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Gatin E, Iordache SM, Gatin DI, Nagy P, Iordache AM, Luculescu C. Periodontal Disease Monitoring by Raman Spectroscopy of Phosphates: New Insights into Pyrophosphate Activity. Diagnostics (Basel) 2023; 14:66. [PMID: 38201375 PMCID: PMC10802175 DOI: 10.3390/diagnostics14010066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/16/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
(1) Background: The intent of this survey was to investigate the quality of the alveolar bone by revealing the different phases for calcified tissues independent of the medical history of the patient in relation to periodontal disease by means of Raman spectroscopy and then to correlate the results by suggesting a possible mechanism for the medical impairment; (2) Methods: The investigation was mainly based on Raman spectroscopy that was performed in vivo during surgery for the selected group of patients. The targeted peaks for the Raman spectra were according to the reference compounds (e.g., calcium phosphates, other phosphates); (3) Results: The variation in the intensity of the spectrum correlated to the specific bone constituents' concentrations highlights the bone quality, while some compounds (such as pyrophosphate, PPi) are strongly related to the patient's medical status, and they provide information regarding a physiological process that occurred in the calcified tissues. Moreover, bone sample fluorescence is related to the collagen (Col) content, enabling a complete evaluation of bone quality, revealing the importance of collagen matrix acting as a load-bearing element for Calcium phosphate (CaP) deposition during the complex bone mineralization process; (4) Conclusions: We highlight that Raman spectroscopy can be considered a viable investigative method for in vivo and rapid bone quality valuation through oral health monitoring.
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Affiliation(s)
- Eduard Gatin
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, Blv. Eroii Sanitari 8, Sector 5, 050474 Bucharest, Romania
- Faculty of Physics, DMSPA Department, University of Bucharest, Atomistilor Str. 405, 077125 Magurele, Romania
| | - Stefan Marian Iordache
- Optospintronics Department, National Institute for Research and Development for Optoelectronics—INOE 2000, Atomistilor Str. 409, 077125 Magurele, Romania; (S.M.I.); (A.-M.I.)
| | - Dina Ilinca Gatin
- Faculty of Dentistry, University of Medicine “Carol Davila”, Calea Plevnei 17-23, Sector 5, 0110221 Bucharest, Romania;
| | - Pal Nagy
- Faculty of Dentistry, Periodontology Department, Semmelweiss University, 1085 Budapest, Hungary;
| | - Ana-Maria Iordache
- Optospintronics Department, National Institute for Research and Development for Optoelectronics—INOE 2000, Atomistilor Str. 409, 077125 Magurele, Romania; (S.M.I.); (A.-M.I.)
| | - Catalin Luculescu
- CETAL Department, National Institute for Laser, Plasma and Radiation Physics, Atomistilor Str. 409, 077125 Magurele, Romania
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2
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Gatin E, Nagy P, Iordache SM, Iordache AM, Luculescu CR, Grygorovskyy V. Preliminary Assessment of In Vivo Raman Spectroscopy Technique for Bone Quality Evaluation of Augmented Maxillary Sinus Floor. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:4789. [PMID: 36981696 PMCID: PMC10049299 DOI: 10.3390/ijerph20064789] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
(1) Background: In oral surgery, bone regeneration is achieved through various types of bone grafts or bone substitutes and its success is usually analyzed by micro-computed tomography and histomorphometry. The aim of this study was to evaluate the usefulness of Raman spectroscopy as an alternative to other techniques for bone quality evaluation during a standard oral surgery procedure. (2) Methods: The preliminary evaluation of bone augmentation during maxillary sinus floor elevation oral surgery was performed by Raman spectroscopy for several (five) patients during and after the surgery and the results were compared with postoperative data from histomorphometry, EDX and SEM analysis. (3) Results: After analyzing all the results for the bone samples according to the four methods (Raman, EDX, SEM and Histology) that were used in our study, the obtained result of the investigation provided a good augmentation process for three of the patients and partly successful augmentation process for two of the patients. The primary evaluation using Raman spectroscopy (in vivo and ex vivo investigation) was confirmed by histological results, thus having a first step for validation of Raman as a new method of imaging for dentistry. (4) Conclusions: Our results show that Raman spectroscopy could provide fast and reliable insight on bone condition during augmentation of the maxillary sinus floor. We emphasize the advantages and drawbacks of the proposed techniques as its accuracy could increase by performing larger size clinical trials. Using the Raman mapping, the method can serve as an alternative to histology.
