ZifBASE: a database of zinc finger proteins and associated resources

<p>Abstract</p> <p>Background</p> <p>Information on the occurrence of zinc finger protein motifs in genomes is crucial to the developing field of molecular genome engineering. The knowledge of their target DNA-binding sequences is vital to develop chimeric proteins for targeted genome engineering and site-specific gene correction. There is a need to develop a computational resource of zinc finger proteins (ZFP) to identify the potential binding sites and its location, which reduce the time of <it>in vivo </it>task, and overcome the difficulties in selecting the specific type of zinc finger protein and the target site in the DNA sequence.</p> <p>Description</p> <p>ZifBASE provides an extensive collection of various natural and engineered ZFP. It uses standard names and a genetic and structural classification scheme to present data retrieved from UniProtKB, GenBank, Protein Data Bank, ModBase, Protein Model Portal and the literature. It also incorporates specialized features of ZFP including finger sequences and positions, number of fingers, physiochemical properties, classes, framework, PubMed citations with links to experimental structures (PDB, if available) and modeled structures of natural zinc finger proteins. ZifBASE provides information on zinc finger proteins (both natural and engineered ones), the number of finger units in each of the zinc finger proteins (with multiple fingers), the synergy between the adjacent fingers and their positions. Additionally, it gives the individual finger sequence and their target DNA site to which it binds for better and clear understanding on the interactions of adjacent fingers. The current version of ZifBASE contains 139 entries of which 89 are engineered ZFPs, containing 3-7F totaling to 296 fingers. There are 50 natural zinc finger protein entries ranging from 2-13F, totaling to 307 fingers. It has sequences and structures from literature, Protein Data Bank, ModBase and Protein Model Portal. The interface is cross linked to other public databases like UniprotKB, PDB, ModBase and Protein Model Portal and PubMed for making it more informative.</p> <p>Conclusion</p> <p>A database is established to maintain the information of the sequence features, including the class, framework, number of fingers, residues, position, recognition site and physio-chemical properties (molecular weight, isoelectric point) of both natural and engineered zinc finger proteins and dissociation constant of few. ZifBASE can provide more effective and efficient way of accessing the zinc finger protein sequences and their target binding sites with the links to their three-dimensional structures. All the data and functions are available at the advanced web-based search interface <url>http://web.iitd.ac.in/~sundar/zifbase</url>.</p

Deciphering Millet Diversity: Proteomic Clusters and Phylogenetic Insights

Millets are renowned for their climatic resilience and possess high nutritive value with wide genetic variations. In countries like India and Africa, millets are part of many people's regular diets with rich sources of protein, dietary fiber, polyphenols, minerals, vitamins, and other nutrients. The proteomic signatures of several millet species, including Fonio, Finger, Proso, Sorghum, and Foxtail millet, were examined in this study. We have performed orthologous analysis to discover both common and distinctive protein clusters among these species by using the OrthoFinder algorithm in conjunction with visualization tools. A total of 16,247 clusters were shared by all species, offering light on similar evolutionary or adaptation mechanisms. The strong representation of Gene Ontology (GO) categories related to osmotic stress, water deprivation, and temperature stresses in the research further highlighted the millets' powerful adaptative responses to various environmental difficulties. Intricate signaling mechanisms for wound, defense, and growth are also revealed by their efficient photosynthetic capacities. However, each species' distinctive clusters, particularly those in Finger millet, highlighted how it differed from other millets. The evolutionary links were further clarified by a phylogenetic tree built using the Maximum likelihood approach and the JTT+CAT evolutionary model, with Foxtail and Proso millets showing a closer kinship. The research sheds light on the complex genetic network of millets, evolutionary histories, and potential adaptive processes. The identification of 2,277 clusters, which are mainly shared by foxtail, proso, fonio, and sorghum millets and support the distinct evolutionary history of finger millet, was especially important. These millets' strong adaptive mechanisms, which are on display in clusters related to different response mechanisms, demonstrate their evolutionary skill and point to prospective directions for crop improvement and resilience techniques

