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D'Angelo CR, Hanel W, Chen Y, Yu M, Yang D, Guo L, Karmali R, Burkart M, Ciccosanti C, David K, Risch Z, Murga-Zamalloa C, Devata S, Wilcox R, Savani M, Courville EL, Bachanova V, Rabinovich E, Peace D, Osman F, Epperla N, Kenkre VP. Impact of initial chemotherapy regimen on outcomes for patients with double-expressor lymphoma: A multi-center analysis. Hematol Oncol 2021; 39:473-482. [PMID: 34347909 DOI: 10.1002/hon.2902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/15/2021] [Accepted: 07/19/2021] [Indexed: 11/12/2022]
Abstract
Diffuse large B-cell lymphoma featuring overexpression of MYC and B-Cell Lymphoma 2 (double expressor lymphoma, DEL) is associated with poor outcomes. Existing evidence suggesting improved outcomes for DEL with the use of more intensive regimens than R-CHOP is restricted to younger patients and based on limited evidence from low patient numbers. We retrospectively evaluated the impact of intensive frontline regimens versus R-CHOP in a multicenter analysis across 7 academic medical centers in the United States. We collected 90 cases of DEL, 46 out of 90 patients (51%) received R-CHOP and 44/90 (49%) received an intensive regimen, which was predominantly DA-EPOCH-R. Treatment cohorts were evenly balanced for demographics and disease characteristics, though the intensive group had a higher lactate dehydrogenase (LDH, 326 vs. 230 U/L p = 0.06) and presence of B-symptoms (50% vs. 22%, p = 0.01) compared to the R-CHOP cohort. There was no difference in PFS (median 53 vs. 38 months, p = 0.49) or overall survival (67 vs. not reached months, p = 0.14) between the R-CHOP and intensive therapy cohorts, respectively. On multivariate analysis, intensive therapy was associated with a hazard ratio of 2.35 (95% CI 0.74-7.41), though this was not statistically significant. Additionally, a subgroup analysis of intermediate high-risk lymphoma defined by IPI ≥3 did not identify a difference in survival outcomes between regimens. We conclude that in our multi-center cohort there is no evidence supporting the use of intensive regimens over R-CHOP, suggesting that R-CHOP remains the standard of care for treating DEL.
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Affiliation(s)
- Christopher R D'Angelo
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Walter Hanel
- Department of Internal Medicine, Division of Hematology/Oncology, The Ohio State University Hospital, Columbus, Ohio, USA
| | - Yi Chen
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Menggang Yu
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David Yang
- Department of Pathology, University of Wisconsin Carbone Cancer Center Madison, Wisconsin, USA
| | - Ling Guo
- The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Reem Karmali
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Madelyn Burkart
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Colleen Ciccosanti
- Department of Internal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA
| | - Kevin David
- Division of Hematology/Oncology, Rutgers Cancer Institute of New Jersey, New Brunswick, New Jersey, USA
| | - Zachary Risch
- The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio, USA
| | | | - Sumana Devata
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Ryan Wilcox
- Department of Internal Medicine, Division of Hematology/Oncology, University of Michigan, Ann Arbor, Michigan, USA
| | - Malvi Savani
- Division of Hematology and Oncology, Department of Medicine, University of Arizona Cancer Center, Tucson, Arizona, USA
| | | | - Veronika Bachanova
- Department of Internal Medicine, Division of Hematology/Oncology, University of Minnesota, Minneapolis, Minnesota, USA
| | - Emma Rabinovich
- Department of Pathology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - David Peace
- Department of Pathology, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Fauzia Osman
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Narendranath Epperla
- The James Cancer Hospital and Solove Research Institute, The Ohio State University, Columbus, Ohio, USA
| | - Vaishalee P Kenkre
- Department of Pathology, University of Wisconsin Carbone Cancer Center Madison, Wisconsin, USA
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Ciccosanti C, Hershey A, Chen C, Moore DF, Stephenson RD, Weiner JP, Koshenkov VP, Silk AW, Mehnert JM, Berger AC, Groisberg R. Evaluating clinical responses to BRAF inhibition in BRAF/TERT promoter mutated melanoma. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.e21551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