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Affiliation(s)
- Eduard Gatin
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, Blv. Eroii Sanitari 8, Sector 5, 050474 Bucharest, Romania
- Faculty of Physics, DMSFAPA Department, University of Bucharest, 405 Atomistilor Str., 077125 Magurele, Romania
| | - Pal Nagy
- Faculty of Dentistry, Periodontology Department, Semmelweiss University, 1085 Budapest, Hungary
| | - Stefan Marian Iordache
- Optospintronics Department, National Institute for Research and Development for Optoelectronics—INOE 2000, 077125 Magurele, Romania
| | - Ana-Maria Iordache
- Optospintronics Department, National Institute for Research and Development for Optoelectronics—INOE 2000, 077125 Magurele, Romania
| | - Catalin Romeo Luculescu
- CETAL Department, National Institute for Laser, Plasma and Radiation Physics, Atomistilor Str. 409, 077125 Magurele, Romania
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3
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Ueda S, Hirata T, Sakasegawa SI. Hypoxanthine-guanine phosphoribosyltransferase is activated via positive cooperativity between guanine and IMP. FEBS Lett 2022; 596:1072-1080. [PMID: 35114018 DOI: 10.1002/1873-3468.14306] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/16/2022] [Accepted: 01/27/2022] [Indexed: 12/31/2022]
Abstract
Hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is a key enzyme in the purine salvage pathway. Here, the reverse reaction of HGPRT from the thermophilic bacterium Hungateiclostridium thermocellum was studied in the presence of IMP and pyrophosphate. As for the human enzyme, the bacterial HGPRT was activated by guanine. Furthermore, guanine was found to operate as both an activator and an inhibitor. Intriguingly, within the concentration range of guanine where it functions as the activator, the Km value for IMP was not influenced by guanine. Consequently, guanine was found to noncompetitively activate the reverse reaction toward IMP. Here, we propose a reaction scheme that explains the activation mechanism in which the enzyme forms a chimeric oligomer bound to both IMP and guanine.
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Affiliation(s)
- Shigeru Ueda
- Department of Health and Medical Sciences, Faculty of Risk and Crisis Management, Chiba Institute of Science, Choshi, Japan
| | - Tatsuya Hirata
- R&D Group, Diagnostics Department, Asahi Kasei Pharma Corporation, Izunokuni-shi, Japan
| | - Shin-Ichi Sakasegawa
- R&D Group, Diagnostics Department, Asahi Kasei Pharma Corporation, Izunokuni-shi, Japan
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4
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Gatin EG, Nagy P, Iordache SM, Iordache AM, Luculescu CR. Raman Spectroscopy: In Vivo Application for Bone Evaluation in Oral Reconstructive (Regenerative) Surgery. Diagnostics (Basel) 2022; 12:diagnostics12030723. [PMID: 35328277 PMCID: PMC8947687 DOI: 10.3390/diagnostics12030723] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/06/2022] [Accepted: 03/10/2022] [Indexed: 12/28/2022] Open
Abstract
The aim of this study was to evaluate the quality of the bone, revealing the different phases for calcified tissues independent of the medical history of the patient in relation to periodontitis by means of in vivo Raman spectroscopy. Raman spectroscopy measurements were performed in vivo during surgery and then ex vivo for the harvested bone samples for the whole group of patients (ten patients). The specific peaks for the Raman spectrum were traced for reference compounds (e.g., calcium phosphates) and bone samples. The variation in the intensity of the spectrum in relation to the specific bone constituents’ concentrations reflects the bone quality and can be strongly related with patient medical status (before dental surgery and after a healing period). Moreover, bone sample fluorescence is related to collagen content, enabling a complete evaluation of bone quality including a “quasi-quantification” of the healing process similar to the bone augmentation procedure. A complete evaluation of the processed spectra offers quantitative/qualitative information on the condition of the bone tissue. We conclude that Raman spectroscopy can be considered a viable investigation method for an in vivo and quick bone quality assessment during oral and periodontal surgery.
