Yuanpeng Janet Huang, Roberto Tejero, Robert Powers, Gaetano T. Montelione
ABSTRACT This article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-constrained...
Yuanpeng Janet Huang, Roberto Tejero, Robert Powers, Gaetano T. Montelione
ABSTRACT This article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-constrained...
Wu, Bin, Yee, Adelinda, Huang, Yuanpeng J., Ramelot, Theresa A., Cort, John R., Semesi, Anthony, ...
The ribosomal protein S17E from the archaeon Methanobacterium thermoautotrophicum is a component of the 30S ribosomal subunit. S17E is a 62-residue protein conserved in archaea and eukaryotes and has...
Comparing Classical Pathways and Modern Networks: Towards the Development of an Edge Ontology (2007)
Lu, Long J., Sboner, Andrea, Huang, Yuanpeng J., Lu, Hao Xin, Gianoulis, Tara A., Yip, Kevin Y., ...
Pathways are integral to systems biology. Their classical representation has proven useful but is inconsistent in the meaning assigned to each arrow (or edge) and inadvertently implies the isolation...
Crystal structure of AGR_C_4470p from Agrobacterium tumefaciens (2007)
Vorobiev, Sergey M., Neely, Helen, Seetharaman, Jayaraman, Ma, Li-Chung, Xiao, Rong, Acton, Thomas B., ...
We report here the crystal structure at 2.0 Å resolution of the AGR_C_4470p protein from the Gram-negative bacterium Agrobacterium tumefaciens. The protein is a tightly associated dimer, each...
Huang, Yuanpeng Janet, Tejero, Roberto, Powers, Robert, Montelione, Gaetano T
This article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-constrained distance...
PubNet: a flexible system for visualizing literature derived networks (2005)
Douglas, Shawn M, Montelione, Gaetano T, Gerstein, Mark
Abstract We have developed PubNet, a web-based tool that extracts several types of relationships returned by PubMed queries and maps them into networks, allowing for graphical visualization, textual...
Powers, Robert, Mirkovic, Nebojsa, Goldsmith-Fischman, Sharon, Acton, Thomas B., Chiang, Yi-wen, Huang, Yuanpeng J., ...
The solution structure of protein AF2095 from the thermophilic archaea Archaeglobus fulgidis, a 123- residue (13.6-kDa) protein, has been determined by NMR methods. The structure of AF2095 is...
Powers, Robert, Mirkovic, Nebojsa, Goldsmith-Fischman, Sharon, Acton, Thomas B., Chiang, Yiwen, Huang, Yuanpeng J., ...
The solution structure of protein AF2095 from the thermophilic archaea Archaeglobus fulgidis, a 123-residue (13.6-kDa) protein, has been determined by NMR methods. The structure of AF2095 is...
Liu, Gaohua, Li, Zhaohui, Chiang, Yiwen, Acton, Thomas, Montelione, Gaetano T., Murray, Diana, ...
The structural biology of proteins mediating iron-sulfur (Fe-S) cluster assembly is central for understanding several important biological processes. Here we present the NMR structure of the 16-kDa...
PubNet: a flexible system for visualizing literature derived networks (2005)
Shawn M Douglas, Gaetano T Montelione, Mark Gerstein
Software
1H, 13C, and 15N assignments for the Archaeglobus fulgidis protein AF2095 (2004)
Powers, Robert, Acton, Thomas B., Chiang, Yi-wen, Rajan, P. K., Cort, John R., Kennedy, Michael A., ...
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...
Zheng, Deyou, Aramini, James M., Montelione, Gaetano T.
Staphylococcal protein A (SpA) is a virulence factor from Staphylococcus aureus that is able to bind to immunoglobulins. The 3D structures of its immunoglobulin (Ig) binding domains have been...
Herve Du Penhoat, Catherine, Atreya, Hanudatta S., Shen, Yang, Liu, Gaohua, Acton, Thomas B., Xiao, Rong, ...
The Archaeoglobus fulgidis gene RS27_ARCFU encodes the 30S ribosomal protein S27e. Here, we present the high-quality NMR solution structure of this archaeal protein, which comprises a C4 zinc finger...
