Open Access. Powered by Scholars. Published by Universities.®
- Keyword
-
- NMR (5)
- NMR screening (2)
- ACP (1)
- ACPS (1)
- Archaeglobus fulgidis (1)
-
- AutoStructure (1)
- Automated NMR structure determination (1)
- CPASS (1)
- Constraint network analysis (1)
- DJ-1 (1)
- Dynamics (1)
- Fatty acids biosynthesis (1)
- Fold topology constraints (1)
- Functional annotation (1)
- Genetics (1)
- Graph theory (1)
- High-throughput NMR (1)
- Hypothetical proteins (1)
- Ligand-defined active sites (1)
- Mass spectrometry (1)
- Molecular mechanisms (1)
- Optimal mixture size (1)
- Parkinson disease (1)
- Parkinson’s Disease (1)
- Protein AF2095 (1)
- Protein structures (1)
- RPF (1)
- Resonance assignments (1)
- Screening NMR mixtures (1)
- Secondary structure (1)
Articles 1 - 14 of 14
Full-Text Articles in Entire DC Network
Multiplatform Untargeted Metabolomics, Micah J. Jeppesen, Robert Powers
Multiplatform Untargeted Metabolomics, Micah J. Jeppesen, Robert Powers
Robert Powers Publications
Metabolomics samples like human urine or serum contain upwards of a few thousand metabolites, but individual analytical techniques can only characterize a few hundred metabolites at best. The uncertainty in metabolite identification commonly encountered in untargeted metabolomics adds to this low coverage problem. A multiplatform (multiple analytical techniques) approach can improve upon the number of metabolites reliably detected and correctly assigned. This can be further improved by applying synergistic sample preparation along with the use of combinatorial or sequential non-destructive and destructive techniques. Similarly, peak detection and metabolite identification strategies that employ multiple probabilistic approaches have led to better annotation …
The Reversible Low-Temperature Instability Of Human Dj-1 Oxidative States, Tessa Andrews, Javier Seravallic, Robert Powers
The Reversible Low-Temperature Instability Of Human Dj-1 Oxidative States, Tessa Andrews, Javier Seravallic, Robert Powers
Robert Powers Publications
DJ-1 is a homodimeric protein that is centrally involved in various human diseases including Parkinson disease (PD). DJ-1 protects against oxidative damage and mitochondrial dysfunction through a homeostatic control of reactive oxygen species (ROS). DJ-1 pathology results from a loss of function, where ROS readily oxidizes a highly conserved and functionally essential cysteine (C106). The over-oxidation of DJ-1 C106 leads to a dynamically destabilized and biologically inactivated protein. An analysis of the structural stability of DJ-1 as a function of oxidative state and temperature may provide further insights into the role the protein plays in PD progression. NMR spectroscopy, circular …
Histidine Enhances The Anticancer Effect Of Gemcitabine Against Pancreatic Cancer Via Disruption Of Amino Acid Homeostasis And Oxidant—Antioxidant Balance, Narendra Kumar, Satyanarayana Rachagani, Gopalakrishnan Natarajan, Alexandra Crook, Thiyagarajan Gopal, Vinothkumar Rajamanickam, Jyoti B. Kaushal, Sirpu N. Nagabhishek, Robert Powers, Surinder K. Batra, Viswanathan Saraswathi
Histidine Enhances The Anticancer Effect Of Gemcitabine Against Pancreatic Cancer Via Disruption Of Amino Acid Homeostasis And Oxidant—Antioxidant Balance, Narendra Kumar, Satyanarayana Rachagani, Gopalakrishnan Natarajan, Alexandra Crook, Thiyagarajan Gopal, Vinothkumar Rajamanickam, Jyoti B. Kaushal, Sirpu N. Nagabhishek, Robert Powers, Surinder K. Batra, Viswanathan Saraswathi
Robert Powers Publications
Simple Summary: Amino acid metabolism is aberrantly altered in pancreatic cancer (PC). Evidence suggests that circulating histidine (His) levels are low in PC. However, the role of His in modulating the progression of PC remains unknown. We determined the role of His in altering the therapeutic effectiveness of gemcitabine (Gem) against PC. We provide evidence that the expression of histidine ammonia lyase (HAL), an enzyme involved in His catabolism, is greatly increased in mouse and human pancreatic tumors. We show that combining His with Gem led to enhanced cytotoxic effects against aggressive PC cell lines. Our metabolomics analysis revealed that …
Review: New Frontiers In Metabolomics: From Measurement To Insight, Eli Riekeberg, Robert Powers
Review: New Frontiers In Metabolomics: From Measurement To Insight, Eli Riekeberg, Robert Powers
Robert Powers Publications
Metabolomics is the newest addition to the “omics” disciplines and has shown rapid growth in its application to human health research because of fundamental advancements in measurement and analysis techniques. Metabolomics has unique and proven advantages in systems biology and biomarker discovery. The next generation of analysis techniques promises even richer and more complete analysis capabilities that will enable earlier clinical diagnosis, drug refinement, and personalized medicine. A review of current advancements in methodologies and statistical analysis that are enhancing and improving the performance of metabolomics is presented along with highlights of some recent successful applications.
