1
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Pandya MJ, Augustyniak W, Cliff MJ, Lindner I, Stinn A, Kahmann J, Temmerman K, Dannatt HRW, Waltho JP, Watson MJ. Backbone 1H, 13C and 15N resonance assignment of the ubiquitin specific protease 7 catalytic domain (residues 208-554) in complex with a small molecule ligand. Biomol NMR Assign 2024; 18:33-44. [PMID: 38472728 DOI: 10.1007/s12104-024-10165-7] [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: 12/08/2023] [Accepted: 02/05/2024] [Indexed: 03/14/2024]
Abstract
The backbone 1H, 13C and 15N resonance assignment of Ubiquitin Specific Protease 7 catalytic domain (residues 208-554) was performed in its complex with a small molecule ligand and in its apo form as a reference. The amide 1H-15N signal intensities were boosted by an amide hydrogen exchange protocol, where expressed 2H, 13C, 15N-labeled protein was unfolded and re-folded to ensure exchange of amide deuterons to protons. The resonance assignments were used to determine chemical shift perturbations on ligand binding, which are consistent with the binding site observed by crystallography.
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Affiliation(s)
- Maya J Pandya
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, United Kingdom
| | - Wojciech Augustyniak
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, United Kingdom.
| | - Matthew J Cliff
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Ilka Lindner
- Biophysics Department, NMR and Protein Production, Evotec SE, Hamburg, Germany
| | - Anne Stinn
- Biophysics Department, NMR and Protein Production, Evotec SE, Hamburg, Germany
| | - Jan Kahmann
- Biophysics Department, NMR and Protein Production, Evotec SE, Hamburg, Germany
| | - Koen Temmerman
- Biophysics Department, NMR and Protein Production, Evotec SE, Hamburg, Germany
| | - Hugh R W Dannatt
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, United Kingdom
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology, University of Manchester, Manchester, United Kingdom
| | - Martin J Watson
- C4X Discovery Ltd, Manchester One, 53 Portland Street, Manchester, M1 3LD, United Kingdom
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2
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L P Hosszu L, Sangar D, Batchelor M, Risse E, Hounslow AM, Collinge J, Waltho JP, Bieschke J. Loss of residues 119 - 136, including the first β-strand of human prion protein, generates an aggregation-competent partially "open" form. J Mol Biol 2023:168158. [PMID: 37244570 DOI: 10.1016/j.jmb.2023.168158] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
In prion replication, the cellular form of prion protein (PrPC) must undergo a full conformational transition to its disease-associated fibrillar form. Transmembrane forms of PrP have been implicated in this structural conversion. The cooperative unfolding of a structural core in PrPC presents a substantial energy barrier to prion formation, with membrane insertion and detachment of parts of PrP presenting a plausible route to its reduction. Here, we examined the removal of residues 119 - 136 of PrP, a region which includes the first β-strand and a substantial portion of the conserved hydrophobic region of PrP, a region which associates with the ER membrane, on the structure, stability and self-association of the folded domain of PrPC. We see an "open" native-like conformer with increased solvent exposure which fibrilises more readily than the native state. These data suggest a stepwise folding transition, which is initiated by the conformational switch to this "open" form of PrPC.
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Affiliation(s)
- Laszlo L P Hosszu
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Daljit Sangar
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Mark Batchelor
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Emmanuel Risse
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
| | - John Collinge
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK; Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jan Bieschke
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK.
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3
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Robertson AJ, Cruz-Navarrete FA, Wood HP, Vekaria N, Hounslow AM, Bisson C, Cliff MJ, Baxter NJ, Waltho JP. An Enzyme with High Catalytic Proficiency Utilizes Distal Site Substrate Binding Energy to Stabilize the Closed State but at the Expense of Substrate Inhibition. ACS Catal 2022; 12:3149-3164. [PMID: 35692864 PMCID: PMC9171722 DOI: 10.1021/acscatal.1c05524] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/10/2022] [Indexed: 02/05/2023]
Abstract
Understanding the factors that underpin the enormous catalytic proficiencies of enzymes is fundamental to catalysis and enzyme design. Enzymes are, in part, able to achieve high catalytic proficiencies by utilizing the binding energy derived from nonreacting portions of the substrate. In particular, enzymes with substrates containing a nonreacting phosphodianion group coordinated in a distal site have been suggested to exploit this binding energy primarily to facilitate a conformational change from an open inactive form to a closed active form, rather than to either induce ground state destabilization or stabilize the transition state. However, detailed structural evidence for the model is limited. Here, we use β-phosphoglucomutase (βPGM) to investigate the relationship between binding a phosphodianion group in a distal site, the adoption of a closed enzyme form, and catalytic proficiency. βPGM catalyzes the isomerization of β-glucose 1-phosphate to glucose 6-phosphate via phosphoryl transfer reactions in the proximal site, while coordinating a phosphodianion group of the substrate(s) in a distal site. βPGM has one of the largest catalytic proficiencies measured and undergoes significant domain closure during its catalytic cycle. We find that side chain substitution at the distal site results in decreased substrate binding that destabilizes the closed active form but is not sufficient to preclude the adoption of a fully closed, near-transition state conformation. Furthermore, we reveal that binding of a phosphodianion group in the distal site stimulates domain closure even in the absence of a transferring phosphoryl group in the proximal site, explaining the previously reported β-glucose 1-phosphate inhibition. Finally, our results support a trend whereby enzymes with high catalytic proficiencies involving phosphorylated substrates exhibit a greater requirement to stabilize the closed active form.
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Affiliation(s)
- Angus J. Robertson
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | | | - Henry P. Wood
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Nikita Vekaria
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Andrea M. Hounslow
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Claudine Bisson
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicola J. Baxter
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- School of Biosciences, The University of Sheffield, Sheffield, S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
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4
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Robertson AJ, Wilson AL, Burn MJ, Cliff MJ, Popelier PLA, Waltho JP. The Relationship between Enzyme Conformational Change, Proton Transfer, and Phosphoryl Transfer in β-Phosphoglucomutase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Angus J. Robertson
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Alex L. Wilson
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Matthew J. Burn
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Matthew J. Cliff
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Paul L. A. Popelier
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, United Kingdom
- Department of Chemistry, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
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5
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Hosszu LLP, Conners R, Sangar D, Batchelor M, Sawyer EB, Fisher S, Cliff MJ, Hounslow AM, McAuley K, Leo Brady R, Jackson GS, Bieschke J, Waltho JP, Collinge J. Structural effects of the highly protective V127 polymorphism on human prion protein. Commun Biol 2020; 3:402. [PMID: 32728168 PMCID: PMC7391680 DOI: 10.1038/s42003-020-01126-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/03/2020] [Indexed: 01/02/2023] Open
Abstract
Prion diseases, a group of incurable, lethal neurodegenerative disorders of mammals including humans, are caused by prions, assemblies of misfolded host prion protein (PrP). A single point mutation (G127V) in human PrP prevents prion disease, however the structural basis for its protective effect remains unknown. Here we show that the mutation alters and constrains the PrP backbone conformation preceding the PrP β-sheet, stabilising PrP dimer interactions by increasing intermolecular hydrogen bonding. It also markedly changes the solution dynamics of the β2-α2 loop, a region of PrP structure implicated in prion transmission and cross-species susceptibility. Both of these structural changes may affect access to protein conformers susceptible to prion formation and explain its profound effect on prion disease.
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Affiliation(s)
- Laszlo L P Hosszu
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Rebecca Conners
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
- University of Bristol, School of Biochemistry, Biomedical Sciences Building, University Walk, Clifton, BS8 1TD, UK
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, UK
| | - Daljit Sangar
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Mark Batchelor
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Elizabeth B Sawyer
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
- London School of Hygiene & Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Stuart Fisher
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
- ESRF, 71, Avenue des Martyrs, CS 40220, 38043, Grenoble Cedex 9, France
| | - Matthew J Cliff
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Katherine McAuley
- Diamond Light Source, Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, UK
| | - R Leo Brady
- University of Bristol, School of Biochemistry, Biomedical Sciences Building, University Walk, Clifton, BS8 1TD, UK
| | - Graham S Jackson
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Jan Bieschke
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Department of Molecular Biology and Biotechnology, University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - John Collinge
- MRC Prion Unit at UCL, UCL Institute of Prion Diseases, 33 Cleveland Street, London, W1W 7FF, UK.
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6
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Wilson AL, Outeiral C, Dowd SE, Doig AJ, Popelier PLA, Waltho JP, Almond A. Deconvolution of conformational exchange from Raman spectra of aqueous RNA nucleosides. Commun Chem 2020; 3:56. [PMID: 36703475 PMCID: PMC9814580 DOI: 10.1038/s42004-020-0298-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 04/06/2020] [Indexed: 01/29/2023] Open
Abstract
Ribonucleic acids (RNAs) are key to the central dogma of molecular biology. While Raman spectroscopy holds great potential for studying RNA conformational dynamics, current computational Raman prediction and assignment methods are limited in terms of system size and inclusion of conformational exchange. Here, a framework is presented that predicts Raman spectra using mixtures of sub-spectra corresponding to major conformers calculated using classical and ab initio molecular dynamics. Experimental optimization allowed purines and pyrimidines to be characterized as predominantly syn and anti, respectively, and ribose into exchange between equivalent south and north populations. These measurements are in excellent agreement with Raman spectroscopy of ribonucleosides, and previous experimental and computational results. This framework provides a measure of ribonucleoside solution populations and conformational exchange in RNA subunits. It complements other experimental techniques and could be extended to other molecules, such as proteins and carbohydrates, enabling biological insights and providing a new analytical tool.
