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Jensen JL, Wu Q, Colbert CL. NMR assignments of the N-terminal signaling domain of the TonB-dependent outer membrane transducer PupB. BIOMOLECULAR NMR ASSIGNMENTS 2018; 12:91-94. [PMID: 29071576 PMCID: PMC5871555 DOI: 10.1007/s12104-017-9785-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 10/20/2017] [Indexed: 06/07/2023]
Abstract
Outer membrane TonB-dependent transducers (TBDTs) actively transport ferric siderophore complexes from the extracellular environment into Gram-negative bacteria. They also participate in a cell-surface signaling regulatory pathway that results in upregulation of the transducer itself, in response to iron-deplete conditions. The TBDT PupB transports ferric pseudobactin, and signals through its N-terminal signaling domain (NTSD), while the TBDT homolog PupA is signaling-inactive. Here, we report the NMR chemical shift assignments of the PupB-NTSD. This information will provide the basis for structural characterization of the PupB-NTSD to further explore its signaling properties.
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Affiliation(s)
- Jaime L Jensen
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37240, USA
| | - Qiong Wu
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Christopher L Colbert
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND, 58102, USA.
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2
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Fritzsching KJ, Hong M, Schmidt-Rohr K. Conformationally selective multidimensional chemical shift ranges in proteins from a PACSY database purged using intrinsic quality criteria. JOURNAL OF BIOMOLECULAR NMR 2016; 64:115-30. [PMID: 26787537 PMCID: PMC4933674 DOI: 10.1007/s10858-016-0013-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 01/08/2016] [Indexed: 05/24/2023]
Abstract
We have determined refined multidimensional chemical shift ranges for intra-residue correlations ((13)C-(13)C, (15)N-(13)C, etc.) in proteins, which can be used to gain type-assignment and/or secondary-structure information from experimental NMR spectra. The chemical-shift ranges are the result of a statistical analysis of the PACSY database of >3000 proteins with 3D structures (1,200,207 (13)C chemical shifts and >3 million chemical shifts in total); these data were originally derived from the Biological Magnetic Resonance Data Bank. Using relatively simple non-parametric statistics to find peak maxima in the distributions of helix, sheet, coil and turn chemical shifts, and without the use of limited "hand-picked" data sets, we show that ~94% of the (13)C NMR data and almost all (15)N data are quite accurately referenced and assigned, with smaller standard deviations (0.2 and 0.8 ppm, respectively) than recognized previously. On the other hand, approximately 6% of the (13)C chemical shift data in the PACSY database are shown to be clearly misreferenced, mostly by ca. -2.4 ppm. The removal of the misreferenced data and other outliers by this purging by intrinsic quality criteria (PIQC) allows for reliable identification of secondary maxima in the two-dimensional chemical-shift distributions already pre-separated by secondary structure. We demonstrate that some of these correspond to specific regions in the Ramachandran plot, including left-handed helix dihedral angles, reflect unusual hydrogen bonding, or are due to the influence of a following proline residue. With appropriate smoothing, significantly more tightly defined chemical shift ranges are obtained for each amino acid type in the different secondary structures. These chemical shift ranges, which may be defined at any statistical threshold, can be used for amino-acid type assignment and secondary-structure analysis of chemical shifts from intra-residue cross peaks by inspection or by using a provided command-line Python script (PLUQin), which should be useful in protein structure determination. The refined chemical shift distributions are utilized in a simple quality test (SQAT) that should be applied to new protein NMR data before deposition in a databank, and they could benefit many other chemical-shift based tools.
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Affiliation(s)
| | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
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Vuister GW, Fogh RH, Hendrickx PMS, Doreleijers JF, Gutmanas A. An overview of tools for the validation of protein NMR structures. JOURNAL OF BIOMOLECULAR NMR 2014; 58:259-285. [PMID: 23877928 DOI: 10.1007/s10858-013-9750-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 06/04/2013] [Indexed: 06/02/2023]
Abstract
Biomolecular structures at atomic resolution present a valuable resource for the understanding of biology. NMR spectroscopy accounts for 11% of all structures in the PDB repository. In response to serious problems with the accuracy of some of the NMR-derived structures and in order to facilitate proper analysis of the experimental models, a number of program suites are available. We discuss nine of these tools in this review: PROCHECK-NMR, PSVS, GLM-RMSD, CING, Molprobity, Vivaldi, ResProx, NMR constraints analyzer and QMEAN. We evaluate these programs for their ability to assess the structural quality, restraints and their violations, chemical shifts, peaks and the handling of multi-model NMR ensembles. We document both the input required by the programs and output they generate. To discuss their relative merits we have applied the tools to two representative examples from the PDB: a small, globular monomeric protein (Staphylococcal nuclease from S. aureus, PDB entry 2kq3) and a small, symmetric homodimeric protein (a region of human myosin-X, PDB entry 2lw9).
