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Lustosa DM, Milo A. Mechanistic Inference from Statistical Models at Different Data-Size Regimes. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Danilo M. Lustosa
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
| | - Anat Milo
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva 84105, Israel
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2
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Barrios B, Mohrhardt B, Doskey PV, Minakata D. Mechanistic Insight into the Reactivities of Aqueous-Phase Singlet Oxygen with Organic Compounds. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8054-8067. [PMID: 34096699 DOI: 10.1021/acs.est.1c01712] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Singlet oxygen (1O2) is a selective reactive oxygen species that plays a key role for the fate of various organic compounds in the aquatic environment under sunlight irradiation, engineered water oxidation systems, atmospheric water droplets, and biomedical systems. While the initial rate-determining charge-transfer reaction mechanisms and kinetics of 1O2 have been studied extensively, no comprehensive studies have been performed to elucidate the reaction mechanisms with organic compounds that have various functional groups. In this study, we use density functional theory calculations to determine elementary reaction mechanisms with a wide variety of organic compounds. The theoretically calculated aqueous-phase free energies of activation of single electron transfer and 1O2 addition reactions are compared to the experimentally determined rate constants in the literature to determine linear free-energy relationships. The theoretically calculated free energies of activation for the groups of phenolates and phenols show excellent correlations with the Hammett constants that accept electron densities by through-resonance. The dominant elementary reaction mechanism is discussed for each group of compounds. As a practical implication, we demonstrate the fate of environmentally relevant organic compounds induced by photochemically produced intermediate species at different pH and evaluate the impact of predicting rate constants to the half-life.
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Affiliation(s)
- Benjamin Barrios
- Department of Civil and Environmental Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Benjamin Mohrhardt
- Department of Civil and Environmental Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
| | - Paul V Doskey
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, Michigan 49931, United States
| | - Daisuke Minakata
- Department of Civil and Environmental Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States
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Wu J, Wang Z, Jin X, Zhang S, Li T, Zhang Y, Xing H, Yu Y, Zhang H, Gao X, Wei H. Hammett Relationship in Oxidase-Mimicking Metal-Organic Frameworks Revealed through a Protein-Engineering-Inspired Strategy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2005024. [PMID: 33283334 DOI: 10.1002/adma.202005024] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/07/2020] [Indexed: 06/12/2023]
Abstract
While the unique physicochemical properties of nanomaterials that enable regulation of nanozyme activities are demonstrated in many systems, quantitative relationships between the nanomaterials structure and their enzymatic activities remain poorly understood, due to the heterogeneity of compositions and active sites in these nanomaterials. Here, inspired by metalloenzymes with well-defined metal-ligand coordination, a set of substituted metal-organic frameworks (MOFs) with similar coordination is employed to investigate the relationship between structure and oxidase-mimicking activity. Both experimental results and density functional theory calculations reveal a Hammett-type structure-activity linear free energy relationship (H-SALR) of MIL-53(Fe) (MIL = Materials of Institute Lavoisier) nanozymes, in which increasing the Hammett σm value with electron-withdrawing ligands increases the oxidase-mimicking activity. As a result, MIL-53(Fe) NO2 with the strongest electron-withdrawing NO2 substituent shows a tenfold higher activity than the unsubstituted MIL-53(Fe). Furthermore, the generality of H-SALR is demonstrated for a range of substrates, one other metal (Cr), and even one other MOF type (MIL-101). Such biologically inspired quantitative studies demonstrate that it is possible to identify quantitative structure-activity relationships of nanozymes, and to provide detailed insight into the catalytic mechanisms as those in native enzymes, making it possible to use these relationships to develop high-performance nanomaterials.