Computer-Aided Drug Design for cancer-causing H-Ras p21 mutant protein

Abstract: GTP-bound mutant form H-Ras (Harvey-Ras) proteins are found in 30% of human tumors. Activation of H-Ras is due to point mutation at positions 12, 13, 59 and/or 61 codon. Mutant form of H-Ras proteins is continuously involved in signal transduction for cell growth and proliferation through interaction of downstream-regulated protein Raf. In this paper, we have reported the virtual screening of lead compounds for H-Ras P 21 mutant protein from ChemBank and DrugBank databases using LigandFit and DrugBank-BLAST. The analysis resulted in 13 hits which were docked and scored to identify structurally active leads that make similar interaction to those of bound complex of H-Ras P 21 mutantRaf. This approach produced two different leads, 3-Aminopropanesulphonic acid (docked energy -3.014 kcal/mol) and Hydroxyurea (docked energy -0.009 kcal/mol) with finest Lipinski&apos;s rule-of-five. Their docked energy scores were better than the complex structure of H-Ras P 21 mutant protein bound with Raf (1.18 kcal/mol). All the leads were docked into effector region forming interaction with ILE36, GLU37, ASP38 and SER39

Unveiling the Potential of Antioxidant Proteins with the Integration of Little Millet Phytochemicals from GC-MS Studies through In silico Approach

Aim: Millet extracts contain bioactive compounds that have antioxidant properties, anti-diabetic, anti-inflammatory, and other health-promoting properties. Little millet contains more protein, minerals, vitamins, and carbohydrates than rice and wheat. The dynamics of soil organic matter may be significantly impacted by the presence of antioxidants compounds in the soil. Antioxidants and protein-modifying substances are dietary components that change numerous characteristics and, in some cases, reverse ageing. Thus, exploring the phytochemicals in little millet is very much essential in understanding its biological functional implications. Methodology: We have carried out the GCMS analysis for the little millet (seed). Further, we have performed the molecular docking and molecular dynamics simulation for the shortlisted phytochemicals.&nbsp;&nbsp; Results: We screened the metabolites using GCMS analysis due to the unexplored phytochemicals of little millet. Docking against the little millet phytochemicals was done with a focus on key antioxidants such as superoxide dismutase, catalase, and glutathione peroxidase. Acetin compound displayed strong binding with superoxide dismutase and glutathione peroxidase, while hexadecenoic acid exhibited best affinity with catalase. Through molecular dynamics simulations, we found the glutathione peroxidase complex to be the most stable. This stability implies enhanced antioxidant activity, crucial in counteracting oxidative stress. Conclusion: This study uncovers the untapped potential of little millet’s phytochemicals. By elucidating their interaction with vital antioxidant proteins, it opens avenues for innovative anti-aging strategies, health interventions and helps in enhancing the plant defence mechanism

Interactions of laminin β3 fragment with β1-integrin receptor: A revisit of the apical ectoplasmic specialization-blood-testis-barrier-hemidesmosome functional axis in the testis

Recent studies have demonstrated the presence of a functional axis that coordinates the events of spermiation and blood-testis barrier (BTB) restructuring which take place simultaneously at the opposite ends of the seminiferous epithelium at stage VIII of the epithelial cycle of spermatogenesis in the rat testis. In short, the disruption of the apical ectoplasmic specialization (apical ES) at the Sertoli cell-elongated spermatid interface, which facilitates the release of sperm at spermiation near the tubule lumen, is coordinated with restructuring at the BTB to accommodate the transit of preleptotene spermatocytes across the immunological barrier near the basement membrane. These two events are likely coordinated by a functional axis involving hemidesmosome at the Sertoli cell-basement membrane interface, and it was designated the apical ES-BTB-hemidesmosome axis. It was demonstrated that fragments of laminin chains (e.g., laminin β3 or γ3 chains) derived from the α6β1-integrin-laminin333 protein complex at the apical ES, which were likely generated via the action of MMP-2 (matrix metalloprotease-2, MMP2) prior to spermiation, acted as biologically active peptides to perturb the BTB permeability function by accelerating protein endocytosis (e.g., occludin) at the site, thereby destabilizing the BTB integrity to facilitate the transit of preleptotene spermatocytes. These laminin fragments also perturbed hemidesmosome function via their action on β1-integrin, a component of hemidesmosome in the testis, which in turn, sent a signal to further destabilize the BTB function. As such, the events of spermiation and BTB restructuring are coordinated via this functional axis. Recent studies using animal models treated with toxicants, such as mono-(2-ethylhexyl) phthalate (MEHP), or adjudin, a male contraceptive under investigation, have also supported the presence of this functional axis in the mouse. In this short review, we critically evaluate the role of this local functional axis in the seminiferous epithelium in spermatogenesis. We also provide molecular modeling information on the interactions between biologically active laminin fragments and β1-integrin, which will be important to assist in the design of more potent laminin-based peptides to disrupt this axis, thereby perturbing spermatogenesis for male contraception and to understand the underlying biology that coordinates spermiation and BTB restructuring during spermatogenesis

