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Your search keyword '"Mandyam, Ramya A."' showing total 8 results
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8 results on '"Mandyam, Ramya A."'

1. Metamorphic response of the CLIC1 chloride intracellular ion channel protein upon membrane interaction

Author

Goodchild, Sophia C., Breit, Samuel N., Curmi, Paul M.G., Brown, Louise J., Mandyam, Ramya A., Sale, Kenneth L., Mazzanti, Michele, Howell, Michael W., and Littler, Dene R.

Subjects
Energy transformation -- Research, Lipid membranes -- Research, Biological sciences, Chemistry
Abstract

The insights into the chloride intracellular channel (CLIC) transmembrane form are obtained by fluorescence resonance energy transfer (FRET) spectroscopy. The studies have shown a large conformational unfolding occurring between the N- and C-domains of CLIC1 upon interaction with the membrane, where the N-terminal domain of CLIC1 has inserted into the lipid bilayer, while the C-domain has remained in solution on the extravesicular side of the membrane.

Published
2010

2. PGTools: A software suite for proteogenomic data analysis and visualization

Author

Hiriyur Nagaraj, Shivashankar, Waddell, Nicola, Madugundu, Anil, Wood, Scott, Jones, Alun, Mandyam, Ramya, Nones, Katia, Pearson, John, Grimmond, Sean, Hiriyur Nagaraj, Shivashankar, Waddell, Nicola, Madugundu, Anil, Wood, Scott, Jones, Alun, Mandyam, Ramya, Nones, Katia, Pearson, John, and Grimmond, Sean

Abstract

We describe PGTools, an open source software suite for analysis and visualization of proteogenomic data. PGTools comprises applications, libraries, customized databases, and visualization tools for analysis of mass-spectrometry data using combined proteomic and genomic backgrounds. A single command is sufficient to search databases, calculate false discovery rates, group and annotate proteins, generate peptide databases from RNA-Seq transcripts, identify altered proteins associated with cancer, and visualize genome scale peptide data sets using sophisticated visualization tools. We experimentally confirm a subset of proteogenomic peptides in human PANC-1 cells and demonstrate the utility of PGTools using a colorectal cancer data set that led to the identification of 203 novel protein coding regions missed by conventional proteomic approaches. PGTools should be equally useful for individual proteogenomic investigations as well as international initiatives such as chromosome-centric Human Proteome Project (C-HPP). PGTools is available at http://qcmg.org/bioinformatics/PGTools.

Published
2015

3. Discovery and Characterization of a Potent Interleukin-6 Binding Peptide with Neutralizing Activity In Vivo

Author

Ranganath, Sheila, primary, Bhandari, Ashok, additional, Avitahl-Curtis, Nicole, additional, McMahon, Jaimee, additional, Wachtel, Derek, additional, Zhang, Jenny, additional, Leitheiser, Christopher, additional, Bernier, Sylvie G., additional, Liu, Guang, additional, Tran, Tran T., additional, Celino, Herodion, additional, Tobin, Jenny, additional, Jung, Joon, additional, Zhao, Hong, additional, Glen, Katie E., additional, Graul, Chris, additional, Griffin, Aliesha, additional, Schairer, Wayne C., additional, Higgins, Carolyn, additional, Reza, Tammi L., additional, Mowe, Eva, additional, Rivers, Sam, additional, Scott, Sonya, additional, Monreal, Alex, additional, Shea, Courtney, additional, Bourne, Greg, additional, Coons, Casey, additional, Smith, Adaline, additional, Tang, Kim, additional, Mandyam, Ramya A., additional, Masferrer, Jaime, additional, Liu, David, additional, Patel, Dinesh V., additional, Fretzen, Angelika, additional, Murphy, Craig A., additional, Milne, G. Todd, additional, Smythe, Mark L., additional, and Carlson, Kenneth E., additional

Published
2015
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5. Structural insights into the organization of the Cavin membrane coat complex

