Recognition of Interaction Interface Residues in Low-Resolution Structures of Protein Assemblies Solely from the Positions of Cα Atoms

Background: The number of available structures of large multi-protein assemblies is quite small. Such structures provide phenomenal insights on the organization, mechanism of formation and functional properties of the assembly. Hence detailed analysis of such structures is highly rewarding. However, the common problem in such analyses is the low resolution of these structures. In the recent times a number of attempts that combine low resolution cryo-EM data with higher resolution structures determined using X-ray analysis or NMR or generated using comparative modeling have been reported. Even in such attempts the best result one arrives at is the very course idea about the assembly structure in terms of trace of the C alpha atoms which are modeled with modest accuracy. Methodology/Principal Findings: In this paper first we present an objective approach to identify potentially solvent exposed and buried residues solely from the position of C alpha atoms and amino acid sequence using residue type-dependent thresholds for accessible surface areas of C alpha. We extend the method further to recognize potential protein-protein interface residues. Conclusion/Significance: Our approach to identify buried and exposed residues solely from the positions of C alpha atoms resulted in an accuracy of 84%, sensitivity of 83-89% and specificity of 67-94% while recognition of interfacial residues corresponded to an accuracy of 94%, sensitivity of 70-96% and specificity of 58-94%. Interestingly, detailed analysis of cases of mismatch between recognition of interface residues from C alpha positions and all-atom models suggested that, recognition of interfacial residues using C alpha atoms only correspond better with intuitive notion of what is an interfacial residue. Our method should be useful in the objective analysis of structures of protein assemblies when positions of only C alpha positions are available as, for example, in the cases of integration of cryo-EM data and high resolution structures of the components of the assembly

Cryopreserved ovine spermatogonial stem cells maintain stemness and colony forming ability in vitro

Objective: To assess the effect of cryopreservation on stemness and proliferation potential of sheep spermatogonial stem cells (SSCs) in vitro. Methods: Sheep testicular cells were isolated and putative SSCs were enriched by the laminin-based differential plating method. Putative SSCs were co-cultured with the Sertoli cell feeder prepared by the Datura Stramonium Agglutinin (DSA-lectin)-based method. The cultured putative SSCs were cryopreserved in Dulbecco's Modified Eagle Medium-10% fetal bovine serum mixture (DMEM-10% FBS) media containing 10% dimethyl sulfoxide (DMSO) alone or 10% DMSO plus 200 mM trehalose. Cryopreserved putative SSCs were evaluated for their proliferation potential using in vitro culture and stemness by immunocytochemistry. Finally, the transfection ability of cryopreserved putative SSCs was analyzed. Results: We isolated 91% viable testicular cells from sheep testes. The majority of the laminin enriched cells expressed the SSC related marker, ITGA6. Co-culture of sheep putative SSCs with Sertoli cell feeder resulted in the generation of stable colonies, and the expression of SSC marker was maintained after several passages. A significantly higher number of viable putative SSCs was recovered from SSCs cryopreserved in media containing 10% DMSO and 200 mM trehalose compared to 10% DMSO alone (P<0.01). Cryopreserved putative SSCs formed colonies and showed SSC marker expression similar to the non-cryopreserved putative SSCs. The appearance of green fluorescent colonies over the Sertoli cell feeder indicated that cryopreserved sheep SSCs were successfully transfected. Conclusions: Cryopreserved putative SSCs can retain their stemness, colony forming ability, and transfection efficiency in vitro. Our research may help in the effective preservation of germplasm and the generation of transgenic ovine species

Biomolecular interactions between the antibacterial ceftolozane and the human inflammatory disease target ADAM17: a drug repurposing study

Inhibition of a disintegrin and metalloproteinase-17 (ADAM17), a metzincin, is proposed as a novel therapeutic strategy to suppress overproduction of the proinflammatory cytokine TNF-α in rheumatoid arthritis and inflammatory bowel disease. Existing ADAM17 inhibitors generate toxic metabolites in-vivo or haven’t progressed in clinical trials. Previous studies suggest that ligands which bind to ADAM17 active site by interacting with the Zn ion and L-shaped hydrophobic S1’- and S3’-pockets and forming favorable hydrogen bonds could act as potential ADAM17 inhibitors. Here, we investigated whether the FDA-approved anti-bacterial drug ceftolozane, a cephalosporin containing aromatic groups and carboxyl groups as probable zinc binding groups (ZBGs), forms non-covalent interactions resulting in its binding in the active site of ADAM17. In this study, the density functional theory (DFT), molecular docking and molecular dynamics calculations with the catalytic chain of ADAM17 show that carboxyl group of ceftolozane acts as moderate ZBG, and its extended geometry forms hydrogen bonds and hydrophobic interactions resulting in a binding affinity comparable to the co-crystallized known ADAM17 inhibitor. The favorable binding interactions identified here suggest the potential of ceftolozane to modulate ADAM17 activity in inflammatory diseases. ADAM17 cleaves and releases epidermal growth factor (EGF) ligands from the cell surface. The shed EGF ligands then bind to the EGF receptors to drive embryonic development. Therefore, our findings also suggest that use of ceftolozane during pregnancy may inhibit ADAM17-mediated shedding of EGF and thus increase the risk of birth defects in humans. Communicated by Ramaswamy H. Sarma</p