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Affiliation(s)
- Alex L. Wilson
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK
| | - Carlos Outeiral
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK
| | - Sarah E. Dowd
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK
| | - Andrew J. Doig
- grid.5379.80000000121662407Division of Neuroscience and Experimental Psychology, Michael Smith Building, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, M13 9PT Manchester, UK
| | - Paul L. A. Popelier
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK
| | - Jonathan P. Waltho
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK ,grid.11835.3e0000 0004 1936 9262Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, S10 2TN Sheffield, UK
| | - Andrew Almond
- grid.5379.80000000121662407Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Science, Faculty of Science and Engineering, The University of Manchester, M1 7DN Manchester, UK
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7
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Cruz-Navarrete FA, Baxter NJ, Wood HP, Hounslow AM, Waltho JP. 1H, 15N and 13C backbone resonance assignments of the P146A variant of β-phosphoglucomutase from Lactococcus lactis in its substrate-free form. Biomol NMR Assign 2019; 13:349-356. [PMID: 31396843 PMCID: PMC6713671 DOI: 10.1007/s12104-019-09904-y] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/20/2019] [Indexed: 06/10/2023]
Abstract
β-Phosphoglucomutase (βPGM) is a magnesium-dependent phosphoryl transfer enzyme that catalyses the reversible isomerisation of β-glucose 1-phosphate and glucose 6-phosphate, via two phosphoryl transfer steps and a β-glucose 1,6-bisphosphate intermediate. Substrate-free βPGM is an essential component of the catalytic cycle and an understanding of its dynamics would present significant insights into βPGM functionality, and enzyme catalysed phosphoryl transfer in general. Previously, 30 residues around the active site of substrate-free βPGMWT were identified as undergoing extensive millisecond dynamics and were unassignable. Here we report 1H, 15N and 13C backbone resonance assignments of the P146A variant (βPGMP146A) in its substrate-free form, where the K145-A146 peptide bond adopts a trans conformation in contrast to all crystal structures of βPGMWT, where the K145-P146 peptide bond is cis. In βPGMP146A millisecond dynamics are suppressed for all but 17 residues, allowing 92% of backbone resonances to be assigned. Secondary structure predictions using TALOS-N reflect βPGM crystal structures, and a chemical shift comparison between substrate-free βPGMP146A and βPGMWT confirms that the solution conformations are very similar, except for the D137-A147 loop. Hence, the isomerisation state of the 145-146 peptide bond has little effect on structure but the cis conformation triggers millisecond dynamics in the hinge (V12-T16), the nucleophile (D8) and residues that coordinate the transferring phosphate group (D8 and S114-S116), and the D137-A147 loop (V141-A142 and K145). These millisecond dynamics occur in addition to those for residues involved in coordinating the catalytic MgII ion and the L44-L53 loop responsible for substrate discrimination.
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Affiliation(s)
- F Aaron Cruz-Navarrete
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Henry P Wood
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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8
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Panova S, Cliff MJ, Macek P, Blackledge M, Jensen MR, Nissink JWM, Embrey KJ, Davies R, Waltho JP. Mapping Hidden Residual Structure within the Myc bHLH-LZ Domain Using Chemical Denaturant Titration. Structure 2019; 27:1537-1546.e4. [DOI: 10.1016/j.str.2019.07.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 05/05/2019] [Accepted: 07/17/2019] [Indexed: 12/25/2022]
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9
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Bennet IA, Finger LD, Baxter NJ, Ambrose B, Hounslow AM, Thompson MJ, Exell JC, Shahari NNBM, Craggs TD, Waltho JP, Grasby JA. Regional conformational flexibility couples substrate specificity and scissile phosphate diester selectivity in human flap endonuclease 1. Nucleic Acids Res 2019; 46:5618-5633. [PMID: 29718417 PMCID: PMC6009646 DOI: 10.1093/nar/gky293] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/09/2018] [Indexed: 02/07/2023] Open
Abstract
Human flap endonuclease-1 (hFEN1) catalyzes the divalent metal ion-dependent removal of single-stranded DNA protrusions known as flaps during DNA replication and repair. Substrate selectivity involves passage of the 5'-terminus/flap through the arch and recognition of a single nucleotide 3'-flap by the α2-α3 loop. Using NMR spectroscopy, we show that the solution conformation of free and DNA-bound hFEN1 are consistent with crystal structures; however, parts of the arch region and α2-α3 loop are disordered without substrate. Disorder within the arch explains how 5'-flaps can pass under it. NMR and single-molecule FRET data show a shift in the conformational ensemble in the arch and loop region upon addition of DNA. Furthermore, the addition of divalent metal ions to the active site of the hFEN1-DNA substrate complex demonstrates that active site changes are propagated via DNA-mediated allostery to regions key to substrate differentiation. The hFEN1-DNA complex also shows evidence of millisecond timescale motions in the arch region that may be required for DNA to enter the active site. Thus, hFEN1 regional conformational flexibility spanning a range of dynamic timescales is crucial to reach the catalytically relevant ensemble.
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Affiliation(s)
- Ian A Bennet
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - L David Finger
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK.,Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, UK
| | - Benjamin Ambrose
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Andrea M Hounslow
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK
| | - Mark J Thompson
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Jack C Exell
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Nur Nazihah B Md Shahari
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Timothy D Craggs
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S10 2TN, UK.,Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester M1 7DN, UK
| | - Jane A Grasby
- Centre for Chemical Biology, Department of Chemistry, Krebs Institute for Biomolecular Research, The University of Sheffield, Sheffield S3 7HF, UK
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10
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Czarnota S, Johannissen LO, Baxter NJ, Rummel F, Wilson AL, Cliff MJ, Levy CW, Scrutton NS, Waltho JP, Hay S. Equatorial Active Site Compaction and Electrostatic Reorganization in Catechol- O-methyltransferase. ACS Catal 2019; 9:4394-4401. [PMID: 31080692 PMCID: PMC6503465 DOI: 10.1021/acscatal.9b00174] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 03/26/2019] [Indexed: 12/18/2022]
Abstract
Catechol-O-methyltransferase (COMT) is a model S-adenosyl-l-methionine (SAM) dependent methyl transferase, which catalyzes the methylation of catecholamine neurotransmitters such as dopamine in the primary pathway of neurotransmitter deactivation in animals. Despite extensive study, there is no consensus view of the physical basis of catalysis in COMT. Further progress requires experimental data that directly probes active site geometry, protein dynamics and electrostatics, ideally in a range of positions along the reaction coordinate. Here we establish that sinefungin, a fungal-derived inhibitor of SAM-dependent enzymes that possess transition state-like charge on the transferring group, can be used as a transition state analog of COMT when combined with a catechol. X-ray crystal structures and NMR backbone assignments of the ternary complexes of the soluble form of human COMT containing dinitrocatechol, Mg2+ and SAM or sinefungin were determined. Comparison and further analysis with the aid of density functional theory calculations and molecular dynamics simulations provides evidence for active site "compaction", which is driven by electrostatic stabilization between the transferring methyl group and "equatorial" active site residues that are orthogonal to the donor-acceptor (pseudo reaction) coordinate. We propose that upon catecholamine binding and subsequent proton transfer to Lys 144, the enzyme becomes geometrically preorganized, with little further movement along the donor-acceptor coordinate required for methyl transfer. Catalysis is then largely facilitated through stabilization of the developing charge on the transferring methyl group via "equatorial" H-bonding and electrostatic interactions orthogonal to the donor-acceptor coordinate.
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Affiliation(s)
- Sylwia Czarnota
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nicola J. Baxter
- Krebs
Institute for Biomolecular Research, Department of Molecular Biology
and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Felix Rummel
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Alex L. Wilson
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Matthew J. Cliff
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Colin W. Levy
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
| | - Jonathan P. Waltho
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
- Krebs
Institute for Biomolecular Research, Department of Molecular Biology
and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, The University
of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
- School
of Chemistry, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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11
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Iorgu AI, Cliff MJ, Waltho JP, Scrutton NS, Hay S. Isotopically labeled flavoenzymes and their uses in probing reaction mechanisms. Methods Enzymol 2019; 620:145-166. [PMID: 31072485 DOI: 10.1016/bs.mie.2019.03.009] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The incorporation of stable isotopes into proteins is beneficial or essential for a range of experiments, including NMR, neutron scattering and reflectometry, proteomic mass spectrometry, vibrational spectroscopy and "heavy" enzyme kinetic isotope effect (KIE) measurements. Here, we present detailed protocols for the stable isotopic labeling of pentaerythritol tetranitrate reductase (PETNR) via recombinant expression in E. coli. PETNR is an ene-reductase belonging to the Old Yellow Enzyme (OYE) family of flavoenzymes, and is regarded as a model system for studying hydride transfer reactions. Included is a discussion of how efficient back-exchange of amide protons in the protein core can be achieved and how the intrinsic flavin mononucleotide (FMN) cofactor can be exchanged, allowing the production of isotopologues with differentially labeled protein and cofactor. In addition to a thorough description of labeling strategies, we briefly exemplify how data analysis and interpretation of "heavy" enzyme KIEs can be performed.
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Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, United Kingdom.
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12
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Iorgu AI, Baxter NJ, Cliff MJ, Levy C, Waltho JP, Hay S, Scrutton NS. Nonequivalence of Second Sphere "Noncatalytic" Residues in Pentaerythritol Tetranitrate Reductase in Relation to Local Dynamics Linked to H-Transfer in Reactions with NADH and NADPH Coenzymes. ACS Catal 2018; 8:11589-11599. [PMID: 31119061 PMCID: PMC6516726 DOI: 10.1021/acscatal.8b02810] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 10/23/2018] [Indexed: 11/28/2022]
Abstract
![]()
Many enzymes that
catalyze hydride transfer reactions work via
a mechanism dominated by quantum mechanical tunneling. The involvement
of fast vibrational modes of the reactive complex is often inferred
in these reactions, as in the case of the NAD(P)H-dependent pentaerythritol
tetranitrate reductase (PETNR). Herein, we interrogated the H-transfer
mechanism in PETNR by designing conservative (L25I and I107L) and
side chain shortening (L25A and I107A) PETNR variants and using a
combination of experimental approaches (stopped-flow rapid kinetics,
X-ray crystallography, isotope/temperature dependence studies of H-transfer
and NMR spectroscopy). X-ray data show subtle changes in the local
environment of the targeted side chains but no major structural perturbation
caused by mutagenesis of these two second sphere active site residues.
However, temperature dependence studies of H-transfer revealed a coenzyme-specific
and complex thermodynamic equilibrium between different reactive configurations
in PETNR–coenzyme complexes. We find that mutagenesis of these
second sphere “noncatalytic” residues affects differently
the reactivity of PETNR with NADPH and NADH coenzymes. We attribute
this to subtle, dynamic structural changes in the PETNR active site,
the effects of which impact differently in the nonequivalent reactive
geometries of PETNR−NADH and PETNR−NADPH complexes.
This inference is confirmed through changes observed in the NMR chemical
shift data for PETNR complexes with unreactive 1,4,5,6-tetrahydro-NAD(P)
analogues. We show that H-transfer rates can (to some extent) be buffered
through entropy–enthalpy compensation, but that use of integrated
experimental tools reveals hidden complexities that implicate a role
for dynamics in this relatively simple H-transfer reaction. Similar
approaches are likely to be informative in other enzymes to understand
the relative importance of (distal) hydrophobic side chains and dynamics
in controlling the rates of enzymatic H-transfer.