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Affiliation(s)
- Eduard Gheorghe Gatin
- Faculty of Medicine, University of Medicine and Pharmacy “Carol Davila”, 050474 Bucharest, Romania
- Faculty of Physics, University of Bucharest, 077125 Magurele, Romania
- Correspondence: (E.G.G.); (S.-M.I.); (A.-M.I.)
| | - Pal Nagy
- Faculty of Dentistry, Semmelweis University, 1085 Budapest, Hungary;
| | - Stefan-Marian Iordache
- Optospintronics Department, National Institute for Research and Development for Optoelectronics—INOE 2000, 077125 Magurele, Romania
- Correspondence: (E.G.G.); (S.-M.I.); (A.-M.I.)
| | - Ana-Maria Iordache
- Optospintronics Department, National Institute for Research and Development for Optoelectronics—INOE 2000, 077125 Magurele, Romania
- Correspondence: (E.G.G.); (S.-M.I.); (A.-M.I.)
| | - Catalin Romeo Luculescu
- National Institute for Laser, Plasma and Radiation Physics, CETAL, 077125 Magurele, Romania;
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5
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Gatin E, Nagy P, Paun I, Dubok O, Bucur V, Windisch P. Raman Spectroscopy: Application in Periodontal and Oral Regenerative Surgery for Bone Evaluation. Ing Rech Biomed 2019. [DOI: 10.1016/j.irbm.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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6
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Abstract
Transition state theory teaches that chemically stable mimics of enzymatic transition states will bind tightly to their cognate enzymes. Kinetic isotope effects combined with computational quantum chemistry provides enzymatic transition state information with sufficient fidelity to design transition state analogues. Examples are selected from various stages of drug development to demonstrate the application of transition state theory, inhibitor design, physicochemical characterization of transition state analogues, and their progress in drug development.
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Affiliation(s)
- Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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7
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Karnawat V, Mehrotra S, Balaram H, Puranik M. Exquisite Modulation of the Active Site of Methanocaldococcus jannaschii Adenylosuccinate Synthetase in Forward Reaction Complexes. Biochemistry 2016; 55:2491-9. [PMID: 27050719 DOI: 10.1021/acs.biochem.5b01386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In enzymes that conduct complex reactions involving several substrates and chemical transformations, the active site must reorganize at each step to complement the transition state of that chemical step. Adenylosuccinate synthetase (ADSS) utilizes a molecule each of guanosine 5'-monophosphate (GTP) and aspartate to convert inosine 5'-monophosphate (IMP) into succinyl adenosine 5'-monophosphate (sAMP) through several kinetic intermediates. Here we followed catalysis by ADSS through high-resolution vibrational spectral fingerprints of each substrate and intermediate involved in the forward reaction. Vibrational spectra show differential ligand distortion at each step of catalysis, and band positions of substrates are influenced by binding of cosubstrates. We found that the bound IMP is distorted toward its N1-deprotonated form even in the absence of any other ligands. Several specific interactions between GTP and active-site amino acid residues result in large Raman shifts and contribute substantially to intrinsic binding energy. When both IMP and GTP are simultaneously bound to ADSS, IMP is converted into an intermediate 6-phosphoryl inosine 5'-monophosphate (6-pIMP). The 6-pIMP·ADSS complex was found to be stable upon binding of the third ligand, hadacidin (HDA), an analogue of l-aspartate. We find that in the absence of HDA, 6-pIMP is quickly released from ADSS, is unstable in solution, and converts back into IMP. HDA allosterically stabilizes ADSS through local conformational rearrangements. We captured this complex and determined the spectra and structure of 6-pIMP in its enzyme-bound state. These results provide important insights into the exquisite tuning of active-site interactions with changing substrate at each kinetic step of catalysis.
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Affiliation(s)
- Vishakha Karnawat
- Indian Institute of Science Education and Research , Pune 411008, India
| | - Sonali Mehrotra
- Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur, Bangalore 560064, India
| | - Hemalatha Balaram
- Jawaharlal Nehru Centre for Advanced Scientific Research , Jakkur, Bangalore 560064, India
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research , Pune 411008, India
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8
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Karnawat V, Gogia S, Balaram H, Puranik M. Differential Distortion of Purine Substrates by Human and Plasmodium falciparum Hypoxanthine-Guanine Phosphoribosyltransferase to Catalyse the Formation of Mononucleotides. Chemphyschem 2015; 16:2172-81. [PMID: 25944719 DOI: 10.1002/cphc.201500084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Indexed: 11/10/2022]
Abstract
Plasmodium falciparum (Pf) hypoxanthine-guanine phosphoribosyltransferase (HGPRT) is a potential therapeutic target. Compared to structurally homologous human enzymes, it has expanded substrate specificity. In this study, 9-deazapurines are used as in situ probes of the active sites of human and Pf HGPRTs. Through the use of these probes it is found that non-covalent interactions stabilise the pre-transition state of the HGPRT-catalysed reaction. Vibrational spectra reveal that the bound substrates are extensively distorted, the carbonyl bond of nucleobase moiety is weakened and the substrate is destabilised along the reaction coordinate. Raman shifts of the human and Pf enzymes are used to quantify the differing degrees of hydrogen bonding in the homologues. A decreased Raman cross-section in enzyme-bound 9-deazaguanine (9DAG) shows that the phenylalanine residue (Phe186 in human and Phe197 in Pf) of HGPRT stacks with the nucleobase. Differential loss of the Raman cross-section suggests that the active site is more compact in human HGPRT as compared to the Pf enzyme, and is more so in the phosphoribosyl pyrophosphate (PRPP) complex 9DAG-PRPP-HGPRT than in 9-deazahypoxanthine (9DAH)-PRPP-HGPRT.
