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Roberts MF, Hedstrom L. High Resolution 31P Field Cycling NMR Reveals Unsuspected Features of Enzyme-Substrate-Cofactor Dynamics. Front Mol Biosci 2022; 9:865519. [PMID: 35433832 PMCID: PMC9009223 DOI: 10.3389/fmolb.2022.865519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 03/16/2022] [Indexed: 11/13/2022] Open
Abstract
The dynamic interactions of enzymes and substrates underpins catalysis, yet few techniques can interrogate the dynamics of protein-bound ligands. Here we describe the use of field cycling NMR relaxometry to measure the dynamics of enzyme-bound substrates and cofactors in catalytically competent complexes of GMP reductase. These studies reveal new binding modes unanticipated by x-ray crystal structures and reaction-specific dynamic networks. Importantly, this work demonstrates that distal interactions not usually considered part of the reaction coordinate can play an active role in catalysis. The commercialization of shuttling apparatus will make field cycling relaxometry more accessible and expand its use to additional nuclei, promising more intriguing findings to come.
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Affiliation(s)
- Mary F. Roberts
- Department of Chemistry, Boston College, Chestnut Hill, MA, United States
| | - Lizbeth Hedstrom
- Departments of Biology and Chemistry, Brandeis University, Waltham, MA, United States
- *Correspondence: Lizbeth Hedstrom,
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2
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Bairagya HR, Tasneem A, Rai GP, Reyaz S. New biochemical insights into the dynamics of water molecules at the GMP or IMP binding site of human GMPR enzyme: A molecular dynamics study. Proteins 2022; 90:200-217. [PMID: 34368983 DOI: 10.1002/prot.26207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 06/24/2021] [Accepted: 07/22/2021] [Indexed: 12/31/2022]
Abstract
Human GMP reductase (hGMPR) enzyme is involved in a cellular metabolic pathway, converting GMP into IMP, and also it is an important target for anti-leukemic agents. Present computational investigations explain dynamical behavior of water molecules during the conformational transition process from GMP to IMP using molecular dynamics simulations. Residues at substrate-binding site of cancerous protein (PDB Id. 2C6Q) are mostly more dynamic in nature than the normal protein (PDB Id. 2BLE). Nineteen conserved water molecules are identified at the GMP/IMP binding site and are classified as (i) conserved stable dynamic and (ii) infrequent dynamic. Water molecules W11, W14, and W16 are classified as conserved stable dynamic due to their immobile character, whereas remaining water molecules (W1, W2, W3, W4, W5, W7, W8, W9, W10, W12, W13, W15, W17, W18, and W19) are infrequent with dynamic nature. Entrance or displacement of these infrequent water molecules at GMP/IMP sites may occur due to forward and backward movement of reference residues involving ligands. Four water molecules of hGMPR-I and nine water molecules of hGMPR-II are observed in repetitive transitions from GMP to IMP pathway, which indicates discrimination between two isoforms of hGMPRs. Water molecules in cancerous protein are more dynamic and unstable compared to normal protein. These water molecules execute rare dynamical events at GMP binding site and could assist in detailed understanding of conformational transitions that influence the hGMPR's biological functionality. The present study should be of interest to the experimental community engaged in leukemia research and drug discovery for CML cancer.
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Affiliation(s)
| | - Alvea Tasneem
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Gyan Prakash Rai
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Saima Reyaz
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
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Bairagya HR, Tasneem A, Rai GP, Reyaz S. Structural and Dynamical Impact of Water Molecules at Substrate- or Product-Binding Sites in Human GMPR Enzyme: A Study by Molecular Dynamics Simulations. J Phys Chem B 2021; 125:1351-1362. [PMID: 33369428 DOI: 10.1021/acs.jpcb.0c08818] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Human guanosine monophosphate reductase (hGMPR) enzyme maintains the intracellular balance between adenine and guanine nucleotide pools, and it is an excellent target for the design of isoform-specific antileukemic agents. In the present study, we have investigated solvation properties of substrate GMP or product inosine-5'-monophosphate (IMP)-binding pocket of hGMPR by employing molecular dynamics simulations on conformations A (substrate GMP), B [substrate GMP with cofactor nicotinamide adenine dinucleotide phosphate (NDP)], C (product IMP with cofactor NDP), and D (product IMP). Nineteen water sites are identified precisely; they are responsible for the catalytic activity of this site, control structural and dynamical integrity, and electronic consequences of GMP or IMP in the binding site of hGMPR. The water sites of category-1 (W1, W4, W5, W6, W13, and W15) in normal protein and category-2 (W2, W3, W7, W8, W10, W17, and W18) in cancerous protein are unique and stabilize the guanosine or inosine group of GMP or IMP for participation in the enzymatic reaction, whereas the remaining water centers either stabilize pentose sugar ribose or the phosphate group of GMP or IMP. Furthermore, water sites of category-4 (W11, W14, and W16) appear to be conserved in all conformations during the entire simulation. The GMP-binding site in cancerous protein 2C6Q is significantly expanded, and its dynamics are very different from normal protein 2BLE. Furthermore, unique interactions of GMP(N1)···W2···Asp129/Asn158, IMP(N1)···W3···Glu289, and IMP(O6)···W10···Ser270 might be used in a water mimic drug design for hGMPR-II. In this context, water finding probability, relative interaction energy (J) associated with water site W, entropy, and topologies of these three water sites are thermodynamically acceptable for the water displacement method by the modified ligand. Hence, their positions in the catalytic pocket may also facilitate future drug discovery for chronic myelogenous leukemia by the design of appropriately oriented chemical groups that may displace these water molecules to mimic their structural, electronic, and thermodynamic properties.
