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Alexandrescu AT, Dregni AJ, Teschke CM. NMR detection and conformational dependence of two, three, and four-bond isotope shifts due to deuteration of backbone amides. JOURNAL OF BIOMOLECULAR NMR 2023; 77:93-109. [PMID: 37093339 PMCID: PMC10724557 DOI: 10.1007/s10858-023-00414-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
NMR isotope shifts occur due to small differences in nuclear shielding when nearby atoms are different isotopes. For molecules dissolved in 1:1 H2O:D2O, the resulting mixture of N-H and N-D isotopes leads to a small splitting of resonances from adjacent nuclei. We used multidimensional NMR to measure isotope shifts for the proteins CUS-3iD and CspA. We observed four-bond 4∆N(ND) isotope shifts in high-resolution 2D 15N-TROSY experiments of the perdeuterated proteins that correlate with the torsional angle psi. Three-bond 3∆C'(ND) isotope shifts detected in H(N)CO spectra correlate with the intraresidue H-O distance, and to a lesser extent with the dihedral angle phi. The conformational dependence of the isotope shifts agree with those previously reported in the literature. Both the 4∆N(ND) and 3∆C'(ND) isotope shifts are sensitive to distances between the atoms giving rise to the isotope shifts and the atoms experiencing the splitting, however, these distances are strongly correlated with backbone dihedral angles making it difficult to resolve distance from stereochemical contributions to the isotope shift. H(NCA)CO spectra were used to measure two-bond 2∆C'(ND) isotope shifts and [D]/[H] fractionation factors. Neither parameter showed significant differences for hydrogen-bonded sites, or changes over a 25° temperature range, suggesting they are not sensitive to hydrogen bonding. Finally, the quartet that arises from the combination of 2∆C'(ND) and 3∆C'(ND) isotope shifts in H(CA)CO spectra was used to measure synchronized hydrogen exchange for the sequence neighbors A315-S316 in the protein CUS-3iD. In many of our experiments we observed minor resonances due to the 10% D2O used for the sample deuterium lock, indicating isotope shifts can be a source of spectral heterogeneity in standard NMR experiments. We suggest that applications of isotope shifts such as conformational analysis and correlated hydrogen exchange could benefit from the larger magnetic fields becoming available.
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Affiliation(s)
- Andrei T Alexandrescu
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269-3125, USA.
| | - Aurelio J Dregni
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Carolyn M Teschke
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269-3125, USA
- Department of Chemistry, University of Connecticut, Storrs, CT, 06269-3060, USA
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2
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Escobedo A, Piccirillo J, Aranda J, Diercks T, Mateos B, Garcia-Cabau C, Sánchez-Navarro M, Topal B, Biesaga M, Staby L, Kragelund BB, García J, Millet O, Orozco M, Coles M, Crehuet R, Salvatella X. A glutamine-based single α-helix scaffold to target globular proteins. Nat Commun 2022; 13:7073. [PMID: 36400768 PMCID: PMC9674830 DOI: 10.1038/s41467-022-34793-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 11/04/2022] [Indexed: 11/19/2022] Open
Abstract
The binding of intrinsically disordered proteins to globular ones can require the folding of motifs into α-helices. These interactions offer opportunities for therapeutic intervention but their modulation with small molecules is challenging because they bury large surfaces. Linear peptides that display the residues that are key for binding can be targeted to globular proteins when they form stable helices, which in most cases requires their chemical modification. Here we present rules to design peptides that fold into single α-helices by instead concatenating glutamine side chain to main chain hydrogen bonds recently discovered in polyglutamine helices. The resulting peptides are uncharged, contain only natural amino acids, and their sequences can be optimized to interact with specific targets. Our results provide design rules to obtain single α-helices for a wide range of applications in protein engineering and drug design.
