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George Priya Doss C.,Center for Nanobiotechnology | Rajith B.,Center for Nanobiotechnology
Cell Biochemistry and Biophysics | Year: 2013

Phosphatase and tensin homolog (PTEN) plays essential roles in cellular processes including survival, proliferation, energy metabolism, and cellular architecture. Activating the mutations of PTEN has long been known to produce a variety of disorders, mainly diabetes and cancer in humans. Owing to the importance of PTEN gene, a functional analysis using different in silico approaches was undertaken to explore the possible associations between genetic mutations and phenotypic variation. SIFT, PolyPhen, I-Mutant 3.0, SNP&GO, and PHD-SNP were used for initial screening of functional nsSNPs. From the observed results, three mutations R47G, H61D, and V343E were selected based on their surface accessibility and total energy change. By molecular dynamics approach, H61D showed increase in flexibility, radius of gyration, solvent accessibility, and deviated more from the native structure which was supported by the decrease in the number of hydrogen bonds. Further from principal component analysis and interaction analysis, we identified significant structural changes that can reasonably explain the involvement of deviations in stability caused by mutations. Our analysis also predicts the involvement of SNPs that could potentially influence post-translational modifications in PTEN gene. These in silico predictions could provide a new insight into structural and functional impact of PTEN polymorphisms. © 2012 Springer Science+Business Media New York.


Sekar G.,Center for Nanobiotechnology | Sivakumar A.,Vellore Institute of Technology | Mukherjee A.,Center for Nanobiotechnology | Chandrasekaran N.,Center for Nanobiotechnology
Journal of Bionanoscience | Year: 2016

Nanoparticles (NPs) with unique physicochemical properties possess distinct properties that are ultimately superior to that of the properties of their bulk counterparts. Hence, their market for industrial applications has counted up to the maximum. Nanoparticle embedded cosmetics, balls, fabrics, water filters, etc. has already occupied their significant part in the commercial sector. Such nanoparticle incorporated products and nano based therapeutics provides enough opportunity for the exposure of nanoparticles to that of human beings from nature either out of pollution or via their biomedical applications. Inhalation or the intentional administration of nano based products into human being results out into the nanoparticle-protein corona that determines the fate of nanoparticle internalization into the body. Such kinds of interaction occurring at the molecular level not only determine the fate of NPs, but also the binding accompanied conformational changes in biomolecules. Also, NPs unique higher surface area to volume ratio promotes the biomolecules aggregation, defined as the protein fibrillation at molecular level. Several spectroscopic techniques occupy prominent position for studying the above phenomena in a much simplified manner. On accounting the above physico-chemical and biological behavioral properties of NPs, the understanding of the impact of nanoparticle on the protein conformation and fibrillation upon binding should be reviewed enough to understand the biocompatibility of nanoparticles for futuristic biomedical applications. Hence, this review encompasses the brief definition and the relationship between nanoparticle, protein corona, and fibrillation process with that of the biophysical methods. Copyright © 2016 American Scientific Publishers.


Lipert R.J.,Iowa State University | Lipert R.J.,Institute for Physical Research and Technology | Porter M.D.,University of Utah | Porter M.D.,Center for Nanobiotechnology | And 11 more authors.
40th International Conference on Environmental Systems, ICES 2010 | Year: 2010

An experimental water monitoring kit for the measurement of iodine and silver(I) was recently delivered to the International Space Station (ISS). The kit is based on Colorimetric Solid Phase Extraction (CSPE) technology, which uses diffuse reflectance spectrophotometry to measure a color change on the surface of indicator disks following exposure to a water sample. To satisfy additional spacecraft potable water monitoring requirements, CSPE has now been extended to encompass the measurement of total I (iodine, iodide, and triiodide). This is accomplished through the introduction of an oxidizing agent, which converts iodide and triiodide to iodine. The sum of the iodine, iodide, and triiodide present in the sample can then be measured using the same iodine sensitive indicator disks currently being tested on ISS. These disks detect iodine, but are insensitive to iodide and triiodide. We report here the operational considerations, design, and ground-based performance of the CSPE method for total I. The results demonstrate that CSPE technology is poised to meet NASA's monitoring requirements for total iodine in potable water. © 2010 by the American Institute of Aeronautics and Astronautics, Inc. All rights reserved.


