Using diffusion distances for flexible molecular shape comparison

Background  

Many molecules are flexible and undergo significant shape deformation as part of their function, and yet most existing molecular shape comparison (MSC) methods treat them as rigid bodies, which may lead to incorrect shape recognition.     

Purification of four gelatin-binding proteins from bovine seminal plasma by affinity chromatography

Bovine seminal plasma contains three similar acidic proteins, which we have previously designated as BSP-A1, BSP-A2, and BSP-A3. These proteins contain two homologous domains that are similar to type II structures present in the gelatin-binding domain of fibronectin. The present data have revealed that these proteins, like fibronectin, also form complexes with gelatin, a denatured collagen. Based on this property, a single step affinity purification method has been developed. In addition to these three proteins BSP-A1, -A2 and -A3, another protein with an apparent molecular weight of 30,000 dalton (named BSP-30-kDa) also bound to the gelatin-agarose column. Elution of these proteins from affinity columns using a linear gradient of either urea or arginine gave essentially the same pattern with a high yield of 90–95%. The purified proteins were homogeneous by SDS-polyacrylamide gel electrophoresis, amino acid composition and HPLC. Chromatography of bull seminal vesicular fluid also exhibited an elution pattern similar to that obtained for bull seminal plasma. The availability of these purified proteins should aid in understanding the physiology of these gelatin-binding proteins.     

Structural organization of cholera toxin gene and its expression in an environmental non-pathogenic strain ofVibrio cholerae

Non-pathogenic, environmental strain ofVibrio cholerae, ELTOR Ogawa EW6 carries a copy of the cholera toxin gene in its chromosome. Restriction enzyme digestion followed by Southern blot analysis revealed that the structure of the cholera toxin gene in this organism is different from that found in the virulent strains. The xbaI site which has been found to be conserved in the cholera toxin of the virulent strains examined so far, is absent here. Results of the RNA dot blot analysis indicated that the cholera toxin gene in EW6 is transcribed much less efficiently compared to the cholera toxin gene present in the virulent strainVibrio cholerae classical Inaba 569B.     

Conformations of peptides containing Z-alpha,beta-dehydroleucine (delta ZLeu). A comparison of Boc-Pro-delta ZLeu-Gly-NHEt and Boc-Pro-delta ZPhe-Gly-NHEt

Two tripeptides of the type Boc-Pro-delta ZX-Gly-NHEt (where X = Leu, Phe) have been synthesized and their solution conformations investigated by 270 MHz 1H n.m.r. and i.r. spectroscopy. These conformational studies indicated that delta ZLeu, similar to delta ZPhe, has a strong tendency to stabilize folded Type II beta-turn conformations when present at i + 2 position.     

Regulation of seed number and female incitation of mate competition by a pH-dependent proteinaceous inhibitor of pollen grain germination in Leucaena leucocephala

Summary Leucaena leucocephala generally produces pods with more than 7–9 seeds. This is regulated by the stigmatic inhibition of pollen grain germination when the pollen grains are less than a critical number in the stigma. This number-dependent inhibition of pollen grain germination is effected by a pH-dependent proteinaceous inhibitor active at the stigmatic pH. Only when the pollen grains in the stigma exceed the critical number, they inactivate the inhibitor by collectively raising the stigmatic pH and thus overcoming the inhibition. The adaptive significance of such pre-fertilization mechanism for the female in inciting mate competition among the pollen grains is discussed. The evolution of en masse pollen grain dispersal units is explained as a sexual selection strategy by males in response to such stigmatic inhibition by females.     

Seed abortion in wind-dispersed pods of Dalbergia sissoo: maternal regulation or sibling rivalry?

Summary Dalbergia sissoo, a wind-dispersed tropical tree, shows a positively skewed distribution of seeds per pod. This is attributed to the enhanced dispersal advantage of few-seeded pods due to their reduced wing loading (ratio of weight to pod surface area) and low settling velocity. The proximate mechanisms causing the positively skewed distribution were investigated. The distribution could not be attributed to the distribution pattern of ovule number per ovary, pollen grain limitation, lack of ovule fertilization, or post-fertilization elimination of many-seeded pods. Rather, it was caused by the post-fertilization abortion of seeds within a pod 2 weeks after fertilization. This intra-pod seed abortion (IPSA) is due to a dominance hierarchy of fertilized ovules from the distal (near stigma) to the basal end, generated by the temporal differences in fertilization. The dominant developing seeds at the distal end cause the abortion of others through the production and diffusion of an aborting agent. When the dominance hierarchy of the siblings is not intense, pods are formed with more than one seed. We argue that the positively skewed distribution of seeds per pod is not due to maternal regulation but is a result of sibling rivalry. We propose that this sibling rivalry is generated by genetic differences in pollen grain fitness and disucss the results in the context of parent-offspring conflict.     

The role of integration host factor In gene expression in Escherichia coli

Integration host factor is a sequence-specific, histone-like, multifunctional DNA-binding and -bending protein of Escherichia coli. The characterization and functional analysis of this protein has been done mainly in bacteriophage lambda and other mobile genetic elements. Less is known concerning the role of integration host factor (IHF) in E. coli, although it has been implicated in a number of processes in this organism including DNA replication, site-specific recombination, and gene expression. This review presents recent work which suggests that IHF alters the activity of an unusually large number of operons in E. coli. We discuss the possible physiological relevance of the involvement of IHF in gene expression and the hypothesis that IHF is a member of a class of functionally redundant proteins that participate in chromosome structure and multiple processes involving DNA.     

Effects of Preweaning Undernutrition and Continued Postweaning Protein Deficiency or Nutritional Rehabilitation on Polyphosphoinositides in Rat Brain

Metabolically inert polyphosphoinositides seem to play an important role in the structural development of neurons, glia, and myelin. The metabolically active pool of PhIpp appears to be important for the functional development of glia and myelin during the postweaning period, whereas PhIp seems to be more important for the functional development of neurons during the preweaning period. Neonatal undernutrition reduces the concentrations of structural polyphosphoinositides and metabolic PhIp while metabolic PhIpp remains unaltered. These effects can be reversed by postweaning nutritional rehabilitation. A continued postweaning protein deficiency of neonatally undernourished rats affects structural PhIpp more than PhIp. Metabolically active PhIpp is drastically reduced.