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Affiliation(s)
- Albert Escobedo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.
| | - Jonathan Piccirillo
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Juan Aranda
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Tammo Diercks
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160, Derio, Spain
| | - Borja Mateos
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Carla Garcia-Cabau
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Macarena Sánchez-Navarro
- Department of Molecular Biology, Instituto de Parasitología y Biomedicina López Neyra (IPBLN-CSIC), Armilla, Granada, Spain
| | - Busra Topal
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Mateusz Biesaga
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Lasse Staby
- REPIN and Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Birthe B Kragelund
- REPIN and Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, DK-2200, Copenhagen N, Denmark
| | - Jesús García
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
| | - Oscar Millet
- CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Science and Technology Park, 48160, Derio, Spain
| | - Modesto Orozco
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain
- Department of Biochemistry and Biomedicine, University of Barcelona, Avinguda Diagonal 645, 08028, Barcelona, Spain
| | - Murray Coles
- Department of Protein Evolution, Max Planck Institute for Biology, Max-Planck-Ring 5, 72076, Tubingen, Germany
| | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Jordi Girona 18-26, 08034, Barcelona, Spain
| | - Xavier Salvatella
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028, Barcelona, Spain.
- ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
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3
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Hansen PE. Isotope effects on chemical shifts in the study of hydrogen bonded biological systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2020; 120-121:109-117. [PMID: 33198966 DOI: 10.1016/j.pnmrs.2020.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/06/2020] [Indexed: 06/11/2023]
Abstract
This review deals with biological systems and with deuterium isotope effects on chemical shifts caused by the replacement of OH, NH or SH protons by deuterons. Hydrogen bonding is clearly of central importance. Isotope effects on chemical shifts seems very suitable for use in studies of structures and reactions in the interior of proteins, as exchange of the label can be expected to be slow. One-bond deuterium isotope effects on 15N chemical shifts, and two-bond effects on 1H chemical shifts for N(D)Hx systems can be used to gauge hydrogen bond strength in proteins as well as in salt bridges. Solvent isotope effects on 19F chemical shifts show promise in monitoring solvent access. Equilibrium isotope effects need in some cases to be taken into account. Schemes for calculation of deuterium isotope effects on chemical shifts are discussed and it is demonstrated how calculations may be used in the study of complex biological systems.
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Affiliation(s)
- Poul Erik Hansen
- Department of Science and Environment, Roskilde University, Universitetsvej 1, DK-4000 Roskilde, Denmark.
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4
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Singh H, Vasa SK, Jangra H, Rovó P, Päslack C, Das CK, Zipse H, Schäfer LV, Linser R. Fast Microsecond Dynamics of the Protein–Water Network in the Active Site of Human Carbonic Anhydrase II Studied by Solid-State NMR Spectroscopy. J Am Chem Soc 2019; 141:19276-19288. [DOI: 10.1021/jacs.9b05311] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Himanshu Singh
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Suresh K. Vasa
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Harish Jangra
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Petra Rovó
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Christopher Päslack
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Chandan K. Das
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Hendrik Zipse
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
| | - Lars V. Schäfer
- Theoretical Chemistry, Ruhr University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Rasmus Linser
- Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Straße 4a, 44227 Dortmund, Germany
- Department of Chemistry, Ludwig-Maximilians-University Munich, Butenandtstraße 5-13, 81377 Munich, Germany
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5
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Brockerman JA, Okon M, Withers SG, McIntosh LP. The pK a values of the catalytic residues in the retaining glycoside hydrolase T26H mutant of T4 lysozyme. Protein Sci 2018; 28:620-632. [PMID: 30537432 DOI: 10.1002/pro.3562] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 12/24/2022]
Abstract
T4 phage lysozyme (T4L) is an enzyme that cleaves bacterial cell wall peptidoglycan. Remarkably, the single substitution of the active site Thr26 to a His (T26H) converts T4L from an inverting to a retaining glycoside hydrolase with transglycosylase activity. It has been proposed that T26H-T4L follows a double displacement mechanism with His26 serving as a nucleophile to form a covalent glycosyl-enzyme intermediate (Kuroki et al., PNAS 1999; 96:8949-8954). To gain further insights into this or alternative mechanisms, we used NMR spectroscopy to measure the acid dissociation constants (pKa values) and/or define the ionization states of the Asp, Glu, His, and Arg residues in the T4L mutant. Most notably, the pKa value of the putative nucleophile His26 is 6.8 ± 0.1, whereas that of the general acid Glu11 is 4.7 ± 0.1. If the proposed mechanism holds true, then T26H-T4L follows a reverse protonation pathway in which only a minor population of the free enzyme is in its catalytically competent ionization state with His26 deprotonated and Glu11 protonated. Our studies also confirm that all arginines in T26H-T4L, including the active site Arg145, are positively charged under neutral pH conditions. BRIEF STATEMENT: The replacement of a single amino acid changes T4 lysozyme from an inverting to a retaining glycoside hydrolase. Using NMR spectroscopy, we measured the pKa values of the ionizable residues in the active site of this mutant enzyme. Along with previously reported data, these results provide important constraints for understanding the catalytic mechanisms by which the wild-type and mutant form of T4 lysozyme cleave bacterial peptidoglycan.