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Affiliation(s)
- Andreea I. Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nicola J. Baxter
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Colin Levy
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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13
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Johnson LA, Robertson AJ, Baxter NJ, Trevitt CR, Bisson C, Jin Y, Wood HP, Hounslow AM, Cliff MJ, Blackburn GM, Bowler MW, Waltho JP. van der Waals Contact between Nucleophile and Transferring Phosphorus Is Insufficient To Achieve Enzyme Transition-State Architecture. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01612] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Luke A. Johnson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Angus J. Robertson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Nicola J. Baxter
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Clare R. Trevitt
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Claudine Bisson
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Yi Jin
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Henry P. Wood
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Andrea M. Hounslow
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - G. Michael Blackburn
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Matthew W. Bowler
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, F-38042 Grenoble, France
| | - Jonathan P. Waltho
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Sheffield S10 2TN, United Kingdom
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester M1 7DN, United Kingdom
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14
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Macek P, Cliff MJ, Embrey KJ, Holdgate GA, Nissink JWM, Panova S, Waltho JP, Davies RA. Myc phosphorylation in its basic helix-loop-helix region destabilizes transient α-helical structures, disrupting Max and DNA binding. J Biol Chem 2018; 293:9301-9310. [PMID: 29695509 DOI: 10.1074/jbc.ra118.002709] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 03/08/2018] [Revised: 04/16/2018] [Indexed: 01/01/2023] Open
Abstract
Myelocytomatosis proto-oncogene transcription factor (Myc) is an intrinsically disordered protein with critical roles in cellular homeostasis and neoplastic transformation. It is tightly regulated in the cell, with Myc phosphorylation playing a major role. In addition to the well-described tandem phosphorylation of Thr-52 and Ser-62 in the Myc transactivation domain linked to its degradation, P21 (RAC1)-activated kinase 2 (PAK2)-mediated phosphorylation of serine and threonine residues in the C-terminal basic helix-loop-helix leucine zipper (bHLH-LZ) region regulates Myc transcriptional activity. Here we report that PAK2 preferentially phosphorylates Myc twice, at Thr-358 and Ser-373, with only a minor fraction being modified at the previously identified Thr-400 site. For transcriptional activity, Myc binds E-box DNA elements, requiring its heterodimerization with Myc-associated factor X (Max) via the bHLH-LZ regions. Using isothermal calorimetry (ITC), we found that Myc phosphorylation destabilizes this ternary protein-DNA complex by decreasing Myc's affinity for Max by 2 orders of magnitude, suggesting a major effect of phosphorylation on this complex. Phosphomimetic substitutions revealed that Ser-373 dominates the effect on Myc-Max heterodimerization. Moreover, a T400D substitution disrupted Myc's affinity for Max. ITC, NMR, and CD analyses of several Myc variants suggested that the effect of phosphorylation on the Myc-Max interaction is caused by secondary structure disruption during heterodimerization rather than by a change in the structurally disordered state of Myc or by phosphorylation-induced electrostatic repulsion in the heterodimer. Our findings provide critical insights into the effects of PAK2-catalyzed phosphorylation of Myc on its interactions with Max and DNA.
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Affiliation(s)
- Pavel Macek
- From AstraZeneca, IMED Discovery Sciences, Alderley Park SK10 4TG, United Kingdom,
| | - Matthew J Cliff
- the Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Kevin J Embrey
- AstraZeneca, IMED Discovery Sciences, Cambridge CB4 0WG, United Kingdom
| | | | | | - Stanislava Panova
- the Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Jonathan P Waltho
- the Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rick A Davies
- From AstraZeneca, IMED Discovery Sciences, Alderley Park SK10 4TG, United Kingdom,
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15
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Iorgu AI, Baxter NJ, Cliff MJ, Waltho JP, Hay S, Scrutton NS. 1H, 15N and 13C backbone resonance assignments of pentaerythritol tetranitrate reductase from Enterobacter cloacae PB2. Biomol NMR Assign 2018; 12:79-83. [PMID: 29168057 PMCID: PMC5869876 DOI: 10.1007/s12104-017-9791-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 08/23/2017] [Accepted: 09/29/2017] [Indexed: 06/07/2023]
Abstract
Pentaerythritol tetranitrate reductase (PETNR) is a flavoenzyme possessing a broad substrate specificity and is a member of the Old Yellow Enzyme family of oxidoreductases. As well as having high potential as an industrial biocatalyst, PETNR is an excellent model system for studying hydrogen transfer reactions. Mechanistic studies performed with PETNR using stopped-flow methods have shown that tunneling contributes towards hydride transfer from the NAD(P)H coenzyme to the flavin mononucleotide (FMN) cofactor and fast protein dynamics have been inferred to facilitate this catalytic step. Herein, we report the near-complete 1H, 15N and 13C backbone resonance assignments of PETNR in a stoichiometric complex with the FMN cofactor in its native oxidized form, which were obtained using heteronuclear multidimensional NMR spectroscopy. A total of 97% of all backbone resonances were assigned, with 333 out of a possible 344 residues assigned in the 1H-15N TROSY spectrum. This is the first report of an NMR structural study of a flavoenzyme from the Old Yellow Enzyme family and it lays the foundation for future investigations of functional dynamics in hydride transfer catalytic mechanism.
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Affiliation(s)
- Andreea I Iorgu
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nicola J Baxter
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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16
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Serimbetov Z, Baxter NJ, Cliff MJ, Waltho JP. 1H, 15N, 13C backbone resonance assignments of human phosphoglycerate kinase in a transition state analogue complex with ADP, 3-phosphoglycerate and magnesium trifluoride. Biomol NMR Assign 2017; 11:251-256. [PMID: 28866776 PMCID: PMC5594045 DOI: 10.1007/s12104-017-9758-3] [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] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/05/2017] [Indexed: 06/07/2023]
Abstract
Human phosphoglycerate kinase (PGK) is an energy generating glycolytic enzyme that catalyses the transfer of a phosphoryl group from 1,3-bisphosphoglycerate (BPG) to ADP producing 3-phosphoglycerate (3PG) and ATP. PGK is composed of two α/β Rossmann-fold domains linked by a central α-helix and the active site is located in the cleft formed between the N-domain which binds BPG or 3PG, and the C-domain which binds the nucleotides ADP or ATP. Domain closure is required to bring the two substrates into close proximity for phosphoryl transfer to occur, however previous structural studies involving a range of native substrates and substrate analogues only yielded open or partly closed PGK complexes. X-ray crystallography using magnesium trifluoride (MgF3-) as a isoelectronic and near-isosteric mimic of the transferring phosphoryl group (PO3-), together with 3PG and ADP has been successful in trapping human PGK in a fully closed transition state analogue (TSA) complex. In this work we report the 1H, 15N and 13C backbone resonance assignments of human PGK in the solution conformation of the fully closed PGK:3PG:MgF3:ADP TSA complex. Assignments were obtained by heteronuclear multidimensional NMR spectroscopy. In total, 97% of all backbone resonances were assigned in the complex, with 385 out of a possible 399 residues assigned in the 1H-15N TROSY spectrum. Prediction of solution secondary structure from a chemical shift analysis using the TALOS-N webserver is in good agreement with the published X-ray crystal structure of this complex.
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Affiliation(s)
- Zhalgas Serimbetov
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nicola J Baxter
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
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17
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Jin Y, Molt RW, Pellegrini E, Cliff MJ, Bowler MW, Richards NGJ, Blackburn GM, Waltho JP. Assessing the Influence of Mutation on GTPase Transition States by Using X-ray Crystallography, 19 F NMR, and DFT Approaches. Angew Chem Int Ed Engl 2017; 56:9732-9735. [PMID: 28498638 PMCID: PMC5575484 DOI: 10.1002/anie.201703074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Indexed: 11/08/2022]
Abstract
We report X-ray crystallographic and 19 F NMR studies of the G-protein RhoA complexed with MgF3- , GDP, and RhoGAP, which has the mutation Arg85'Ala. When combined with DFT calculations, these data permit the identification of changes in transition state (TS) properties. The X-ray data show how Tyr34 maintains solvent exclusion and the core H-bond network in the active site by relocating to replace the missing Arg85' sidechain. The 19 F NMR data show deshielding effects that indicate the main function of Arg85' is electronic polarization of the transferring phosphoryl group, primarily mediated by H-bonding to O3G and thence to PG . DFT calculations identify electron-density redistribution and pinpoint why the TS for guanosine 5'-triphosphate (GTP) hydrolysis is higher in energy when RhoA is complexed with RhoGAPArg85'Ala relative to wild-type (WT) RhoGAP. This study demonstrates that 19 F NMR measurements, in combination with X-ray crystallography and DFT calculations, can reliably dissect the response of small GTPases to site-specific modifications.
