1
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Ng HQ, Li Q, Kang C. 1H, 13C and 15N resonance assignments of the first BIR domain of cellular inhibitor of apoptosis protein 1. Biomol NMR Assign 2022; 16:91-95. [PMID: 35061233 DOI: 10.1007/s12104-022-10065-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Cellular inhibitor of apoptosis protein-1 (cIAP-1) is member of inhibitor of apoptosis proteins (IAPs) which can affect apoptosis through interactions with caspases. cIAP-1 is a multi-domain protein and able to regulate apoptosis through interactions with proteins such as caspases and possesses E3 ligase activity. Human cIAP-1 contains three baculovirus IAP repeat (BIR) domains which are critical for protein-protein interactions. Here, we report NMR resonance assignments of the first BIR domain of human cIAP. Its secondary structures in solution were determined based on the assigned resonances. The dynamics of this domain was obtained, and our hydrogen-deuterium exchange experiment reveals that the first helix in BIR1 is exposed to the solvent. The availability of assignments of backbone and side chain resonances will be useful for probing protein-protein interactions.
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Affiliation(s)
- Hui Qi Ng
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore, 138670, Singapore
| | - Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, 510316, China
| | - Congbao Kang
- Experimental Drug Development Centre (EDDC), Agency for Science, Technology and Research (A*STAR), Singapore, 138670, Singapore.
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2
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Benjamin SV, Creeke PI, Henry AJ, McDonnell JM. NMR backbone assignment of the Cε4 domain of immunoglobulin E. Biomol NMR Assign 2020; 14:151-155. [PMID: 32108310 PMCID: PMC7069932 DOI: 10.1007/s12104-020-09936-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/21/2020] [Indexed: 06/10/2023]
Abstract
Immunoglobulin E (IgE) plays a central role in allergic reactions. IgE is a dynamic molecule that is capable of undergoing large conformational changes. X-ray crystal structures of the Fc region of IgE in complex with various ligands have shown that IgE-Fc can exist in extended and various bent conformations. IgE-Fc consists of three domains: Cε2, Cε3 and Cε4. While the complete NMR backbone assignments of the Cε2 and Cε3 domains have been reported previously, the Cε4 domain has not been assigned. Here, we report the complete backbone assignment of the Cε4 homodimer. Cε4 can be used as a model system to study dynamics and allostery in IgE, as both molecules exist as homodimers and exhibit similar binding properties to a number of ligands.
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Affiliation(s)
- Stefi V Benjamin
- Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK
| | - Paul I Creeke
- UCB Pharma, 216 Bath Road, Slough, Berkshire, SL1 3WE, UK
| | | | - James M McDonnell
- Randall Centre for Cell & Molecular Biophysics, King's College London, New Hunt's House, Guy's Campus, London, SE1 1UL, UK.
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3
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Li Y, Zhong W, Koay AZ, Ng HQ, Nah Q, Wong YH, Hill J, Lescar J, Dedon PC, Kang C. Backbone resonance assignment for the full length tRNA-(N 1G37) methyltransferase of Pseudomonas aeruginosa. Biomol NMR Assign 2019; 13:327-332. [PMID: 31175551 DOI: 10.1007/s12104-019-09900-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 05/31/2019] [Indexed: 06/09/2023]
Abstract
Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) plays important roles in translation, making it an important target for the development of new antibacterial compounds. TrmD comprises two domains with the N-terminal domain binding to the S-adenosyl-L-methionine (SAM) cofactor and the C-terminal domain critical for tRNA binding. Bacterial TrmD is functional as a dimer. Here we report the backbone NMR resonance assignments for the full length TrmD protein of Pseudomonas aeruginosa. Most resonances were assigned and the secondary structure for each amino acid was determined according to the assigned backbone resonances. The availability of the assignment will be valuable for exploring molecular interactions of TrmD with ligands, inhibitors and tRNA.
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Affiliation(s)
- Yan Li
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, 430030, Hubei, People's Republic of China
| | - Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
| | - Ann Zhufang Koay
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Hui Qi Ng
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Yee Hwa Wong
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jeffrey Hill
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore.
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - CongBao Kang
- Experimental Drug Development Centre, 10 Biopolis Road, #05-01, Singapore, 138670, Singapore.