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Affiliation(s)
- Hridoy R Bairagya
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Alvea Tasneem
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi 110025, India
| | - Gyan Prakash Rai
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi 110025, India
| | - Saima Reyaz
- Department of Computer Science, Jamia Millia Islamia, Jamia Nagar, Okhla, New Delhi 110025, India
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Rosenberg MM, Yao T, Patton GC, Redfield AG, Roberts MF, Hedstrom L. Enzyme-Substrate-Cofactor Dynamical Networks Revealed by High-Resolution Field Cycling Relaxometry. Biochemistry 2020; 59:2359-2370. [PMID: 32479091 PMCID: PMC8364753 DOI: 10.1021/acs.biochem.0c00212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The remarkable power and specificity of enzyme catalysis rely on the dynamic alignment of the enzyme, substrates, and cofactors, yet the role of dynamics has usually been approached from the perspective of the protein. We have been using an underappreciated NMR technique, subtesla high-resolution field cycling 31P NMR relaxometry, to investigate the dynamics of the enzyme-bound substrates and cofactor on guanosine-5'-monophosphate reductase (GMPR). GMPR forms two dead end, yet catalytically competent, complexes that mimic distinct steps in the catalytic cycle: E·IMP·NADP+ undergoes a partial hydride transfer reaction, while E·GMP·NADP+ undergoes a partial deamination reaction. A different cofactor conformation is required for each partial reaction. Here we report the effects of mutations designed to perturb cofactor conformation and ammonia binding with the goal of identifying the structural features that contribute to the distinct dynamic signatures of the hydride transfer and deamination complexes. These experiments suggest that Asp129 is a central cog in a dynamic network required for both hydride transfer and deamination. In contrast, Lys77 modulates the conformation and mobility of substrates and cofactors in a reaction-specific manner. Thr105 and Tyr318 are part of a deamination-specific dynamic network that includes the 2'-OH of GMP. These residues have comparatively little effect on the dynamic properties of the hydride transfer complex. These results further illustrate the potential of high-resolution field cycling NMR relaxometry for the investigation of ligand dynamics. In addition, exchange experiments indicate that NH3/NH4+ has a high affinity for the deamination complex but a low affinity for the hydride transfer complex, suggesting that the movement of ammonia may gate the cofactor conformational change. Collectively, these experiments reinforce the view that the enzyme, substrates, and cofactor are linked in intricate, reaction-specific, dynamic networks and demonstrate that distal portions of the substrates and cofactors are critical features in these networks.
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Affiliation(s)
- Masha M. Rosenberg
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
| | - Tianjiong Yao
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
| | - Gregory C. Patton
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
| | - Alfred G. Redfield
- Department of Biochemistry, Brandeis University, MS009, 415 South Street, Waltham, MA 02453-9110 USA
| | - Mary F. Roberts
- Department of Chemistry, Boston College, 140 Commonwealth Avenue, Chestnut Hill, MA 02467-9110 USA
| | - Lizbeth Hedstrom
- Department of Biology, Brandeis University, MS009, 415 South St., Waltham MA 02453-9110 USA
- Department of Chemistry, Brandeis University, 415 South Street, Waltham, MA 02453-3808 USA
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5
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Sommerville EW, Dalla Rosa I, Rosenberg MM, Bruni F, Thompson K, Rocha M, Blakely EL, He L, Falkous G, Schaefer AM, Yu‐Wai‐Man P, Chinnery PF, Hedstrom L, Spinazzola A, Taylor RW, Gorman GS. Identification of a novel heterozygous guanosine monophosphate reductase (GMPR) variant in a patient with a late-onset disorder of mitochondrial DNA maintenance. Clin Genet 2020; 97:276-286. [PMID: 31600844 PMCID: PMC7004030 DOI: 10.1111/cge.13652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 09/18/2019] [Accepted: 09/27/2019] [Indexed: 12/18/2022]
Abstract
Autosomal dominant progressive external ophthalmoplegia (adPEO) is a late-onset, Mendelian mitochondrial disorder characterised by paresis of the extraocular muscles, ptosis, and skeletal-muscle restricted multiple mitochondrial DNA (mtDNA) deletions. Although dominantly inherited, pathogenic variants in POLG, TWNK and RRM2B are among the most common genetic defects of adPEO, identification of novel candidate genes and the underlying pathomechanisms remains challenging. We report the clinical, genetic and molecular investigations of a patient who presented in the seventh decade of life with PEO. Oxidative histochemistry revealed cytochrome c oxidase-deficient fibres and occasional ragged red fibres showing subsarcolemmal mitochondrial accumulation in skeletal muscle, while molecular studies identified the presence of multiple mtDNA deletions. Negative candidate screening of known nuclear genes associated with PEO prompted diagnostic exome sequencing, leading to the prioritisation of a novel heterozygous c.547G>C variant in GMPR (NM_006877.3) encoding guanosine monophosphate reductase, a cytosolic enzyme required for maintaining the cellular balance of adenine and guanine nucleotides. We show that the novel c.547G>C variant causes aberrant splicing, decreased GMPR protein levels in patient skeletal muscle, proliferating and quiescent cells, and is associated with subtle changes in nucleotide homeostasis protein levels and evidence of disturbed mtDNA maintenance in skeletal muscle. Despite confirmation of GMPR deficiency, demonstrating marked defects of mtDNA replication or nucleotide homeostasis in patient cells proved challenging. Our study proposes that GMPR is the 19th locus for PEO and highlights the complexities of uncovering disease mechanisms in late-onset PEO phenotypes.
