Exploration of disorder in protein structures by X-ray restrained molecular dynamics

Conformational disorder in crystal structures of ribonuclease-A and crambin is studied by including two independent structures in least-squares optimizations against X-ray data. The optimizations are carried out by X-ray restrained molecular dynamics (simulated annealing refinement) and by conventional least-squares optimization. Starting from two identical structures, the optimizations against X-ray data lead to significant deviations between the two, with rms backbone displacements of 0.45 A for refinement of ribonuclease at 1.53 A resolution, and 0.31 A for crambin at 0.945 A. More than 15 independent X-ray restrained molecular dynamics runs have been carried out for ribonuclease, and the displacements between the resulting structures are highly reproducible for most atoms. These include residues with two or more conformations with significant dihedral angle differences and alternative hydrogen bonding, as well as groups of residues that undergo displacements that are suggestive of rigid-body librations. The crystallographic R-values obtained are approximately 13%, as compared to 15.3% for a comparable refinement with a single structure. Least-squares optimization without an intervening restrained molecular dynamics stage is sufficient to reproduce most of the observed displacements. Similar results are obtained for crambin, where the higher resolution of the X-ray data allows for refinement of unconstrained individual anisotropic temperature factors. These are shown to be correlated with the displacements in the two-structure refinements.     

Role of 3-methyladenine-DNA glycosylase in host-cell reactivation of methylated T7 bacteriophage

Purified T7 phage, treated with methyl methanesulfonate, was assayed on four Escherichia coli K12 host cells: (1) AB1157, wild-type; (2) PK432-1, lacking 3-methyladenine-DNA glycosylase (tag); (3) NH5016, lacking apurinic endonuclease VI (xthA); (4) p3478, lacking DNA polymerase I (polA), the latter three strains being deficient in enzymes of the base excision repair pathway. For inactivation measured immediately after alkylation, phage survival was lowest on strains PK432-1 and p3478; for delayed inactivation, measured after partial depurination of alkylated phage, survival was much lower on strain p3478 than on PK432-1. These results demonstrate the important role played by 3-methyladenine-DNA glycosylase in the survival of methylated T7 phage. Quantitative analysis of the data, using the results of Verly et al. (Verly, W.G., Crine, P., Bannon, P. and Forget, A. (1974) Biochim. Biophys. Acta 349, 204–213) to correlate the dose with the number of methyl groups introduced into phage DNA, revealed that 5–10 3-methyladenine residues per T7 DNA constituted an inactivation hit for the tag mutant. Thus, 3-methyladenine may be as toxic a lesion as an apurinic site.     

Physical mapping of the genome and sequence analysis at the inverted terminal repetition of adenovirus type 4 DNA

The genome of adenovirus type 4 (Ad4), the unique member of Ad group E, has been mapped with nine restriction endonucleases. Comparison of the occurrence of restriction endonuclease cleavage sites on Ad2, Ad7, Ad12 and Ad4 indicates that there is very little homology between these serotypes. Sequence analysis at the ITR of Ad4 showed that the "CAT" box which is present in all the ITRs of Ad's so far sequenced is absent in Ad4. The length of 116 bp for the ITR of Ad4 is also different from that of other Ad subgroups.     

Kin-structured migration and the rate of advance of an advantageous gene

Hemoglobin E, an allele generally considered to confer malarial resistance in heterozygotes, is found in high frequencies across a wide area of Southeast Asia. Apparently it originated as a single-point mutation which was spread by gene flow. The rate of diffusion of this adaptive allele is studied using four computer simulation models. It is shown that in small populations deterministic equations for gene flow may overestimate rates of diffusion. Other aspects of population structure, however, such as kin-structuring of migrant groups, increase the rate of advance. Finally, population growth coupled with the spread of the allele leads to much more rapid diffusion. These results suggest that population structure can be an important factor affecting the diffusion of advantageous genes.     

On the origin of mitochondria: a reexamination of the molecular structure and kinetic properties of pyruvate dehydrogenase complex from brewer''s yeast

45Ca2+ incorporated in response to glucose was selectively mobilized from the beta-cell-rich pancreatic islets of ob/ob-mice after raising the intracellular Na+ by removal of K+ or addition of ouabain or veratridine. Also studies of insulin release indicated opposite effects of glucose and Na+ on the intracellular sequestration of calcium. The fact that glucose inhibits insulin release induced by raised intracellular Na+ indicates that this sugar can lower the cytoplasmic [Ca2+]. The concept of a dual action of glucose on the cytoplasmic [Ca2+]. The concept of a dual action of glucose on the cytoplasmic [Ca2+] might well explain previous observations of an inhibitory component in the glucose action on the 45Ca2+ efflux.     