ZHENG, DEYOU, ARAMINI, JAMES M., MONTELIONE, GAETANO T.
Staphylococcal protein A (SpA) is a virulence factor from Staphylococcus aureus that is able to bind to immunoglobulins. The 3D structures of its immunoglobulin (Ig) binding domains have been...
Chern-sing Goh, Ning Lan, Nathaniel Echols, Shawn M. Douglas, Duncan Milburn, Paul Bertone, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at
Access the most recent version at doi: 10.1110/ps.0300203 References (2003)
Deyou Zheng, Yuanpeng J. Huang, Rong Xiao, James Aramini, ...
Automated protein fold determination using a minimal NMR
Automated protein fold determination using a minimal NMR constraint strategy (2003)
Zheng, Deyou, Huang, Yuanpeng J., Moseley, Hunter N.B., Xiao, Rong, Aramini, James, Swapna, G.V.T., ...
Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold...
Goh, Chern-Sing, Lan, Ning, Echols, Nathaniel, Douglas, Shawn M., Milburn, Duncan, Bertone, Paul, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium,...
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii (2003)
Aramini, James M., Huang, Yuanpeng J., Cort, John R., Goldsmith-Fischman, Sharon, Xiao, Rong, Shih, Liang-Yu, ...
We report NMR assignments and solution structure of the 71-residue 30S ribosomal protein S28E from the archaean Pyrococcus horikoshii, target JR19 of the Northeast Structural Genomics Consortium. The...
Bertone, Paul, Kluger, Yuval, Lan, Ning, Zheng, Deyou, Christendat, Dinesh, Yee, Adelinda, ...
High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information...
Campion, Stephen R., Biamonti, Clelia, Montelione, Gaetano T., Niyogi, Salil K.
The highly conserved asparagine residue at position 32 (Asn32) in the 'hinge' region of epidermal growth factor (EGF) separates the N- and C-terminal structural motifs of the EGF molecule and is...
Montelione, Gaetano T., Wagner, Gerhard
Peer Reviewed
Montelione, Gaetano T., Winkler, Marjorie E., Rauenbuehler, Peter, Wagner, Gerhard
Peer Reviewed
Bertone, Paul, Kluger, Yuval, Lan, Ning, Zheng, Deyou, Christendat, Dinesh, Yee, Adelinda, ...
High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information...
Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment
Szyperski, Thomas, Yeh, Deok C., Sukumaran, Dinesh K., Moseley, Hunter N. B., Montelione, Gaetano T.
A suite of reduced-dimensionality 13C,15N,1H-triple-resonance NMR experiments is presented for rapid and complete protein resonance assignment. Even when using short measurement times, these...
SPINE 2: a system for collaborative structural proteomics within a federated database framework
Goh, Chern-Sing, Lan, Ning, Echols, Nathaniel, Douglas, Shawn M., Milburn, Duncan, Bertone, Paul, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium,...
Das, Kalyan, Acton, Thomas, Chiang, Yiwen, Shih, Lydia, Arnold, Eddy, Montelione, Gaetano T.
The RlmA class of enzymes (RlmAI and RlmAII) catalyzes N1-methylation of a guanine base (G745 in Gram-negative and G748 in Gram-positive bacteria) of hairpin 35 of 23S rRNA. We have determined the...
Forouhar, Farhad, Yang, Yue, Kumar, Dhirendra, Chen, Yang, Fridman, Eyal, Park, Sang Wook, ...
Salicylic acid (SA) is a critical signal for the activation of plant defense responses against pathogen infections. We recently identified SA-binding protein 2 (SABP2) from tobacco as a protein that...
NMR data collection and analysis protocol for high-throughput protein structure determination
Liu, Gaohua, Shen, Yang, Atreya, Hanudatta S., Parish, David, Shao, Ying, Sukumaran, Dinesh K., ...
A standardized protocol enabling rapid NMR data collection for high-quality protein structure determination is presented that allows one to capitalize on high spectrometer sensitivity: a set of five...
PubNet: a flexible system for visualizing literature derived networks
Douglas, Shawn M, Montelione, Gaetano T, Gerstein, Mark
PubNet is a web-based tool to extract several types of relationships returned by PubMed queries and map them into networks.
