Solvated protein–DNA docking using HADDOCK

Interfacial water molecules play an important role in many aspects of protein–DNA specificity and recognition. Yet they have been mostly neglected in the computational modeling of these complexes. We present here a solvated docking protocol that allows explicit inclusion of water molecules in the docking of protein–DNA complexes and demonstrate its feasibility on a benchmark of 30 high-resolution protein–DNA complexes containing crystallographically-determined water molecules at their interfaces. Our protocol is capable of reproducing the solvation pattern at the interface and recovers hydrogen-bonded water-mediated contacts in many of the benchmark cases. Solvated docking leads to an overall improvement in the quality of the generated protein–DNA models for cases with limited conformational change of the partners upon complex formation. The applicability of this approach is demonstrated on real cases by docking a representative set of 6 complexes using unbound protein coordinates, model-built DNA and knowledge-based restraints. As HADDOCK supports the inclusion of a variety of NMR restraints, solvated docking is also applicable for NMR-based structure calculations of protein–DNA complexes.     

Integrating structure-based machine learning and co-evolution to investigate specificity in plant sesquiterpene synthases

Sesquiterpene synthases (STSs) catalyze the formation of a large class of plant volatiles called sesquiterpenes. While thousands of putative STS sequences from diverse plant species are available, only a small number of them have been functionally characterized. Sequence identity-based screening for desired enzymes, often used in biotechnological applications, is difficult to apply here as STS sequence similarity is strongly affected by species. This calls for more sophisticated computational methods for functionality prediction. We investigate the specificity of precursor cation formation in these elusive enzymes. By inspecting multi-product STSs, we demonstrate that STSs have a strong selectivity towards one precursor cation. We use a machine learning approach combining sequence and structure information to accurately predict precursor cation specificity for STSs across all plant species. We combine this with a co-evolutionary analysis on the wealth of uncharacterized putative STS sequences, to pinpoint residues and distant functional contacts influencing cation formation and reaction pathway selection. These structural factors can be used to predict and engineer enzymes with specific functions, as we demonstrate by predicting and characterizing two novel STSs from Citrus bergamia.     

Inhibitory and stimulatory action of vasopressin on the secretion of corticotrophin in rats : structure-activity study

The effect of intracerebroventricular injection of graded amounts of vasopressin and related peptides on plasma ACTH levels was investigated. Picogram amounts of vasopressin and oxytocin suppressed ACTH levels whereas nanogram amounts of vasopressin resulted in a pronounced increase in plasma ACTH levels. The time course of this stimulatory action was found to be different to that of the inhibitory action. The desglycinamide analogue of vasopressin was less potent in suppressing ACTH release and the C-terminal tripeptide did not affect plasma ACTH levels. However, the C-terminal tripeptide of oxytocin suppressed ACTH release while the desglycinamide analogue was ineffective. Vasotocin and its desglycinamide analogue appeared to be equipotent, although both were less active than vasopressin and oxytocin in this respect. We conclude that the entire vasopressin molecule is needed to suppress ACTH release while oxytocin may exert its inhibitory action through a smaller fragment of the molecule.     

Plasma calcium difference between man and vertebrates

1. Literature data about the plasma content of total calcium, ionized calcium and inorganic phosphate in healthy animals and man of different age and sex were collected. 2. It was established that under normal conditions ionized calcium is about 45% of total calcium. 3. The degree of saturation of these blood samples with respect to octocalcium phosphate OCP was calculated. 4. In young animals and man the blood plasma has a higher degree of saturation than in adult animals and man. 5. The blood plasma of healthy animals is supersaturated with respect to OCP during their whole life. 6. However, the blood plasma of healthy human adults is slightly undersaturated with respect to OCP.     

Maternal effects in the highly communal sociable weaver may exacerbate brood reduction and prepare offspring for a competitive social environment

Maternal effects can influence offspring phenotype with short- and long-term consequences. Yet, how the social environment may influence egg composition is not well understood. Here, we investigate how laying order and social environment predict maternal effects in the sociable weaver, Philetairus socius, a species that lives in massive communal nests which may be occupied by only a few to 100+ individuals in a single nest. This range of social environments is associated with variation in a number of phenotypic and life-history traits. We investigate whether maternal effects are adjusted accordingly. We found no evidence for the prediction that females might benefit from modifying brood hierarchies through an increased deposition of androgens with laying order. Instead, females appear to exacerbate brood reduction by decreasing the costly production of yolk mass and antioxidants with laying order. Additionally, we found that this effect did not depend on colony size. Finally, in accordance with an expected increased intensity of environmental stress with increasing colony size, we found that yolk androgen concentration increased with colony size. This result suggests that females may enhance the competitive ability of offspring raised in larger colonies, possibly preparing the offspring for a competitive social environment.     

Development and characterization of microsatellite markers for Liporrhopalum tentacularis Grandi,the pollinator fig wasp of Ficus montana Blume

Microsatellite markers for the pollinator fig wasp Liporrhopalum tentacularis were developed using genomic libraries enriched for di‐, tri‐ and tetranucleotide repeats. A subset of 31 positive clones was sequenced and primers were designed. Eleven primer pairs produced polymorphic amplification products in L. tentacularis. Eight markers gave unambiguously scorable patterns and were further characterized on 29 individuals collected from different fruits of the dioecious host fig Ficus montana in Indonesia. Three to 19 alleles per locus were detected in this set of samples. The observed heterozygosity ranged between 0.10 and 0.55.