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Affiliation(s)
- Vishakha Karnawat
- Indian Institute of Science Education and Research, Pune-411008 (India)
| | - Spriha Gogia
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore-560065 (India)
| | - Hemalatha Balaram
- Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur, Bangalore-560064 (India).
| | - Mrinalini Puranik
- Indian Institute of Science Education and Research, Pune-411008 (India).
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9
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Jensen KF, Hansen MR, Jensen KS, Christoffersen S, Poulsen JCN, Mølgaard A, Kadziola A. Adenine phosphoribosyltransferase from Sulfolobus solfataricus is an enzyme with unusual kinetic properties and a crystal structure that suggests it evolved from a 6-oxopurine phosphoribosyltransferase. Biochemistry 2015; 54:2323-34. [PMID: 25790177 DOI: 10.1021/bi501334m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The adenine phosphoribosyltransferase (APRTase) encoded by the open reading frame SSO2342 of Sulfolobus solfataricus P2 was subjected to crystallographic, kinetic, and ligand binding analyses. The enzyme forms dimers in solution and in the crystals, and binds one molecule of the reactants 5-phosphoribosyl-α-1-pyrophosphate (PRPP) and adenine or the product adenosine monophosphate (AMP) or the inhibitor adenosine diphosphate (ADP) in each active site. The individual subunit adopts an overall structure that resembles a 6-oxopurine phosphoribosyltransferase (PRTase) more than known APRTases implying that APRT functionality in Crenarchaeotae has its evolutionary origin in this family of PRTases. Only the N-terminal two-thirds of the polypeptide chain folds as a traditional type I PRTase with a five-stranded β-sheet surrounded by helices. The C-terminal third adopts an unusual three-helix bundle structure that together with the nucleobase-binding loop undergoes a conformational change upon binding of adenine and phosphate resulting in a slight contraction of the active site. The inhibitor ADP binds like the product AMP with both the α- and β-phosphates occupying the 5'-phosphoribosyl binding site. The enzyme shows activity over a wide pH range, and the kinetic and ligand binding properties depend on both pH and the presence/absence of phosphate in the buffers. A slow hydrolysis of PRPP to ribose 5-phosphate and pyrophosphate, catalyzed by the enzyme, may be facilitated by elements in the C-terminal three-helix bundle part of the protein.
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Affiliation(s)
- Kaj Frank Jensen
- †University of Copenhagen, Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Michael Riis Hansen
- †University of Copenhagen, Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Kristine Steen Jensen
- †University of Copenhagen, Department of Biology, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
| | - Stig Christoffersen
- ‡University of Copenhagen, Department of Chemistry, Center of Crystallographic Studies, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Jens-Christian Navarro Poulsen
- ‡University of Copenhagen, Department of Chemistry, Center of Crystallographic Studies, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Anne Mølgaard
- ‡University of Copenhagen, Department of Chemistry, Center of Crystallographic Studies, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
| | - Anders Kadziola
- ‡University of Copenhagen, Department of Chemistry, Center of Crystallographic Studies, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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10
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Vetticatt MJ, Itin B, Evans GB, Schramm VL. Distortional binding of transition state analogs to human purine nucleoside phosphorylase probed by magic angle spinning solid-state NMR. Proc Natl Acad Sci U S A 2013; 110:15991-6. [PMID: 24043827 PMCID: PMC3791767 DOI: 10.1073/pnas.1313657110] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Transition state analogs mimic the geometry and electronics of the transition state of enzymatic reactions. These molecules bind to the active site of the enzyme much tighter than substrate and are powerful noncovalent inhibitors. Immucillin-H (ImmH) and 4'-deaza-1'-aza-2'-deoxy-9-methylene Immucillin-H (DADMe-ImmH) are picomolar inhibitors of human purine nucleoside phosphorylase (hPNP). Although both molecules are electronically similar to the oxocarbenium-like dissociative hPNP transition state, DADMe-ImmH is more potent than ImmH. DADMe-ImmH captures more of the transition state binding energy by virtue of being a closer geometric match to the hPNP transition state than ImmH. A consequence of these similarities is that the active site of hPNP exerts greater distortional forces on ImmH than on DADMe-ImmH to "achieve" the hPNP transition state geometry. By using magic angle spinning solid-state NMR to investigate stable isotope-labeled ImmH and DADMe-ImmH, we have explored the difference in distortional binding of these two inhibitors to hPNP. High-precision determinations of internuclear distances from NMR recoupling techniques, rotational echo double resonance, and rotational resonance, have provided unprecedented atomistic insight into the geometric changes that occur upon binding of transition state analogs. We conclude that hPNP stabilizes conformations of these chemically distinct analogs having distances between the cation and leaving groups resembling those of the known transition state.