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Affiliation(s)
- Yi Jin
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.,School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK
| | - Robert W Molt
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,ENSCO, Inc., Melbourne, FL, 32940, USA
| | - Erika Pellegrini
- Structural Biology Group, ESRF-The European Synchrotron, CS40220, 38043, Grenoble, Cedex 9, France
| | - Matthew J Cliff
- Manchester Institute of Biotechnology, Manchester, M1 7DN, UK
| | - Matthew W Bowler
- Structural Biology Group, ESRF-The European Synchrotron, CS40220, 38043, Grenoble, Cedex 9, France.,European Molecular Biology Laboratory, Grenoble Outstation CS90181, 38042, Grenoble, Cedex 9, France
| | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Sheffield, S10 2TN, UK.,Manchester Institute of Biotechnology, Manchester, M1 7DN, UK
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18
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Jin Y, Molt RW, Pellegrini E, Cliff MJ, Bowler MW, Richards NGJ, Blackburn GM, Waltho JP. Assessing the Influence of Mutation on GTPase Transition States by Using X‐ray Crystallography,
19
F NMR, and DFT Approaches. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703074] [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: 11/11/2022]
Affiliation(s)
- Yi Jin
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
- School of ChemistryCardiff University Cardiff CF10 3AT UK
| | - Robert W. Molt
- School of ChemistryCardiff University Cardiff CF10 3AT UK
- Department of Biochemistry and Molecular BiologyIndiana University School of Medicine Indianapolis IN 46202 USA
- ENSCO, Inc. Melbourne FL 32940 USA
| | - Erika Pellegrini
- Structural Biology GroupESRF-The European Synchrotron, CS40220 38043 Grenoble, Cedex 9 France
| | | | - Matthew W. Bowler
- Structural Biology GroupESRF-The European Synchrotron, CS40220 38043 Grenoble, Cedex 9 France
- European Molecular Biology Laboratory, Grenoble Outstation CS90181 38042 Grenoble, Cedex 9 France
| | | | - G. Michael Blackburn
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
| | - Jonathan P. Waltho
- Department of Molecular Biology and BiotechnologyKrebs InstituteUniversity of Sheffield Sheffield S10 2TN UK
- Manchester Institute of Biotechnology Manchester M1 7DN UK
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19
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Blackburn GM, Cherfils J, Moss GP, Richards NGJ, Waltho JP, Williams NH, Wittinghofer A. How to name atoms in phosphates, polyphosphates, their derivatives and mimics, and transition state analogues for enzyme-catalysed phosphoryl transfer reactions (IUPAC Recommendations 2016). PURE APPL CHEM 2017. [DOI: 10.1515/pac-2016-0202] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AbstractProcedures are proposed for the naming of individual atoms, P, O, F, N, and S in phosphate esters, amidates, thiophosphates, polyphosphates, their mimics, and analogues of transition states for enzyme-catalyzed phosphoryl transfer reactions. Their purpose is to enable scientists in very different fields, e.g. biochemistry, biophysics, chemistry, computational chemistry, crystallography, and molecular biology, to share standard protocols for the labelling of individual atoms in complex molecules. This will facilitate clear and unambiguous descriptions of structural results, as well as scientific intercommunication concerning them. At the present time, perusal of the Protein Data Bank (PDB) and other sources shows that there is a limited degree of commonality in nomenclature, but a large measure of irregularity in more complex structures. The recommendations described here adhere to established practice as closely as possible, in particular to IUPAC and IUBMB recommendations and to “best practice” in the PDB, especially to its atom labelling of amino acids, and particularly to Cahn-Ingold-Prelog rules for stereochemical nomenclature. They are designed to work in complex enzyme sites for binding phosphates but also to have utility for non-enzymatic systems. Above all, the recommendations are designed to be easy to comprehend and user-friendly.
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Affiliation(s)
- G. Michael Blackburn
- 1Department of Molecular Biology, Krebs Institute, University of Sheffield, S10 2TN, UK
| | - Jacqueline Cherfils
- 2Laboratoire de Biologie et Pharmacologie Appliquée, CNRS – École Normale Supérieure Paris-Saclay, Cachan, France. http://orcid.org/0000-0002-8966-3067
| | - Gerard P. Moss
- 3Queen Mary University of London, School of Biological and Chemical Sciences, London E1 4NS, UK
| | - Nigel G. J. Richards
- 4Department of Chemistry, Indiana University Purdue University Indianapolis, IL 46202, USA; and School of Chemistry, Cardiff University, Cardiff CF10 3AT, UK
| | | | | | - Alfred Wittinghofer
- 7Group for Structural Biology, Max-Planck-Institut für Molekulare Physiologie, 44227 Dortmund, Deutschland
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20
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Czarnota S, Baxter NJ, Cliff MJ, Waltho JP, Scrutton NS, Hay S. 1H, 15N, 13C backbone resonance assignments of human soluble catechol O-methyltransferase in complex with S-adenosyl-L-methionine and 3,5-dinitrocatechol. Biomol NMR Assign 2017; 11:57-61. [PMID: 27981425 PMCID: PMC5343089 DOI: 10.1007/s12104-016-9720-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 08/23/2016] [Accepted: 11/30/2016] [Indexed: 06/06/2023]
Abstract
Catechol O-methyltransferase (COMT) is an enzyme that plays a major role in catechol neurotransmitter deactivation. Inhibition of COMT can increase neurotransmitter levels, which provides a means of treatment for Parkinson's disease, schizophrenia and depression. COMT exists as two isozymes: a soluble cytoplasmic form (S-COMT), expressed in the liver and kidneys and a membrane-bound form (MB-COMT), found mostly in the brain. Here we report the backbone 1H, 15N and 13C chemical shift assignments of S-COMT in complex with S-adenosyl-L-methionine, 3,5-dinitrocatechol and Mg2+. Assignments were obtained by heteronuclear multidimensional NMR spectroscopy. In total, 97 % of all backbone resonances were assigned in the complex, with 205 out of a possible 215 residues assigned in the 1H-15N TROSY spectrum. Prediction of solution secondary structure from a chemical shift analysis using the TALOS+ webserver is in good agreement with published X-ray crystal structures.
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Affiliation(s)
- Sylwia Czarnota
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Nicola J Baxter
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK.
| | - Matthew J Cliff
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, The University of Sheffield, Firth Court, Western Bank, Sheffield, S10 2TN, UK
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Sam Hay
- Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK.
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21
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Jin Y, Richards NG, Waltho JP, Blackburn GM. Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes. Angew Chem Int Ed Engl 2017; 56:4110-4128. [PMID: 27862756 DOI: 10.1002/anie.201606474] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Indexed: 12/27/2022]
Abstract
The 1994 structure of a transition-state analogue with AlF4- and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO3- ) groups. The number of enzyme structures in the PDB containing metal fluorides (MFx ) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF3- that mimic ground-state phosphates; 2) octahedral complexes, primarily based on AlF4- , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF3- and putative AlF30 moieties, which mimic the geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding into the behavior and manipulation of phosphate monoesters in molecular biology. This Review provides a comprehensive overview of these structures, their uses, and their computational development.
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Affiliation(s)
- Yi Jin
- Department of Chemistry, University of York, York, YO10 5DD, UK
| | | | | | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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Affiliation(s)
- Yi Jin
- Department of Chemistry; University of York; York YO10 5DD Großbritannien
| | - Nigel G. Richards
- School of Chemistry; Cardiff University; Cardiff CF10 3AT Großbritannien
| | | | - G. Michael Blackburn
- Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN Großbritannien
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Jin Y, Molt RW, Waltho JP, Richards NGJ, Blackburn GM. (19)F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA-Catalyzed GTP Hydrolysis. Angew Chem Int Ed Engl 2016; 55:3318-22. [PMID: 26822702 PMCID: PMC4770445 DOI: 10.1002/anie.201509477] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 01/14/2016] [Indexed: 11/13/2022]
Abstract
Molecular details for RhoA/GAP catalysis of the hydrolysis of GTP to GDP are poorly understood. We use (19)F NMR chemical shifts in the MgF3(-) transition state analogue (TSA) complex as a spectroscopic reporter to indicate electron distribution for the γ-PO3(-) oxygens in the corresponding TS, implying that oxygen coordinated to Mg has the greatest electron density. This was validated by QM calculations giving a picture of the electronic properties of the transition state (TS) for nucleophilic attack of water on the γ-PO3(-) group based on the structure of a RhoA/GAP-GDP-MgF3(-) TSA complex. The TS model displays a network of 20 hydrogen bonds, including the GAP Arg85' side chain, but neither phosphate torsional strain nor general base catalysis is evident. The nucleophilic water occupies a reactive location different from that in multiple ground state complexes, arising from reorientation of the Gln-63 carboxamide by Arg85' to preclude direct hydrogen bonding from water to the target γ-PO3(-) group.
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Affiliation(s)
- Yi Jin
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert W Molt
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA
| | - Jonathan P Waltho
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.
- Manchester Institute of Biotechnology, Manchester, M1 7DN, UK.
| | - Nigel G J Richards
- Department of Chemistry and Chemical Biology, Indiana University Purdue University Indianapolis, Indianapolis, IN, 46202, USA.
- School of Chemistry, Cardiff University, Cardiff, CF10 3AT, UK.
| | - G Michael Blackburn
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK.
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Jin Y, Molt RW, Waltho JP, Richards NGJ, Blackburn GM. 19F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA-Catalyzed GTP Hydrolysis. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201509477] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yi Jin
- Krebs Institute, Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN UK
| | - Robert W. Molt
- Department of Chemistry and Chemical Biology; Indiana University Purdue University Indianapolis; Indianapolis IN 46202 USA
| | - Jonathan P. Waltho
- Krebs Institute, Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN UK
- Manchester Institute of Biotechnology; Manchester M1 7DN UK
| | - Nigel G. J. Richards
- Department of Chemistry and Chemical Biology; Indiana University Purdue University Indianapolis; Indianapolis IN 46202 USA
- School of Chemistry; Cardiff University; Cardiff CF10 3AT UK
| | - G. Michael Blackburn
- Krebs Institute, Department of Molecular Biology and Biotechnology; University of Sheffield; Sheffield S10 2TN UK
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25
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Davis PJ, Holmes D, Waltho JP, Staniforth RA. Limited Proteolysis Reveals That Amyloids from the 3D Domain-Swapping Cystatin B Have a Non-Native β-Sheet Topology. J Mol Biol 2015; 427:2418-2434. [DOI: 10.1016/j.jmb.2015.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2015] [Revised: 05/08/2015] [Accepted: 05/15/2015] [Indexed: 01/21/2023]
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26
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Kiraly P, Adams RW, Paudel L, Foroozandeh M, Aguilar JA, Timári I, Cliff MJ, Nilsson M, Sándor P, Batta G, Waltho JP, Kövér KE, Morris GA. Real-time pure shift ¹⁵N HSQC of proteins: a real improvement in resolution and sensitivity. J Biomol NMR 2015; 62:43-52. [PMID: 25737243 PMCID: PMC4432093 DOI: 10.1007/s10858-015-9913-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 12/19/2014] [Accepted: 02/20/2015] [Indexed: 06/01/2023]
Abstract
Spectral resolution in proton NMR spectroscopy is reduced by the splitting of resonances into multiplets due to the effect of homonuclear scalar couplings. Although these effects are often hidden in protein NMR spectroscopy by low digital resolution and routine apodization, behind the scenes homonuclear scalar couplings increase spectral overcrowding. The possibilities for biomolecular NMR offered by new pure shift NMR methods are illustrated here. Both resolution and sensitivity are improved, without any increase in experiment time. In these experiments, free induction decays are collected in short bursts of data acquisition, with durations short on the timescale of J-evolution, interspersed with suitable refocusing elements. The net effect is real-time (t 2) broadband homodecoupling, suppressing the multiplet structure caused by proton-proton interactions. The key feature of the refocusing elements is that they discriminate between the resonances of active (observed) and passive (coupling partner) spins. This can be achieved either by using band-selective refocusing or by the BIRD element, in both cases accompanied by a nonselective 180° proton pulse. The latter method selects the active spins based on their one-bond heteronuclear J-coupling to (15)N, while the former selects a region of the (1)H spectrum. Several novel pure shift experiments are presented, and the improvements in resolution and sensitivity they provide are evaluated for representative samples: the N-terminal domain of PGK; ubiquitin; and two mutants of the small antifungal protein PAF. These new experiments, delivering improved sensitivity and resolution, have the potential to replace the current standard HSQC experiments.