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Affiliation(s)
- Geerten W Vuister
- Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK,
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Blaum BS, Wünsche W, Benie AJ, Kusov Y, Peters H, Gauss-Müller V, Peters T, Sczakiel G. Functional binding of hexanucleotides to 3C protease of hepatitis A virus. Nucleic Acids Res 2012; 40:3042-55. [PMID: 22156376 PMCID: PMC3326307 DOI: 10.1093/nar/gkr1152] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2010] [Revised: 11/09/2011] [Accepted: 11/10/2011] [Indexed: 12/01/2022] Open
Abstract
Oligonucleotides as short as 6 nt in length have been shown to bind specifically and tightly to proteins and affect their biological function. Yet, sparse structural data are available for corresponding complexes. Employing a recently developed hexanucleotide array, we identified hexadeoxyribonucleotides that bind specifically to the 3C protease of hepatitis A virus (HAV 3C(pro)). Inhibition assays in vitro identified the hexanucleotide 5'-GGGGGT-3' (G(5)T) as a 3C(pro) protease inhibitor. Using (1)H NMR spectroscopy, G(5)T was found to form a G-quadruplex, which might be considered as a minimal aptamer. With the help of (1)H, (15)N-HSQC experiments the binding site for G(5)T was located to the C-terminal β-barrel of HAV 3C(pro). Importantly, the highly conserved KFRDI motif, which has previously been identified as putative viral RNA binding site, is not part of the G(5)T-binding site, nor does G(5)T interfere with the binding of viral RNA. Our findings demonstrate that sequence-specific nucleic acid-protein interactions occur with oligonucleotides as small as hexanucleotides and suggest that these compounds may be of pharmaceutical relevance.
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Affiliation(s)
- Bärbel S. Blaum
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Winfried Wünsche
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Andrew J. Benie
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Yuri Kusov
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Hannelore Peters
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Verena Gauss-Müller
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Thomas Peters
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
| | - Georg Sczakiel
- Institute of Chemistry, Institute of Molecular Medicine, Institute for Virology and Cell Biology and Institute for Biochemistry, University of Luebeck, Center for Structural and Cell Biology in Medicine (CSCM), Ratzeburger Allee 160, D-23538 Luebeck, Germany
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Stratmann D, Boelens R, Bonvin AMJJ. Quantitative use of chemical shifts for the modeling of protein complexes. Proteins 2011; 79:2662-70. [PMID: 21744392 DOI: 10.1002/prot.23090] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2011] [Revised: 04/27/2011] [Accepted: 05/09/2011] [Indexed: 11/10/2022]
Abstract
Despite recent advances in the modeling of protein-protein complexes by docking, additional information is often required to identify the best solutions. For this purpose, NMR data deliver valuable restraints that can be used in the sampling and/or the scoring stage, like in the data-driven docking approach HADDOCK that can make use of NMR chemical shift perturbation (CSP) data to define the binding site on each protein and drive the docking. We show here that a quantitative use of chemical shifts (CS) in the scoring stage can help to resolve ambiguities. A quantitative CS-RMSD score based on (1) H(α) ,(13) C(α) , and (15) N chemical shifts ranks the best solutions always at the top, as demonstrated on a small benchmark of four complexes. It is implemented in a new docking protocol, CS-HADDOCK, which combines CSP data as ambiguous interaction restraints in the sampling stage with the CS-RMSD score in the final scoring stage. This combination of qualitative and quantitative use of chemical shifts increases the reliability of data-driven docking for the structure determination of complexes from limited NMR data.