e21551 Background: Combined BRAF/MEK inhibition results in improved progression free and overall survival in BRAF mutated melanoma, but significant response is not universally observed. TERT promoter activating mutations often co-occur with BRAF mutations and have been associated with aggressive features and poorer prognosis. The TERT promotor inhibits apoptosis via a mechanism dependent upon BRAF mutant MAPK activation. Preclinical data in mouse models suggests that BRAF/TERT genetic duet melanomas are associated with improved response to BRAF/MEK inhibition as compared with BRAF mutant/TERT-WT melanomas. Methods: We performed a single center retrospective analysis of adults with melanoma with confirmed BRAF mutations +/- TERT promoter mutations. Responses and progression free survival in response to BRAF/MEK inhibition was assessed. Differences in RR and PFS were compared using Kaplan-Meier and Log-Rank. Results: 52 cases of BRAF/TERT genetic duet and BRAF mutated/TERT-WT melanomas were assessed. A total of 24 patients received BRAF/MEK inhibitors over the course of treatment meeting criteria for study inclusion; 9 (37.5%) BRAF/TERT genetic duet and 15 (62.5%) BRAF mutated/TERT-WT. BRAF V600E was present in 19/24 (79.2%) and V600K in 5/24 (20.8%). In the genetic duets, TERT -146C > T was present in 4/9 (44.4%), -124C > T in 2/9 (22.2%), -139_-138CC > TT in 2/9 (22.2%), and a SNV in 1/9 (11.1%). Mean age at diagnosis was 56 ± 13.5 years and 62.5% were male. ECOG PFS was 0-1 in 15/24 (62.5%), 2-3 in 6/24 (25%), and unreported in 3/24 (12.5%). Mean LDH at start of therapy was 391 (range 81-1664). At initial diagnosis 20.8% were Stage I, 25% Stage II, 37.5% Stage III, and 16.7% Stage IV. Two or more sites of disease were present in 10/24 (41.7%) and 2/24 (8.3%) had CNS metastases. BRAF/MEK directed therapy was first line in 6/24 (25%) of patients, others received prior immunotherapy. No significant differences between groups were observed in baseline demographics, disease state at diagnosis, or treatment history. In BRAF/TERT genetic duet melanomas CR was observed in 1/9 (11.1%), PR in 7/9 (77.8%), and NR in 1/9 (11.1%). In BRAF mutated/TERT-WT CR was observed in 3/15 (20%), PR in 11/15 (73.3%), and NR in 1/15 (6.7%). BRAF/TERT genetic duets were observed to initially have somewhat better PFS on first exposure to BRAF/MEK directed therapy but the PFS curves crossed at about 5 months with no significant difference observed overall (p = 0.40). Conclusions: This study is the first to report on outcomes of BRAF/MEK directed therapy in BRAF/TERT genetic duet vs BRAF mutated/TERT-WT melanomas in humans. While preclinical data from mouse models observed an improved response to BRAF/MEK inhibition in genetic duet tumors, no significant difference was observed. Our study is limited by small sample size. A multicenter analysis may be of interest to better understand the effects of BRAF inhibition in patients with BRAF/TERT genetic duet melanoma.
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Affiliation(s)
- Colleen Ciccosanti
- Department of Internal Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ
| | | | - Chunxia Chen
- Biometrics, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | - Dirk F. Moore
- Biometrics, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | | | | | | | - Ann W. Silk
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | | | - Adam C. Berger
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
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Feldmann EA, Seetharaman J, Ramelot TA, Lew S, Zhao L, Hamilton K, Ciccosanti C, Xiao R, Acton TB, Everett JK, Tong L, Montelione GT, Kennedy MA. Solution NMR and X-ray crystal structures of Pseudomonas syringae Pspto_3016 from protein domain family PF04237 (DUF419) adopt a "double wing" DNA binding motif. ACTA ACUST UNITED AC 2012; 13:155-62. [PMID: 22865330 DOI: 10.1007/s10969-012-9140-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 07/03/2012] [Indexed: 01/13/2023]
Abstract
The protein Pspto_3016 is a 117-residue member of the protein domain family PF04237 (DUF419), which is to date a functionally uncharacterized family of proteins. In this report, we describe the structure of Pspto_3016 from Pseudomonas syringae solved by both solution NMR and X-ray crystallography at 2.5 Å resolution. In both cases, the structure of Pspto_3016 adopts a "double wing" α/β sandwich fold similar to that of protein YjbR from Escherichia coli and to the C-terminal DNA binding domain of the MotA transcription factor (MotCF) from T4 bacteriophage, along with other uncharacterized proteins. Pspto_3016 was selected by the Protein Structure Initiative of the National Institutes of Health and the Northeast Structural Genomics Consortium (NESG ID PsR293).