Bertone, Paul, Kluger, Yuval, Lan, Ning, Zheng, Deyou, Christendat, Dinesh, Yee, Adelinda, ...
High-throughput structural proteomics is expected to generate considerable amounts of data on the progress of structure determination for many proteins. For each protein this includes information...
Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment
Szyperski, Thomas, Yeh, Deok C., Sukumaran, Dinesh K., Moseley, Hunter N. B., Montelione, Gaetano T.
A suite of reduced-dimensionality 13C,15N,1H-triple-resonance NMR experiments is presented for rapid and complete protein resonance assignment. Even when using short measurement times, these...
SPINE 2: a system for collaborative structural proteomics within a federated database framework
Goh, Chern-Sing, Lan, Ning, Echols, Nathaniel, Douglas, Shawn M., Milburn, Duncan, Bertone, Paul, ...
We present version 2 of the SPINE system for structural proteomics. SPINE is available over the web at http://nesg.org. It serves as the central hub for the Northeast Structural Genomics Consortium,...
Das, Kalyan, Acton, Thomas, Chiang, Yiwen, Shih, Lydia, Arnold, Eddy, Montelione, Gaetano T.
The RlmA class of enzymes (RlmAI and RlmAII) catalyzes N1-methylation of a guanine base (G745 in Gram-negative and G748 in Gram-positive bacteria) of hairpin 35 of 23S rRNA. We have determined the...
Forouhar, Farhad, Yang, Yue, Kumar, Dhirendra, Chen, Yang, Fridman, Eyal, Park, Sang Wook, ...
Salicylic acid (SA) is a critical signal for the activation of plant defense responses against pathogen infections. We recently identified SA-binding protein 2 (SABP2) from tobacco as a protein that...
NMR data collection and analysis protocol for high-throughput protein structure determination
Liu, Gaohua, Shen, Yang, Atreya, Hanudatta S., Parish, David, Shao, Ying, Sukumaran, Dinesh K., ...
A standardized protocol enabling rapid NMR data collection for high-quality protein structure determination is presented that allows one to capitalize on high spectrometer sensitivity: a set of five...
PubNet: a flexible system for visualizing literature derived networks
Douglas, Shawn M, Montelione, Gaetano T, Gerstein, Mark
PubNet is a web-based tool to extract several types of relationships returned by PubMed queries and map them into networks.
Molecular insights into substrate recognition and catalysis by tryptophan 2,3-dioxygenase
Forouhar, Farhad, Anderson, J. L. Ross, Mowat, Christopher G., Vorobiev, Sergey M., Hussain, Arif, Abashidze, Mariam, ...
Tryptophan 2,3-dioxygenase (TDO) and indoleamine 2,3-dioxygenase (IDO) constitute an important, yet relatively poorly understood, family of heme-containing enzymes. Here, we report extensive...
Crystal structure of AGR_C_4470p from Agrobacterium tumefaciens
Vorobiev, Sergey M., Neely, Helen, Seetharaman, Jayaraman, Ma, Li-Chung, Xiao, Rong, Acton, Thomas B., ...
We report here the crystal structure at 2.0 Å resolution of the AGR_C_4470p protein from the Gram-negative bacterium Agrobacterium tumefaciens. The protein is a tightly associated dimer, each...
Powers, Robert, Mirkovic, Nebojsa, Goldsmith-Fischman, Sharon, Acton, Thomas B., Chiang, Yiwen, Huang, Yuanpeng J., ...
The solution structure of protein AF2095 from the thermophilic archaea Archaeglobus fulgidis, a 123-residue (13.6-kDa) protein, has been determined by NMR methods. The structure of AF2095 is...
Liu, Gaohua, Li, Zhaohui, Chiang, Yiwen, Acton, Thomas, Montelione, Gaetano T., Murray, Diana, ...
The structural biology of proteins mediating iron-sulfur (Fe-S) cluster assembly is central for understanding several important biological processes. Here we present the NMR structure of the 16-kDa...
Zheng, Deyou, Aramini, James M., Montelione, Gaetano T.
