Simanti Bhattacharya

Hypoglycosylation of dystroglycan due to T192M mutation: a molecular insight behind the fact.

Abnormal glycosylation of dystroglycan (DG), a transmembrane glycoprotein, results in a group of diseases known as dystroglycanopathy. A severe dystroglycanopathy known as the limb girdle disease MDDGC9 [OMIM: 613818] occurs as a result of hypoglycosylation of alpha subunit of DG. Reasons behind this has been traced back to a point mutation (T192M) in DG that leads to weakening of interactions of DG protein with laminin and subsequent loss of signal flow through the DG protein. In this work we have tried to analyze the molecular details of the interactions between DG and laminin1 in order to propose a mechanism about the onset of the disease MDDGC9. We have observed noticeable changes between the modeled structures of wild type and mutant DG proteins. We also have employed molecular docking techniques to study and compare the binding interactions between laminin1 and both the wild type and mutant DG proteins. The docking simulations have revealed that the mutant DG has weaker interactions with laminin1 as compared to the wild type DG. Till date there are no previous reports that deal with the elucidation of the interactions of DG with laminin1 from the molecular level. Our study is therefore the first of its kind which analyzes the differences in binding patterns of laminin1 with both the wild type and mutant DG proteins. Our work would therefore facilitate analysis of the molecular mechanism of the disease MDDGC9. Future work based on our results may be useful for the development of suitable drugs against this disease.

Analyses of the presence of mutations in Dystrophin protein to predict their relative influences in the onset of Duchenne Muscular Dystrophy

Muscle plays a vital role in the life of vertebrates like humans. Muscle contraction is the only criterion required for locomotion. Muscle fibers also play a vital role as the provider of mechanical strength and act as a large repository of building blocks for protein synthesis in living beings. Muscles function as per the messages received from the extra-cellular signals. One of the central players responsible for capturing and transmission of extra-cellular signals to maintain the integrity of muscle function is the protein called Dystrophin (Dp). However, the wild type Dp protein accumulates some mutations which lead to a severe disease called Duchenne Muscular Dystrophy (DMD). The disease is so frequent that it is known to affect 1 in 3500 newborns per year. There are a number of reports that identify the mutations leading to DMD. Interestingly, it is also observed that the type of mutations affects the severity of the disease. But the biochemical mechanism of the DMD onset is still obscure. In the present scenario, an attempt has been made to analyze the mutations in the development of the disease. We analyzed the changes in secondary structure, solvent accessibility and stability of the Dp protein associated with the mutations. We tried to correlate the type of mutations with the severity of the disease. So far this is the first report that deals with the analyses of the mutations leading to DMD. This study would therefore be essential to come up with a plausible mechanism of DMD disease onset.

In-silico characterization of Formin Binding Protein 4 Family of proteins

Members of the Formin Binding Protein 4 Family or the FNBP4 were indirectly reported to be associated with many of the biological processes. These proteins possess two WW domains. So far there are practically no reports regarding the characterization and classification of the protein by any means. Keeping in mind the importance of the proteins from this FNBP4 family, we have tried an in silico approach to come up with a comprehensive analysis of the proteins. We have analyzed the proteins by considering their sequence conservation, their phylogenetic distributions among the different organisms. We have also investigated the functional properties of the WW domains in the proteins. Finally, we have made an attempt to elucidate the structural details of the domains and predicted the possible modes of their interactions. Our findings show that FNBP4 is eukaryotic in its distribution and follows a trend of evolution where animal and plant homologues have evolved in an independent manner. While the WW domain is the only common motif present across the FNBP4 family of proteins, there are different classes (mainly two) of WW domains that are found among different FNBP4 proteins. Structure function predictions indicate a possible role of FNBP4 in either protein stabilization control or transcript processing. Our study on FNBP4 may therefore open up new avenues to generate new interest in this highly important but largely unexplored class of proteins. Future studies with proteins from this family may answer many important questions of protein-protein interactions in different biologically important processes.

Implication from the predicted docked interaction of sigma H and exploration of its interaction with RNA polymerase in Mycobacterium tuberculosis.