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4
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Li Y, Zhong W, Koay AZ, Ng HQ, Koh-Stenta X, Nah Q, Lim SH, Larsson A, Lescar J, Hill J, Dedon PC, Kang C. Backbone resonance assignment for the N-terminal region of bacterial tRNA-(N 1G37) methyltransferase. Biomol NMR Assign 2019; 13:49-53. [PMID: 30298375 DOI: 10.1007/s12104-018-9849-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 09/15/2018] [Indexed: 06/08/2023]
Abstract
Bacterial tRNA (guanine37-N1)-methyltransferase (TrmD) is an important antibacterial target due to its essential role in translation. TrmD has two domains connected with a flexible linker. The N-terminal domain (NTD) of TrmD contains the S-adenosyl-L-methionine (SAM) cofactor binding site and the C-terminal domain is critical for tRNA binding. Here we report the backbone NMR resonance assignments for NTD of Pseudomonas aeruginosa TrmD. Its secondary structure was determined based on the assigned resonances. Relaxation analysis revealed that NTD existed as dimers in solution. NTD also exhibited thermal stability in solution. Its interactions with SAM and other compounds suggest it can be used for evaluating SAM competitive inhibitors by NMR.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Road, Wuhan, Hubei, 430030, People's Republic of China
| | - Wenhe Zhong
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Ann Zhufang Koay
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Xiaoying Koh-Stenta
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore
| | - Qianhui Nah
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore
| | - Siau Hoi Lim
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Experimental Biotherapeutics Centre, 30 Biopolis Street, #08-01 Matrix, Singapore, 138671, Singapore
| | - Andreas Larsson
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Julien Lescar
- NTU Institute of Structural Biology, Nanyang Technological University, Singapore, 636921, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore.
| | - Peter C Dedon
- Infectious Disease and Antimicrobial Resistance Interdisciplinary Research Groups, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Antimicrobial Resistance Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, 1 CREATE Way, Singapore, 138602, Singapore.
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | - CongBao Kang
- Experimental Therapeutics Centre, 31 Biopolis Way, #03-01 Nanos, Singapore, 138669, Singapore.
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5
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Bastiray A, Giri M, Singh M. Sequential backbone resonance assignment of AT-rich interaction domain of human BAF200. Biomol NMR Assign 2019; 13:115-119. [PMID: 30535613 DOI: 10.1007/s12104-018-9862-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 12/04/2018] [Indexed: 06/09/2023]
Abstract
BAF200 is a subunit of PBAF chromatin remodeling complex that contains an N-terminal AT-rich interaction domain (ARID). ARID domain in general has been shown to bind to the AT-rich DNA sequences. The human BAF200 ARID (~ 110 residues) has the potential to bind the DNA sequences with high affinity, however, the structure and the exact contribution of hBAF200 ARID in PBAF functions as well its DNA binding specificities have not been established. In this study, we have expressed and purified the hBAF200 ARID for NMR studies. We report the complete backbone 1H, 13C, and 15N chemical shift assignment and secondary structure of hBAF200 ARID domain.
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Affiliation(s)
- Abhishek Bastiray
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
- Undergraduate Department, Indian Institute of Science, Bengaluru, 560012, India
| | - Malyasree Giri
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Mahavir Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India.
- NMR Research Centre, Indian Institute of Science, Bengaluru, 560012, India.
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6
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Henrich E, Löhr F, Mezhyrova J, Laguerre A, Bernhard F, Dötsch V. Synthetic Biology-Based Solution NMR Studies on Membrane Proteins in Lipid Environments. Methods Enzymol 2018; 614:143-185. [PMID: 30611423 DOI: 10.1016/bs.mie.2018.08.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Although membrane proteins are in the focus of biochemical research for many decades the general knowledge of this important class is far behind soluble proteins. Despite several recent technical developments, the most challenging feature still is the generation of high-quality samples in environments suitable for the selected application. Reconstitution of membrane proteins into lipid bilayers will generate the most native-like environment and is therefore commonly desired. However, it poses tremendous problems to solution-state NMR analysis due to the dramatic increase in particle size resulting in high rotational correlation times. Nevertheless, a few promising strategies for the solution NMR analysis of membrane inserted proteins are emerging and will be discussed in this chapter. We focus on the generation of membrane protein samples in nanodisc membranes by cell-free systems and will describe the characteristic advantages of that platform in providing tailored protein expression and folding environments. We indicate frequent problems that have to be overcome in cell-free synthesis, nanodisc preparation, and customization for samples dedicated for solution-state NMR. Detailed instructions for sample preparation are given, and solution NMR approaches suitable for membrane proteins in bilayers are compiled. We further discuss the current strategies applied for signal detection from such difficult samples and describe the type of information that can be extracted from the various experiments. In summary, a comprehensive guideline for the analysis of membrane proteins in native-like membrane environments by solution-state NMR techniques will be provided.
