Sequence and structural features of binding site residues in protein-protein complexes: comparison with protein-nucleic acid complexes

<p>Abstract</p> <p>Background</p> <p>Protein-protein interactions are important for several cellular processes. Understanding the mechanism of protein-protein recognition and predicting the binding sites in protein-protein complexes are long standing goals in molecular and computational biology.</p> <p>Methods</p> <p>We have developed an energy based approach for identifying the binding site residues in protein–protein complexes. The binding site residues have been analyzed with sequence and structure based parameters such as binding propensity, neighboring residues in the vicinity of binding sites, conservation score and conformational switching.</p> <p>Results</p> <p>We observed that the binding propensities of amino acid residues are specific for protein-protein complexes. Further, typical dipeptides and tripeptides showed high preference for binding, which is unique to protein-protein complexes. Most of the binding site residues are highly conserved among homologous sequences. Our analysis showed that 7% of residues changed their conformations upon protein-protein complex formation and it is 9.2% and 6.6% in the binding and non-binding sites, respectively. Specifically, the residues Glu, Lys, Leu and Ser changed their conformation from coil to helix/strand and from helix to coil/strand. Leu, Ser, Thr and Val prefer to change their conformation from strand to coil/helix.</p> <p>Conclusions</p> <p>The results obtained in this study will be helpful for understanding and predicting the binding sites in protein-protein complexes.</p

Multifarious pigment producing fungi of Western Ghats and their potential

Concerns about the negative impacts of synthetic colorants on both consumers and the environment have sparked a surge of interest in natural colorants. This has boosted the global demand for natural colorants in the food, cosmetics and textile industries. Pigments and colorants derived from plants and microorganisms are currently the principal sources used by modern industry. When compared to the hazardous effects of synthetic dyes on human health, natural colors are quickly degradable and have no negative consequences. In fact, fungal pigments have multidimensional bioactivity spectra too. Western Ghats, a biodiversity hotspot has a lot of unique ecological niches known to harbor potential endophytic pigment-producing fungi having enumerable industrial and medical applications. Most of the fungi have coevolved with the plants in a geographical niche and hence the endophytic associations can be thought to bring about many mutually beneficial traits. The current review aims to highlight the potential of fungal pigments found in the Western ghats of India depicting various methods of isolation and screening, pigment extraction and uses. There is an urgent need for bioprospecting for the identification and characterization of extremophilic endophytic fungi to meet industry demands and attain sustainability and balance in nature, especially from geographic hotspots like the Western Ghats

Exploring the Potential of Bacillus velezensis, an Endophytic Bacteria Isolated from Alternanthera philoxeroides for Plant Growth Promotion and Bioremediation Properties

The current work was done to analyse the bioremediation and plant growth promotion (PGP) traits of endophytic bacteria isolated from Alternanthera philoxeroides from Bellandur Lake, Bangalore, India. Twenty-nine endophytic bacteria were isolated and tested for their PGP traits like indole acetic acid (IAA), ammonia, nitrogen fixation, 1-aminocyclopropane-1- carboxylate (ACC) deaminase production, phosphate solubilization etc. Endophytic bacterium, BEBAphL1 obtained from leaves of A. philoxeroides exhibited significant plant growth promotion properties and the isolate was identified as Bacillus velezensis OQ874364 using 16S rRNA sequencing. The bacterium showed potential IAA, ammonia production, nitrogen fixation, phosphate solubilization, and ACC deaminase production. The results indicate that this endophyte is promising as a growth-promoting inoculant, reducing the reliance on chemical inputs in conventional agricultural practices while enhancing nutrient uptake and stress resilience in plants. B. velezensis exhibited tolerance to high levels of chromium (500 mg/L) and NaCl (15%) and was also able to decolourize Congo red by 70% at 0.005% concentration of dye. Characterization of dye samples pre- and post-bacterial treatment was done using Fourier-transform infrared spectroscopy (FTIR) and Gas Chromatography-Mass Spectrometry (GC-MS) analysis. The findings of the study indicate that B. velezensis shows promise as a plant growth stimulator capable of withstanding heavy metal exposure and breaking down dyes

