Sujay Ray

Molecular level biodegradation of phenol and its derivatives through dmp operon of Pseudomonas putida：A bio-molecular modeling and docking analysis

Participation of Pseudomonas putida-derived methyl phenol (dmp) operon and DmpR protein in the biodegradation of phenol or other harmful, organic, toxic pollutants was investigated at a molecular level. Documentation documents that P. putida has DmpR protein which positively regulates dmp operon in the presence of inducers; like phenols. From the operon, phenol hydroxylase encoded by dmpN gene, participates in degrading phenols after dmp operon is expressed. For the purpose, the 3-D models of the four domains from DmpR protein and of the DNA sequences from the two Upstream Activation Sequences (UAS) present at the promoter region of the operon were demonstrated using discrete molecular modeling techniques. The best modeled structures satisfying their stereo-chemical properties were selected in each of the cases. To stabilize the individual structures, energy optimization was performed. In the presence of inducers, probable interactions among domains and then the two independent DNA structures with the fourth domain were perused by manifold molecular docking simulations. The complex structures were made to be stable by minimizing their overall energy. Responsible amino acid residues, nucleotide bases and binding patterns for the biodegradation, were examined. In the presence of the inducers, the biodegradation process is initiated by the interaction of phe50 from the first protein domain with the inducers. Only after the interaction of the last domain with the DNA sequences individually, the operon is expressed. This novel residue level study is paramount for initiating transcription in the operon; thereby leading to expression of phenol hydroxylase followed by phenol biodegradation.

Molecular modeling, mutational analysis and conformational switching in IL27: An in silico structural insight towards AIDS research

The advancement in proteomics and bioinformatics provokes to discern the molecular-level probe for HIV inhibitor; human interleukin-27 (IL27). Documentation documents that tyrosine residues in IL27 play a pivotal role for interacting with HIV, causing apoptosis of the HIV+ cells. Primarily, 3D structure of human wild-type (WT) IL27 was built through manifold molecular modeling techniques after the satisfaction of stereo-chemical properties. Its essential tyrosine residues were identified. Two mutant models for IL27 were prepared following the similar protocol by first substituting the tyrosine residues with glycine (MT_G) and then with alanine (MT_A) in the WT protein. Molecular dynamics (MD) simulation was performed to obtain a stable conformation. Conformational alterations in WT, MT_G and MT_A (before and after MD simulation) disclosed that MT_A was the steadiest one with the best secondary structure conformation supported by statistical significances. Though huge RMSD variations were observed on superimposing the MT structures on WT individually, the MTs were examined to share similar SCOP/CATH fold with TM-score=0.8, indicating that they retained their functionality even after mutation. Electrostatic surface potential again unveiled MT_A to be the most stable one. MT_A was thereby revealed to be the potent peptide inhibitor for HIV. This probe presents a pathway to investigate and compare the bio-molecular interaction of WT IL27 and MT_A IL27 (strongest model) with HIV in the future. This is the first report regarding the structural biology of IL27 accompanied by alteration at its genetic level and delving into the unknown residue-level and functional biochemistry for bringing about an annihilation towards AIDS.

Molecular Computing and Residual Binding Mode in ERα and bZIP Proteins from Homo Sapiens : An Insight into the Signal Transduction in Breast Cancer Metastasis

The most provoking reason for death in breast cancer patients is the metastasis of breast cancer. Accumulating documentation states that signal transduction in human breast cancers initiate in estrogen-dependent manner with the signaling of estrogen receptor α-subunit (ERα) and XBP-1 (bZIP-domain) proteins. So, molecular level insight into the signaling mechanism is indispensable for future pathological and therapeutic developments. Thus, this current study discloses the stable residual participation of the two crucial human proteins for enhancing the signaling mechanism in breast tumor malignancies. For this purpose, 3D homology models of the respective proteins were prepared after the satisfaction of their stereo-chemical features. The protein–protein interaction was studied and protein complex was energy optimized. Revelation from the stability calculating parameters, solvent accessibility areas and interaction probes led to the inference of the most stable optimized complex and its residual participation (exceptional contribution of polar charged residues) for metastasis progression in breast cancer cells.