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Affiliation(s)
- Jiangjiexing Wu
- College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Zhenzhen Wang
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanophotonic Materials and Devices, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Xin Jin
- College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Shuo Zhang
- College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Tong Li
- College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Yihong Zhang
- College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, 410082, China
| | - Yang Yu
- Department of Biochemical Engineering and Institute for Synthetic Biosystem, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, China
| | - Huigang Zhang
- College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210093, China
| | - Xingfa Gao
- Laboratory of Theoretical and Computational Nanoscience, CAS Key Laboratory of Nanophotonic Materials and Devices, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hui Wei
- College of Engineering and Applied Sciences, Nanjing National Laboratory of Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Nanjing University, Nanjing, Jiangsu, 210093, China
- State Key Laboratory of Analytical Chemistry for Life Science and State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, Jiangsu, 210023, China
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Hu QH, Williams MT, Shulgina I, Fossum CJ, Weeks KM, Adams LM, Reinhardt CR, Musier-Forsyth K, Hati S, Bhattacharyya S. Editing Domain Motions Preorganize the Synthetic Active Site of Prolyl-tRNA Synthetase. ACS Catal 2020; 10:10229-10242. [PMID: 34295570 DOI: 10.1021/acscatal.0c02381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate tRNAs, an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and the "prokaryotic-like" ProRSs are distinguished from "eukaryotic-like" ProRSs by the presence of an editing domain (INS) inserted between motifs 2 and 3 of the main catalytic domain. Earlier studies suggested the presence of coupled-domain dynamics could contribute to catalysis; however, the role that the distal, highly mobile INS domain plays in catalysis at the synthetic active site is not completely understood. In the present study, a combination of theoretical and experimental approaches has been used to elucidate the precise role of INS domain dynamics. Quantum mechanical/molecular mechanical simulations were carried out to model catalytic Pro-AMP formation by Enterococcus faecalis ProRS. The energetics of the adenylate formation by the wild-type enzyme was computed and contrasted with variants containing active site mutations, as well as a deletion mutant lacking the INS domain. The combined results revealed that two distinct types of dynamics contribute to the enzyme's catalytic power. One set of motions is intrinsic to the INS domain and leads to conformational preorganization that is essential for catalysis. A second type of motion, stemming from the electrostatic reorganization of active site residues, impacts the height and width of the energy profile and has a critical role in fine tuning the substrate orientation to facilitate reactive collisions. Thus, motions in a distal domain can preorganize the active site of an enzyme to optimize catalysis.
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Affiliation(s)
- Quin H. Hu
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Murphi T. Williams
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Irina Shulgina
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Carl J. Fossum
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Katelyn M. Weeks
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Lauren M. Adams
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Clorice R. Reinhardt
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry and Center for RNA Biology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin, Eau Claire, Wisconsin 54701, United States
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5
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Kulkarni Y, Kamerlin SCL. Computational physical organic chemistry using the empirical valence bond approach. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2019. [DOI: 10.1016/bs.apoc.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Roston D, Lu X, Fang D, Demapan D, Cui Q. Analysis of Phosphoryl-Transfer Enzymes with QM/MM Free Energy Simulations. Methods Enzymol 2018; 607:53-90. [PMID: 30149869 DOI: 10.1016/bs.mie.2018.05.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We discuss the application of quantum mechanics/molecular mechanics (QM/MM) free energy simulations to the analysis of phosphoryl transfers catalyzed by two enzymes: alkaline phosphatase and myosin. We focus on the nature of the transition state and the issue of mechanochemical coupling, respectively, in the two enzymes. The results illustrate unique insights that emerged from the QM/MM simulations, especially concerning the interpretation of experimental data regarding the nature of enzymatic transition states and coupling between global structural transition and catalysis in the active site. We also highlight a number of technical issues worthy of attention when applying QM/MM free energy simulations, and comment on a number of technical and mechanistic issues that require further studies.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Dong Fang
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Darren Demapan
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, WI, United States.