M. tuberculosis is adapted to remain active in the extreme environmental condition due to the presence of atypical sigma factors commonly called extra cytoplasmic function (ECF) sigma factors. Among the 13 sigma factors of M. tuberculosis, 10 are regarded as the ECF sigma factor that exerts their attributes in various stress response. Therefore it is of interest to describe the structural prediction of one of the ECF sigma factors, sigma H (SigH), involved in oxidative and heat stress having interaction with the β׳ subunit of M. tuberculosis. RNA polymerase (Mtb-RNAP). The model of Mtb-SigH was build using the commercial package of Discovery Studio version 2.5 from Accelerys (San Diego, CA, USA) containing the inbuilt MODELER module and that of β׳ subunit of Mtb-RNAP using Phyre Server. Further, the protein models were docked using the fully automated web tool ClusPro (cluspro.bu.edu/login.php). Mtb-SigH is a triple helical structure having a putative DNA-binding site and the β׳ subunit of MtbRNAP consists of 18-beta sheets and 22 helices. The SigH-Mtb-RNAP β׳ interaction studies showed that Arg26, Gln19 andAsp18, residues of SigH protein are involved in binding with Arg137, Gln140, Arg152, Asn133 and Asp144 of β׳ subunit of Mtb-RNAP. The predicted model helps to explore the molecular mechanism in the control of gene regulation with a novel unique target for potential new generation inhibitor.

Structural and Functional Characterization of Arabidopsis thaliana WW Domain Containing Protein F4JC80

WW domains are the smallest known independently foldable protein structural motifs that are involved in cellular events like protein turnover, splicing, development, and tumor growth control. These motifs bind the polyproline rich ligands. While the WW domains of animal origin are well characterized, the same from plant origin are not well documented yet. Despite the small repertoire of WW proteome of plants (in comparison to animal WW proteome) functional diversity is reported to be equally vivid for plants also. Here, for the first time, we report the structural and functional properties of an Arabidopsis thaliana (At) WW domain containing protein F4JC80 by using homology modeling and docking techniques. Our findings report that the At F4JC80 protein contains two WW domains which bear the standard triple β sheet structure and structurally and functionally resemble Class I WW domains of E3 ubiquitin ligase family but their structural differences impact their polypeptide binding abilities differently.

Understanding the Interaction of Human Formin Binding Protein 4 with Formin FMN1

The proline rich formin homolog 1 (FH1) region of mouse formin FMN1 was initially reported to bind to WW domains and mediate its interaction with formin binding protein 4 (FNBP4) via the WW domain of FNBP4. However further structural, biochemical and functional details about this interaction have never been reported. The nature of the study that first reported this interaction, along with lack of further information, later created doubt about the possibility of this interaction under cellular environment. In this context, this computational study confirms the binding of mouse formin FMN1 FH1 with the 1st WW domain of FNBP4. Combined with our previous reports, this study concludes that only the 1st WW domain of FNBP4 is able to mediate its interaction with formins FH1 regions and its binding is stronger to the PPXXPP motif compared to the PPXP or PPXPP motifs, all of which are found in formin FH1 region.

The Effect of T192M Mutation in Stability of Alpha Dystroglycan: Study with Molecular Dynamics Simulation

Alpha-dystroglycan (α-DG), a cell surface receptor links extracellular matrix with cellular cytoskeleton. Its post translational modification is carried out with number of glycosyltransferases, depending on cell types to make the ligand specific mature α-DG receptor protein. However, T192M mutation in α-DG has been found to cause hypo-glycosylation of the protein disabling its Laminin binding form and thereby triggering the onset of a limb girdle muscular dystrophy affecting early childhood. Here for the first time we exploit the effect of this mutation in protein conformational stability. We have found that this mutation leads to significant changes in secondary structure of the protein as well as in the accessible surface area. All these changes also hamper the crucial disulfide bond that is required to maintain the globular fold at the N terminus of α-DG. This molecular insight will therefore be useful for developing new therapeutic approaches to overcome the disease state.

Computational analyses of the length and compositional variations of the FNBP4 gene across 10 different species.