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Affiliation(s)
- Erik Henrich
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Löhr
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Julija Mezhyrova
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Aisha Laguerre
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Frank Bernhard
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry, Centre for Biomolecular Magnetic Resonance, J.W. Goethe-University, Frankfurt am Main, Germany.
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7
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Bowles DP, Yuan C, Stephany KR, Lavinder JJ, Hansen AL, Magliery TJ. Resonance assignments of wild-type and two cysteine-free variants of the four-helix bundle protein, Rop. Biomol NMR Assign 2018; 12:345-350. [PMID: 30159810 DOI: 10.1007/s12104-018-9837-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/09/2018] [Indexed: 06/08/2023]
Abstract
Repressor of primer (Rop, or ROM, RNA I modulator) is a 63 amino acid four-helix bundle protein that exists in solution as an anti-parallel homodimer. This protein has been extensively studied, including by X-ray crystallography, NMR, rational design, and combinatorial mutagenesis. Previous NMR experiments with wild-type Rop were carried out at pH 2.3 and pH 6.3. In this paper, we report complete N-H backbone assignments for three variants of Rop under the same pH 6.3 conditions: wild-type Rop; a cysteine-free pseudo-wild type variant (C38A C52V); and a core-repacked variant of the Cys-free variant (T19V L41V C38A C52V). These assignments enable functional and dynamic studies of wild-type and Cys-free variants of Rop.
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Affiliation(s)
- David P Bowles
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA
| | - Chunhua Yuan
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Ave 209 Biomedical Research Tower, Columbus, OH, 43210, USA
| | - Kimberly R Stephany
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA
| | - Jason J Lavinder
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH, 43210, USA
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA
| | - Alexandar L Hansen
- Campus Chemical Instrument Center, The Ohio State University, 460 W. 12th Ave 209 Biomedical Research Tower, Columbus, OH, 43210, USA
| | - Thomas J Magliery
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Ave., Columbus, OH, 43210, USA.
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8
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Paithankar H, Jadhav PV, Naglekar AS, Sharma S, Chugh J. 1H, 13C and 15N resonance assignment of domain 1 of trans-activation response element (TAR) RNA binding protein isoform 1 (TRBP2) and its comparison with that of isoform 2 (TRBP1). Biomol NMR Assign 2018; 12:189-194. [PMID: 29445910 DOI: 10.1007/s12104-018-9807-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
TAR RNA binding protein (TRBP) is a double-stranded RNA binding protein involved in various biological processes like cell growth, development, death, etc. The protein exists as two isoforms TRBP2 and TRBP1. TRBP2 contains additional 21 amino acids at its N-terminus, which are proposed to be involved in its membrane localization, when compared to TRBP1. The resonance assignment (19-228) of the double-stranded RNA binding domains (dsRBD 1 and 2) of TRBP2 has been reported earlier. Here, we report 1H, 13C and 15N resonance assignment for dsRBD1 of TRBP2 (1-105) containing the additional N-terminal residues. This assignment will provide deeper insights to understand the effect of these residues on the structure and dynamics of TRBP2 and would therefore help in further elucidating the differences in the role of these isoforms.
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Affiliation(s)
- Harshad Paithankar
- Department of Chemistry, Indian Institute of Science Education & Research, Dr Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Pankaj V Jadhav
- Department of Biotechnology, Savitrabai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411007, India
| | - Amit S Naglekar
- Department of Biotechnology, Savitrabai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411007, India
| | - Shilpy Sharma
- Department of Biotechnology, Savitrabai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411007, India
| | - Jeetender Chugh
- Department of Chemistry, Indian Institute of Science Education & Research, Dr Homi Bhabha Road, Pashan, Pune, 411008, India.
- Department of Biology, Indian Institute of Science Education & Research, Dr Homi Bhabha Road, Pashan, Pune, 411008, India.