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Affiliation(s)
- Mathew J. Vetticatt
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461
| | - Boris Itin
- New York Structural Biology Center, New York, NY 10027; and
| | - Gary B. Evans
- Carbohydrate Chemistry Team, Callaghaninnovation, Lower Hutt 5040, New Zealand
| | - Vern L. Schramm
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, Bronx, NY 10461
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11
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Deng H. Enzyme active site interactions by Raman/FTIR, NMR, and ab initio calculations. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2013; 93:153-82. [PMID: 24018325 PMCID: PMC5484042 DOI: 10.1016/b978-0-12-416596-0.00005-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Characterization of enzyme active site structure and interactions at high resolution is important for the understanding of the enzyme catalysis. Vibrational frequency and NMR chemical shift measurements of enzyme-bound ligands are often used for such purpose when X-ray structures are not available or when higher resolution active site structures are desired. This review is focused on how ab initio calculations may be integrated with vibrational and NMR chemical shift measurements to quantitatively determine high-resolution ligand structures (up to 0.001 Å for bond length and 0.01 Å for hydrogen bonding distance) and how interaction energies between bound ligand and its surroundings at the active site may be determined. Quantitative characterization of substrate ionic states, bond polarizations, tautomeric forms, conformational changes and its interactions with surroundings in enzyme complexes that mimic ground state or transition state can provide snapshots for visualizing the substrate structural evolution along enzyme-catalyzed reaction pathway. Our results have shown that the integration of spectroscopic studies with theoretical computation greatly enhances our ability to interpret experimental data and significantly increases the reliability of the theoretical analysis.
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Affiliation(s)
- Hua Deng
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York, USA.
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12
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Gong B, Klein DJ, Ferré-D’Amaré AR, Carey PR. The glmS ribozyme tunes the catalytically critical pK(a) of its coenzyme glucosamine-6-phosphate. J Am Chem Soc 2011; 133:14188-91. [PMID: 21848325 PMCID: PMC3174766 DOI: 10.1021/ja205185g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The glmS ribozyme riboswitch is the first known natural catalytic RNA that employs a small-molecule cofactor. Binding of glucosamine-6-phosphate (GlcN6P) uncovers the latent self-cleavage activity of the RNA, which adopts a catalytically competent conformation that is nonetheless inactive in the absence of GlcN6P. Structural and analogue studies suggest that the amine of GlcN6P functions as a general acid-base catalyst, while its phosphate is important for binding affinity. However, the solution pK(a) of the amine is 8.06 ± 0.05, which is not optimal for proton transfer. Here we used Raman crystallography directly to determine the pK(a)'s of GlcN6P bound to the glmS ribozyme. Binding to the RNA lowers the pK(a) of the amine of GlcN6P to 7.26 ± 0.09 and raises the pK(a) of its phosphate to 6.35 ± 0.09. Remarkably, the pK(a)'s of these two functional groups are unchanged from their values for free GlcN6P (8.06 ± 0.05 and 5.98 ± 0.05, respectively) when GlcN6P binds to the catalytically inactive but structurally unperturbed G40A mutant of the ribozyme, thus implicating the ribozyme active site guanine in pK(a) tuning. This is the first demonstration that a ribozyme can tune the pK(a) of a small-molecule ligand. Moreover, the anionic glmS ribozyme in effect stabilizes the neutral amine of GlcN6P by lowering its pK(a). This is unprecedented and illustrates the chemical sophistication of ribozyme active sites.