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7
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Duo T, Robinson K, Greig IR, Chen HM, Patrick BO, Withers SG. Remarkable Reactivity Differences between Glucosides with Identical Leaving Groups. J Am Chem Soc 2017; 139:15994-15999. [PMID: 29035043 DOI: 10.1021/jacs.7b09645] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Two isomeric aryl 2-deoxy-2-fluoro-β-glucosides react with a β-glucosidase at rates differing by 106-fold, despite the fact that they release the same aromatic aglycone. In contrast, the equivalent glucoside substrates react with essentially identical rate constants. Insight into the source of these surprising rate differences was obtained through a comprehensive study of the nonenzymatic (spontaneous) hydrolysis of these same substrates, wherein an approximate 105-fold difference in rates was measured, clarifying that the differences were inherent rather than being due to specific interactions with the enzyme. The possibility that an alternate nucleophilic aryl substitution mechanism was responsible for the rapid reaction of the faster substrate was excluded through 18O-labeling studies. Further exploration of the origins of these rate differences involved analysis of X-ray crystal structures as well as quantum chemical calculations, which surprisingly revealed that ground state destabilization and transition state stabilizing effects contribute almost equally to the observed reactivity differences. These studies highlight the dangers of using simple reference equilibria such as pKa values as measures of leaving group ability.
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Affiliation(s)
- Tianmeng Duo
- Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Kyle Robinson
- Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ian R Greig
- Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Hong-Ming Chen
- Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Brian O Patrick
- Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia , 2036 Main Mall, Vancouver, British Columbia V6T 1Z1, Canada
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8
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Cupp-Sutton KA, Ashby MT. Biological Chemistry of Hydrogen Selenide. Antioxidants (Basel) 2016; 5:E42. [PMID: 27879667 PMCID: PMC5187540 DOI: 10.3390/antiox5040042] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 12/13/2022] Open
Abstract
There are no two main-group elements that exhibit more similar physical and chemical properties than sulfur and selenium. Nonetheless, Nature has deemed both essential for life and has found a way to exploit the subtle unique properties of selenium to include it in biochemistry despite its congener sulfur being 10,000 times more abundant. Selenium is more easily oxidized and it is kinetically more labile, so all selenium compounds could be considered to be "Reactive Selenium Compounds" relative to their sulfur analogues. What is furthermore remarkable is that one of the most reactive forms of selenium, hydrogen selenide (HSe- at physiologic pH), is proposed to be the starting point for the biosynthesis of selenium-containing molecules. This review contrasts the chemical properties of sulfur and selenium and critically assesses the role of hydrogen selenide in biological chemistry.
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Affiliation(s)
- Kellye A Cupp-Sutton
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
| | - Michael T Ashby
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA.
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Roston D, Cui Q. Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects. J Am Chem Soc 2016; 138:11946-57. [PMID: 27541005 PMCID: PMC5705178 DOI: 10.1021/jacs.6b07347] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Enzymes are powerful catalysts, and a thorough understanding of the sources of their catalytic power will facilitate many medical and industrial applications. Here we have studied the catalytic mechanism of alkaline phosphatase (AP), which is one of the most catalytically proficient enzymes known. We have used quantum mechanics calculations and hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to model a variety of isotope effects relevant to the reaction of AP. We have calculated equilibrium isotope effects (EIEs), binding isotope effects (BIEs), and kinetic isotope effects (KIEs) for a range of phosphate mono- and diester substrates. The results agree well with experimental values, but the model for the reaction's transition state (TS) differs from the original interpretation of those experiments. Our model indicates that isotope effects on binding make important contributions to measured KIEs on V/K, which complicated interpretation of the measured values. Our results provide a detailed interpretation of the measured isotope effects and make predictions that can test the proposed model. The model indicates that the substrate is deformed in the ground state (GS) of the reaction and partially resembles the TS. The highly preorganized active site preferentially binds conformations that resemble the TS and not the GS, which induces the substrate to adapt to the enzyme, rather than the other way around-as with classic "induced fit" models. The preferential stabilization of the TS over the GS is what lowers the barrier to the chemical step.
