The high-resolution NMR structure of the R21A Spc-SH3:P41 complex: Understanding the determinants of binding affinity by comparison with Abl-SH3

Background  

SH3 domains are small protein modules of 60–85 amino acids that bind to short proline-rich sequences with moderate-to-low affinity and specificity. Interactions with SH3 domains play a crucial role in regulation of many cellular processes (some are related to cancer and AIDS) and have thus been interesting targets in drug design. The decapeptide APSYSPPPPP (p41) binds with relatively high affinity to the SH3 domain of the Abl tyrosine kinase (Abl-SH3), while it has a 100 times lower affinity for the α-spectrin SH3 domain (Spc-SH3).     

Transmembrane protein structures without X-rays

Transmembrane (TM) proteins constitute 15-30% of the genome, but <1% of the structures in the Protein Data Bank. This discrepancy is disturbing, and emphasizes that structure determination of TM proteins remains challenging. The challenge is greatest for proteins from eukaryotes, the structures of which remain intractable despite tremendous advances that have been made towards structure determination of bacterial TM proteins. Notably, >50% of the membrane protein families in eukaryotes lack bacterial homologs. Therefore, it is conceivable that many more years will elapse before high-resolution structures of eukaryotic TM proteins emerge. Until then, integrated approaches that combine biochemical and computational analyses with low-resolution structures are likely to have increasingly important roles in providing frameworks for the mechanistic understanding of membrane-protein structure and function.     

Motion perception and visual signal design in Anolis lizards

Anolis lizards communicate with displays consisting of motion of the head and body. Early portions of long-distance displays require movements that are effective at eliciting the attention of potential receivers. We studied signal-motion efficacy using a two-dimensional visual-motion detection (2DMD) model consisting of a grid of correlation-type elementary motion detectors. This 2DMD model has been shown to accurately predict Anolis lizard behavioural response. We tested different patterns of artificially generated motion and found that an abrupt 0.3° shift of position in less than 100 ms is optimal. We quantified motion in displays of 25 individuals from five species. Four species employ near-optimal movement patterns. We tested displays of these species using the 2DMD model on scenes with and without moderate wind. Display movements can easily be detected, even in the presence of windblown vegetation. The fifth species does not typically use the most effective display movements and display movements cannot be discerned by the 2DMD model in the presence of windblown vegetation. A number of Anolis species use abrupt up-and-down head movements approximately 10 mm in amplitude in displays, and these movements appear to be extremely effective for stimulating the receiver visual system.     

Functional consequences of DECTIN-1 early stop codon polymorphism Y238X in rheumatoid arthritis

Introduction

We have previously demonstrated that ex vivo inhibition of costimulatory molecules on antigen-pulsed dendritic cells (DCs) can be useful for induction of antigen-specific immune deviation and suppression of autoimmune arthritis in the collagen induced arthritis (CIA) model. The current study evaluated a practical method of immune modulation through temporary systemic inhibition of the costimulatory molecule CD40.

Methods

Mice with collagen II (CII)-induced arthritis (CIA) were administered siRNA targeting the CD40 molecule. Therapeutic effects were evaluated by clinical symptoms, histopathology, Ag-specific T cell and B cell immune responses.

Results

Systemic administration of CD40-targeting siRNA can inhibit antigen-specific T cell response to collagen II, as well as prevent pathogenesis of disease in both a pre- and post-immunization manner in the CIA model. Disease amelioration was associated with suppression of Th1 cytokines, attenuation of antibody production, and upregulation of T regulatory cells.

Conclusions

These studies support the feasibility of transient gene silencing at a systemic level as a mechanism of resetting autoreactive immunity.     

