3D modeling and molecular dynamics simulation of an immune-regulatory cytokine, interleukin-10, from the Indian major carp, Catla catla

Molecular analysis of the type III interferon complex and its applications in protein engineering

Type III interferons (IFNλs) are cytokines with critical roles in the immune system and are attractive therapeutic candidates due to their tissue-specific activity. Despite entering several clinical trials, results have demonstrated limited efficacy and potency, partially attributed to low-affinity protein-protein interactions (PPIs) responsible for receptor complex formation. Subsequently, structural studies of the native IFNλ signaling complexes remain inaccessible. While protein engineering can overcome affinity limitations, tools to investigate low-affinity systems like these remain limited. To provide insights into previous efforts to strengthen the PPIs within this complex, we perform a molecular analysis of the extracellular ternary complexes of IFNλ3 using both computational and experimental approaches. We first use molecular simulations and modeling to quantify differences in PPIs and residue strain fluctuations, generate detailed free energy landscapes, and reveal structural differences between an engineered, high-affinity complex, and a model of the wild-type, low-affinity complex. This analysis illuminates distinct behaviors of these ligands, yielding mechanistic insights into IFNλ complex formation. We then apply these computational techniques in protein engineering and design by utilizing simulation data to identify hotspots of interaction to rationally engineer the native cytokine-receptor complex for increased stability. These simulations are then validated by experimental techniques, showing that a single mutation at a computationally predicted site of interaction between the two receptors increases PPIs and improves complex formation for all IFNλs. This study highlights the power of molecular dynamics simulations for protein engineering and design as applied to the IFNλ family but also presents a potential tool for analysis and engineering of other systems with low-affinity PPIs.

Cloning of interleukin-10 from African clawed frog (Xenopus tropicalis), with the Finding of IL-19/20 homologue in the IL-10 locus

Interleukin-10 (IL-10) is a pleiotropic cytokine that plays an important role in immune system. In the present study, the IL-10 gene of African clawed frog (Xenopus tropicalis) was first cloned, and its expression pattern and 3D structure were also analyzed. The frog IL-10 mRNA encoded 172 amino acids which possessed several conserved features found in IL-10s from other species, including five-exon/four-intron genomic structure, conserved four cysteine residues, IL-10 family motif, and six α-helices. Real-time PCR showed that frog IL-10 mRNA was ubiquitous expressed in all examined tissues, highly in some immune related tissues including kidney, spleen, and intestine and lowly in heart, stomach, and liver. The frog IL-10 mRNA was upregulated at 24 h after LPS stimulation, indicating that it plays a part in the host immune response to bacterial infection. Another IL, termed as IL-20, was identified from the frog IL-10 locus, which might be the homologue of mammalian IL-19/20 according to the analysis results of the phylogenetic tree and the sequence identities.

Structural elucidation of SrtA enzyme in Enterococcus faecalis: an emphasis on screening of potential inhibitors against the biofilm formation

Enterococcus faecalis is a pathogenic Gram-positive bacterium, which mainly infects humans through urinary tract infections. SrtA is an essential enzyme for survival of E. faecalis, and inhibition of this particular enzyme will reduce the virulence of biofilm formation. It is proved to be associated with the microbial surface protein embedded signal transduction mechanism and promising as a suitable anti-microbial drug target for E. faecalis. The present work gives an inclusive description of SrtA isolated from E. faecalis through computational and experimental methodologies. For exploring the mechanism of SrtA and to screen potential leads against E. faecalis, we have generated three-dimensional models through homology modeling. The 3D model showed conformational stability over time, confirming the quality of the starting 3D model. Large scale 100 ns molecular dynamics simulations show the intramolecular changes occurring in SrtA, and multiple conformations of structure based screening elucidate potential leads against this pathogen. Experimental results showed that the screened compounds are active showing anti-microbial and anti-biofilm activity, as SrtA is known to play an important role in E. faecalis biofilm formation. Experimental results also suggest that SrtA specific screened compounds have better anti-biofilm activity than the available inhibitors. Therefore, we believe that development of these compounds would be an impetus to design the novel chief SrtA inhibitors against E. faecalis.