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Affiliation(s)
- Daniel Roston
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin , Madison, Wisconsin 53706, United States
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10
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Neel AJ, Milo A, Sigman MS, Toste FD. Enantiodivergent Fluorination of Allylic Alcohols: Data Set Design Reveals Structural Interplay between Achiral Directing Group and Chiral Anion. J Am Chem Soc 2016; 138:3863-75. [PMID: 26967114 PMCID: PMC5176255 DOI: 10.1021/jacs.6b00356] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Enantioselectivity values represent relative rate measurements that are sensitive to the structural features of the substrates and catalysts interacting to produce them. Therefore, well-designed enantioselectivity data sets are information rich and can provide key insights regarding specific molecular interactions. However, if the mechanism for enantioselection varies throughout a data set, these values cannot be easily compared. This premise, which is the crux of free energy relationships, exposes a challenging issue of identifying mechanistic breaks within multivariate correlations. Herein, we describe an approach to addressing this problem in the context of a chiral phosphoric acid catalyzed fluorination of allylic alcohols using aryl boronic acids as transient directing groups. By designing a data set in which both the phosphoric and boronic acid structures were systematically varied, key enantioselectivity outliers were identified and analyzed. A mechanistic study was executed to reveal the structural origins of these outliers, which was consistent with the presence of several mechanistic regimes within the data set. While 2- and 4-substituted aryl boronic acids favored the (R)-enantiomer with most of the studied catalysts, meta-alkoxy substituted aryl boronic acids resulted in the (S)-enantiomer when used in combination with certain (R)-phosphoric acids. We propose that this selectivity reversal is the result of a lone pair-π interaction between the substrate ligated boronic acid and the phosphate. On the basis of this proposal, a catalyst system was identified, capable of producing either enantiomer in high enantioselectivity (77% (R)-2 to 92% (S)-2) using the same chiral catalyst by subtly changing the structure of the achiral boronic acid.
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Affiliation(s)
- Andrew J. Neel
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, and Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Anat Milo
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
- Department of Chemistry, Ben-Gurion University of the Negev, Beer Sheva, 84105, Israel
| | - Matthew S. Sigman
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112, United States
| | - F. Dean Toste
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, and Department of Chemistry, University of California, Berkeley, California 94720, United States
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Minakata D, Mezyk SP, Jones JW, Daws BR, Crittenden JC. Development of linear free energy relationships for aqueous phase radical-involved chemical reactions. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2014; 48:13925-13932. [PMID: 25368975 DOI: 10.1021/es504491z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aqueous phase advanced oxidation processes (AOPs) produce hydroxyl radicals (HO•) which can completely oxidize electron rich organic compounds. The proper design and operation of AOPs require that we predict the formation and fate of the byproducts and their associated toxicity. Accordingly, there is a need to develop a first-principles kinetic model that can predict the dominant reaction pathways that potentially produce toxic byproducts. We have published some of our efforts on predicting the elementary reaction pathways and the HO• rate constants. Here we develop linear free energy relationships (LFERs) that predict the rate constants for aqueous phase radical reactions. The LFERs relate experimentally obtained kinetic rate constants to quantum mechanically calculated aqueous phase free energies of activation. The LFERs have been applied to 101 reactions, including (1) HO• addition to 15 aromatic compounds; (2) addition of molecular oxygen to 65 carbon-centered aliphatic and cyclohexadienyl radicals; (3) disproportionation of 10 peroxyl radicals, and (4) unimolecular decay of nine peroxyl radicals. The LFERs correlations predict the rate constants within a factor of 2 from the experimental values for HO• reactions and molecular oxygen addition, and a factor of 5 for peroxyl radical reactions. The LFERs and the elementary reaction pathways will enable us to predict the formation and initial fate of the byproducts in AOPs. Furthermore, our methodology can be applied to other environmental processes in which aqueous phase radical-involved reactions occur.
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Affiliation(s)
- Daisuke Minakata
- Department of Civil and Environmental Engineering, Michigan Technological University, 1400 Townsend Drive, Houghton, Michigan 49931, United States.