Citrus for wellness: Exploring the bioactive properties of Citrus medica fruit peel with emphasis on its anticancer, antioxidant, antimicrobial and anthelmintic properties

Citrus medica (Citron) is an underutilised plant consisting of various bioactive elements with numerous medicinal benefits. The present study aimed to evaluate the bioactive properties, including anthelmintic, antimicrobial, antioxidant and anticancer activities, of chloroform extract obtained from the of fruit peel of C. medica. The different types of phytochemicals present in the chloroform extract were analysed using GC-MS. The major components detected included n-hexadecanoic acid, octadecanoic acid, t-tetradecenal, 1-nonadecene etc. Anthelmintic study was conducted using Eisenia fetida as a test organism, revealing a significant anthelmintic effect in the C. medica fruit peel extract compared to the standard drug. Antimicrobial properties were assessed against five test bacterial and fungal strains. Antibacterial tests showed zones of inhibition ranging from 8 to 11 mm, while no prominent zones of inhibition were observed in antifungal tests. The DPPH assay demonstrated significant antioxidant properties of Citron fruit peel extract compared to the standard ascorbic acid. The Chloroform extract of citron fruit peel exhibited significant cytotoxic properties against FaDu (human hypopharyngeal tumour) cell line. The present study indicates the potential of the chloroform extract of C. medica fruit peel to be employed as an anthelmintic, antibacterial, antioxidant and anticancer agent. Hence, it emphasises the prominence that can be given to the dietary consumption of citrus fruit peel in various forms, such as dried peel, powder etc

Differential Laccase Production among Diverse Fungal Endophytes in Aquatic Plants of Hulimavu Lake in Bangalore, India

The ability of plants to acclimatise and thrive in stressed environments can be attributed, in part, to the reserve of endophytic fungi that they harbour, that help enhance physiological and immunological defence and tolerance to various biotic and abiotic stressors. The present work has focussed on screening laccase producing endophytic fungi residing in different aquatic plants isolated from Hulimavu Lake, Bengaluru. This lake is well known for its water pollution contributed by anthropogenic factors. Survival of plants in this lake can hence be associated with their rich repertoire of endophytic fungi that enhance host plant defence towards stressors. Upon isolation and culturing of endophytic fungi, qualitative laccase detection using laccase specific growth media and quantitative laccase estimation using ABTS (2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) substrate were performed. Differential production rates were observed for the laccase enzyme by different endophytic fungi; production rates also varied between fungi isolated from different parts like node, stem, root and leaf of the same plant species too. Phylogenetic analysis of fungal isolates with highest laccase production was performed and the species was found to be Cladosporium tenuissimum. Even the crude extract of this strain displayed laccase production of 42.16U/L, as revealed by ABTS assay. Hence this strain is a promising candidate for optimization studies for utilisation in the domain of bioremediation and industrial applications

Understanding the Role of Antimicrobial Peptides in Neutrophil Extracellular Traps Promoting Autoimmune Disorders

AMPs are small oligopeptides acting as integral elements of the innate immune system and are of tremendous potential in the medical field owing to their antimicrobial and immunomodulatory activities. They offer a multitude of immunomodulatory properties such as immune cell differentiation, inflammatory responses, cytokine production, and chemoattraction. Aberrancy in neutrophil or epithelial cell-producing AMPs leads to inflammation culminating in various autoimmune responses. In this review, we have tried to explore the role of prominent mammalian AMPs—defensins and cathelicidins, as immune regulators with special emphasis on their role in neutrophil extracellular traps which promotes autoimmune disorders. When complexed with self-DNA or self-RNA, AMPs act as autoantigens which activate plasmacytoid dendritic cells and myeloid dendritic cells leading to the production of interferons and cytokines. These trigger a series of self-directed inflammatory reactions, leading to the emergence of diverse autoimmune disorders. Since AMPs show both anti- and pro-inflammatory abilities in different ADs, there is a dire need for a complete understanding of their role before developing AMP-based therapy for autoimmune disorders