staufen protein. Yfia and HI0257 differ in their surface charges and in the composition of their flexible C-termini, indicating their specificity to different target molecules. Both proteins exhibit a hydrophobic and polar region, which probably functions as interaction site for protein complex formation. Despite their similarity to the dsRBD fold, Yfia does not bind to model fragments of 16S ribosomal RNA as determined by NMR titration and gel shift experiments.     

Laser probing of the plasma in the S-300 facility

A method for the laser probing of an imploding plasma in the S-300 high-current generator (I=4 MA, Z=0.15 Ω, and τ=100 ns) with the use of a YAG: Nd laser is described. The first version of the method enables obtaining three-frame shadow and schlieren photographs of the plasma of the accelerator load with an exposure of 10 ns and an interval between frames of 25 ns. The second version enables the five-frame probing of the plasma with an exposure of 1 ns and an interval between frames of 10 ns. Stimulated Brillouin scattering in carbon tetrachloride is used to compress the probing laser pulse. A series of shadow and schlieren photographs of the plasma of different liners and Z-pinches are obtained. Mechanisms for the image formation are discussed. The magnitude and gradients of the plasma density are estimated.     

Mutants of Escherichia coli K-12 with increased resistance to ionizing radiation. VI. Increased radioresistance and heat shock proteins

By means of one-dimensional electrophoresis, it is shown that in radiation-resistant Gamr444 and Gamr445 mutants of Escherichia coli K-12 high-molecular weight heat shock proteins are hyperproduced at 32-37 degrees C and are induced more intensively during heat shock (in comparison to the parental wild-type strain AB1157). When the missense htpR15 mutation of the positive regulatory htpR gene for heat shock proteins was introduced by transduction into the genome of the Gamr444 mutant, its enhanced radiation-resistance disappeared but could be restored upon introduction of pKV3 plasmid bearing the htpR+ gene. These data show that heat shock proteins are participating in the enhanced radioresistance of Gamr mutants.     

Use of growth hormone genes for the diagnosis of the disease of dwarfism

The pattern of BamHI fragments of DNA from three children suggested to suffer the isolated growth hormone deficiency type. IA was not different from normal pattern registered in blot hybridization with [32P]cDNA of the growth hormone gene. The data permits one to exclude the above mentioned disease that is characterized by the deletion of HGH-N gene. The analogous DNA restriction analysis using HindIII restriction endonuclease has shown, that neither the sick children, nor their parents carry the deletion in heterozygotic state. The study of normal polymorphism of the restriction fragments length has shown that as for as the frequency of polymorphic MspI restriction endonuclease sites A and B in the growth hormone gene cluster (0.67 and 0.75 respectively) is concerned the Russian population in Moscow is closer to Mediterranean one than to North-european.     

Escherichia coli K-12 mutants with enhanced resistance to ionizing radiation. IV. Recombination characteristics of Gamr mutants

In the radiation-resistant Gamr444 mutant the inheritance frequency of long F' episomes ORF1 (purE+ tsx+ procC+ lac+) and F'14 (ilv+--argE+) is lower, and the frequencies of chromosome mobilization and integrative suppression of temperature-sensitive dnaA46 mutation by the sex factor F are much higher than those in the wild-type strain AB1157 and another radiation-resistant mutant Gamr445. In this respect, the mutant Gamr444 is very similar to the recRC sbcB mutant (RecF-pathway of recombination).     

W-reactivation and W-mutagenesis in UV-irradiated phage phil05 of Bacillus subtilis]

The survival of UV-irradiated phage ?105 on the lawns of several strains of Bacillus subtilis: wild type (strain 168) and 11 recombination-defficient mutants (recA1, recB2, recB3, recB19, recD27, recF15, recF18, recK4, recM13, recL16 and recO61) was investigated. All rec mutants have the phenotype Hcr+, i.e. normally host-cell reactivate UV-damaged phage. Small doses of UV-irradiation given to the wild type (rec+) cells increase the probability of survival of UV-irradiated ?105 phage (W-reactivation) and significantly enhance the frequency of c-mutants (W-mutagenesis). Maximal frequency of clear mutations in conditions of W-mutagenesis is 3-10(-3), i.e. is 100 times higher than the spontaneous background. Various rec mutations of host cells only diminish the level of W-reactivation but do not eliminate it completely. The most deficient in W-reactivation is recD27 mutant. Mutations recB2, B3, B19 and O61 have no effect on W-mutagenesis of UV-irradiated phage ?105 and on UV-induction of ?105, F15,F18 and L16 mutants. UV-irradiation of lysogenic cells of these mutants does not induce ?105 prophage.