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35 results on '"Venkatakrishnan, Balasubramanian"'

1. Small Molecule Assembly Agonist Alters the Dynamics of Hepatitis B Virus Core Protein Dimer and Capsid

Author

Kant, Ravi, Lee, Lye-Siang, Patterson, Angela, Gibes, Nora, Venkatakrishnan, Balasubramanian, Zlotnick, Adam, and Bothner, Brian

Abstract

Chronic hepatitis B virus (HBV) poses a significant public health burden worldwide, encouraging the search for curative antivirals. One approach is capsid assembly modulators (CAMs), which are assembly agonists. CAMs lead to empty and defective capsids, inhibiting the formation of new viruses, and can also lead to defects in the release of the viral genome, inhibiting new infections. In this study, we employed hydrogen–deuterium exchange mass spectrometry (HDX-MS) to assess the impact of one such CAM, HAP18, on HBV dimers, capsids composed of 120 (or 90) capsid protein dimers, and cross-linked capsids (xl-capsids). HDX analysis revealed hydrogen bonding networks within and between the dimers. HAP18 disrupted the hydrogen bonding network of dimers, demonstrating a previously unappreciated impact on the dimer structure. Conversely, HAP18 stabilized both unmodified and cross-linked capsids. Intriguingly, cross-linking the capsid, which was accomplished by forming disulfides between an engineered C-terminal cysteine, increased the overall rate of HDX. Moreover, HAP18 binding induced conformational changes beyond the binding sites. Our findings provide evidence for allosteric communication within and between capsid protein dimers. These results show that CAMs are capable of harnessing this allosteric network to modulate the dimer and capsid dynamics.

Published
2024
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3. X− Dominating colour transversals in graphs

Author

Venkatakrishnan Balasubramanian Yanamandram, C. Natarajan, and S. K. Ayyaswamy

Subjects
X−dominating set, X−dominating colour transversal set, X−chromatic partition, Mathematics, QA1-939
Abstract

Let G = (X, Y,E) be a bipartite graph. A X-dominating set D ⊆ X is called a X−dominating colour transversal set of a graph G if D is a transversal of at least one $chi$−partition of G.The minimum cardinal- ity of a X−dominating colour transversal set is called X−dominating colour transversal number and is denoted by $chi_{dct}(G)$. We find the bounds of X−dominating colour transversal number and characterize the graphs attaining the bound.

Published
2016
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4. Adaptation of Web Pages for Hand-Held Devices

Author

Venkatakrishnan, Balasubramanian Appiah, Murugesan, San, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Lowe, David, editor, and Gaedke, Martin, editor

Published
2005
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6. Contributors

Author

K.C.A. Alam, Abdur Rahman Ansari, M.T. Arif, Neha Arora, Muhammad Arshad, Venkatakrishnan Balasubramanian, Dhinesh Balasubramaniyam, Suresh Bhargava, Awais Bokhari, Apinya Chanthakett, Arooj Fatima, V. Edwin Geo, Pobitra Halder, Nawshad Haque, Muddasser Inayat, Frankowski Jakub, Sadia Javed, Zobaidul Kabir, Imran Khan, Mohammad Masud Kamal Khan, Asif Hussain Khoja, Sazal Kundu, Srinivasan Madapusi, M. Taqi Mehran, M. Naqvi, Salman Raza Naqvi, Aman M.T. Oo, Rajarathinam Parthasarathy, Savankumar Patel, George P. Philippidis, Biplob Pramanik, Suvash C. Saha, Nor Aishah Saidina Amin, Ali M. Sefidan, Kalpit Shah, Muhammad Shahbaz, Mirza Imran Shahzad, Atta Sojoudi, Ankit Sonthalia, Shaharin A. Sulaiman, Muhammad Ikhsan Taipabu, Syed Ali Ammar Taqvi, S. Thiyagarajan, Karthickeyan Viswanathan, Karthikeyan Viswanathan, Shuang Wang, Wei Wu, and M.A. Yusuf

Published
2021
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7. Techno-economic evaluation methodology for hydrogen energy systems

Author

Suresh K. Bhargava, Srinivasan Madapusi, Nawshad Haque, Rajarathinam Parthasarathy, and Venkatakrishnan Balasubramanian

Subjects
Hydrogen, Process (engineering), business.industry, chemistry.chemical_element, Sizing, Renewable energy, chemistry, Hydrogen fuel, Environmental science, Process simulation, business, Process engineering, Operating cost, Hydrogen production
Abstract