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Affiliation(s)
- Peter Kiraly
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Ralph W. Adams
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Liladhar Paudel
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
- Department of Anesthesiology and Pain Medicine, Mitochondria and Metabolism Center, University of Washington, 850 Republican St, Seattle, WA 98109 USA
| | | | - Juan A. Aguilar
- Department of Chemistry, Durham University, South Road, Durham, DH1 3LE UK
| | - István Timári
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary
| | - Matthew J. Cliff
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Mathias Nilsson
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
| | - Péter Sándor
- Agilent Technologies R&D and Marketing GmbH & Co. KG, Hewlett-Packard Strasse 8, 76337 Waldbronn, Germany
| | - Gyula Batta
- Department of Organic Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary
| | - Jonathan P. Waltho
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN UK
| | - Katalin E. Kövér
- Department of Inorganic and Analytical Chemistry, University of Debrecen, Egyetem tér 1, Debrecen, 4032 Hungary
| | - Gareth A. Morris
- School of Chemistry, University of Manchester, Oxford Road, Manchester, M13 9PL UK
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Volk M, Milanesi L, Waltho JP, Hunter CA, Beddard GS. The roughness of the protein energy landscape results in anomalous diffusion of the polypeptide backbone. Phys Chem Chem Phys 2015; 17:762-82. [DOI: 10.1039/c4cp03058c] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Recombination of photolysed protein disulfide bonds confirms subdiffusional backbone motion and measures the roughness of the protein's energy landscape.
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Affiliation(s)
- Martin Volk
- Department of Chemistry
- University of Liverpool
- Liverpool
- UK
| | - Lilia Milanesi
- School of Chemical and Biological Sciences
- Queen Mary
- University of London
- London
- UK
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology
- University of Sheffield
- Sheffield
- UK
- Manchester Institute of Biotechnology
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28
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Jin Y, Bhattasali D, Pellegrini E, Forget SM, Baxter NJ, Cliff MJ, Bowler MW, Jakeman DL, Blackburn GM, Waltho JP. α-Fluorophosphonates reveal how a phosphomutase conserves transition state conformation over hexose recognition in its two-step reaction. Proc Natl Acad Sci U S A 2014; 111:12384-9. [PMID: 25104750 PMCID: PMC4151737 DOI: 10.1073/pnas.1402850111] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
β-Phosphoglucomutase (βPGM) catalyzes isomerization of β-D-glucose 1-phosphate (βG1P) into D-glucose 6-phosphate (G6P) via sequential phosphoryl transfer steps using a β-D-glucose 1,6-bisphosphate (βG16BP) intermediate. Synthetic fluoromethylenephosphonate and methylenephosphonate analogs of βG1P deliver novel step 1 transition state analog (TSA) complexes for βPGM, incorporating trifluoromagnesate and tetrafluoroaluminate surrogates of the phosphoryl group. Within an invariant protein conformation, the β-D-glucopyranose ring in the βG1P TSA complexes (step 1) is flipped over and shifted relative to the G6P TSA complexes (step 2). Its equatorial hydroxyl groups are hydrogen-bonded directly to the enzyme rather than indirectly via water molecules as in step 2. The (C)O-P bond orientation for binding the phosphate in the inert phosphate site differs by ∼ 30° between steps 1 and 2. By contrast, the orientations for the axial O-Mg-O alignment for the TSA of the phosphoryl group in the catalytic site differ by only ∼ 5°, and the atoms representing the five phosphorus-bonded oxygens in the two transition states (TSs) are virtually superimposable. The conformation of βG16BP in step 1 does not fit into the same invariant active site for step 2 by simple positional interchange of the phosphates: the TS alignment is achieved by conformational change of the hexose rather than the protein.
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Affiliation(s)
- Yi Jin
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Debabrata Bhattasali
- Department of Chemistry, College of Pharmacy, Dalhousie University, Halifax, NS, Canada B3H 4R2
| | - Erika Pellegrini
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom; Structural Biology Group, European Synchrotron Radiation Facility, 38042 Grenoble, Cedex 9, France; European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, Cedex 9, France
| | - Stephanie M Forget
- Department of Chemistry, College of Pharmacy, Dalhousie University, Halifax, NS, Canada B3H 4R2
| | - Nicola J Baxter
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom
| | - Matthew J Cliff
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom; Manchester Institute of Biotechnology, Manchester M1 7DN, United Kingdom; and
| | - Matthew W Bowler
- Structural Biology Group, European Synchrotron Radiation Facility, 38042 Grenoble, Cedex 9, France; European Molecular Biology Laboratory, Grenoble Outstation, 38042 Grenoble, Cedex 9, France; Unit of Virus Host Cell Interactions, University of Grenoble Alpes-European Molecular Biology Laboratory-Centre National de la Recherche Scientifique, 38042 Grenoble, Cedex 9, France
| | - David L Jakeman
- Department of Chemistry, College of Pharmacy, Dalhousie University, Halifax, NS, Canada B3H 4R2;
| | - G Michael Blackburn
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom;
| | - Jonathan P Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom; Manchester Institute of Biotechnology, Manchester M1 7DN, United Kingdom; and
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Trevitt CR, Hosszu LLP, Batchelor M, Panico S, Terry C, Nicoll AJ, Risse E, Taylor WA, Sandberg MK, Al-Doujaily H, Linehan JM, Saibil HR, Scott DJ, Collinge J, Waltho JP, Clarke AR. N-terminal domain of prion protein directs its oligomeric association. J Biol Chem 2014; 289:25497-508. [PMID: 25074940 PMCID: PMC4162156 DOI: 10.1074/jbc.m114.566588] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The self-association of prion protein (PrP) is a critical step in the pathology of prion diseases. It is increasingly recognized that small non-fibrillar β-sheet-rich oligomers of PrP may be of crucial importance in the prion disease process. Here, we characterize the structure of a well defined β-sheet-rich oligomer, containing ∼12 PrP molecules, and often enclosing a central cavity, formed using full-length recombinant PrP. The N-terminal region of prion protein (residues 23-90) is required for the formation of this distinct oligomer; a truncated form comprising residues 91-231 forms a broad distribution of aggregated species. No infectivity or toxicity was found using cell and animal model systems. This study demonstrates that examination of the full repertoire of conformers and assembly states that can be accessed by PrP under specific experimental conditions should ideally be done using the full-length protein.
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Affiliation(s)
- Clare R Trevitt
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Laszlo L P Hosszu
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Mark Batchelor
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Silvia Panico
- the Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX
| | - Cassandra Terry
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Andrew J Nicoll
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Emmanuel Risse
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - William A Taylor
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Malin K Sandberg
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Huda Al-Doujaily
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Jacqueline M Linehan
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Helen R Saibil
- the Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX
| | - David J Scott
- the National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, the ISIS Spallation Neutron and Muon Source and Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, and
| | - John Collinge
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG
| | - Jonathan P Waltho
- the Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Anthony R Clarke
- From the Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, Queen Square, London WC1N 3BG,
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Krishnan R, Tsubery H, Proschitsky MY, Asp E, Lulu M, Gilead S, Gartner M, Waltho JP, Davis PJ, Hounslow AM, Kirschner DA, Inouye H, Myszka DG, Wright J, Solomon B, Fisher RA. A Bacteriophage Capsid Protein Provides a General Amyloid Interaction Motif (GAIM) That Binds and Remodels Misfolded Protein Assemblies. J Mol Biol 2014; 426:2500-19. [DOI: 10.1016/j.jmb.2014.04.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Revised: 03/21/2014] [Accepted: 04/14/2014] [Indexed: 01/08/2023]
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31
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Paudel L, Adams RW, Király P, Aguilar JA, Foroozandeh M, Cliff MJ, Nilsson M, Sándor P, Waltho JP, Morris GA. Simultaneously enhancing spectral resolution and sensitivity in heteronuclear correlation NMR spectroscopy. Angew Chem Int Ed Engl 2013; 52:11616-9. [PMID: 24014213 PMCID: PMC4065349 DOI: 10.1002/anie.201305709] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Indexed: 11/26/2022]
Abstract
BIRD's eye view: Adding periodic BIRD J-refocusing (BIRD=bilinear rotation decoupling) to data acquisition in an HSQC experiment causes broadband homonuclear decoupling, giving a single signal for each proton chemical shift. This pure shift method improves both resolution and signal-to-noise ratio, without the need for special data processing.
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Affiliation(s)
- Liladhar Paudel
- School of Chemistry, University of ManchesterOxford Road, Manchester, M13 9PL (UK)
| | - Ralph W Adams
- School of Chemistry, University of ManchesterOxford Road, Manchester, M13 9PL (UK)
| | - Péter Király
- School of Chemistry, University of ManchesterOxford Road, Manchester, M13 9PL (UK)
- Institute of Organic Chemistry, Hungarian Academy of SciencesPusztaszeri út 59–67, 1025 Budapest (Hungary)
| | - Juan A Aguilar
- School of Chemistry, University of ManchesterOxford Road, Manchester, M13 9PL (UK)
- Department of Chemistry, Durham UniversitySouth Road, Durham, DH1 3LE (UK)
| | | | - Matthew J Cliff
- Manchester Institute of Biotechnology131 Princess Street, Manchester, M1 7DN (UK)
| | - Mathias Nilsson
- School of Chemistry, University of ManchesterOxford Road, Manchester, M13 9PL (UK)
- Department of Food Science, University of CopenhagenRolighedsvej 30, 1958 Frederiksberg C (Denmark)
| | - Péter Sándor
- Agilent Technologies R & D a. Marketing GmbH & Co. KGHewlett–Packard Strasse 8, 76337 Waldbronn (Germany)
| | - Jonathan P Waltho
- Manchester Institute of Biotechnology131 Princess Street, Manchester, M1 7DN (UK)
| | - Gareth A Morris
- School of Chemistry, University of ManchesterOxford Road, Manchester, M13 9PL (UK)
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32
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Paudel L, Adams RW, Király P, Aguilar JA, Foroozandeh M, Cliff MJ, Nilsson M, Sándor P, Waltho JP, Morris GA. Simultaneously Enhancing Spectral Resolution and Sensitivity in Heteronuclear Correlation NMR Spectroscopy. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201305709] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Abstract
Early studies on chemical synthesis of biological molecules can be seen to progress to preparation and biological evaluation of phosphonates as analogues of biological phosphates, with emphasis on their isosteric and isopolar character. Work with such mimics progressed into structural studies with a range of nucleotide-utilising enzymes. The arrival of metal fluorides as analogues of the phosphoryl group, PO(3)(-), for transition state (TS) analysis of enzyme reactions stimulated the symbiotic deployment of (19)F NMR and protein crystallography. Characteristics of enzyme transition state analogues are reviewed for a range of reactions. From the available MF(x) species, trifluoroberyllate gives tetrahedral mimics of ground states (GS) in which phosphate is linked to carboxylate and phosphate oxyanions. Tetrafluoroaluminate is widely employed as a TS mimic, but it necessarily imposes octahedral geometry on the assembled complexes, whereas phosphoryl transfer involves trigonal bipyramidal (tbp) geometry. Trifluoromagnesate (MgF(3)(-)) provides the near-ideal solution, delivering tbp geometry and correct anionic charge. Some of the forty reported tbp structures assigned as having AlF(3)(0) cores have been redefined as trifluoromagnesate complexes. Transition state analogues for a range of kinases, mutases, and phosphatases provide a detailed description of mechanism for phosphoryl group transfer, supporting the concept of charge balance in their TS and of concerted-associative pathways for biocatalysis. Above all, superposition of GS and TS structures reveals that in associative phosphoryl transfer, the phosphorus atom migrates through a triangle of three, near-stationary, equatorial oxygens. The extension of these studies to near attack conformers further illuminates enzyme catalysis of phosphoryl transfer.