Metabolic Investigations Of The Molecular Mechanisms Associated With Parkinson’S Disease, Robert Powers, Shulei Lei, Annadurai Anandhan, Darrell D. Marshall, Bradley Worley, Ronald Cerny, Eric D. Dodds, Yuting Huang, Mihalis I. Panayiotidis, Aglaia Pappa, Rodrigo Franco
Metabolic Investigations Of The Molecular Mechanisms Associated With Parkinson’S Disease, Robert Powers, Shulei Lei, Annadurai Anandhan, Darrell D. Marshall, Bradley Worley, Ronald Cerny, Eric D. Dodds, Yuting Huang, Mihalis I. Panayiotidis, Aglaia Pappa, Rodrigo Franco
Robert Powers Publications
Parkinson’s disease (PD) is a neurodegenerative disorder characterized by fibrillar cytoplasmic aggregates of α-synuclein (i.e., Lewy bodies) and the associated loss of dopaminergic cells in the substantia nigra. Mutations in genes such as α -synuclein (SNCA) account for only 10% of PD occurrences. Exposure to environmental toxicants including pesticides and metals (e.g., paraquat (PQ) and manganese (Mn)) is also recognized as an important PD risk factor. Thus, aging, genetic alterations, and environmental factors all contribute to the etiology of PD. In fact, both genetic and environmental factors are thought to interact in the promotion of idiopathic PD, but the mechanisms …
Mvapack: A Complete Data Handling Package For Nmr Metabolomics, Bradley Worley, Robert Powers
Mvapack: A Complete Data Handling Package For Nmr Metabolomics, Bradley Worley, Robert Powers
Robert Powers Publications
Data handling in the field of NMR metabolomics has historically been reliant on either in-house mathematical routines or long chains of expensive commercial software. Thus, while the relatively simple biochemical protocols of metabolomics maintain a low barrier to entry, new practitioners of metabolomics experiments are forced to either purchase expensive software packages or craft their own data handling solutions from scratch. This inevitably complicates the standardization and communication of data handling protocols in the field. We report a newly developed open-source platform for complete NMR metabolomics data handling, MVAPACK, and describe its application on an example metabolic fingerprinting data set.
Searching The Protein Structure Database For Ligand-Binding Site Similarities Using Cpass V.2, Robert Powers, Jennifer C. Copeland, Jaime L. Stark, Adam Caprez, Ashu Guru, David R. Swanson
Searching The Protein Structure Database For Ligand-Binding Site Similarities Using Cpass V.2, Robert Powers, Jennifer C. Copeland, Jaime L. Stark, Adam Caprez, Ashu Guru, David R. Swanson
Robert Powers Publications
Background: A recent analysis of protein sequences deposited in the NCBI RefSeq database indicates that ~8.5 million protein sequences are encoded in prokaryotic and eukaryotic genomes, where ~30% are explicitly annotated as “hypothetical” or “uncharacterized” protein. Our Comparison of Protein Active-Site Structures (CPASS v.2) database and software compares the sequence and structural characteristics of experimentally determined ligand binding sites to infer a functional relationship in the absence of global sequence or structure similarity. CPASS is an important component of our Functional Annotation Screening Technology by NMR (FAST-NMR) protocol and has been successfully applied to aid the annotation of a number …
List Of Publications: Robert Powers
List Of Publications: Robert Powers
Robert Powers Publications
Chronological list of 57 published articles and chapters in chemistry. Current through August 2006.