Australia has an advantage of having an abundant source of solar- and wind-based renewable energy. It can be utilized for renewable hydrogen production via liquid ammonia (NH3) pathway. Countries importing renewable ammonia can decompose it back to pure hydrogen using CSIRO (Commonwealth Scientific and Industrial Research Organization) metal membrane technology. The membrane separates ultrahigh pure hydrogen from ammonia while blocking all other gases. Re-cracked hydrogen can be used for fuel cell vehicles and other energy applications. The assessment of the economic viability of the abovementioned process chain requires a techno-economic evaluation (TEE) that involves process simulation, mass and energy balances, plant sizing, capital and operating cost estimations, and cash-flow and sensitivity analyses. This chapter presents the TEE methodology for a hydrogen energy system and it can be used in assessing engineering, research and development impact, scale-up, and the feasibility of the production system.

Published
2021
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10. Adeno-Associated Virus (AAV) Capsid Stability and Liposome Remodeling During Endo/Lysosomal pH Trafficking

Author

Lins-Austin, Bridget, primary, Patel, Saajan, additional, Mietzsch, Mario, additional, Brooke, Dewey, additional, Bennett, Antonette, additional, Venkatakrishnan, Balasubramanian, additional, Van Vliet, Kim, additional, Smith, Adam N., additional, Long, Joanna R., additional, McKenna, Robert, additional, Potter, Mark, additional, Byrne, Barry, additional, Boye, Sanford L., additional, Bothner, Brian, additional, Heilbronn, Regine, additional, and Agbandje-McKenna, Mavis, additional

Published
2020
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11. Studies on the use of sodium polyacrylate (SPA) for low-salt animal skin preservation

Author

Suresha P. Ranganath, Manohar V. Badiger, Venkatakrishnan Balasubramanian, Vedaraman Nagarajan, Velappan Kandukalpatti Chinnaraj, Brindha Velappan, Sandhya Kurvilla Vijayan, Hepzibah Jabamani, Muralidharan Chellappa, and John Sundar Victor

Subjects
Absorption of water, Magnetic Resonance Spectroscopy, Spectrophotometry, Infrared, Sodium polyacrylate, Health, Toxicology and Mutagenesis, Sodium, Organoleptic, Acrylic Resins, chemistry.chemical_element, Salt (chemistry), 010501 environmental sciences, Sodium Chloride, 01 natural sciences, chemistry.chemical_compound, Water Pollution, Chemical, Environmental Chemistry, Animals, Recycling, Curing (chemistry), 0105 earth and related environmental sciences, Skin, chemistry.chemical_classification, Pollutant, Calorimetry, Differential Scanning, Chemistry, Tanning, General Medicine, Pulp and paper industry, Total dissolved solids, Pollution, Microscopy, Electron, Scanning
Abstract

Salt-based preservation is practiced for decades in the leather industry because of its versatility, cost-effectiveness, and availability. The salt removed from the soaking process causes significant pollution including organic and elevated total dissolved solids (TDS). Hence, a low-salt skin preservation method using commercial sodium polyacrylate with a reduced quantity of sodium chloride aiming to retain leather properties and pollution reduction was the principal focus of the study. Commercial sodium polyacrylate initially characterized for water absorption capacity along with structural and functional properties is confirmed by NMR and IR spectroscopic techniques. In preliminary experiments, the process parameters attained optimized conditions of sodium polyacrylate (SPA) quantity (5%), a minimal amount of salt (15%), and contact time (4 h) required for skin preservation. Besides, reusability studies after SPA recovery (95%) were applied to skins with an optimized quantity of SPA and salt subsequently stored for 15 days along with control (40% salt). The results revealed that SPA with low salt aided an adequate curing efficiency with a substantial reduction (> 65%) of TDS and comparable physical and organoleptic properties on par with the conventional method. Overall, SPA supported low-salt skin preservation reduces pollutant load (TDS) caused due to using of 40% sodium chloride in the conventional curing process.