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Affiliation(s)
- G M Blackburn
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK.
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Pudney CR, Guerriero A, Baxter NJ, Johannissen LO, Waltho JP, Hay S, Scrutton NS. Fast protein motions are coupled to enzyme H-transfer reactions. J Am Chem Soc 2013; 135:2512-7. [PMID: 23373704 DOI: 10.1021/ja311277k] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [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
Coupling of fast protein dynamics to enzyme chemistry is controversial and has ignited considerable debate, especially over the past 15 years in relation to enzyme-catalyzed H-transfer. H-transfer can occur by quantum tunneling, and the temperature dependence of kinetic isotope effects (KIEs) has emerged as the "gold standard" descriptor of these reactions. The anomalous temperature dependence of KIEs is often rationalized by invoking fast motions to facilitate H-transfer, yet crucially, direct evidence for coupled motions is lacking. The fast motions hypothesis underpinning the temperature dependence of KIEs is based on inference. Here, we have perturbed vibrational motions in pentaerythritol tetranitrate reductase (PETNR) by isotopic substitution where all non-exchangeable atoms were replaced with the corresponding heavy isotope ((13)C, (15)N, and (2)H). The KIE temperature dependence is perturbed by heavy isotope labeling, demonstrating a direct link between (promoting) vibrations in the protein and the observed KIE. Further we show that temperature-independent KIEs do not necessarily rule out a role for fast dynamics coupled to reaction chemistry. We show causality between fast motions and enzyme chemistry and demonstrate how this impacts on experimental KIEs for enzyme reactions.
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Affiliation(s)
- Christopher R Pudney
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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35
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Milanesi L, Waltho JP, Hunter CA, Shaw DJ, Beddard GS, Reid GD, Dev S, Volk M. Measurement of energy landscape roughness of folded and unfolded proteins. Proc Natl Acad Sci U S A 2012; 109:19563-8. [PMID: 23150572 PMCID: PMC3511724 DOI: 10.1073/pnas.1211764109] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The dynamics of protein conformational changes, from protein folding to smaller changes, such as those involved in ligand binding, are governed by the properties of the conformational energy landscape. Different techniques have been used to follow the motion of a protein over this landscape and thus quantify its properties. However, these techniques often are limited to short timescales and low-energy conformations. Here, we describe a general approach that overcomes these limitations. Starting from a nonnative conformation held by an aromatic disulfide bond, we use time-resolved spectroscopy to observe nonequilibrium backbone dynamics over nine orders of magnitude in time, from picoseconds to milliseconds, after photolysis of the disulfide bond. We find that the reencounter probability of residues that initially are in close contact decreases with time following an unusual power law that persists over the full time range and is independent of the primary sequence. Model simulations show that this power law arises from subdiffusional motion, indicating a wide distribution of trapping times in local minima of the energy landscape, and enable us to quantify the roughness of the energy landscape (4-5 k(B)T). Surprisingly, even under denaturing conditions, the energy landscape remains highly rugged with deep traps (>20 k(B)T) that result from multiple nonnative interactions and are sufficient for trapping on the millisecond timescale. Finally, we suggest that the subdiffusional motion of the protein backbone found here may promote rapid folding of proteins with low contact order by enhancing contact formation between nearby residues.
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Affiliation(s)
- Lilia Milanesi
- Departments of Molecular Biology and Biotechnology and
- Chemistry, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Jonathan P. Waltho
- Departments of Molecular Biology and Biotechnology and
- Manchester Institute of Biotechnology, Manchester M1 7DN, United Kingdom
| | | | - Daniel J. Shaw
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; and
| | - Godfrey S. Beddard
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; and
| | - Gavin D. Reid
- School of Chemistry, University of Leeds, Leeds LS2 9JT, United Kingdom; and
| | - Sagarika Dev
- Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
| | - Martin Volk
- Department of Chemistry, University of Liverpool, Liverpool L69 3BX, United Kingdom
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Jin Y, Cliff MJ, Baxter NJ, Dannatt HRW, Hounslow AM, Bowler MW, Blackburn GM, Waltho JP. Charge-Balanced Metal Fluoride Complexes for Protein Kinase A with Adenosine Diphosphate and Substrate Peptide SP20. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204266] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Jin Y, Cliff MJ, Baxter NJ, Dannatt HRW, Hounslow AM, Bowler MW, Blackburn GM, Waltho JP. Charge-balanced metal fluoride complexes for protein kinase A with adenosine diphosphate and substrate peptide SP20. Angew Chem Int Ed Engl 2012; 51:12242-5. [PMID: 23125010 DOI: 10.1002/anie.201204266] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 10/10/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Yi Jin
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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38
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Paramore R, Morgan GJ, Davis PJ, Sharma CA, Hounslow A, Taler-Verčič A, Žerovnik E, Waltho JP, Cliff MJ, Staniforth RA. Mapping local structural perturbations in the native state of stefin B (cystatin B) under amyloid forming conditions. Front Mol Neurosci 2012; 5:94. [PMID: 23091450 PMCID: PMC3469841 DOI: 10.3389/fnmol.2012.00094] [Citation(s) in RCA: 6] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 08/27/2012] [Indexed: 11/17/2022] Open
Abstract
Unlike a number of amyloid-forming proteins, stefins, and in particular stefin B (cystatin B) form amyloids under conditions where the native state predominates. In order to trigger oligomerization processes, the stability of the protein needs to be compromised, favoring structural re-arrangement however, accelerating fibril formation is not a simple function of protein stability. We report here on how optimal conditions for amyloid formation lead to the destabilization of dimeric and tetrameric states of the protein in favor of the monomer. Small, highly localized structural changes can be mapped out that allow us to visualize directly areas of the protein which eventually become responsible for triggering amyloid formation. These regions of the protein overlap with the Cu (II)-binding sites which we identify here for the first time. We hypothesize that in vivo modulators of amyloid formation may act similarly to painstakingly optimized solvent conditions developed in vitro. We discuss these data in the light of current structural models of stefin B amyloid fibrils based on H-exchange data, where the detachment of the helical part and the extension of loops were observed.
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Affiliation(s)
- Robert Paramore
- Department of Molecular Biology and Biotechnology, University of SheffieldSheffield, UK
| | - Gareth J. Morgan
- Department of Molecular Biology and Biotechnology, University of SheffieldSheffield, UK
| | - Peter J. Davis
- Department of Molecular Biology and Biotechnology, University of SheffieldSheffield, UK
| | - Carrie-anne Sharma
- Department of Molecular Biology and Biotechnology, University of SheffieldSheffield, UK
| | - Andrea Hounslow
- Department of Molecular Biology and Biotechnology, University of SheffieldSheffield, UK
| | - Ajda Taler-Verčič
- Department of Biochemistry and Molecular and Structural Biology, Institute Jožef StefanLjubljana, Slovenia
| | - Eva Žerovnik
- Department of Biochemistry and Molecular and Structural Biology, Institute Jožef StefanLjubljana, Slovenia
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, University of SheffieldSheffield, UK
- Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, University of ManchesterManchester, UK
| | - Matthew J. Cliff
- Department of Molecular Biology and Biotechnology, University of SheffieldSheffield, UK
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Milanesi L, Hunter CA, Tzokova N, Waltho JP, Tomas S. Versatile low-molecular-weight hydrogelators: achieving multiresponsiveness through a modular design. Chemistry 2011; 17:9753-61. [PMID: 21793058 DOI: 10.1002/chem.201100640] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [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] [Received: 02/28/2011] [Indexed: 01/28/2023]
Abstract
Multiresponsive low-molecular-weight hydrogelators (LMWHs) are ideal candidates for the development of smart, soft, nanotechnology materials. The synthesis is however very challenging. On the one hand, de novo design is hampered by our limited ability to predict the assembly of small molecules in water. On the other hand, modification of pre-existing LMWHs is limited by the number of different stimuli-sensitive chemical moieties that can be introduced into a small molecule without seriously disrupting the ability to gelate water. Herein we report the synthesis and characterization of multistimuli LMWHs, based on a modular design, composed of a hydrophobic, disulfide, aromatic moiety, a maleimide linker, and a hydrophilic section based on an amino acid, here N-acetyl-L-cysteine (NAC). As most LMWHs, these gelators experience reversible gel-to-sol transition following temperature changes. Additionally, the NAC moiety allows reversible control of the assembly of the gel by pH changes. The reduction of the aromatic disulfide triggers a gel-to-sol transition that, depending on the design of the particular LMWH, can be reverted by reoxidation of the resulting thiol. Finally, the hydrolysis of the cyclic imide moieties provides an additional trigger for the gel-to-sol transition with a timescale that is appropriate for use in drug-delivery applications. The efficient response to the multiple external stimuli, coupled to the modular design makes these LMWHs an excellent starting point for the development of smart nanomaterials with applications that include controlled drug release. These hydrogelators, which were discovered by serendipity rather than design, suggest nonetheless a general strategy for the introduction of multiple stimuli-sensitive chemical moieties, to offset the introduction of hydrophilic moieties with additional hydrophobic ones, in order to minimize the upsetting of the critical hydrophobic-hydrophilic balance of the LMWH.