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Affiliation(s)
- Jacob A Brockerman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Mark Okon
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Lawrence P McIntosh
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, V6T 1Z1, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
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6
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Adsorption Capacity of a Volcanic Rock—Used in ConstructedWetlands—For Carbamazepine Removal, and Its Modification with Biofilm Growth. WATER 2017. [DOI: 10.3390/w9090721] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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7
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Cao C, Chen JL, Yang Y, Huang F, Otting G, Su XC. Selective (15)N-labeling of the side-chain amide groups of asparagine and glutamine for applications in paramagnetic NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2014; 59:251-61. [PMID: 25002097 DOI: 10.1007/s10858-014-9844-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 07/01/2014] [Indexed: 05/24/2023]
Abstract
The side-chain amide groups of asparagine and glutamine play important roles in stabilizing the structural fold of proteins, participating in hydrogen-bonding networks and protein interactions. Selective (15)N-labeling of side-chain amides, however, can be a challenge due to enzyme-catalyzed exchange of amide groups during protein synthesis. In the present study, we developed an efficient way of selectively labeling the side chains of asparagine, or asparagine and glutamine residues with (15)NH2. Using the biosynthesis pathway of tryptophan, a protocol was also established for simultaneous selective (15)N-labeling of the side-chain NH groups of asparagine, glutamine, and tryptophan. In combination with site-specific tagging of the target protein with a lanthanide ion, we show that selective detection of (15)N-labeled side-chains of asparagine and glutamine allows determination of magnetic susceptibility anisotropy tensors based exclusively on pseudocontact shifts of amide side-chain protons.
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Affiliation(s)
- Chan Cao
- State Key Laboratory of Elemento-Organic Chemistry, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Nankai University, Tianjin, 300071, China
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8
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Tugarinov V. Indirect use of deuterium in solution NMR studies of protein structure and hydrogen bonding. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 77:49-68. [PMID: 24411830 DOI: 10.1016/j.pnmrs.2013.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 08/15/2013] [Indexed: 06/03/2023]
Abstract
A description of the utility of deuteration in protein NMR is provided with an emphasis on quantitative evaluation of the effects of deuteration on a number of NMR parameters of proteins: (1) chemical shifts, (2) scalar coupling constants, (3) relaxation properties (R1 and R2 rates) of nuclei directly attached to one or more deuterons as well as protons of methyl groups in a highly deuterated environment, (4) scalar relaxation of 15N and 13C nuclei in 15N-D and 13C-D spin systems as a measure of hydrogen bonding strength, and (5) NOE-based applications of deuteration in NMR studies of protein structure. The discussion is restricted to the 'indirect' use of deuterium in the sense that the description of NMR parameters and properties of the nuclei affected by nearby deuterons (15N, 13C, 1H) is provided rather than those of deuterium itself.
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Affiliation(s)
- Vitali Tugarinov
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, United States.