Rajith B.,Center for Nanobiotechnology | Doss C.G.P.,Center for Nanobiotechnology
Applied Biochemistry and Biotechnology | Year: 2013

In-depth computationally based structural analysis of human fibroblast growth factor type 1 (FGFR1) protein carrying disease-causing mutation was performed in this study. Gain or loss of function due to missense mutations in FGFR1 is responsible for a variety of disorders including Kallmann syndrome, Apert syndrome, Pfeiffer syndrome, Crouzon syndrome, etc. The mutant model of the human FGFR1 protein was subjected to various in silico analysis, and most deleterious SNPs were screened out. Furthermore, docking and long molecular dynamics simulations were carried out with an intention of studying the possible impact of these mutations on the protein structure and hence its function. Analysis of various structural properties-especially of those of the functionally important regions: the extracellular immunoglobulin domain and intracellular Tyrosine kinase domain-gave some insights into the possible structural characteristics of the disease mutant and the wild-type forms of the protein. In a nutshell, compared to the wild-type protein, the mutant structures V273M and S685F are associated with significant changes, and the functionally important regions seem to adopt such structures that are not conducive for the wild-type-like functionality. © Springer Science+Business Media New York 2013.


PubMed | Center for Nanobiotechnology
Type: Journal Article | Journal: Cell biochemistry and biophysics | Year: 2013

Phosphatase and tensin homolog (PTEN) plays essential roles in cellular processes including survival, proliferation, energy metabolism, and cellular architecture. Activating the mutations of PTEN has long been known to produce a variety of disorders, mainly diabetes and cancer in humans. Owing to the importance of PTEN gene, a functional analysis using different in silico approaches was undertaken to explore the possible associations between genetic mutations and phenotypic variation. SIFT, PolyPhen, I-Mutant 3.0, SNP&GO, and PHD-SNP were used for initial screening of functional nsSNPs. From the observed results, three mutations R47G, H61D, and V343E were selected based on their surface accessibility and total energy change. By molecular dynamics approach, H61D showed increase in flexibility, radius of gyration, solvent accessibility, and deviated more from the native structure which was supported by the decrease in the number of hydrogen bonds. Further from principal component analysis and interaction analysis, we identified significant structural changes that can reasonably explain the involvement of deviations in stability caused by mutations. Our analysis also predicts the involvement of SNPs that could potentially influence post-translational modifications in PTEN gene. These in silico predictions could provide a new insight into structural and functional impact of PTEN polymorphisms.


George Priya Doss C.,Center for Nanobiotechnology | Nagasundaram N.,Center for Nanobiotechnology | Tanwar H.,Center for Nanobiotechnology
Interdisciplinary Sciences: Computational Life Sciences | Year: 2012

Functional alteration in SMAD proteins leads to dis-regulation of its mechanism results in possibilities of high risk diseases like fibrosis, cancer, juvenile polyposis etc. Studying single nucleotide polymorphism (SNP) in SMAD genes helps understand the malfunction of these proteins. In this study, we focused on deleterious effects of nsSNPs in both structural and functional level using publically available bioinformatics tools. We have mainly focused on identifying deleterious nsSNPs in both structural and functional level in SMAD genes by using SIFT, PolyPhen, SNPs&GO, I-Mutant 3.0, MUpro and PANTHER. Structure analysis was carried out with the major mutation that occurred in the native protein coded by SMAD genes and its amino acid positions (R358W, K306S, R310G, S433R and R361C). SRide was used to check the stability of the native and mutant modelled proteins. In addition, we used MAPPER to identify SNPs present in transcription factor binding sites. These findings demonstrate that the in silico approaches can be used efficiently to identify potential candidate SNPs in large scale analysis. © 2012 International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg.

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