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Affiliation(s)
- Bo Gong
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
| | - Daniel J. Klein
- Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
| | - Adrian R. Ferré-D’Amaré
- Laboratory of RNA Biophysics and Cellular Physiology, National Heart, Lung and Blood Institute, 50 South Drive, Bethesda, MD 20892, USA
| | - Paul R. Carey
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
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13
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Andrews LD, Deng H, Herschlag D. Isotope-edited FTIR of alkaline phosphatase resolves paradoxical ligand binding properties and suggests a role for ground-state destabilization. J Am Chem Soc 2011; 133:11621-31. [PMID: 21692505 DOI: 10.1021/ja203370b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Escherichia coli alkaline phosphatase (AP) can hydrolyze a variety of chemically diverse phosphate monoesters while making contacts solely to the transferred phosphoryl group and its incoming and outgoing atoms. Strong interactions between AP and the transferred phosphoryl group are not present in the ground state despite the apparent similarity of the phosphoryl group in the ground and transition states. Such modest ground-state affinity is required to curtail substrate saturation and product inhibition and to allow efficient catalysis. To investigate how AP achieves limited affinity for its ground state, we first compared binding affinities of several related AP ligands. This comparison revealed a paradox: AP has a much stronger affinity for inorganic phosphate (P(i)) than for related compounds that are similar to P(i) geometrically and in overall charge but lack a transferable proton. We postulated that the P(i) proton could play an important role via transfer to the nearby anion, the active site serine nucleophile (Ser102), resulting in the attenuation of electrostatic repulsion between bound P(i) and the Ser102 oxyanion and the binding of P(i) in its trianionic form adjacent to a now neutral Ser residue. To test this model, isotope-edited Fourier transform infrared (FTIR) spectroscopy was used to investigate the ionic structure of AP-bound P(i). The FTIR results indicate that the P(i) trianion is bound and, in conjunction with previous studies of pH-dependent P(i) binding and other results, suggest that P(i) dianion transfers its proton to the Ser102 anion of AP. This internal proton-transfer results in stronger P(i) binding presumably because the additional negative charge on the trianionic P(i) allows stronger electrostatic interactions within the AP active site and because the electrostatic repulsion between bound P(i) and anionic Ser102 is eliminated when the transferred P(i) proton neutralizes Ser102. Indeed, when Ser102 is neutralized the P(i) trianion binds AP with a calculated K(d) of ≤290 fM. These results suggest that electrostatic repulsion between Ser102 and negatively charged phosphate ester substrates contributes to catalysis by the preferential destabilization of the reaction's E·S ground state.
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Affiliation(s)
- Logan D Andrews
- Department of Chemical and Systems Biology, Stanford University, Stanford, California 94305, USA
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14
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Zhang Y, Deng H, Schramm VL. Leaving group activation and pyrophosphate ionic state at the catalytic site of Plasmodium falciparum orotate phosphoribosyltransferase. J Am Chem Soc 2010; 132:17023-31. [PMID: 21067187 DOI: 10.1021/ja107806j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Plasmodium falciparum orotate phosphoribosyltransferase (PfOPRT) catalyzes the reversible pyrophosphorolysis of orotidine 5'-monophosphate (OMP). Transition-state analysis from kinetic isotope effects supports a dianionic orotic acid (OA) leaving group. Isotope-edited Fourier transform infrared (FTIR) spectrometry complemented by homology modeling and quantum chemical calculations were used to characterize the orotate hydrogen-bond network for PfOPRT. Bond stretch frequencies for C(2)═O and C(4)═O of OMP were established from (13)C-edited FTIR difference spectra. Both frequencies were shifted downward by 20 cm(-1) upon formation of the Michaelis complex. Hydrogen-bond interactions to the orotate moiety induce strong leaving group polarization by ground-state destabilization. The C(2)═O bond is 2.7 Å from two conserved water molecules, and the C(4)═O bond is within 2.4 Å of the NH(2)(ω) of Arg241 and the peptide NH of Phe97. Relative to free OMP, the N1 atom of PfOPRT-bound OMP indicates a ΔpK(a) of -4.6. The decreased basicity of N1 supports leaving group activation through a hydrogen-bond network at the PfOPRT active site. PfOPRT in complex with (18)O-PPi and a proposed transition-state analogue revealed a trianionic PPi nucleophile with no significant P··O bond polarization, supporting a mechanism proceeding through the migration of the ribocation toward the PPi. These results along with previous PfOPRT transition-state analyses provide reaction coordinate information for the PfOPRT-catalyzed OMP pyrophosphorolysis reaction.
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Affiliation(s)
- Yong Zhang
- Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, United States
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