Translocation of colicin E1 through cytoplasmic membrane of Escherichia coli

The product of the malE—lacZ gene fusion was reported to compete with some proteins including outer membrane lipoprotein in the protein translocation across the Echerichia coli membrane. The fusion product also inhibited colicin E1 export. Furthermore, globomycin, which accumulated prolipoprotein in the membrane, inhibited the translocation of colicin E1 in the wild-type cells, but not in lipoprotein-negative mutant cells. Since colicin E1 contains the internal signal-like sequence [Proc. Natl. Acad. Sci. USA (1982) 79, 2827–2831], these results suggest that colicin E1 is exported by the aid of this sequence at a common site for maltose-binding protein and lipoprotein translocation.     

Sex pheromone components of the leafroller moth Pandemis cerasana

Female-tip washings of the leafroller moth, Pandemis cerasana, were found to contain (E)-11-tetradecenyl acetate, (Z)-11-tetradecenyl acetate, (E)-11-tetradecenol, (Z)-11-tetradecenol and tetradecyl acetate, based on chemical analysis and electroantennogram tests. The relative amounts of these compounds in the gland were ca. 64:21:10:3:2 in the order named. Only (E)-11 and (Z)-11-tetradecenyl acetate were required for attraction of males to trap dispensed in the ratio 3:1, respectively.     

Chemical equilibrium and E value of Zn (ZnE) in inceptisols and entisols of tropical india

Summary The chemical equilibrium and E value for Zn was calculated in 9 soils of Haryana (India) which represented mainly entisol and inceptisols. The rate of isotopic exchange between⁶⁵Zn and native soil Zn was quite rapid and radioactivity reduced to about 0.2 per cent of initial activity after 3 days but total Zn concentration in soil solution did not decrease. In 5 out of 9 soils equilibrium was established in 2 to 3 days. In typic ustochrepts having high clay content (3,4) equilibrium was attained in two days. In typic udipsamments (2), typic camborthids (8) and aquic vertic ustichrepts (9) it took 3 days to set equilibrium. Typic ustochrepts (5) took 5 days for equilibrium whereas typic ustipssaments (6) and typic camborthids of high O.C. did not attain equilibrium even in 7 days. This indicated that the chemistry and availability of Zn in soil would depend on soil types. When Zn_E was estimated by applying activity after equilibrium with carrier Zn and by applying activity with carrier Zn before equilibrium was set, there was no agreement in Zn_E in two methods. Increasing Zn_E with increasing Zn dose was observed by both methods only in alkaline typic ustochrept (4). In some soils higher E values than added amounts were observed, whereas, in soil 8 negative E values were obtained. The E values become erratic and are over estimated where complex reactions take place due to high pH, high O.C. and high complex forming elements.     

Regulation of Muscarinic Receptor-Mediated Cyclic GMP Synthesis by Cultured Mouse Neuroblastoma Cells

Mouse neuroblastoma clone N1E-115 has muscarinic acetylcholine receptors that mediate cyclic GMP synthesis. This receptor-mediated response is not significantly higher than background until the cells have been maintained in the stationary phase for at least 1 week. The basis of the influence of time in culture on the cyclic GMP response was investigated. The relative amount of cyclic GMP synthesized by intact cells was measured by radioactively labeling the GTP pool with [³H]guanine, incubating cells with agonists, and then chromatographically isolating [³H]cyclic GMP. Carbamylcholine-, ionophore X-537A-, and sodium azide-induced cyclic GMP formation increased with time in culture to a maximum of 13-, 9-, and 2.5-fold above basal, respectively. There was no change in the number or the apparent affinity of the muscarinic receptors as measured by [³H]quinuclidinyl benzylate ([³H]QNB) binding. In addition, there was no change in the apparent affinity of the receptors for agonist as measured by the ability of carbamylcholine to displace the specific binding of [³H]QNB. Guanylate cyclase activity per milligram protein and per cell in-creased six- and sevenfold, respectively, from day 0 to day 22. However, this increase in guanylate cyclase appeared to precede the marked increase in sensitivity of the cells to agonists. These data suggest that, in addition to guanylate cyclase and muscarinic receptors, there is another factor which is responsible for the development of this muscarinic receptor-mediated response.     

Morphine addiction and withdrawal alters brain peptide concentrations

This study demonstrates that, during morphine addiction and withdrawal in rats profound alterations in the concentrations of a variety of brain peptides occur. Somatostatin, cholecystokinin, neurotensin and substance P concentrations increased during morphine addiction. Naloxone-induced withdrawal decreased brain concentrations of TRH, somatostatin, neurotensin and substance P. Naloxone alone decreased thalamic substance P and neurotensin concentrations. Vasoactive intestinal peptide concentrations were unaltered by any of the treatments. The fall in the tissue concentration of somatostatin during naloxone-induced withdrawal correlated well with the fall in the circulating growth hormone, suggesting that this could be secondary to somatostatin release. Our data support the hypothesis that brain peptides, acting locally in the brain as neuromodulators, play an important role in the genesis of the syndromes of morphine addiction and withdrawal.