Published
2019

13. GAC inhibitors with a 4-hydroxypiperidine spacer: Requirements for potency

Author

Lee Apostle Mcdermott, Mackenzie Geedy, David Ryan Koes, Shabber Mohammed, Melissa Boby, Richard A. Cerione, William P. Katt, Venkatakrishnan Balasubramanian, and Prema Iyer

Subjects
Models, Molecular, Clinical Biochemistry, Allosteric regulation, Pharmaceutical Science, Antineoplastic Agents, Breast Neoplasms, 01 natural sciences, Biochemistry, Article, Small Molecule Libraries, Glutaminase, Piperidines, Drug Discovery, Tumor Cells, Cultured, Humans, Potency, Moiety, Enzyme Inhibitors, Molecular Biology, Cell Proliferation, chemistry.chemical_classification, Molecular Structure, 010405 organic chemistry, Chemistry, Organic Chemistry, Combinatorial chemistry, 0104 chemical sciences, 010404 medicinal & biomolecular chemistry, Enzyme, Molecular Medicine, Female
Abstract

Allosteric inhibitors of glutaminase (GAC), such as BPTES, CB-839 and UPGL00019, have great promise as inhibitors of cancer cell growth, but potent inhibitors with drug-like qualities have been difficult to achieve. Here, a small library of GAC inhibitors based on the UPGL00019 core is described. This set of derivatives was designed to assess if one or both of the phenylacetyl groups flanking the UPGL00019 core can be replaced by smaller simple aliphatic acyl groups without loss in potency. We found that one of the phenylacetyl moieties can be replaced by a set of small aliphatic moieties without loss in potency. We also found that enzymatic potency co-varies with the VDW volume or the maximum projection area of the groups used as replacements of the phenylacetyl moiety and used literature X-ray data to provide an explanation for this finding.

Published
2019
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17. Apo-human carbonic anhydrase II revisited: implications of the loss of a metal in protein structure, stability, and solvent network

Author

Avvaru, Balendu Sankara, Busby, Scott A., Chalmers, Michael J., Griffin, Patrick R., Venkatakrishnan, Balasubramanian, Agbandje-McKenna, Mavis, Silverman, David N., and McKenna, Robert

Subjects
Bicarbonates -- Chemical properties, Enzymes -- Chemical properties, Hydration (Chemistry) -- Analysis, Solvation -- Analysis, Zinc -- Chemical properties, Proteins -- Structure, Proteins -- Analysis, Biological sciences, Chemistry
Abstract

The important role of zinc towards the structural stability of human carbonic anhydrase II (HCA II) which is a monomeric zinc-containing metalloenzyme that catalyzes the hydration of C[O.sub.2] to form bicarbonate and a proton is reported. The results suggested that removal of zinc from the active site have no effect on either the topological fold of the enzyme or the ordered water network in the active site but altered the collective electrostatics of the apo-HCA II.

Published
2009

24. From Research Management System to Digital Repository: Managing and storing research outputs at the University of Sydney

Author

Browne, Gary, Appia, Venkatakrishnan Balasubramanian, and Christensen, Sten

Subjects
Digital Repository, Interface, DSpace, Research Information Management System
Abstract

This poster demonstrates a system for transferring data and objects from the University of Sydney Research Office research management system (RMS) to a Library supported digital repository (DSpace).

Published
2008

26. Comparative Analysis of Adeno-Associated Virus Capsid Stability and Dynamics

Author

Rayaprolu, Vamseedhar, primary, Kruse, Shannon, additional, Kant, Ravi, additional, Venkatakrishnan, Balasubramanian, additional, Movahed, Navid, additional, Brooke, Dewey, additional, Lins, Bridget, additional, Bennett, Antonette, additional, Potter, Timothy, additional, McKenna, Robert, additional, Agbandje-McKenna, Mavis, additional, and Bothner, Brian, additional

Published
2013
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27. Structure and Dynamics of Adeno-Associated Virus Serotype 1 VP1-Unique N-Terminal Domain and Its Role in Capsid Trafficking

Author

Venkatakrishnan, Balasubramanian, primary, Yarbrough, Joseph, additional, Domsic, John, additional, Bennett, Antonette, additional, Bothner, Brian, additional, Kozyreva, Olga G., additional, Samulski, R. Jude, additional, Muzyczka, Nicholas, additional, McKenna, Robert, additional, and Agbandje-McKenna, Mavis, additional

Published
2013
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31. Insights into Mycoplasma genitalium metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein

Author

Sippel, Katherine H., primary, Venkatakrishnan, Balasubramanian, additional, Boehlein, Susan K., additional, Sankaran, Banumathi, additional, Quirit, Jeanne G., additional, Govindasamy, Lakshamanan, additional, Agbandje-McKenna, Mavis, additional, Goodison, Steve, additional, Rosser, Charles J., additional, and McKenna, Robert, additional

Published
2010
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32. Adaptation of Web Pages for Hand-Held Devices.