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Affiliation(s)
- Erik A Feldmann
- Department of Chemistry and Biochemistry, Miami University, Oxford, OH 45056, USA
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Yang Y, Ramelot TA, Cort JR, Wang H, Ciccosanti C, Jiang M, Janjua H, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA. Solution NMR structure of Dsy0195 homodimer from Desulfitobacterium hafniense: first structure representative of the YabP domain family of proteins involved in spore coat assembly. J Struct Funct Genomics 2011; 12:175-9. [PMID: 21904870 DOI: 10.1007/s10969-011-9117-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 08/26/2011] [Indexed: 11/24/2022]
Abstract
Protein domain family YabP (PF07873) is a family of small protein domains that are conserved in a wide range of bacteria and involved in spore coat assembly during the process of sporulation. The 62-residue fragment of Dsy0195 from Desulfitobacterium hafniense, which belongs to the YabP family, exists as a homodimer in solution under the conditions used for structure determination using NMR spectroscopy. The structure of the Dsy0195 homodimer contains two identical 62-residue monomeric subunits, each consisting of five anti-parallel beta strands (β1, 23-29; β2, 31-38; β3, 41-46; β4, 49-59; β5, 69-80). The tertiary structure of the Dsy0195 monomer adopts a cylindrical fold composed of two beta sheets. The two monomer subunits fold into a homodimer about a single C2 symmetry axis, with the interface composed of two anti-parallel beta strands, β1-β1' and β5b-β5b', where β5b refers to the C-terminal half of the bent β5 strand, without any domain swapping. Potential functional regions of the Dsy0195 structure were predicted based on conserved sequence analysis. The Dsy0195 structure reported here is the first representative structure from the YabP family.
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Affiliation(s)
- Yunhuang Yang
- Department of Chemistry and Biochemistry, Miami University, 701 East High Street, Oxford, OH 45056, USA
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Yang Y, Ramelot TA, Cort JR, Wang D, Ciccosanti C, Hamilton K, Nair R, Rost B, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA. Solution NMR structure of photosystem II reaction center protein Psb28 from Synechocystis sp. Strain PCC 6803. Proteins 2011; 79:340-4. [PMID: 21058299 DOI: 10.1002/prot.22876] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Yunhuang Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, USA
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6
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Ramelot TA, Smola MJ, Lee HW, Ciccosanti C, Hamilton K, Acton TB, Xiao R, Everett JK, Prestegard JH, Montelione GT, Kennedy MA. Solution structure of 4'-phosphopantetheine - GmACP3 from Geobacter metallireducens: a specialized acyl carrier protein with atypical structural features and a putative role in lipopolysaccharide biosynthesis. Biochemistry 2011; 50:1442-53. [PMID: 21235239 PMCID: PMC3063093 DOI: 10.1021/bi101932s] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
GmACP3 from Geobacter metallireducens is a specialized acyl carrier protein (ACP) whose gene, gmet_2339, is located near genes encoding many proteins involved in lipopolysaccharide (LPS) biosynthesis, indicating a likely function for GmACP3 in LPS production. By overexpression in Escherichia coli, about 50% holo-GmACP3 and 50% apo-GmACP3 were obtained. Apo-GmACP3 exhibited slow precipitation and non-monomeric behavior by (15)N NMR relaxation measurements. Addition of 4'-phosphopantetheine (4'-PP) via enzymatic conversion by E. coli holo-ACP synthase resulted in stable >95% holo-GmACP3 that was characterized as monomeric by (15)N relaxation measurements and had no indication of conformational exchange. We have determined a high-resolution solution structure of holo-GmACP3 by standard NMR methods, including refinement with two sets of NH residual dipolar couplings, allowing for a detailed structural analysis of the interactions between 4'-PP and GmACP3. Whereas the overall four helix bundle topology is similar to previously solved ACP structures, this structure has unique characteristics, including an ordered 4'-PP conformation that places the thiol at the entrance to a central hydrophobic cavity near a conserved hydrogen-bonded Trp-His pair. These residues are part of a conserved WDSLxH/N motif found in GmACP3 and its orthologs. The helix locations and the large hydrophobic cavity are more similar to medium- and long-chain acyl-ACPs than to other apo- and holo-ACP structures. Taken together, structural characterization along with bioinformatic analysis of nearby genes suggests that GmACP3 is involved in lipid A acylation, possibly by atypical long-chain hydroxy fatty acids, and potentially is involved in synthesis of secondary metabolites.