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Affiliation(s)
- Dirk Stratmann
- Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Han B, Liu Y, Ginzinger SW, Wishart DS. SHIFTX2: significantly improved protein chemical shift prediction. JOURNAL OF BIOMOLECULAR NMR 2011; 50:43-57. [PMID: 21448735 PMCID: PMC3085061 DOI: 10.1007/s10858-011-9478-4] [Citation(s) in RCA: 491] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 01/28/2011] [Indexed: 05/03/2023]
Abstract
A new computer program, called SHIFTX2, is described which is capable of rapidly and accurately calculating diamagnetic (1)H, (13)C and (15)N chemical shifts from protein coordinate data. Compared to its predecessor (SHIFTX) and to other existing protein chemical shift prediction programs, SHIFTX2 is substantially more accurate (up to 26% better by correlation coefficient with an RMS error that is up to 3.3× smaller) than the next best performing program. It also provides significantly more coverage (up to 10% more), is significantly faster (up to 8.5×) and capable of calculating a wider variety of backbone and side chain chemical shifts (up to 6×) than many other shift predictors. In particular, SHIFTX2 is able to attain correlation coefficients between experimentally observed and predicted backbone chemical shifts of 0.9800 ((15)N), 0.9959 ((13)Cα), 0.9992 ((13)Cβ), 0.9676 ((13)C'), 0.9714 ((1)HN), 0.9744 ((1)Hα) and RMS errors of 1.1169, 0.4412, 0.5163, 0.5330, 0.1711, and 0.1231 ppm, respectively. The correlation between SHIFTX2's predicted and observed side chain chemical shifts is 0.9787 ((13)C) and 0.9482 ((1)H) with RMS errors of 0.9754 and 0.1723 ppm, respectively. SHIFTX2 is able to achieve such a high level of accuracy by using a large, high quality database of training proteins (>190), by utilizing advanced machine learning techniques, by incorporating many more features (χ(2) and χ(3) angles, solvent accessibility, H-bond geometry, pH, temperature), and by combining sequence-based with structure-based chemical shift prediction techniques. With this substantial improvement in accuracy we believe that SHIFTX2 will open the door to many long-anticipated applications of chemical shift prediction to protein structure determination, refinement and validation. SHIFTX2 is available both as a standalone program and as a web server ( http://www.shiftx2.ca ).
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Affiliation(s)
- Beomsoo Han
- Department of Computing Science, University of Alberta, Edmonton, AB Canada
| | - Yifeng Liu
- Department of Computing Science, University of Alberta, Edmonton, AB Canada
| | - Simon W. Ginzinger
- Department of Molecular Biology, Division of Bioinformatics, Center of Applied Molecular Engineering, University of Salzburg, Hellbrunnerstr. 34/3.OG, 5020 Salzburg, Austria
| | - David S. Wishart
- Department of Computing Science, University of Alberta, Edmonton, AB Canada
- Department of Biological Sciences, University of Alberta, Edmonton, AB Canada
- National Research Council, National Institute for Nanotechnology (NINT), Edmonton, AB T6G 2E8 Canada
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Breukels V, Konijnenberg A, Nabuurs SM, Doreleijers JF, Kovalevskaya NV, Vuister GW. Overview on the use of NMR to examine protein structure. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2011; Chapter 17:Unit17.5. [PMID: 21488042 DOI: 10.1002/0471140864.ps1705s64] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Any protein structure determination process contains several steps, starting from obtaining a suitable sample, then moving on to acquiring data and spectral assignment, and lastly to the final steps of structure determination and validation. This unit describes all of these steps, starting with the basic physical principles behind NMR and some of the most commonly measured and observed phenomena such as chemical shift, scalar and residual coupling, and the nuclear Overhauser effect. Then, in somewhat more detail, the process of spectral assignment and structure elucidation is explained. Furthermore, the use of NMR to study protein-ligand interaction, protein dynamics, or protein folding is described.
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Affiliation(s)
- Vincent Breukels
- Protein Biophysics, Institute for Molecules and Materials, Radboud University Nijmegen, Nijmegen, The Netherlands
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Wishart DS. Interpreting protein chemical shift data. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2011; 58:62-87. [PMID: 21241884 DOI: 10.1016/j.pnmrs.2010.07.004] [Citation(s) in RCA: 184] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2010] [Accepted: 07/29/2010] [Indexed: 05/12/2023]
Affiliation(s)
- David S Wishart
- Department of Biological Sciences, National Institute for Nanotechnology (NINT), Edmonton, AB, Canada T6G 2E8.
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