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9
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Voehler M, Ashoka MA, Meiler J, Bock PE. Carbon and amide detect backbone assignment methods of a novel repeat protein from the staphylocoagulase in S. aureus. Biomol NMR Assign 2017; 11:243-249. [PMID: 28819722 PMCID: PMC6057470 DOI: 10.1007/s12104-017-9757-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
The C-terminal repeat domain of staphylocoagulase that is secreted by the S. aureus is believed to play an important role interacting with fibrinogen and promotes blood clotting. To study this interaction by NMR, full assignment of each amide residue in the HSQC spectrum was required. Despite of the short sequence of the repeat construct, the HSQC spectrum contained a substantial amount of overlapped and exchange broadened resonances, indicating little secondary or tertiary structure. This caused severe problems while using the conventional, amide based NMR method for the backbone assignment. With the growing interest in small apparently disordered proteins, these issues are being faced more frequently. An alternative strategy to improve the backbone assignment capability involved carbon direct detection methods. Circumventing the amide proton detection offers a larger signal dispersion and more uniform signal intensity. For peptides with higher concentrations and in combination with the cold carbon channels of new cryoprobes, higher fields, and sufficiently long relaxation times, the disadvantage of the lower sensitivity of the 13C nucleus can be overcome. Another advantage of this method is the assignment of the proline backbone residues. Complete assignment with the carbon-detected strategy was achieved with a set of only two 3D, one 2D, and a HNCO measurement, which was necessary to translate the information to the HSQC spectrum.
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Affiliation(s)
- Markus Voehler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232-8725, USA.
| | - Maddur Appajaiah Ashoka
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jens Meiler
- Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37232-8725, USA
| | - Paul E Bock
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
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10
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Li Y, Ng HQ, Ngo A, Liu S, Tan YW, Kwek PZ, Hung AW, Joy J, Hill J, Keller TH, Kang C. Backbone resonance assignments for the SET domain of human methyltransferase NSD3 in complex with its cofactor. Biomol NMR Assign 2017; 11:225-229. [PMID: 28808922 DOI: 10.1007/s12104-017-9753-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
NSD3 is a histone H3 methyltransferase that plays an important role in chromatin biology. A construct containing the methyltransferase domain encompassing residues Q1049-K1299 of human NSD3 was obtained and biochemical activity was demonstrated using histone as a substrate. Here we report the backbone HN, N, Cα, C', and side chain Cβ assignments of the construct in complex with S-adenosyl-L-methionine (SAM). Based on these assignments, secondary structures of NSD3/SAM complex in solution were determined.
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Affiliation(s)
- Yan Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Hui Qi Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Anna Ngo
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Shuang Liu
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Yih Wan Tan
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Perlyn Zekui Kwek
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Alvin W Hung
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Joma Joy
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - Thomas H Keller
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore
| | - CongBao Kang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research, 31 Biopolis Way Nanos, #03-01, Singapore, 138669, Singapore.
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11
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Xia Y, Rossi P, Tonelli M, Huang C, Kalodimos CG, Veglia G. Optimization of 1H decoupling eliminates sideband artifacts in 3D TROSY-based triple resonance experiments. J Biomol NMR 2017; 69:45-52. [PMID: 28887770 PMCID: PMC5693675 DOI: 10.1007/s10858-017-0133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 09/05/2017] [Indexed: 05/09/2023]
Abstract
TROSY-based triple resonance experiments are essential for protein backbone assignment of large biomolecular systems by solution NMR spectroscopy. In a survey of the current Bruker pulse sequence library for TROSY-based experiments we found that several sequences were plagued by artifacts that affect spectral quality and hamper data analysis. Specifically, these experiments produce sidebands in the 13C(t 1) dimension with inverted phase corresponding to 1HN resonance frequencies, with approximately 5% intensity of the parent 13C crosspeaks. These artifacts originate from the modulation of the 1HN frequency onto the resonance frequency of 13Cα and/or 13Cβ and are due to 180° pulses imperfections used for 1H decoupling during the 13C(t 1) evolution period. These sidebands can become severe for CAi, CAi-1 and/or CBi, CBi-1 correlation experiments such as TROSY-HNCACB. Here, we implement three alternative decoupling strategies that suppress these artifacts and, depending on the scheme employed, boost the sensitivity up to 14% on Bruker spectrometers. A class of comparable Agilent/Varian pulse sequences that use WALTZ16 1H decoupling can also be improved by this method resulting in up to 60-80% increase in sensitivity.
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Affiliation(s)
- Youlin Xia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Paolo Rossi
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Marco Tonelli
- NMRFAM, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chengdong Huang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Charalampos G Kalodimos
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
| | - Gianluigi Veglia
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, 55455, USA.
- Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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12
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Bobby R, Peciak K, Milbradt AG. Backbone resonance assignments for the SET domain of the human methyltransferase NSD2. Biomol NMR Assign 2016; 10:307-310. [PMID: 27368234 DOI: 10.1007/s12104-016-9689-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 06/22/2016] [Indexed: 06/06/2023]
Abstract
Aberrant NSD2 methyltransferase activity is implicated as the oncogenic driver in multiple myeloma, suggesting opportunities for novel therapeutic intervention. The methyltransferase activity of NSD2 resides in its catalytic SET domain, which is conserved among most lysine methyltransferases. Here we report the backbone [Formula: see text], N, C[Formula: see text], [Formula: see text] and side-chain [Formula: see text] assignments of a 25 kDa NSD2 SET domain construct, spanning residues 991-1203. A chemical shift analysis of C[Formula: see text], [Formula: see text] and [Formula: see text] resonances predicts a secondary structural pattern that is in agreement with homology models.
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Affiliation(s)
- Romel Bobby
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Alderley Park, SK10 4TG, UK
| | - Karolina Peciak
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Alderley Park, SK10 4TG, UK
| | - Alexander G Milbradt
- Discovery Sciences, Innovative Medicines and Early Development Biotech Unit, AstraZeneca, Alderley Park, SK10 4TG, UK.
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Walser R, Renshaw J, Milbradt AG. Backbone resonance assignments for the PHD-Bromo dual-domain of the human chromatin reader TRIM24. Biomol NMR Assign 2016; 10:207-211. [PMID: 26878853 DOI: 10.1007/s12104-016-9668-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 02/05/2016] [Indexed: 06/05/2023]
Abstract
Plant homeodomains (PHD) and Bromo domains are both chromatin reader domains that recognise histone methylation degree and acetylation state, respectively. The tripartite motif protein TRIM24 is a multidomain protein carrying a PHD-Bromo motif at its C-terminus, through which it is able to bind to histone 3 (H3) N-terminal tails with a specific modification pattern, namely unmethylated at K4 and acetylated at K23 (H3-K4me0K23ac). Here we report the 1H, 13C and 15N backbone resonance assignment of this 23 kDa motif, which we have obtained by heteronuclear multidimensional NMR spectroscopy. Furthermore we show that the secondary Cα and Cβ chemical shifts are in good agreement with a previously published crystal structure.
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Affiliation(s)
- Reto Walser
- Structure and Biophysics, AstraZeneca Discovery Sciences, Alderley Park, SK10 4TG, United Kingdom.
| | - Jonathan Renshaw
- RAD, AstraZeneca Discovery Sciences, Alderley Park, SK10 4TG, United Kingdom
| | - Alexander G Milbradt
- Structure and Biophysics, AstraZeneca Discovery Sciences, Alderley Park, SK10 4TG, United Kingdom
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Harden BJ, Mishra SH, Frueh DP. Effortless assignment with 4D covariance sequential correlation maps. J Magn Reson 2015; 260:83-8. [PMID: 26432397 PMCID: PMC4628886 DOI: 10.1016/j.jmr.2015.09.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Accepted: 09/11/2015] [Indexed: 05/13/2023]
Abstract
Traditional Nuclear Magnetic Resonance (NMR) assignment procedures for proteins rely on preliminary peak-picking to identify and label NMR signals. However, such an approach has severe limitations when signals are erroneously labeled or completely neglected. The consequences are especially grave for proteins with substantial peak overlap, and mistakes can often thwart entire projects. To overcome these limitations, we previously introduced an assignment technique that bypasses traditional pick peaking altogether. Covariance Sequential Correlation Maps (COSCOMs) transform the indirect connectivity information provided by multiple 3D backbone spectra into direct (H, N) to (H, N) correlations. Here, we present an updated method that utilizes a single four-dimensional spectrum rather than a suite of three-dimensional spectra. We demonstrate the advantages of 4D-COSCOMs relative to their 3D counterparts. We introduce improvements accelerating their calculation. We discuss practical considerations affecting their quality. And finally we showcase their utility in the context of a 52 kDa cyclization domain from a non-ribosomal peptide synthetase.
