Stock and parental effects on embryonic and early larval development of winter flounder Pseudopleuronectes americanus (Walbaum)

A hierarchical breeding design was used to determine if winter flounder Pseudopleuronectes americanus embryos and yolk-sac larvae sired by Georges Bank males developed and grew larger than fish sired by Passamaquoddy Bay males, and to examine parental contributions to variations in fertilization success, time to 50% hatch, hatch success and larval morphological development. Significant stock effects were detected for time to hatch and larval development. Eggs fertilized by Passamaquoddy Bay males reached 50% hatch significantly earlier than eggs fertilized by Georges Bank males. Larvae sired by Georges Bank males were significantly larger during larval development for four of the six traits measured at 12 days post-hatch: head depth, jaw length, myotome height and body area. Embryo and larval development were strongly influenced by maternal contributions; there were significant maternal variance components for the majority of the variables measured. Paternal variance components were significant for fertilization success, time to hatch, larval jaw length and larval head depth, however, they acted principally through parental interactions. This information has important implications for the long-term sustainable development of winter flounder for aquaculture purposes as well as for understanding winter flounder genetic variation in the wild.     

Lifetime reproductive success in reproductively suppressed female voles

A population of the grey red-backed vole, Clethrionomys rufocanus bedfordiae, was investigated on a 1 ha control grid and a 1 ha grid on which the voles were fed within a 2.1 ha outdoor enclosure in Hokkaido, Japan by live trapping from 1984 to 1986, for testing the Reproductive Suppression Model of Wasser and Barash (1983)-females can optimize their lifetime reproductive success by suppressing reproduction when future conditions for the survival of offspring are likely to be sufficiently better than present ones as to exceed the costs of the suppression itself. Age at the first pregnancy more varied in a higher density population on the experimental grid and females could be classified into the early and the late reproductive type in two generations (A: females born from February to June 1985; B: females born from September to November 1985). Lifetime reproductive success (the number of pregnancies, the number of successful litters, and the number of offspring) was not different between the early and the late reproducing females. The late reproducing females lived for longer periods than the early reproducing females, so that the loss by delayed start of reproduction was compensated for by a longer life span. Life span was not different between offspring of the early and the late reproducing females. These facts supported the Reproductive Suppression Model.     

PDB-wide identification of physiological hetero-oligomeric assemblies based on conserved quaternary structure geometry

1. Download : Download high-res image (339KB)
2. Download : Download full-size image

     

RCSB Protein Data Bank: Enabling biomedical research and drug discovery

Analyses of publicly available structural data reveal interesting insights into the impact of the three‐dimensional (3D) structures of protein targets important for discovery of new drugs (e.g., G‐protein‐coupled receptors, voltage‐gated ion channels, ligand‐gated ion channels, transporters, and E3 ubiquitin ligases). The Protein Data Bank (PDB) archive currently holds > 155,000 atomic‐level 3D structures of biomolecules experimentally determined using crystallography, nuclear magnetic resonance spectroscopy, and electron microscopy. The PDB was established in 1971 as the first open‐access, digital‐data resource in biology, and is now managed by the Worldwide PDB partnership (wwPDB; wwPDB.org ). US PDB operations are the responsibility of the Research Collaboratory for Structural Bioinformatics PDB (RCSB PDB). The RCSB PDB serves millions of RCSB.org users worldwide by delivering PDB data integrated with ～40 external biodata resources, providing rich structural views of fundamental biology, biomedicine, and energy sciences. Recently published work showed that the PDB archival holdings facilitated discovery of ～90% of the 210 new drugs approved by the US Food and Drug Administration 2010–2016. We review user‐driven development of RCSB PDB services, examine growth of the PDB archive in terms of size and complexity, and present examples and opportunities for structure‐guided drug discovery for challenging targets (e.g., integral membrane proteins).     