Author

Lowe, David, Gaedke, Martin, Venkatakrishnan, Balasubramanian Appiah, and Murugesan, San

Abstract

Web browsing using hand-held devices is becoming more common. But the relatively small display area of hand-held devices, compared to desktop computers, requires that Web pages designed for desktops are adapted to suit hand-held devices for convenient browsing. Web page adaptation techniques for hand-held devices takes into account device's screen size, limited bandwidth and input capabilities. Although several techniques have been proposed to adapt Web pages for smaller screen, each of them is better suited for specific scenarios and requirements. Hence a better understanding of the features and limitations of these techniques are required for successful development of Web pages for mobile devices. This paper presents a concise overview and comparative evaluation of the state-of-the-art of the techniques for adapting Web pages for hand-held devices. [ABSTRACT FROM AUTHOR]

Published
2005
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34. Insights into Mycoplasma genitalium metabolism revealed by the structure of MG289, an extracytoplasmic thiamine binding lipoprotein.

Author

Sippel, Katherine H., Venkatakrishnan, Balasubramanian, Boehlein, Susan K., Sankaran, Banumathi, Quirit, Jeanne G., Govindasamy, Lakshamanan, Agbandje-McKenna, Mavis, Goodison, Steve, Rosser, Charles J., and McKenna, Robert

Abstract

Mycoplasma genitalium is one of the smallest organisms capable of self-replication and its sequence is considered a starting point for understanding the minimal genome required for life. MG289, a putative phosphonate substrate binding protein, is considered to be one of these essential genes. The crystal structure of MG289 has been solved at 1.95 Å resolution. The structurally identified thiamine binding region reveals possible mechanisms for ligand promiscuity. MG289 was determined to be an extracytoplasmic thiamine binding lipoprotein. Computational analysis, size exclusion chromatography, and small angle X-ray scattering indicates that MG289 homodimerizes in a concentration-dependant manner. Comparisons to the thiamine pyrophosphate binding homolog Cypl reveal insights into the metabolic differences between mycoplasmal species including identifying possible kinases for cofactor phosphorylation and describing the mechanism of thiamine transport into the cell. These results provide a baseline to build our understanding of the minimal metabolic requirements of a living organism. Proteins 2011. © 2010 Wiley-Liss, Inc. [ABSTRACT FROM AUTHOR]

Published
2011
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35. Structural differences between the Woodchuck hepatitis virus core protein in dimer and capsid states are consistent with entropic and conformational regulation of assembly.

Author

Zhongchao Zhao, Che-Yen Wang, Joseph, Gonzalez-Gutierrez, Giovanni, Venkatakrishnan, Balasubramanian, Khaykelson, Daniel, Raviv, Uri, and Zlotnick, Adam

Subjects
*HEPATITIS viruses, *VIRAL proteins, *HEPATITIS B virus, *DNA viruses, *PROTEIN-protein interactions
Abstract

Hepadnaviruses are hepatotropic enveloped DNA viruses with an icosahedral capsid. Hepatitis B virus (HBV) causes chronic infection in an estimated 240 million people; Woodchuck Hepatitis virus (WHV), an HBV homologue, has been an important model system for drug development. The dimeric capsid protein (Cp) plays multiple functions during the viral life cycle and thus has become an important target for a new generation of antivirals. Purified HBV and WHV Cp spontaneously assemble into 120-dimer capsids. Though they have 65% identity, WHV Cp has error-prone assembly with stronger protein-protein association. We have taken advantage of the differences in assembly to investigate the basis of assembly regulation. We determined the structures of the WHV capsid to 4.5 Å resolution by cryo-EM and the WHV Cp dimer to 2.9 Å resolution by crystallography and examined the biophysical properties of the dimer. We found, in dimer, the subdomain that makes protein-protein interactions is partially disordered and rotated 21° from its position in capsid. This subdomain is susceptible to proteolysis, consistent with local disorder. WHV assembly shows similar susceptibility to HBV antiviral molecules, suggesting that HBV assembly follows similar transitions. These data show there is an entropic cost for assembly that is compensated for by the energetic gain of burying hydrophobic interprotein contacts. We propose a series of stages in assembly that incorporate disorder-to order transition and structural shifts. We suggest that a cascade of structural changes may be a common mechanism for regulating high fidelity capsid assembly in HBV and other viruses. [ABSTRACT FROM AUTHOR]

Published
2019
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