Formin binding protein 4 (FNBP4) interacts with formins and other proteins via its WW domains. Previously, we reported the structural and phylogenetic clustering of FNBP4 across a wide range of organisms from different taxonomic groups along with characterizing its plant variant (Arabidopsis thaliana F4JC80). Recently, the FNBP4 gene is reported to be associated with a congenital disorder Microphthalmia with Limb Anomalies. Except these reports, FNBP4 is mostly uncharacterized, especially the FNBP4 gene. In this context, we have attempted to characterize the FNBP4 gene in terms of its length and compositional variations across 10 different organisms from different taxonomic groups. Our findings highlight that the length of the FNBP4 gene varies greatly among different species. Introns, UTRs and the entire gene were AT rich while CDS and mRNAs were GC rich. The RSCU values were also different for the different organisms indicating a possible impact on translational efficiency of this protein. Comparative analyses highlight gene element and base proportions related characteristics specific to highly expression regulated genes like FNBP4.

In-silico structural analysis of E509K mutation in LARGE and T192M mutation in Alpha Dystroglycan in the inhibition of glycosylation of Alpha Dystroglycan by LARGE

Impaired glycosylation of cellular receptor Alpha Dystroglycan (α-DG) leads to dystroglycanopathy. Glycoprotein α-DG is the receptor protein in the Dystrophin Associated Protein Complex (DAPC), a macromolecular gathering on muscle cell membrane to form a bridge between extracellular matrix (ECM) and cellular actin cytoskeleton. Proper glycosylation of α-DG is mediated by the glycosylating enzyme LARGE. Mutations either in α-DG or in LARGE lead to improper glycosylations of α-DG thereby hampering the formation of final Laminin binding form α-DG resulting in dystroglycanopathy. In our current work, we explored the structural changes associated with the presence of mutations in α-DG as well as in the enzyme LARGE. We further extended our research to understand the effect of the mutations onto protein-enzyme interactions. Moreover, since LARGE transfers the sugar moiety (glucuronic acid; GlcA) onto α-DG, we tried to analyze what effect the mutation in LARGE confers on this enzyme ligand interaction. This work for the first time addressed the molecular changes occurring in the structures α-DG, LARGE and their interactions and shed lights on the as yet poorly understood mechanism behind the dystroglycanopathy onset.

LCMV Interaction Changes with T192M Mutation in Alpha-Dystroglycan

Limb girdle muscular dystrophy (OMIM: 613818) is a severe disease in humans, which broadly affects brain development. The disease is caused by T192M mutation in the protein alpha-dystroglycan (α-DG). α-DG is an important component of dystrophin–dystroglycan complex which links extracellular matrices with actin cytoskeleton and thereby maintains signalling cascades essential for the development of tissues and organs. The mutation T192M in α-DG hampers proper glycosylation of α-DG thereby developing limb girdle muscular dystrophy. Prototype virus for Old World Arenaviruses (OWV), Lymphocytic Choriomeningitis virus (LCMV) also uses this α-DG as host cell receptor and invades the host cell causing a disease called Lymphocytic choriomeningitis, an infection to meninges. Thereby, interaction of α-DG and LCMV has become an interesting object of study to predict the mode of the disease onset. In our current work, we have used homology modelling, molecular docking and molecular dynamics (MD) with temperature variation. We have identified significant structural differences between wild type (WT) and mutant (MT) α-DG in terms of spatiotemporal orientations of amino acids. This change in the folding patterns of the WT and MT α-DG has brought forth a different interaction pattern of the WT and MT α-DG with GP1 protein from LCMV as reflected in our docking simulations. Further MD simulations with the complexes over tropical and temperate environment have revealed that MT-α-DG-LCMV GP1 complex is relatively more stable than the wild type counterpart. It has also been found that LCMV GP1 has interacted strongly with mutant α-DG. Our studies therefore has shed light on the structure and molecular interaction pattern of LCMV with MT α-DG and also indicate a possibility of T192M mutant in α-DG making the receptor to interact strongly with LCMV GP1. These insights also provide clues to develop possible therapeutic approaches.