Structure of the DNA-bound BRCA1 C-terminal Region from Human Replication Factor C p140 and Model of the Protein-DNA Complex

BRCA1 C-terminal domain (BRCT)-containing proteins are found widely throughout the animal and bacteria kingdoms where they are exclusively involved in cell cycle regulation and DNA metabolism. Whereas most BRCT domains are involved in protein-protein interactions, a small subset has bona fide DNA binding activity. Here, we present the solution structure of the BRCT region of the large subunit of replication factor C bound to DNA and a model of the structure-specific complex with 5′-phosphorylated double-stranded DNA. The replication factor C BRCT domain possesses a large basic patch on one face, which includes residues that are structurally conserved and ligate the phosphate in phosphopeptide binding BRCT domains. An extra α-helix at the N terminus, which is required for DNA binding, inserts into the major groove and makes extensive contacts to the DNA backbone. The model of the protein-DNA complex suggests 5′-phosphate recognition by the BRCT domains of bacterial NAD⁺-dependent ligases and a nonclamp loading role for the replication factor C complex in DNA transactions.     

Identifying potential survival strategies of HIV-1 through virus-host protein interaction networks

Background  

The National Institute of Allergy and Infectious Diseases has launched the HIV-1 Human Protein Interaction Database in an effort to catalogue all published interactions between HIV-1 and human proteins. In order to systematically investigate these interactions functionally and dynamically, we have constructed an HIV-1 human protein interaction network. This network was analyzed for important proteins and processes that are specific for the HIV life-cycle. In order to expose viral strategies, network motif analysis was carried out showing reoccurring patterns in virus-host dynamics.     

pANT: a method for the pairwise assessment of nonfunctionalization times of processed pseudogenes

We present a method for pairwise Assessment of Nonfunctionalization Times (pANT) in processed pseudogenes. Contrary to existing methods for estimating nonfunctionalization times, pANT utilizes previously calculated probabilities of nucleotide substitution as explicit rate measurements, rather than assume that the substitution rates are the same for all nucleotides. Thus, the method allows a more accurate computation of the time that has elapsed since the nonfunctionalization of a pseudogene. Whereas existing methods require the sequence of an orthologous functional gene, which is not always at hand, pANT only uses the pairwise alignment of the gene/pseudogene pair, thus expanding the range of problems that can be tackled. To estimate evolutionary times in nonfunctional sequences, pANT measures the differences in the pairwise alignment of a gene and its paralogous processed pseudogene, using only the first and second codon positions. It assumes that, because of functional constraints, these positions in the sequence of the functional homolog have not changed since the time of nonfunctionalization of the pseudogene. Hence, the sequence of the gene may be used as the ancestor of the pseudogene. We show that the method's reliance on a detailed substitution matrix, which is derived separately for each species, makes it more accurate than existing methods. We applied pANT to the case of the unitary alpha-1,3-galactosyltransferase human pseudogene and found that our estimate of the nonfunctionalization time was in agreement with that obtained by taxonomic and paleontological considerations pertaining to the divergence between platyrrhines (New World monkeys) and cattarhines (Old World monkeys).     

Evidence for habitat partitioning based on adaptation to environmental light in a pair of sympatric lizard species

Terrestrial habitats exhibit a variety of light environments. If species exhibit evolutionary adaptations of their visual system or signals to habitat light conditions, then these conditions can directly influence the structure of communities. We evaluated habitat light characteristics and visual-signal design in a pair of sympatric species of lizards: Anolis cooki and Anolis cristatellus. We found that each species occupies a distinct microhabitat with respect to light intensity and spectral quality. We measured the relative retinal spectral sensitivity and found significant differences between the species that correlate with differences in habitat spectral quality. We measured the spectral reflectance of the dewlaps (colourful throat fans used in communication), and found that the A. cooki dewlap reflects little ultraviolet (UV), while that of A. cristatellus reflects strongly in the UV. For both species downwelling light (irradiance) is rich in UV. However the background light (radiance) is rich in UV for A. cooki, but low in UV for A. cristatellus. Thus, the dewlap of each species creates a high contrast with the background in the UV. Our findings strongly suggest that these two species are partitioning their habitat through specializations of the visual system and signal design to microhabitat light conditions.     

Different incorporation of glucocorticoid hormone into diploid and tetraploid liver nuclei

Tetraploid parenchymal rat liver nuclei incorporate about twice as much (³H)dexamethasone as diploid parenchymal nuclei both in vivo and in vitro. This suggests that the ability of hepatic nuclei to incorporate glucocorticoid hormone is influenced by the number of copies of the genome in these nuclei.