Author

Kovtun, Oleksiy, Tillu, Vikas, Jung, WooRam, Leneva, Natalya, Ariotti, Nicholas, Chaudhary, Natasha, Mandyam, Ramya, Ferguson, Charles, Morgan, Garry, Johnston, Wayne, Harrop, Stephen, Alexandrov, Kirill, Parton, Robert, Collins, Brett, Kovtun, Oleksiy, Tillu, Vikas, Jung, WooRam, Leneva, Natalya, Ariotti, Nicholas, Chaudhary, Natasha, Mandyam, Ramya, Ferguson, Charles, Morgan, Garry, Johnston, Wayne, Harrop, Stephen, Alexandrov, Kirill, Parton, Robert, and Collins, Brett

Abstract

Free to read at publisher's site.
Summary Caveolae are cell-surface membrane invaginations that play critical roles in cellular processes including signaling and membrane homeostasis. The cavin proteins, in cooperation with caveolins, are essential for caveola formation. Here we show that a minimal N-terminal domain of the cavins, termed HR1, is required and sufficient for their homo- and hetero-oligomerization. Crystal structures of the mouse cavin1 and zebrafish cavin4a HR1 domains reveal highly conserved trimeric coiled-coil architectures, with intersubunit interactions that determine the specificity of cavin-cavin interactions. The HR1 domain contains a basic surface patch that interacts with polyphosphoinositides and coordinates with additional membrane-binding sites within the cavin C terminus to facilitate membrane association and remodeling. Electron microscopy of purified cavins reveals the existence of large assemblies, composed of a repeating rod-like structural element, and we propose that these structures polymerize through membrane-coupled interactions to form the unique striations observed on the surface of caveolae in vivo.

Published
2014

6. Structural Insights into the Organization of the Cavin Membrane Coat Complex

Author

Kovtun, Oleksiy, primary, Tillu, Vikas A., additional, Jung, WooRam, additional, Leneva, Natalya, additional, Ariotti, Nicholas, additional, Chaudhary, Natasha, additional, Mandyam, Ramya A., additional, Ferguson, Charles, additional, Morgan, Garry P., additional, Johnston, Wayne A., additional, Harrop, Stephen J., additional, Alexandrov, Kirill, additional, Parton, Robert G., additional, and Collins, Brett M., additional

Published
2014
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7. Comparison of vertebrate and invertebrate CLIC proteins: The crystal structures ofCaenorhabditis elegans EXC-4 andDrosophila melanogaster DmCLIC

Author

Littler, Dene R., primary, Harrop, Stephen J., additional, Brown, Louise J., additional, Pankhurst, Greg J., additional, Mynott, Andrew V., additional, Luciani, Paolo, additional, Mandyam, Ramya A., additional, Mazzanti, Michele, additional, Tanda, Soichi, additional, Berryman, Mark A., additional, Breit, Samuel N., additional, and Curmi, Paul M. G., additional

Published
2008
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8. Comparison of vertebrate and invertebrate CLIC proteins: The crystal structures of Caenorhabditis elegans EXC-4 and Drosophila melanogaster DmCLIC.

Author

Littler, Dene R., Harrop, Stephen J., Brown, Louise J., Pankhurst, Greg J., Mynott, Andrew V., Luciani, Paolo, Mandyam, Ramya A., Mazzanti, Michele, Tanda, Soichi, Berryman, Mark A., Breit, Samuel N., and Curmi, Paul M. G.

Abstract

The crystal structures of two CLIC family members DmCLIC and EXC-4 from the invertebrates Drosophila melanogaster and Caenorhabditis elegans, respectively, have been determined. The proteins adopt a glutathione S-transferase (GST) fold. The structures are highly homologous to each other and more closely related to the known structures of the human CLIC1 and CLIC4 than to GSTs. The invertebrate CLICs show several unique features including an elongated C-terminal extension and a divalent metal binding site. The latter appears to alter the ancestral glutathione binding site, and thus, the invertebrate CLICs are unlikely to bind glutathione in the same manner as the GST proteins. Purified recombinant DmCLIC and EXC-4 both bind to lipid bilayers and can form ion channels in artificial lipid bilayers, albeit at low pH. EXC-4 differs from other CLIC proteins in that the conserved redox-active cysteine at the N-terminus of helix 1 is replaced by an aspartic acid residue. Other key distinguishing features of EXC-4 include the fact that it binds to artificial bilayers at neutral pH and this binding is not sensitive to oxidation. These differences with other CLIC family members are likely to be due to the substitution of the conserved cysteine by aspartic acid. Proteins 2008. © 2007 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Published
2008
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