Structural insight, mutation and interactions in human Beta-catenin and SOX17 protein: A molecular-level outlook for organogenesis

Essential human proteins; SOX17-HMG domain and beta-catenin uphold a major responsibility for vertebrate gastrulation and embryonic development. Earlier experimental assays document their interaction and states that upon M76A and G103R mutation, their interaction varied. Till date, there was no computational analysis for either of proteins as well as their respective residues for the interaction. The present study extracted and analyzed the experimentally validated 3D models of SOX17-HMG domain and beta-catenin. After analysis of the evolutionarily conserved residues and the sequence-level alteration, the mutated SOX17-HMG protein was re-modeled, demonstrated and energy minimized. Molecular dynamics simulation was performed upon the docked complex of beta-catenin with wild-type and mutant-type protein, individually. Comparable analysis for interaction studies revealed reduction of predominant ionic interactions from 16 (wild-type) to 5 (mutant-type). Glu residues from wild-type protein played a pivotal role forming 50% of the ionic interactions alone. Fascinatingly, statistically significant deductions for several stability calculations deduced the mutant-type protein/complex to form unsteady interaction with beta-catenin. Again, helix-to-coil transition in mutant-type protein supported its weaker conformation. This probe depicts the paramount molecular-level detailed scrutiny for the essential human proteins and disclosure of the mutational analysis, which might tend to hinder the signal transduction. It instigates the future development for the pharmaceutical research.

A Computational Structural Biology of SoxR and DNA: A Modelling and Interactive Discern to Express the Sox Operon in Pseudaminobacter salicylatoxidans (KCT001) for Global Sulphur Oxidation

Computational and microbial molecular-level participation of sox operon and its repressor protein (SoxR) in sulphur oxidation from Pseudaminobacter salicylatoxidans (KCT001) was investigated. Documentation reveals that P. salicylatoxidans (KCT001) has sox TRSVWXYZABCD operon that is regulated by a repressor protein (SoxR). Previously, various experimental procedures such as DMS-mediated DNA methylations and hydroxyl radical footprinting have disclosed that SoxR interacts first with an operator region-sv (present in between soxS and soxV). Detailed computational studies were accomplished in the present study. 3D models of repressor protein and the DNA sequence from operon’s promoter region were demonstrated using molecular modelling techniques. Molecular docking simulation was performed to predict DNA–protein interaction. Amino acid residues and nucleotide bases responsible for interaction were identified by PyMOL and Discovery Studio software suite. This novel residue-level study is paramount for initiating transcription in the operon, thereby leading to sulphur oxidation.

Insight into the Conformational Variations in SoxYZ Protein Complex from Two Different Members of the β-Proteobacterial Family Involved in Sulfur Oxidation

Sulfur anions serve as the important environmental pollutants. Microbes use hydrogen sulfide in different redox reactions and thus make the environment pollution-free. The sulfur redox processes are performed by a gene cluster called the sox operon, possessed by a diverse set of microorganisms. However, most of the previous studies were confined to α-proteobacteria. In this work, we tried to elucidate the mechanistic details of sulfur oxidation in β-proteobacteria. We compared the molecular mechanism of sulfur oxidation process using Dechloromonas aromatica and Thiobacillus denitrificans. Dechloromonas aromatica possesses the entire sox operon, whereas T. denitrificans lacks SoxCD. In both the organisms, SoxYZ complex formation is essential for thiosulfate oxidation. This SoxYZ protein complex interacts with SoxCD and SoxAX, respectively, for recycling the thiosulfate-bound SoxY protein. For this purpose, individual proteins were modeled via manifold modeling techniques. Protein–protein docking studies were executed to generate duo- and quadro-protein complexes. Different stability parameters such as free energy of folding, solvent accessibility area (for final complexes), and electrostatic surface potential (for SoxYZ complexes) were calculated and analyzed. Fifteen strengthening ionic interactions were accomplished in the SoxYZAX complex, whereas eight such interactions were observed in SoxYZCD complex. From the result, SoxYZAX complex was found to be more stable and interactive one. This study is the first of its kind that analyzes the comparative aspects of the binding interactions of the proteins involved in redox reactions of sulfur anions. This study may, therefore, be helpful in tailoring the microorganisms to function in a better way to remove the environmental sulfur pollutants.Graphical Abstract

Mutations and interactions in human ERα and bZIP proteins: An in silico approach for cell signaling in breast oncology