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Affiliation(s)
- Lilia Milanesi
- Institute of Structural and Molecular Biology, Department of Biological Sciences, School of Science, Birkbeck University of London, London, UK.
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40
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Xiaoxia L, Marston JP, Baxter NJ, Hounslow AM, Yufen Z, Blackburn GM, Cliff MJ, Waltho JP. Prioritization of charge over geometry in transition state analogues of a dual specificity protein kinase. J Am Chem Soc 2011; 133:3989-94. [PMID: 21348513 DOI: 10.1021/ja1090035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The direct observation of a transition state analogue (TSA) complex for tyrosine phosphorylation by a signaling kinase has been achieved using (19)F NMR analysis of MEK6 in complex with tetrafluoroaluminate (AlF(4)(-)), ADP, and p38α MAP kinase (acceptor residue: Tyr182). Solvent-induced isotope shifts and chemical shifts for the AlF(4)(-) moiety indicate that two fluorine atoms are coordinated by the two catalytic magnesium ions of the kinase active site, while the two remaining fluorides are liganded by protein residues only. An equivalent, yet distinct, AlF(4)(-) complex involving the alternative acceptor residue in p38α (Thr180) is only observed when the Tyr182 is mutated to phenylalanine. The formation of octahedral AlF(4)(-) species for both acceptor residues, rather than the trigonal bipyramidal AlF(3)(0) previously identified in the only other metal fluoride complex with a protein kinase, shows the requirement of MEK6 for a TSA that is isoelectronic with the migrating phosphoryl group. This requirement has hitherto only been demonstrated for proteins having a single catalytic magnesium ion.
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Affiliation(s)
- Liu Xiaoxia
- Krebs Institute and Department of Molecular Biology & Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
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41
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Nicoll AJ, Trevitt CR, Tattum MH, Risse E, Quarterman E, Ibarra AA, Wright C, Jackson GS, Sessions RB, Farrow M, Waltho JP, Clarke AR, Collinge J. Pharmacological chaperone for the structured domain of human prion protein. Proc Natl Acad Sci U S A 2010; 107:17610-5. [PMID: 20876144 PMCID: PMC2955083 DOI: 10.1073/pnas.1009062107] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In prion diseases, the misfolded protein aggregates are derived from cellular prion protein (PrP(C)). Numerous ligands have been reported to bind to human PrP(C) (huPrP), but none to the structured region with the affinity required for a pharmacological chaperone. Using equilibrium dialysis, we screened molecules previously suggested to interact with PrP to discriminate between those which did not interact with PrP, behaved as nonspecific polyionic aggregates or formed a genuine interaction. Those that bind could potentially act as pharmacological chaperones. Here we report that a cationic tetrapyrrole [Fe(III)-TMPyP], which displays potent antiprion activity, binds to the structured region of huPrP. Using a battery of biophysical techniques, we demonstrate that Fe(III)-TMPyP forms a 11 complex via the structured C terminus of huPrP with a K(d) of 4.5 ± 2 μM, which is in the range of its IC(50) for curing prion-infected cells of 1.6 ± 0.4 μM and the concentration required to inhibit protein-misfolding cyclic amplification. Therefore, this molecule tests the hypothesis that stabilization of huPrP(C), as a principle, could be used in the treatment of human prion disease. The identification of a binding site with a defined 3D structure opens up the possibility of designing small molecules that stabilize huPrP and prevent its conversion into the disease-associated form.
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Affiliation(s)
| | - Clare R. Trevitt
- Medical Research Council Prion Unit, University College of London Institute of Neurology, Queen Square, London WCN1 3BG, United Kingdom
| | - M. Howard Tattum
- Medical Research Council Prion Unit, University College of London Institute of Neurology, Queen Square, London WCN1 3BG, United Kingdom
| | | | | | - Amaurys Avila Ibarra
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom; and
| | | | - Graham S. Jackson
- Medical Research Council Prion Unit, University College of London Institute of Neurology, Queen Square, London WCN1 3BG, United Kingdom
| | - Richard B. Sessions
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom; and
| | | | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Anthony R. Clarke
- Medical Research Council Prion Unit, University College of London Institute of Neurology, Queen Square, London WCN1 3BG, United Kingdom
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom; and
| | - John Collinge
- Department of Neurodegenerative Disease and
- Medical Research Council Prion Unit, University College of London Institute of Neurology, Queen Square, London WCN1 3BG, United Kingdom
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Hosszu LLP, Tattum MH, Jones S, Trevitt CR, Wells MA, Waltho JP, Collinge J, Jackson GS, Clarke AR. The H187R mutation of the human prion protein induces conversion of recombinant prion protein to the PrP(Sc)-like form. Biochemistry 2010; 49:8729-38. [PMID: 20718410 DOI: 10.1021/bi100572j] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [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: 12/20/2022]
Abstract
Prion diseases are associated with a conformational switch in the prion protein (PrP) from its normal cellular form (denoted PrP(C)) to a disease-associated "scrapie" form (PrP(Sc)). A number of PrP(Sc)-like conformations can be generated by incubating recombinant PrP(C) at low pH, indicating that protonation of key residues is likely to destabilize PrP(C), facilitating its conversion to PrP(Sc). Here, we examine the stability of human PrP(C) with pH and find that PrP(C) fold stability is significantly reduced by the protonation of two histidine residues, His187 and His155. Mutation of His187 to an arginine, which imposes a permanently positively charged residue in this region of the protein, has a dramatic effect on the folding of PrP(C), resulting in a molecule that displays a markedly increased propensity to oligomerize. The oligomeric form is characterized by an increased β-sheet content, loss of fixed side chain interactions, and partial proteinase resistance. Hence, the protonation state of H187 appears to be crucial in determining the conformation of PrP; the unprotonated form favors native PrP(C), while the protonated form favors PrP(Sc)-like conformations. These results are relevant to the pathogenic H187R mutation found in humans, which is associated with an inherited prion disease [also termed Gerstmann-Sträussler-Scheinker (GSS) syndrome] with unusual features such as childhood neuropsychiatric illness. Our data imply that the intrinsic instability of the PrP(C) conformation in this variant is caused by a positive charge at this site in the protein. This mutation is distinct from all those associated with GSS, which have much more subtle physical consequences. The degree of instability might be the cause of the unusually early onset of mental disturbance in affected individuals.
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Affiliation(s)
- Laszlo L P Hosszu
- MRC Prion Unit, UCL Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG, UK
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43
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Cliff MJ, Bowler MW, Varga A, Marston JP, Szabó J, Hounslow AM, Baxter NJ, Blackburn GM, Vas M, Waltho JP. Transition state analogue structures of human phosphoglycerate kinase establish the importance of charge balance in catalysis. J Am Chem Soc 2010; 132:6507-16. [PMID: 20397725 DOI: 10.1021/ja100974t] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Transition state analogue (TSA) complexes formed by phosphoglycerate kinase (PGK) have been used to test the hypothesis that balancing of charge within the transition state dominates enzyme-catalyzed phosphoryl transfer. High-resolution structures of trifluoromagnesate (MgF(3)(-)) and tetrafluoroaluminate (AlF(4)(-)) complexes of PGK have been determined using X-ray crystallography and (19)F-based NMR methods, revealing the nature of the catalytically relevant state of this archetypal metabolic kinase. Importantly, the side chain of K219, which coordinates the alpha-phosphate group in previous ground state structures, is sequestered into coordinating the metal fluoride, thereby creating a charge environment complementary to the transferring phosphoryl group. In line with the dominance of charge balance in transition state organization, the substitution K219A induces a corresponding reduction in charge in the bound aluminum fluoride species, which changes to a trifluoroaluminate (AlF(3)(0)) complex. The AlF(3)(0) moiety retains the octahedral geometry observed within AlF(4)(-) TSA complexes, which endorses the proposal that some of the widely reported trigonal AlF(3)(0) complexes of phosphoryl transfer enzymes may have been misassigned and in reality contain MgF(3)(-).
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Affiliation(s)
- Matthew J Cliff
- The Krebs Institute & The Department of Molecular Biology and Biotechnology, The University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, UK
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44
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Baxter NJ, Bowler MW, Alizadeh T, Cliff MJ, Hounslow AM, Wu B, Berkowitz DB, Williams NH, Blackburn GM, Waltho JP. Atomic details of near-transition state conformers for enzyme phosphoryl transfer revealed by MgF-3 rather than by phosphoranes. Proc Natl Acad Sci U S A 2010; 107:4555-60. [PMID: 20164409 PMCID: PMC2842025 DOI: 10.1073/pnas.0910333106] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Prior evidence supporting the direct observation of phosphorane intermediates in enzymatic phosphoryl transfer reactions was based on the interpretation of electron density corresponding to trigonal species bridging the donor and acceptor atoms. Close examination of the crystalline state of beta-phosphoglucomutase, the archetypal phosphorane intermediate-containing enzyme, reveals that the trigonal species is not PO-3 , but is MgF-3 (trifluoromagnesate). Although MgF-3 complexes are transition state analogues rather than phosphoryl group transfer reaction intermediates, the presence of fluorine nuclei in near-transition state conformations offers new opportunities to explore the nature of the interactions, in particular the independent measures of local electrostatic and hydrogen-bonding distributions using 19F NMR. Measurements on three beta-PGM-MgF-3 -sugar phosphate complexes show a remarkable relationship between NMR chemical shifts, primary isotope shifts, NOEs, cross hydrogen bond F...H-N scalar couplings, and the atomic positions determined from the high-resolution crystal structure of the beta-PGM-MgF--3 -G6P complex. The measurements provide independent validation of the structural and isoelectronic MgF--3 model of near-transition state conformations.