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9
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Tugarinov V. Four-bond deuterium isotope effects on the chemical shifts of amide nitrogens in proteins. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2013; 51:722-728. [PMID: 24038445 DOI: 10.1002/mrc.4007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Revised: 07/19/2013] [Accepted: 08/18/2013] [Indexed: 06/02/2023]
Abstract
An approach towards precision NMR measurements of four-bond deuterium isotope effects on the chemical shifts of backbone amide nitrogen nuclei in proteins is described. Three types of four-bond (15) N deuterium isotope effects are distinguished depending on the site of proton-to-deuterium substitution: (4)ΔN(N(i-1)D), (4)ΔN(N(i+1)D) and (4)ΔN(Cβ,(i-1)D). All the three types of isotope shifts are quantified in the (partially) deuterated protein ubiquitin. The (4)ΔN(N(i+1)D) and (4)ΔN(C(β,i-1)D) effects are by far the largest in magnitude and vary between 16 and 75 ppb and -18 and 46 ppb, respectively. A semi-quantitative correlation between experimental (4)ΔN(N(i+1)D) and (4)ΔN(C(β,i-1)D) values and the distances between nitrogen nuclei and the sites of (1)H-to-D substitution is noted. The largest isotope shifts in both cases correspond to the shortest inter-nuclear distances.
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Affiliation(s)
- Vitali Tugarinov
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20742, USA
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10
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Zhang D, Tugarinov V. Accurate measurements of the effects of deuteration at backbone amide positions on the chemical shifts of ¹⁵N, ¹³Cα, ¹³Cβ, ¹³CO and ¹Hα nuclei in proteins. JOURNAL OF BIOMOLECULAR NMR 2013; 56:169-182. [PMID: 23612994 DOI: 10.1007/s10858-013-9733-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/18/2013] [Indexed: 06/02/2023]
Abstract
An approach towards accurate NMR measurements of deuterium isotope effects on the chemical shifts of all backbone nuclei in proteins ((15)N, (13)Cα, (13)CO, (1)Hα) and (13)Cβ nuclei arising from (1)H-to-D substitutions at amide nitrogen positions is described. Isolation of molecular species with a defined protonation/deuteration pattern at successive backbone nitrogen positions in the polypeptide chain allows quantifying all deuterium isotope shifts of these nuclei from the first to the fourth order. Some of the deuterium isotope shifts measured in the proteins ubiquitin and GB1 can be interpreted in terms of backbone geometry via empirical relationships describing their dependence on (φ; ψ) backbone dihedral angles. Because of their relatively large variability and notable dependence on the protein secondary structure, the two- and three-bond (13)Cα isotope shifts, (2)ΔCα(NiD) and (3)ΔCα(Ni+1D), and three-bond (13)Cβ isotope shifts, (3)ΔCβ(NiD), are useful reporters of the local geometry of the protein backbone.
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Affiliation(s)
- Daoning Zhang
- Department of Chemistry and Biochemistry, University of Maryland, Biomolecular Sci. Bldg./CBSO, College Park, MD 20742, USA
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11
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Boeckx B, Maes G. Simulating the Interaction between Amino Acids and DNA: A Combined Matrix-Isolation FT-IR and Theoretical Study of the 1-Methyluracil·Glycine H-Bond Complexes Using a Dual Sublimation Furnace. J Phys Chem B 2012; 116:11890-8. [DOI: 10.1021/jp307388e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bram Boeckx
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, Leuven, Belgium
| | - Guido Maes
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, Leuven, Belgium
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12
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Sun H, Tugarinov V. Precision Measurements of Deuterium Isotope Effects on the Chemical Shifts of Backbone Nuclei in Proteins: Correlations with Secondary Structure. J Phys Chem B 2012; 116:7436-48. [DOI: 10.1021/jp304300n] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hechao Sun
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Vitali Tugarinov
- Department
of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
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13