I. BACKGROUND Metastasis of breast cancer serves the most aggravating cause for transience in breast cancer patients. Accumulating evidences suggest that signal transduction in human breast cancers commences in estrogen-reliant pattern via signaling of the estrogen-receptor α-subunit (ERα) and XBP-1 (bZIP-domain) proteins. Furthermore, earlier investigations from SAGE and GST pull-down assay, also state that a point mutation in ERα leads to a risky factor by resulting into hyper-responsiveness towards estrogen and increased proliferation of breast cancer cells. So, a molecular-level exploration into the signaling mechanism is a prime requisite for future clinical and therapeutic progress. II. METHODS AND RESULTS Present study explores primarily the residual participation of the two essential proteins from humans to boost the signaling mechanism in malignant breast tumors. So, 3D structures of the respective monomer proteins were demonstrated and mutated protein was homology modeled after the satisfaction of the stereo-chemical features. The functionality was observed to be conserved after mutation. Abrupt increment in protein-protein interactions was studied for the individual optimized and Molecular Dynamics simulated protein complexes. Revelation from supportive statistical significances for several energy calculations, solvent accessibility areas, electrostatic surface potentials and interaction studies led to confer that after mutation, the complex and the individual protein were the most stable and the best interactive one. For metastasis in breast cancer cells, polar charged residues hold a significant contribution. III. CONCLUSION Therefore, this investigation provides a cogent framework for the interactive studies associated with breast cancer and an exposure towards the lethal impact on mutation.

Structural Exploration and Conformational Transitions in MDM2 upon DHFR Interaction from Homo sapiens: A Computational Outlook for Malignancy via Epigenetic Disruption

Structural basis for exploration into MDM2 and MDM2-DHFR interaction plays a vital role in analyzing the obstruction in folate metabolism, nonsynthesis of purines, and further epigenetic regulation in Homo sapiens. Therefore, it leads to suppression of normal cellular behavior and malignancy. This has been earlier documented via yeast two-hybrid assays. So, with a novel outlook, this study explores the molecular level demonstration of the best satisfactory MDM2 model selection after performing manifold modeling techniques. Z-scores and other stereochemical features were estimated for comparison. Further, protein-protein docking was executed with MDM2 and the experimentally validated X-ray crystallographic DHFR. Residual disclosure from the best suited simulated protein complex disclosed 18 side chain and 3 ionic interactions to strongly accommodate MDM2 protein into the pocket-like zone in DHFR due to the positive environment by charged residues. Lysine residues from MDM2 played a predominant role. Moreover, evaluation from varied energy calculations, folding rate, and net area for solvent accessibility implied the active participation of MDM2 with DHFR. Fascinatingly, conformational transitions from coils to helices and β-sheets after interaction with DHFR affirm the conformational strength and firmer interaction of human MDM2-DHFR. Therefore, this probe instigates near-future clinical research and interactive computational investigations with mutations.

An In-Silico Structural Analysis of the Interactions of SoxY and SoxZ from Moderately Thermophilic Betaproteobacterium, Hydrogenophilus thermoluteolus in the Global Sulfur Oxidation Cycle

Microbial redox reactions are mediated by a diverse set of sulfur-oxidising bacteria. These redox reactions are important to maintain the environmental sulfur balance. The sulfur oxidation reactions are performed by sulfur-oxidizing gene cluster called the sox operon comprising of genes soxEFCDYZAXBH. However, the mechanistic details of sulfur oxidation process by Hydrogenophilus thermoluteolus are yet to be determined. In this study, the three-dimensional structures of SoxY and SoxZ proteins were constructed by homology modeling. Protein-protein docking generated SoxY–Z complex. Responsible amino acid residues for the protein interactions were identified after molecular dynamics simulation of SoxY–Z complex. The best binding mode of thiosulfate with SoxY–Z complex was identified through their molecular docking. Current study thereby, provides a rational frame-work to discern molecular mechanism and biophysical characterization of sulfur-oxidation process.

Computational structural biology and modes of interaction between human annexin A6 with influenza A virus protein M2: a possible mechanism for reducing viral infection

Influenza-A virus is a prime lethal causative factor for influenza. The M2 protein of influenza A virus plays an important responsibility in the cycle of viral replication. The human Annexin A6 protein targets and stops the viral budding for influenza A virus. Here, molecular level interactions between Annexin A6 and influenza A virus M2 protein were examined. Executing the techniques for molecular modelling, the 3D structures of the two proteins were built via energy optimisations. Interactions between the two proteins were analysed by molecular docking studies. Both Annexin A6 and M2 protein interacted strongly with a pivotal role of Asp and Lys residues, respectively. A conformational shift from helices and sheets to coils was observed in the M2 protein after its interaction with Annexin A6. This probe therefore helped to understand the molecular mechanism of the two proteins and the negative modulation of Annexin A6 on the M2 protein from influenza A virus.