Environmental toxicants and male reproductive function

Environmental toxicants, such as cadmium and bisphenol A (BPA) are endocrine disruptors. In utero, perinatal or neonatal exposure of BPA to rats affect the male reproductive function, such as the blood-testis barrier (BTB) integrity. This effect of BPA on BTB integrity in immature rats is likely mediated via a loss of gap junction function at the BTB, failing to coordinate tight junction and anchoring junction function at the site to maintain the immunological barrier integrity. This in turn activates the extracellular signal-regulated kinases 1/2 (Erk1/2) downstream and an increase in protein endocytosis, destabilizing the BTB. The cadmium-induced disruption of testicular dysfunction is mediated initially via its effects on the occludin/ZO-1/focal adhesion kinase (FAK) complex at the BTB, causing redistribution of proteins at the Sertoli-Sertoli cell interface, leading to the BTB disruption. The damaging effects of these toxicants to testicular function are mediated by mitogen-activated protein kinases (MAPK) downstream, which in turn perturbs the actin bundling and accelerates the actin-branching activity, causing disruption of the Sertoli cell tight junction (TJ)-barrier function at the BTB and perturbing spermatid adhesion at the apical ectoplasmic specialization (apical ES, a testis-specific anchoring junction type) that leads to premature release of germ cells from the testis. However, the use of specific inhibitors against MAPK was shown to block or delay the cadmium-induced testicular injury, such as BTB disruption and germ cell loss. These findings suggest that there may be a common downstream p38 and/or Erk1/2 MAPK-based signaling pathway involving polarity proteins and actin regulators that is shared between different toxicants that induce male reproductive dysfunction. As such, the use of inhibitors and/or antagonists against specific MAPKs can possibly be used to “manage” the illnesses caused by these toxicants and/or “protect” industrial workers being exposed to high levels of these toxicants in their work environment

Regulation of blood-testis barrier dynamics by desmosome, gap junction, hemidesmosome and polarity proteins: An unexpected turn of events

The blood-testis barrier (BTB) is a unique ultrastructure in the mammalian testis. Unlike other blood-tissue barriers, such as the blood-brain barrier and the blood-ocular (or blood-retina) barrier which formed by tight junctions (TJ) between endothelial cells of the microvessels, the BTB is constituted by coexisting TJ, basal ectoplasmic specialization (basal ES), desmosomes and gap junctions between adjacent Sertoli cells near the basement membrane of the seminiferous tubule. The BTB also divides the seminiferous epithelium into the apical (or adluminal) and basal compartments so that meiosis I and II and post-meiotic germ cell development can all take place in a specialized microenvironment in the apical compartment behind the BTB. While the unusual anatomical features of the BTB have been known for decades, the physiological function of the coexisting junctions, in particular the desmosome and gap junction, that constitute the BTB was unknown until recently. Based on recently published findings, we critically evaluate the role of the desmosome and gap junction that serve as a signaling platform to coordinate the “opening” and “closing” of the TJ-permeability barrier conferred by TJ and basal ES during the seminiferous epithelial cycle of spermatogenesis. This is made possible by polarity proteins working in concert with nonreceptor protein tyrosine kinases, such as focal adhesion kinase (FAK) and c-Src, at the site to regulate endosome-mediated protein trafficking events (e.g., endocytosis, transcytosis, recycling or protein degradation). These events not only serve to destabilize the existing “old” BTB above preleptotene spermatocytes in transit in “clones” at the BTB, but also contribute to the assembly of “new” BTB below the transiting spermatocytes. Furthermore, hemidesmosomes at the Sertoli cell-basement membrane interface also contribute to the BTB restructuring events at stage VIII of the epithelial cycle. Additionally, the findings that a gap junction at the BTB provides a possible route for the passage of toxicants [e.g., bisphenol A (BPA)] and potential male contraceptives (e.g., adjudin) across the BTB also illustrate that these coexisting junctions, while helpful to maintain the immunological barrier integrity during the transit of spermatocytes, can be the “gateway” to making the BTB so vulnerable to toxicants and/or chemicals, causing male reproductive dysfunction