Staphylococcal protein A (SpA) is a virulence factor from Staphylococcus aureus that is able to bind to immunoglobulins. The 3D structures of its immunoglobulin (Ig) binding domains have been...
Herve Du Penhoat, Catherine, Atreya, Hanudatta S., Shen, Yang, Liu, Gaohua, Acton, Thomas B., Xiao, Rong, ...
The Archaeoglobus fulgidis gene RS27_ARCFU encodes the 30S ribosomal protein S27e. Here, we present the high-quality NMR solution structure of this archaeal protein, which comprises a C4 zinc finger...
Automated protein fold determination using a minimal NMR constraint strategy
Zheng, Deyou, Huang, Yuanpeng J., Moseley, Hunter N.B., Xiao, Rong, Aramini, James, Swapna, G.V.T., ...
Determination of precise and accurate protein structures by NMR generally requires weeks or even months to acquire and interpret all the necessary NMR data. However, even medium-accuracy fold...
Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii
Aramini, James M., Huang, Yuanpeng J., Cort, John R., Goldsmith-Fischman, Sharon, Xiao, Rong, Shih, Liang-Yu, ...
We report NMR assignments and solution structure of the 71-residue 30S ribosomal protein S28E from the archaean Pyrococcus horikoshii, target JR19 of the Northeast Structural Genomics Consortium. The...
Consistent blind protein structure generation from NMR chemical shift data
Shen, Yang, Lange, Oliver, Delaglio, Frank, Rossi, Paolo, Aramini, James M., Liu, Gaohua, ...
Protein NMR chemical shifts are highly sensitive to local structure. A robust protocol is described that exploits this relation for de novo protein structure generation, using as input experimental...
Wu, Bin, Yee, Adelinda, Huang, Yuanpeng J., Ramelot, Theresa A., Cort, John R., Semesi, Anthony, ...
The ribosomal protein S17E from the archaeon Methanobacterium thermoautotrophicum is a component of the 30S ribosomal subunit. S17E is a 62-residue protein conserved in archaea and eukaryotes and has...
Structural basis for suppression of a host antiviral response by influenza A virus
Das, Kalyan, Ma, Li-Chung, Xiao, Rong, Radvansky, Brian, Aramini, James, Zhao, Li, ...
Influenza A viruses are responsible for seasonal epidemics and high mortality pandemics. A major function of the viral NS1A protein, a virulence factor, is the inhibition of the production of IFN-β...
Vila, Jorge A., Aramini, James M., Rossi, Paolo, Kuzin, Alexandre, Su, Min, Seetharaman, Jayaraman, ...
A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those...
Molecular Insights into the Biosynthesis of the F420 Coenzyme*
Forouhar, Farhad, Abashidze, Mariam, Xu, Huimin, Grochowski, Laura L., Seetharaman, Jayaraman, Hussain, Munif, ...
Coenzyme F420, a hydride carrier, is found in Archaea and some bacteria and has crucial roles in methanogenesis, antibiotic biosynthesis, DNA repair, and activation of antitubercular compounds. CofD,...
Unique opportunities for NMR methods in structural genomics
Montelione, Gaetano T., Arrowsmith, Cheryl, Girvin, Mark E., Kennedy, Michael A., Markley, John L., Powers, Robert, ...
This Perspective, arising from a workshop held in July 2008 in Buffalo NY, provides an overview of the role NMR has played in the United States Protein Structure Initiative (PSI), and a vision of how...
Structural genomics is the largest contributor of novel structural leverage
Nair, Rajesh, Liu, Jinfeng, Soong, Ta-Tsen, Acton, Thomas B., Everett, John K., Kouranov, Andrei, ...
The Protein Structural Initiative (PSI) at the US National Institutes of Health (NIH) is funding four large-scale centers for structural genomics (SG). These centers systematically target many large...
Targeting the Human Cancer Pathway Protein Interaction Network by Structural Genomics*
Huang, Yuanpeng Janet, Hang, Dehua, Lu, Long Jason, Tong, Liang, Gerstein, Mark B., Montelione, Gaetano T.
Structural genomics provides an important approach for characterizing and understanding systems biology. As a step toward better integrating protein three-dimensional (3D) structural information in...