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Affiliation(s)
- Theresa A. Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
| | - Matthew J. Smola
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
| | - Hsiau-Wei Lee
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States and the Northeast Structural Genomics Consortium
| | - Colleen Ciccosanti
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Keith Hamilton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Thomas B. Acton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - John K. Everett
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
| | - James H. Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States and the Northeast Structural Genomics Consortium
| | - Gaetano T. Montelione
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States and the Northeast Structural Genomics Consortium
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey, 08854, United States
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056, United States and the Northeast Structural Genomics Consortium
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7
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Acton TB, Xiao R, Anderson S, Aramini J, Buchwald WA, Ciccosanti C, Conover K, Everett J, Hamilton K, Huang YJ, Janjua H, Kornhaber G, Lau J, Lee DY, Liu G, Maglaqui M, Ma L, Mao L, Patel D, Rossi P, Sahdev S, Shastry R, Swapna GVT, Tang Y, Tong S, Wang D, Wang H, Zhao L, Montelione GT. Preparation of protein samples for NMR structure, function, and small-molecule screening studies. Methods Enzymol 2011; 493:21-60. [PMID: 21371586 DOI: 10.1016/b978-0-12-381274-2.00002-9] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
In this chapter, we concentrate on the production of high-quality protein samples for nuclear magnetic resonance (NMR) studies. In particular, we provide an in-depth description of recent advances in the production of NMR samples and their synergistic use with recent advancements in NMR hardware. We describe the protein production platform of the Northeast Structural Genomics Consortium and outline our high-throughput strategies for producing high-quality protein samples for NMR studies. Our strategy is based on the cloning, expression, and purification of 6×-His-tagged proteins using T7-based Escherichia coli systems and isotope enrichment in minimal media. We describe 96-well ligation-independent cloning and analytical expression systems, parallel preparative scale fermentation, and high-throughput purification protocols. The 6×-His affinity tag allows for a similar two-step purification procedure implemented in a parallel high-throughput fashion that routinely results in purity levels sufficient for NMR studies (>97% homogeneity). Using this platform, the protein open reading frames of over 17,500 different targeted proteins (or domains) have been cloned as over 28,000 constructs. Nearly 5000 of these proteins have been purified to homogeneity in tens of milligram quantities (see Summary Statistics, http://nesg.org/statistics.html), resulting in more than 950 new protein structures, including more than 400 NMR structures, deposited in the Protein Data Bank. The Northeast Structural Genomics Consortium pipeline has been effective in producing protein samples of both prokaryotic and eukaryotic origin. Although this chapter describes our entire pipeline for producing isotope-enriched protein samples, it focuses on the major updates introduced during the last 5 years (Phase 2 of the National Institute of General Medical Sciences Protein Structure Initiative). Our advanced automated and/or parallel cloning, expression, purification, and biophysical screening technologies are suitable for implementation in a large individual laboratory or by a small group of collaborating investigators for structural biology, functional proteomics, ligand screening, and structural genomics research.