Comparison Of Protein Active Site Structures For Functional Annotation Of Proteins And Drug Design, Robert Powers, Jennifer C. Copeland, Katherine Germer, Kelly A. Mercier, Viswanathan Ramanathan, Peter Revesz
Comparison Of Protein Active Site Structures For Functional Annotation Of Proteins And Drug Design, Robert Powers, Jennifer C. Copeland, Katherine Germer, Kelly A. Mercier, Viswanathan Ramanathan, Peter Revesz
Robert Powers Publications
Rapid and accurate functional assignment of novel proteins is increasing in importance, given the completion of numerous genome sequencing projects and the vastly expanding list of unannotated proteins. Traditionally, global primary-sequence and structure comparisons have been used to determine putative function. These approaches, however, do not emphasize similarities in active site configurations that are fundamental to a protein’s activity and highly conserved relative to the global and more variable structural features. The Comparison of Protein Active Site Structures (CPASS) database and software enable the comparison of experimentally identified ligand-binding sites to infer biological function and aid in drug discovery. The …
A Topology-Constrained Distance Network Algorithm For Protein Structure Determination From Noesy Data, Yuanpeng Janet Huang, Roberto Tejero, Robert Powers, Gaetano T. Montelione
A Topology-Constrained Distance Network Algorithm For Protein Structure Determination From Noesy Data, Yuanpeng Janet Huang, Roberto Tejero, Robert Powers, Gaetano T. Montelione
Robert Powers Publications
This article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-constrained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology- constrained distance network analysis algorithm and iteratively generates structures using the three-dimensional (3D) protein structure calculation programs XPLOR/CNS or DYANA. The minimum input for AutoStructure includes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D-NOESY cross peaks. AutoStructure can also analyze homodimeric proteins when X-filtered NOESY experiments are available. The quality …
Determining The Optimal Size Of Small Molecule Mixtures For High Throughput Nmr Screening, Kelly A. Mercier, Robert Powers
Determining The Optimal Size Of Small Molecule Mixtures For High Throughput Nmr Screening, Kelly A. Mercier, Robert Powers
Robert Powers Publications
High-throughput screening (HTS) using NMR spectroscopy has become a common component of the drug discovery effort and is widely used throughout the pharmaceutical industry. NMR provides additional information about the nature of small molecule-protein interactions compared to traditional HTS methods. In order to achieve comparable efficiency, small molecules are often screened as mixtures in NMR-based assays. Nevertheless, an analysis of the efficiency of mixtures and a corresponding determination of the optimum mixture size (OMS) that minimizes the amount of material and instrumentation time required for an NMR screen has been lacking. A model for calculating OMS based on the application …
1H, 13C, And 15N Assignments For The Archaeglobus Fulgidis Protein Af2095, Robert Powers, Thomas B. Acton, Yi-Wen Chiang, P. K. Rajan, John R. Cort, Michael A. Kennedy, Jinfeng Liu, Lichung Ma, Burkhard Rost, Gaetano T. Montelione
1H, 13C, And 15N Assignments For The Archaeglobus Fulgidis Protein Af2095, Robert Powers, Thomas B. Acton, Yi-Wen Chiang, P. K. Rajan, John R. Cort, Michael A. Kennedy, Jinfeng Liu, Lichung Ma, Burkhard Rost, Gaetano T. Montelione
Robert Powers Publications
Structural genomics is providing a means to determine the molecular and cellular function for the vast amount of proteins in the Human proteome that lack any explicit experimental information by characterizing the complete range of protein folds (Montelione, 2001). The Northeast Structural Genomics Consortium (NESG; http://www.nesg.org/) is a pilot project funded by the National Institutes of Health Protein Structure Initiative, focusing on proteins from eukaryotic model organisms including humans. The thermophillic archaea Archaeglobus fulgidis AF2095 protein is an example of a protein of unknown biological function targeted for structural analysis by NESG. AF2095 belongs to the Pfam family PF01981 – …
Applications Of Nmr To Structure-Based Drug Design In Structural Genomics, Robert Powers
Applications Of Nmr To Structure-Based Drug Design In Structural Genomics, Robert Powers
Robert Powers Publications
Structural genomics is poised to have a tremendous impact on traditional structure-based drug design programs. As a result, there is a growing need to obtain rapid structural information in a reliable form that is amenable to rational drug design. In this manner, NMR has been expanding and evolving its role in aiding the design process. A variety of NMR methodologies that cover a range of inherent resolution are described in the context of structure-based drug design in the era of structural genomics.
Solution Structure Of B. Subtilis Acyl Carrier Protein, Guang-Yi Xu, Amy Tam, Laura Lin, Jeffrey Hixon, Christian C. Fritz, Robert Powers
Solution Structure Of B. Subtilis Acyl Carrier Protein, Guang-Yi Xu, Amy Tam, Laura Lin, Jeffrey Hixon, Christian C. Fritz, Robert Powers
Robert Powers Publications
Background: Acyl carrier protein (ACP) is a fundamental component of fatty acid biosynthesis in which the fatty acid chain is elongated by the fatty acid synthetase system while attached to the 4’-phosphopantetheine prosthetic group (4’- PP) of ACP. Activation of ACP is mediated by holo-acyl carrier protein synthase (ACPS) when ACPS transfers the 4’-PP moiety from coenzyme A (CoA) to Ser36 of apo-ACP. Both ACP and ACPS have been identified as essential for E. coli viability and potential targets for development of antibiotics. Results: The solution structure of B. subtilis ACP (9 kDa) has been determined using two-dimensional and three-dimensional …