The heterodimerization of platelet-derived chemokines

Chemokines encompass a large family of proteins that act as chemoattractants and are involved in many biological processes. In particular, chemokines guide the migration of leukocytes during normal and inflammatory conditions. Recent studies reveal that the heterophilic interactions between chemokines significantly affect their biological activity, possibly representing a novel regulatory mechanism of the chemokine activities. The co-localization of platelet-derived chemokines in vivo allows them to interact. Here, we used nano-spray ionization mass spectrometry to screen eleven different CXC and CC platelet-derived chemokines for possible interactions with the two most abundant chemokines present in platelets, CXCL4 and CXCL7. Results indicate that many screened chemokines, although not all of them, form heterodimers with CXCL4 and/or CXCL7. In particular, a strong heterodimerization was observed between CXCL12 and CXCL4 or CXCL7. Compared to other chemokines, the main structural difference of CXCL12 is in the orientation and packing of the C-terminal alpha-helix in relation to the beta-sheet. The analysis of one possible structure of the CXCL4/CXCL12 heterodimer, CXC-type structure, using molecular dynamics (MD) trajectory reveals that CXCL4 may undergo a conformational transition to alter the alpha helix orientation. In this new orientation, the alpha-helix of CXCL4 aligns in parallel with the CXCL12 alpha-helix, an energetically more favorable conformation. Further, we determined that CXCL4 and CXCL12 physically interact to form heterodimers by co-immunoprecipitations from human platelets. Overall, our results highlight that many platelet-derived chemokines are capable of heterophilic interactions and strongly support future studies of the biological impact of these interactions.     

Enhancement of thermal stability of chondroitinase ABC I by site-directed mutagenesis: An insight from Ramachandran plot

The application of chondroitinase ABC I (cABC I) in damaged nervous tissue is believed to prune glycosaminoglycan chains of proteoglycans, thereby facilitates axon regeneration. However, the utilization of cABC I as therapeutics is notably restricted due to its thermal instability. In the present study, we have explored the possibility of thermostabilization of cABC I through release of its conformational strain using Ramachandran plot information. In this regard, Gln140 with non-optimal φ and ψ values were replaced with Gly, Ala and Asn. The results indicated that Q140G and Q140A mutants were able to improve both activity and thermal stability of the enzyme while Q140N variant reduced the enzyme activity and destabilized it. Moreover, the two former variants displayed a remarkable resistance to trypsin degradation. Structural analysis of all mutants showed an increase in intrinsic fluorescence intensity and secondary structure content of Q140G and Q140A compared to the wild type which indicated more compact structure upon mutation. This investigation demonstrated that relief of conformational tension can be considered as a possible approach to increase the stability of the protein.     

Records of fishes from the West Norfolk Ridge,north-west of New Zealand

Abstract

A total of 89 species of elasmobranch and teleost fish was recorded from the West Norfolk Ridge in 1986. Between 50 and 60 of these have not previously been reported from the area. Fish species were caught in bottom trawls at depths between 100 m and 1100 m, principally on the Wanganella Bank. Depth distribution is discussed. Species composition is very similar to that of northern New Zealand.     

In Human Pseudouridine Synthase 1 (hPus1), a C-Terminal Helical Insert Blocks tRNA from Binding in the Same Orientation as in the Pus1 Bacterial Homologue TruA,Consistent with Their Different Target Selectivities

Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8 Å resolution. The structures are the first of a mammalian Ψ synthase from the set of five Ψ synthase families common to all kingdoms of life. hPus1 adopts a fold similar to bacterial Ψ synthases, with a central antiparallel β-sheet flanked by helices and loops. A flexible hinge at the base of the sheet allows the enzyme to open and close around an electropositive active-site cleft. In one crystal form, a molecule of Mes [2-(N-morpholino)ethane sulfonic acid] mimics the target uridine of an RNA substrate. A positively charged electrostatic surface extends from the active site towards the N-terminus of the catalytic domain, suggesting an extensive binding site specific for target RNAs. Two α-helices C-terminal to the core domain, but unique to hPus1, extend along the back and top of the central β-sheet and form the walls of the RNA binding surface. Docking of tRNA to hPus1 in a productive orientation requires only minor conformational changes to enzyme and tRNA. The docked tRNA is bound by the electropositive surface of the protein employing a completely different binding mode than that seen for the tRNA complex of the Escherichia coli homologue TruA.     

Computational Design of a Protein-Based Enzyme Inhibitor

While there has been considerable progress in designing protein–protein interactions, the design of proteins that bind polar surfaces is an unmet challenge. We describe the computational design of a protein that binds the acidic active site of hen egg lysozyme and inhibits the enzyme. The design process starts with two polar amino acids that fit deep into the enzyme active site, identifies a protein scaffold that supports these residues and is complementary in shape to the lysozyme active-site region, and finally optimizes the surrounding contact surface for high-affinity binding. Following affinity maturation, a protein designed using this method bound lysozyme with low nanomolar affinity, and a combination of NMR studies, crystallography, and knockout mutagenesis confirmed the designed binding surface and orientation. Saturation mutagenesis with selection and deep sequencing demonstrated that specific designed interactions extending well beyond the centrally grafted polar residues are critical for high-affinity binding.