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Affiliation(s)
- Ewen W. Sommerville
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Ilaria Dalla Rosa
- Department of Clinical and Movement Neurosciences, UCL Queens Square Institute of Neurology, Royal Free CampusUniversity College LondonLondonUK
| | | | - Francesco Bruni
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of Bari “ldo Moro”BariItaly
| | - Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Mariana Rocha
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Emma L. Blakely
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Andrew M. Schaefer
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Patrick Yu‐Wai‐Man
- NIHR Biomedical Research Centre at Moorfields Eye Hospital and UCL Institute of OphthalmologyLondonUK
- MRC Mitochondrial Biology UnitUniversity of CambridgeCambridgeUK
- Cambridge Centre for Brain Repair, Department of Clinical NeurosciencesUniversity of CambridgeCambridgeUK
| | - Patrick F. Chinnery
- Department of Clinical Neuroscience & Medical Research Council Mitochondrial Biology UnitSchool of Clinical Medicine, University of CambridgeCambridgeUK
| | - Lizbeth Hedstrom
- Department of BiologyBrandeis UniversityWalthamMA
- Department of ChemistryBrandeis University, 415 South St.WalthamMA
| | - Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queens Square Institute of Neurology, Royal Free CampusUniversity College LondonLondonUK
- MRC Centre for Neuromuscular DiseasesUCL Institute of Neurology and National Hospital for Neurology and NeurosurgeryLondonUK
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Gráinne S. Gorman
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
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Rosenberg MM, Redfield AG, Roberts MF, Hedstrom L. Dynamic Characteristics of Guanosine-5'-monophosphate Reductase Complexes Revealed by High-Resolution 31P Field-Cycling NMR Relaxometry. Biochemistry 2018; 57:3146-3154. [PMID: 29547266 DOI: 10.1021/acs.biochem.8b00142] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The ability of enzymes to modulate the dynamics of bound substrates and cofactors is a critical feature of catalysis, but the role of dynamics has largely been approached from the perspective of the protein. Here, we use an underappreciated NMR technique, subtesla high-resolution field-cycling 31P NMR relaxometry, to interrogate the dynamics of enzyme bound substrates and cofactors in guanosine-5'-monophosphate reductase (GMPR). These experiments reveal distinct binding modes and dynamic profiles associated with the 31P nuclei in the Michaelis complexes for the deamination and hydride transfer steps of the catalytic cycle. Importantly, the substrate is constrained and the cofactor is more dynamic in the deamination complex E·GMP·NADP+, whereas the substrate is more dynamic and the cofactor is constrained in the hydride transfer complex E·IMP·NADP+. The presence of D2O perturbed the relaxation of the 31P nuclei in E·IMP·NADP+ but not in E·GMP·NADP+, providing further evidence of distinct binding modes with different dynamic properties. dIMP and dGMP are poor substrates, and the dynamics of the cofactor complexes of dGMP/dIMP are disregulated relative to GMP/IMP. The substrate 2'-OH interacts with Asp219, and mutation of Asp219 to Ala decreases the value of Vmax by a factor of 30. Counterintuitively, loss of Asp219 makes both substrates and cofactors less dynamic. These observations suggest that the interactions between the substrate 2'-OH and Asp219 coordinate the dynamic properties of the Michaelis complexes, and these dynamics are important for progression through the catalytic cycle.
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Affiliation(s)
- Masha M Rosenberg
- Department of Biology , Brandeis University , MS009, 415 South Street , Waltham , Massachusetts 02453-9110 , United States
| | - Alfred G Redfield
- Department of Biochemistry , Brandeis University , MS009, 415 South Street , Waltham , Massachusetts 02453-9110 , United States
| | - Mary F Roberts
- Department of Chemistry , Boston College , 140 Commonwealth Avenue , Chestnut Hill , Massachusetts 02467-9110 , United States
| | - Lizbeth Hedstrom
- Department of Biology , Brandeis University , MS009, 415 South Street , Waltham , Massachusetts 02453-9110 , United States.,Department of Chemistry , Brandeis University , 415 South Street , Waltham , Massachusetts 02453-3808 , United States
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