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12
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Probing the catalytic mechanism of bovine CD38/NAD+ glycohydrolase by site directed mutagenesis of key active site residues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:1317-31. [PMID: 24721563 DOI: 10.1016/j.bbapap.2014.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Revised: 03/28/2014] [Accepted: 03/31/2014] [Indexed: 01/14/2023]
Abstract
Bovine CD38/NAD(+) glycohydrolase catalyzes the hydrolysis of NAD(+) to nicotinamide and ADP-ribose and the formation of cyclic ADP-ribose via a stepwise reaction mechanism. Our recent crystallographic study of its Michaelis complex and covalently-trapped intermediates provided insights into the modalities of substrate binding and the molecular mechanism of bCD38. The aim of the present work was to determine the precise role of key conserved active site residues (Trp118, Glu138, Asp147, Trp181 and Glu218) by focusing mainly on the cleavage of the nicotinamide-ribosyl bond. We analyzed the kinetic parameters of mutants of these residues which reside within the bCD38 subdomain in the vicinity of the scissile bond of bound NAD(+). To address the reaction mechanism we also performed chemical rescue experiments with neutral (methanol) and ionic (azide, formate) nucleophiles. The crucial role of Glu218, which orients the substrate for cleavage by interacting with the N-ribosyl 2'-OH group of NAD(+), was highlighted. This contribution to catalysis accounts for almost half of the reaction energy barrier. Other contributions can be ascribed notably to Glu138 and Asp147 via ground-state destabilization and desolvation in the vicinity of the scissile bond. Key interactions with Trp118 and Trp181 were also proven to stabilize the ribooxocarbenium ion-like transition state. Altogether we propose that, as an alternative to a covalent acylal reaction intermediate with Glu218, catalysis by bCD38 proceeds through the formation of a discrete and transient ribooxocarbenium intermediate which is stabilized within the active site mostly by electrostatic interactions.
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13
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Mohamed MF, Hollfelder F. Efficient, crosswise catalytic promiscuity among enzymes that catalyze phosphoryl transfer. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:417-24. [PMID: 22885024 DOI: 10.1016/j.bbapap.2012.07.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2012] [Revised: 07/19/2012] [Accepted: 07/26/2012] [Indexed: 11/25/2022]
Abstract
The observation that one enzyme can accelerate several chemically distinct reactions was at one time surprising because the enormous efficiency of catalysis was often seen as inextricably linked to specialization for one reaction. Originally underreported, and considered a quirk rather than a fundamental property, enzyme promiscuity is now understood to be important as a springboard for adaptive evolution. Owing to the large number of promiscuous enzymes that have been identified over the last decade, and the increased appreciation for promiscuity's evolutionary importance, the focus of research has shifted to developing a better understanding of the mechanistic basis for promiscuity and the origins of tolerant or restrictive specificity. We review the evidence for widespread crosswise promiscuity amongst enzymes that catalyze phosphoryl transfer, including several members of the alkaline phosphatase superfamily, where large rate accelerations between 10(6) and 10(17) are observed for both native and multiple promiscuous reactions. This article is part of a Special Issue entitled: Chemistry and mechanism of phosphatases, diesterases and triesterases.