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Wang J, Sklenak S, Liu A, Felczak K, Wu Y, Li Y, Yan H. Role of glutamate 64 in the activation of the prodrug 5-fluorocytosine by yeast cytosine deaminase. Biochemistry 2011; 51:475-86. [PMID: 22208667 DOI: 10.1021/bi201540z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Yeast cytosine deaminase (yCD) catalyzes the hydrolytic deamination of cytosine to uracil as well as the deamination of the prodrug 5-fluorocytosine (5FC) to the anticancer drug 5-fluorouracil. In this study, the role of Glu64 in the activation of the prodrug 5FC was investigated by site-directed mutagenesis, biochemical, nuclear magnetic resonance (NMR), and computational studies. Steady-state kinetics studies showed that the mutation of Glu64 causes a dramatic decrease in k(cat) and a dramatic increase in K(m), indicating Glu64 is important for both binding and catalysis in the activation of 5FC. (19)F NMR experiments showed that binding of the inhibitor 5-fluoro-1H-pyrimidin-2-one (5FPy) to the wild-type yCD causes an upfield shift, indicating that the bound inhibitor is in the hydrated form, mimicking the transition state or the tetrahedral intermediate in the activation of 5FC. However, binding of 5FPy to the E64A mutant enzyme causes a downfield shift, indicating that the bound 5FPy remains in an unhydrated form in the complex with the mutant enzyme. (1)H and (15)N NMR analysis revealed trans-hydrogen bond D/H isotope effects on the hydrogen of the amide of Glu64, indicating that the carboxylate of Glu64 forms two hydrogen bonds with the hydrated 5FPy. ONIOM calculations showed that the wild-type yCD complex with the hydrated form of the inhibitor 1H-pyrimidin-2-one is more stable than the initial binding complex, and in contrast, with the E64A mutant enzyme, the hydrated inhibitor is no longer favored and the conversion has a higher activation energy, as well. The hydrated inhibitor is stabilized in the wild-type yCD by two hydrogen bonds between it and the carboxylate of Glu64 as revealed by (1)H and (15)N NMR analysis. To explore the functional role of Glu64 in catalysis, we investigated the deamination of cytosine catalyzed by the E64A mutant by ONIOM calculations. The results showed that without the assistance of Glu64, both proton transfers before and after the formation of the tetrahedral reaction intermediate become partially rate-limiting steps. The results of the experimental and computational studies together indicate that Glu64 plays a critical role in both the binding and the chemical transformation in the conversion of the prodrug 5FC to the anticancer drug 5-fluorouracil.
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Affiliation(s)
- Jifeng Wang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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14
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Abildgaard J, Hansen PE, Manalo MN, LiWang A. Deuterium isotope effects on 15N backbone chemical shifts in proteins. JOURNAL OF BIOMOLECULAR NMR 2009; 44:119-26. [PMID: 19455282 PMCID: PMC2697368 DOI: 10.1007/s10858-009-9316-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Accepted: 04/06/2009] [Indexed: 05/09/2023]
Abstract
Quantum mechanical calculations are presented that predict that one-bond deuterium isotope effects on the (15)N chemical shift of backbone amides of proteins, (1)Delta(15)N(D), are sensitive to backbone conformation and hydrogen bonding. A quantitative empirical model for (1)Delta(15)N(D) including the backbone dihedral angles, Phi and Psi, and the hydrogen bonding geometry is presented for glycine and amino acid residues with aliphatic side chains. The effect of hydrogen bonding is rationalized in part as an electric-field effect on the first derivative of the nuclear shielding with respect to N-H bond length. Another contributing factor is the effect of increased anharmonicity of the N-H stretching vibrational state upon hydrogen bonding, which results in an altered N-H/N-D equilibrium bond length ratio. The N-H stretching anharmonicity contribution falls off with the cosine of the N-H...O bond angle. For residues with uncharged side chains a very good prediction of isotope effects can be made. Thus, for proteins with known secondary structures, (1)Delta(15)N(D) can provide insights into hydrogen bonding geometries.
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Affiliation(s)
- Jens Abildgaard
- Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark
| | - Poul Erik Hansen
- Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark
| | - Marlon N. Manalo
- Department of Chemistry & Biochemistry, UC San Diego, La Jolla, CA USA
| | - Andy LiWang
- School of Natural Sciences, UC Merced, Merced, CA USA
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