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Affiliation(s)
- Bradley J Harden
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 701 Hunterian, 725 N Wolfe St, Baltimore, MD 21205, United States
| | - Subrata H Mishra
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 701 Hunterian, 725 N Wolfe St, Baltimore, MD 21205, United States
| | - Dominique P Frueh
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 701 Hunterian, 725 N Wolfe St, Baltimore, MD 21205, United States
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Kumar D. Reduced dimensionality tailored HN(C)N experiments for facile backbone resonance assignment of proteins through unambiguous identification of sequential HSQC peaks. J Magn Reson 2013; 237:85-91. [PMID: 24161682 DOI: 10.1016/j.jmr.2013.09.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2013] [Revised: 09/06/2013] [Accepted: 09/27/2013] [Indexed: 06/02/2023]
Abstract
Two novel reduced dimensionality (RD) tailored HN(C)N [S.C. Panchal, N.S. Bhavesh, R.V. Hosur, Improved 3D triple resonance experiments, HNN and HN(C)N, for HN and 15N sequential correlations in (13C, 15N) labeled proteins: application to unfolded proteins, J. Biomol. NMR 20 (2001) 135-147] experiments are proposed to facilitate the backbone resonance assignment of proteins both in terms of its accuracy and speed. These experiments - referred here as (4,3)D-hNCOcaNH and (4,3)D-hNcoCANH - exploit the linear combination of backbone (15)N and (13)C'/(13)C(α) chemical shifts simultaneously to achieve higher peak dispersion and randomness along their respective F1 dimensions. Simply, this has been achieved by modulating the backbone (15)N(i) chemical shifts with that of (13)C' (i-1)/(13)C(α) (i-1) spins following the established reduced dimensionality NMR approach [T. Szyperski, D.C. Yeh, D.K. Sukumaran, H.N. Moseley, G.T. Montelione, Reduced-dimensionality NMR spectroscopy for high-throughput protein resonance assignment, Proc. Natl. Acad. Sci. USA 99 (2002) 8009-8014]. Though the modification is simple it has resulted an ingenious improvement of HN(C)N both in terms of peak dispersion and easiness of establishing the sequential connectivities. The increased dispersion along F1 dimension solves two purposes here: (i) resolves the ambiguities arising because of degenerate (15)N chemical shifts and (ii) reduces the signal overlap in F2((15)N)-F3((1)H) planes (an important requisite in HN(C)N based assignment protocol for facile and unambiguous identification of sequentially connected HSQC peaks). The performance of both these experiments and the assignment protocol has been demonstrated using bovine apo Calbindin-d9k (75 aa) and urea denatured UNC60B (a 152 amino acid ADF/cofilin family protein of Caenorhabditis elegans), as representatives of folded and unfolded protein systems, respectively.
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Affiliation(s)
- Dinesh Kumar
- Centre of Biomedical Research (CBMR), Sanjay Gandhi Post-Graduate Institute of Medical Sciences Campus, Raibareli Road, Lucknow 226014, Uttar Pradesh, India.
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Shi P, Li D, Lai C, Zhang L, Tian C. Intracellular segment between transmembrane helices S0 and S1 of BK channel α subunit contains two amphipathic helices connected by a flexible loop. Biochem Biophys Res Commun 2013; 437:408-12. [PMID: 23831469 DOI: 10.1016/j.bbrc.2013.06.091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [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: 06/21/2013] [Accepted: 06/24/2013] [Indexed: 01/31/2023]
Abstract
The BK channel, a tetrameric potassium channel with very high conductance, has a central role in numerous physiological functions. The BK channel can be activated by intracellular Ca(2+) and Mg(2+), as well as by membrane depolarization. Unlike other tetrameric potassium channels, the BK channel has seven transmembrane helices (S0-S6) including an extra helix S0. The intracellular segment between S0 and S1 (BK-IS1) is essential to BK channel functions and Asp99 in BK-IS1 is reported to be responsible for Mg(2+) coordination. In this study, BK-IS1 (44-113) was over-expressed using a bacterial system and purified in the presence of detergent micelles for multidimensional heteronuclear nuclear magnetic resonance (NMR) structural studies. Backbone resonance assignment and secondary structure analysis showed that BK-IS1 contains two amphipathic helices connected by a 36-residue loop. Amide (1)H-(15)N heteronuclear NOE analysis indicated that the loop is very flexible, while the two amphipathic helices are possibly stabilized through interaction with the membrane. A solution NMR-based titration assay of BK-IS1 was performed with various concentrations of Mg(2+). Two residues (Thr45 and Leu46) with chemical shift changes were observed but no, or very minor, chemical shift difference was observed for Asp99, indicating a possible site for binding divalent ions or other modulation partners.
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Affiliation(s)
- Pan Shi
- Hefei National Laboratory of Microscale Physical Sciences, School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, 230027, PR China
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