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Affiliation(s)
- Mark F Mohamed
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, EU, UK
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14
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Ishizuka T, Sankar M, Yamada Y, Fukuzumi S, Kojima T. Porphyrin nanochannels reinforced by hydrogen bonding. Chem Commun (Camb) 2012; 48:6481-3. [DOI: 10.1039/c2cc31142a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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15
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Babtie AC, Lima MF, Kirby AJ, Hollfelder F. Kinetic and computational evidence for an intermediate in the hydrolysis of sulfonate esters. Org Biomol Chem 2012; 10:8095-101. [DOI: 10.1039/c2ob25699a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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16
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Maxwell CI, Liu CT, Neverov AA, Mosey NJ, Brown RS. Transition from concerted to stepwise processes as a function of leaving group ability: density functional theory and experimental study of lyoxide-promoted cleavages of phosphorothioate and phosphate triesters in water and methanol. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1938] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - C. Tony Liu
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Alexei A. Neverov
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Nicholas J. Mosey
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
| | - Robert Stan Brown
- Department of Chemistry; Queen's University; Kingston Ontario Canada K7L 3N6
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Lee SS, Hong SY, Errey JC, Izumi A, Davies GJ, Davis BG. Mechanistic evidence for a front-side, SNi-type reaction in a retaining glycosyltransferase. Nat Chem Biol 2011; 7:631-8. [DOI: 10.1038/nchembio.628] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 06/10/2011] [Indexed: 01/14/2023]
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18
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Minakata D, Crittenden J. Linear free energy relationships between aqueous phase hydroxyl radical reaction rate constants and free energy of activation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2011; 45:3479-3486. [PMID: 21410278 DOI: 10.1021/es1020313] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The hydroxyl radical (HO(•)) is a strong oxidant that reacts with electron-rich sites on organic compounds and initiates complex radical chain reactions in aqueous phase advanced oxidation processes (AOPs). Computer based kinetic modeling requires a reaction pathway generator and predictions of associated reaction rate constants. Previously, we reported a reaction pathway generator that can enumerate the most important elementary reactions for aliphatic compounds. For the reaction rate constant predictor, we develop linear free energy relationships (LFERs) between aqueous phase literature-reported HO(•) reaction rate constants and theoretically calculated free energies of activation for H-atom abstraction from a C-H bond and HO(•) addition to alkenes. The theoretical method uses ab initio quantum mechanical calculations, Gaussian 1-3, for gas phase reactions and a solvation method, COSMO-RS theory, to estimate the impact of water. Theoretically calculated free energies of activation are found to be within approximately ±3 kcal/mol of experimental values. Considering errors that arise from quantum mechanical calculations and experiments, this should be within the acceptable errors. The established LFERs are used to predict the HO(•) reaction rate constants within a factor of 5 from the experimental values. This approach may be applied to other reaction mechanisms to establish a library of rate constant predictions for kinetic modeling of AOPs.
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Affiliation(s)
- Daisuke Minakata
- School of Civil and Environmental Engineering, Georgia Institute of Technology , 800 West Peachtree Street, Suite 400 F-H, Atlanta, Georgia 30332-0595, United States.
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Schelwies M, Brinson D, Otsuki S, Hong YH, Lotz MK, Wong CH, Hanson SR. Glucosamine-6-sulfamate analogues of heparan sulfate as inhibitors of endosulfatases. Chembiochem 2010; 11:2393-7. [PMID: 20973023 PMCID: PMC3086843 DOI: 10.1002/cbic.201000401] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Indexed: 01/13/2023]
Abstract
Keeping Sulfate. The extracellular endosulfatases, which modulate signalling pathways by removing sulfate groups from heparan, can be inhibited by replacing the 6-sulfate destined for cleavage with an inhibitory sulfamate motif, as demonstrated by simple glucosamine-6-sulfamate analogs of heparan sulfate.
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Affiliation(s)
- Mathias Schelwies
- Dr. M. Schelwies, Prof. Dr. C.-H. Wong, Dr. S. R. Hanson Department of Chemistry and Skaggs Institute for Chemical Biology The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Diana Brinson
- D. Brinson, Dr. Y.-H. Hong, Dr. S. Otsuki, Prof. Dr. M. K. Lotz, Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Shuhei Otsuki
- D. Brinson, Dr. Y.-H. Hong, Dr. S. Otsuki, Prof. Dr. M. K. Lotz, Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Young-Hoon Hong
- D. Brinson, Dr. Y.-H. Hong, Dr. S. Otsuki, Prof. Dr. M. K. Lotz, Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Martin K. Lotz
- D. Brinson, Dr. Y.-H. Hong, Dr. S. Otsuki, Prof. Dr. M. K. Lotz, Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Chi-Huey Wong
- Dr. M. Schelwies, Prof. Dr. C.-H. Wong, Dr. S. R. Hanson Department of Chemistry and Skaggs Institute for Chemical Biology The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
| | - Sarah R. Hanson
- Dr. M. Schelwies, Prof. Dr. C.-H. Wong, Dr. S. R. Hanson Department of Chemistry and Skaggs Institute for Chemical Biology The Scripps Research Institute 10550 North Torrey Pines Road, La Jolla, CA 92037 (USA)
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