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Affiliation(s)
- Thomas B Acton
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Northeast Structural Genomics Consortium, Rutgers University, Piscataway, New Jersey, USA
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Tang Y, Xiao R, Ciccosanti C, Janjua H, Lee DY, Everett JK, Swapna GVT, Acton TB, Rost B, Montelione GT. Solution NMR structure of Lin0431 protein from Listeria innocua reveals high structural similarity with domain II of bacterial transcription antitermination protein NusG. Proteins 2010; 78:2563-8. [PMID: 20602357 DOI: 10.1002/prot.22760] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yuefeng Tang
- Department of Molecular Biology and Biochemistry, Rutgers, Center for Advanced Biotechnology and Medicine, The State University of New Jersey, Piscataway, New Jersey 08854, USA
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9
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Yang Y, Ramelot TA, McCarrick RM, Ni S, Feldmann EA, Cort JR, Wang H, Ciccosanti C, Jiang M, Janjua H, Acton TB, Xiao R, Everett JK, Montelione GT, Kennedy MA. Combining NMR and EPR methods for homodimer protein structure determination. J Am Chem Soc 2010; 132:11910-3. [PMID: 20698532 PMCID: PMC3057626 DOI: 10.1021/ja105080h] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There is a general need to develop more powerful and more robust methods for structural characterization of homodimers, homo-oligomers, and multiprotein complexes using solution-state NMR methods. In recent years, there has been increasing emphasis on integrating distinct and complementary methodologies for structure determination of multiprotein complexes. One approach not yet widely used is to obtain intermediate and long-range distance constraints from paramagnetic relaxation enhancements (PRE) and electron paramagnetic resonance (EPR)-based techniques such as double electron electron resonance (DEER), which, when used together, can provide supplemental distance constraints spanning to 10-70 A. In this Communication, we describe integration of PRE and DEER data with conventional solution-state nuclear magnetic resonance (NMR) methods for structure determination of Dsy0195, a homodimer (62 amino acids per monomer) from Desulfitobacterium hafniense. Our results indicate that combination of conventional NMR restraints with only one or a few DEER distance constraints and a small number of PRE constraints is sufficient for the automatic NMR-based structure determination program CYANA to build a network of interchain nuclear Overhauser effect constraints that can be used to accurately define both the homodimer interface and the global homodimer structure. The use of DEER distances as a source of supplemental constraints as described here has virtually no upper molecular weight limit, and utilization of the PRE constraints is limited only by the ability to make accurate assignments of the protein amide proton and nitrogen chemical shifts.
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Affiliation(s)
- Yunhuang Yang
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
| | - Theresa A. Ramelot
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
| | - Robert M. McCarrick
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Shuisong Ni
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
| | - Erik A. Feldmann
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
| | - John R. Cort
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352
| | - Huang Wang
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Colleen Ciccosanti
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Mei Jiang
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Haleema Janjua
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Thomas B. Acton
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Rong Xiao
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - John K. Everett
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
| | - Gaetano T. Montelione
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
- Department of Molecular Biology and Biochemistry, Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854
| | - Michael A. Kennedy
- Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio 45056
- Northeast Structural Genomics Consortium, Piscataway, New Jersey 08854
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Xiao R, Anderson S, Aramini J, Belote R, Buchwald WA, Ciccosanti C, Conover K, Everett JK, Hamilton K, Huang YJ, Janjua H, Jiang M, Kornhaber GJ, Lee DY, Locke JY, Ma LC, Maglaqui M, Mao L, Mitra S, Patel D, Rossi P, Sahdev S, Sharma S, Shastry R, Swapna GVT, Tong SN, Wang D, Wang H, Zhao L, Montelione GT, Acton TB. The high-throughput protein sample production platform of the Northeast Structural Genomics Consortium. J Struct Biol 2010; 172:21-33. [PMID: 20688167 DOI: 10.1016/j.jsb.2010.07.011] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2010] [Revised: 07/24/2010] [Accepted: 07/28/2010] [Indexed: 11/15/2022]
Abstract
We describe the core Protein Production Platform of the Northeast Structural Genomics Consortium (NESG) and outline the strategies used for producing high-quality protein samples. The platform is centered on the cloning, expression and purification of 6X-His-tagged proteins using T7-based Escherichia coli systems. The 6X-His tag allows for similar purification procedures for most targets and implementation of high-throughput (HTP) parallel methods. In most cases, the 6X-His-tagged proteins are sufficiently purified (>97% homogeneity) using a HTP two-step purification protocol for most structural studies. Using this platform, the open reading frames of over 16,000 different targeted proteins (or domains) have been cloned as>26,000 constructs. Over the past 10 years, more than 16,000 of these expressed protein, and more than 4400 proteins (or domains) have been purified to homogeneity in tens of milligram quantities (see Summary Statistics, http://nesg.org/statistics.html). Using these samples, the NESG has deposited more than 900 new protein structures to the Protein Data Bank (PDB). The methods described here are effective in producing eukaryotic and prokaryotic protein samples in E. coli. This paper summarizes some of the updates made to the protein production pipeline in the last 5 years, corresponding to phase 2 of the NIGMS Protein Structure Initiative (PSI-2) project. The NESG Protein Production Platform is suitable for implementation in a large individual laboratory or by a small group of collaborating investigators. These advanced automated and/or parallel cloning, expression, purification, and biophysical screening technologies are of broad value to the structural biology, functional proteomics, and structural genomics communities.
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Affiliation(s)
- Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey and Robert Wood Johnson Medical School, and Northeast Structural Genomics Consortium, Piscataway, NJ 08854, USA
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