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Affiliation(s)
- Nicola J. Baxter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Matthew W. Bowler
- Structural Biology Group, European Synchrotron Radiation Facility, 6 rue Jules Horowitz, F-38043 Grenoble, France
| | - Tooba Alizadeh
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Matthew J. Cliff
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Andrea M. Hounslow
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Bin Wu
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - David B. Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, NE 68588
| | - Nicholas H. Williams
- Centre for Chemical Biology, Department of Chemistry, University of Sheffield, Sheffield S3 7HF, United Kingdom; and
| | - G. Michael Blackburn
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
- Faculty of Life Sciences and Manchester Interdisciplinary Biocentre, University of Manchester, Manchester, M1 7DN, United Kingdom
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45
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Marston JP, Cliff MJ, Reed MAC, Blackburn GM, Hounslow AM, Craven CJ, Waltho JP. Structural tightening and interdomain communication in the catalytic cycle of phosphoglycerate kinase. J Mol Biol 2010; 396:345-60. [PMID: 19944703 DOI: 10.1016/j.jmb.2009.11.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 11/16/2009] [Accepted: 11/19/2009] [Indexed: 11/25/2022]
Abstract
Changes in amide-NH chemical shift and hydrogen exchange rates as phosphoglycerate kinase progresses through its catalytic cycle have been measured to assess whether they correlate with changes in hydrogen bonding within the protein. Four representative states were compared: the free enzyme, a product complex containing 3-phosphoglyceric acid (3PG), a substrate complex containing ADP and a transition-state analogue (TSA) complex containing a 3PG-AlF(4)(-)-ADP moiety. There are an overall increases in amide protection from hydrogen exchange when the protein binds the substrate and product ligands and an additional increase when the TSA complex is formed. This is consistent with stabilisation of the protein structure by ligand binding. However, there is no correlation between the chemical shift changes and the protection factor changes, indicating that the protection factor changes are not associated with an overall shortening of hydrogen bonds in the protected ground state, but rather can be ascribed to the properties of the high-energy, exchange-competent state. Therefore, an overall structural tightening mechanism is not supported by the data. Instead, we observed that some cooperativity is exhibited in the N-domain, such that within this domain the changes induced upon forming the TSA complex are an intensification of those induced by binding 3PG. Furthermore, chemical shift changes induced by 3PG binding extend through the interdomain region to the C-domain beta-sheet, highlighting a network of hydrogen bonds between the domains that suggests interdomain communication. Interdomain communication is also indicated by amide protection in one domain being significantly altered by binding of substrate to the other, even where no associated change in the structure of the substrate-free domain is indicated by chemical shifts. Hence, the communication between domains is also manifested in the accessibility of higher-energy, exchange-competent states. Overall, the data that are consistent with structural tightening relate to defined regions and are close to the 3PG binding site and in the hinge regions of 3-phosphoglycerate kinase.
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Affiliation(s)
- James P Marston
- Department of Molecular Biology and Biotechnology, Firth Court, The University of Sheffield, Western Bank, Sheffield, UK
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46
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47
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Baxter NJ, Hounslow AM, Bowler MW, Williams NH, Blackburn GM, Waltho JP. MgF(3)(-) and alpha-galactose 1-phosphate in the active site of beta-phosphoglucomutase form a transition state analogue of phosphoryl transfer. J Am Chem Soc 2009; 131:16334-5. [PMID: 19852484 DOI: 10.1021/ja905972m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
(19)F-based NMR analysis and hydrogen/deuterium primary isotope shifts establish the formation of a highly populated solution-state trigonal bipyramidal complex involving beta-phosphoglucomutase (beta-PGM), alpha-galactose 1-phosphate (alphaGal1P), and trifluoromagnesate (MgF(3)(-)), PGM-MgF(3)-alphaGal1P, that is a transition state analogue for phosphoryl transfer. Full backbone resonance assignment of the protein shows that its structure is in the closed conformation required for catalytic activity and is closely related to the corresponding complex with glucose 6-phosphate, which we have recently identified using NMR analysis in solution and X-ray crystallography in the solid state. The previous identification of three structural waters in a PGM-alphaGal1P binary substrate complex had indicated that, in the presence of alphaGal1P, magnesium ions, and fluoride, beta-PGM should indeed form a PGM-MgF(3)-alphaGal1P-TSA complex whereas, in the solid-state, apparently it did not. This cast doubt on the validity of the interpretation of MgF(3)(-) complexes. The present work establishes that, in solution, the expectation that a PGM-MgF(3)-alphaGal1P-TSA complex should readily form is fulfilled. These results thus refute the final evidence used to claim that the trigonal bipyramidal species observed in some solid-state structures of complexes involving beta-PGM are pentaoxyphosphorane intermediates.
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Affiliation(s)
- Nicola J Baxter
- Department of Molecular Biology & Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
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48
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Hosszu LLP, Trevitt CR, Jones S, Batchelor M, Scott DJ, Jackson GS, Collinge J, Waltho JP, Clarke AR. Conformational properties of beta-PrP. J Biol Chem 2009; 284:21981-21990. [PMID: 19369250 PMCID: PMC2755922 DOI: 10.1074/jbc.m809173200] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [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] [Received: 12/05/2008] [Revised: 03/19/2009] [Indexed: 11/06/2022] Open
Abstract
Prion propagation involves a conformational transition of the cellular form of prion protein (PrPC) to a disease-specific isomer (PrPSc), shifting from a predominantly alpha-helical conformation to one dominated by beta-sheet structure. This conformational transition is of critical importance in understanding the molecular basis for prion disease. Here, we elucidate the conformational properties of a disulfide-reduced fragment of human PrP spanning residues 91-231 under acidic conditions, using a combination of heteronuclear NMR, analytical ultracentrifugation, and circular dichroism. We find that this form of the protein, which similarly to PrPSc, is a potent inhibitor of the 26 S proteasome, assembles into soluble oligomers that have significant beta-sheet content. The monomeric precursor to these oligomers exhibits many of the characteristics of a molten globule intermediate with some helical character in regions that form helices I and III in the PrPC conformation, whereas helix II exhibits little evidence for adopting a helical conformation, suggesting that this region is a likely source of interaction within the initial phases of the transformation to a beta-rich conformation. This precursor state is almost as compact as the folded PrPC structure and, as it assembles, only residues 126-227 are immobilized within the oligomeric structure, leaving the remainder in a mobile, random-coil state.
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Affiliation(s)
- Laszlo L. P. Hosszu
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
- the Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, and
| | - Clare R. Trevitt
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Samantha Jones
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Mark Batchelor
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - David J. Scott
- the National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, United Kingdom
| | - Graham S. Jackson
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - John Collinge
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
| | - Jonathan P. Waltho
- the Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, and
| | - Anthony R. Clarke
- From the MRC Prion Unit, Department of Neurodegenerative Disease, Institute of Neurology, Queen Square, London WC1N 3BG
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49
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Menon BRK, Waltho JP, Scrutton NS, Heyes DJ. Cryogenic and laser photoexcitation studies identify multiple roles for active site residues in the light-driven enzyme protochlorophyllide oxidoreductase. J Biol Chem 2009; 284:18160-6. [PMID: 19439417 PMCID: PMC2709359 DOI: 10.1074/jbc.m109.020719] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [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] [Received: 01/21/2009] [Revised: 05/13/2009] [Indexed: 11/06/2022] Open
Abstract
The light-activated enzyme NADPH-protochlorophyllide oxidoreductase (POR) catalyzes the trans addition of hydrogen across the C-17-C-18 double bond of protochlorophyllide (Pchlide), a key step in chlorophyll biosynthesis. Similar to other members of the short chain alcohol dehydrogenase/reductase family of enzymes, POR contains a conserved Tyr and Lys residue in the enzyme active site, which are implicated in a proposed reaction mechanism involving proton transfer from the Tyr hydoxyl group to Pchlide. We have analyzed a number of POR variant enzymes altered in these conserved residues using a combination of steady-state turnover, laser photoexcitation studies, and low temperature fluorescence spectroscopy. None of the mutations completely abolished catalytic activity. We demonstrate their importance to catalysis by defining multiple roles in the overall reaction pathway. Mutation of either residue impairs formation of the ground state ternary enzyme-substrate complex, pointing to a key role in substrate binding. By analyzing the most active variant (Y193F), we show that Tyr-193 participates in proton transfer to Pchlide and stabilizes the Pchlide excited state, enabling hydride transfer from NADPH to Pchilde. Thus, in addition to confirming the probable identity of the proton donor in Pchlide reduction, our work defines additional roles for these residues in facilitating hydride transfer through stabilization of the ground and excited states of the ternary enzyme complex.
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Affiliation(s)
- Binuraj R. K. Menon
- From the Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Jonathan P. Waltho
- From the Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- From the Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Derren J. Heyes
- From the Faculty of Life Sciences, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom
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Hart T, Hosszu LLP, Trevitt CR, Jackson GS, Waltho JP, Collinge J, Clarke AR. Folding kinetics of the human prion protein probed by temperature jump. Proc Natl Acad Sci U S A 2009; 106:5651-6. [PMID: 19321423 PMCID: PMC2667024 DOI: 10.1073/pnas.0811457106] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Indexed: 11/18/2022] Open
Abstract
Temperature-jump perturbation was used to examine the relaxation kinetics of folding of the human prion protein. Measured rates were very fast (approximately 3,000 s(-1)), with the extrapolated folding rate constant at approximately 20 degrees C in physiological conditions reaching 20,000 s(-1). By a mutational analysis of core residues, we found that only 2, on the interface of helices 2 and 3, have significant phi-values in the transition state. Interestingly, a mutation sandwiched between the above 2 residues on the helix-helix contact interface had very little effect on the overall free energy of folding but led to the formation of a monomeric misfolded state, which had to unfold to acquire the native PrP(C) conformation. Another mutation that led to a marked destabilization of the native fold also formed a misfolded intermediate, but this was aggregation-prone despite the native state of this mutant being soluble. Taken together, the data imply that this fast-folding protein has a transition state that is not compact (m value analysis gives a beta(t) value of only 0.3) but contains a developing nucleus between helices 2 and 3. The fact that a mutation in this nucleus had a negligible effect on stability but still led to formation of aberrant conformations during folding implies an easily perturbed folding mechanism. It is notable that in inherited forms of human prion disease, where point mutations produce a lethal dominant condition, 20 of the 33 amino acid replacements occur in the helix-2/3 sequence.
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Affiliation(s)
- Tanya Hart
- Medical Research Council Prion Unit, Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom; and
| | - Laszlo L. P. Hosszu
- Medical Research Council Prion Unit, Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom; and
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Clare R. Trevitt
- Medical Research Council Prion Unit, Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom; and
| | - Graham S. Jackson
- Medical Research Council Prion Unit, Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom; and
| | - Jonathan P. Waltho
- Department of Molecular Biology and Biotechnology, Krebs Institute for Biomolecular Research, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - John Collinge
- Medical Research Council Prion Unit, Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom; and
| | - Anthony R. Clarke
- Medical Research Council Prion Unit, Institute of Neurology, Queen Square, London WC1N 3BG, United Kingdom; and
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