1
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Poddar A, Zhao D, Ayers PW, Liu S, Chattaraj PK. What Dictates the α-Effect in Gas-Phase S N2 Reactions? A Density Functional Theory Study. J Phys Chem A 2025; 129:1847-1855. [PMID: 39908015 DOI: 10.1021/acs.jpca.4c08694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2025]
Abstract
The α-effect is an important concept in chemistry and biochemistry, namely that for a bimolecular nucleophilic substitution (SN2) reaction, the nucleophilicity of an atom is increased if its adjacent (α) atom has a lone pair of electrons, lowering the reaction barrier height and increasing the reaction rate. However, exceptions exist, even for very similar structural motifs. We investigate what underlies the α-effect in gas-phase SN2 reactions using two total energy decomposition schemes based on density functional theory (DFT) and find that steric effects play an important role, but that there exists a strong linear correlation between the α-effect and electrostatic contribution, suggesting that it is the electrostatic interaction that stabilizes the transition state and leads to the α-effect in gas-phase SN2 reactions. This multifaceted explanation resolves the long-standing uncertainty about the α-effect. We show that the α-effect increases with the branching of the central carbon atom.
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Affiliation(s)
- Arpita Poddar
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Dongbo Zhao
- Institute of Biomedical Research, Yunnan University, Kunming, Yunnan 650500, China
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton ONL8S4M1, Canada
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599-3420, United States
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599-3290, United States
| | - Pratim K Chattaraj
- Department of Chemistry, Birla Institute of Technology Mesra, Ranchi, Jharkhand 835215, India
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2
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David R, Tuñón I, Laage D. Competing Reaction Mechanisms of Peptide Bond Formation in Water Revealed by Deep Potential Molecular Dynamics and Path Sampling. J Am Chem Soc 2024; 146:14213-14224. [PMID: 38739765 DOI: 10.1021/jacs.4c03445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The formation of an amide bond is an essential step in the synthesis of materials and drugs, and in the assembly of amino acids to form peptides. The mechanism of this reaction has been studied extensively, in particular to understand how it can be catalyzed, but a representation capable of explaining all the experimental data is still lacking. Numerical simulation should provide the necessary molecular description, but the solvent involvement poses a number of challenges. Here, we combine the efficiency and accuracy of neural network potential-based reactive molecular dynamics with the extensive and unbiased exploration of reaction pathways provided by transition path sampling. Using microsecond-scale simulations at the density functional theory level, we show that this method reveals the presence of two competing distinct mechanisms for peptide bond formation between alanine esters in aqueous solution. We describe how both reaction pathways, via a general base catalysis mechanism and via direct cleavage of the tetrahedral intermediate respectively, change with pH. This result contrasts with the conventional mechanism involving a single pathway in which only the barrier heights are affected by pH. We show that this new proposal involving two competing mechanisms is consistent with the experimental data, and we discuss the implications for peptide bond formation under prebiotic conditions and in the ribosome. Our work shows that integrating deep potential molecular dynamics with path sampling provides a powerful approach for exploring complex chemical mechanisms.
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Affiliation(s)
- Rolf David
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Iñaki Tuñón
- Departamento de Química Física, Universitat de Valencia, Burjassot, 46100 Valencia, Spain
| | - Damien Laage
- PASTEUR, Department of Chemistry, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
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3
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Fındık V, Ruiz-López MF, Erdem SS. Mechanistic insights into lysine-targeting covalent inhibition through a theoretical study of ester aminolysis. Org Biomol Chem 2021; 19:9996-10004. [PMID: 34755747 DOI: 10.1039/d1ob01963e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Development of targeted covalent inhibitors in drug design has a broad and important interest and many efforts are currently being made in this direction. Targeted covalent inhibitors have special relevance in oncology due to the possibilities they offer to overcome the problems of acquired resistance. In recent experiments, lysine-targeting has been envisaged for the irreversible inhibition of the heterodimeric lipid kinase phosphoinositide 3-kinase delta (PI3Kδ). Activated esters have been evaluated and shown to be promising inhibitors of this enzyme, but the reaction mechanisms display specificities that are not yet fully understood. In the present work, we have carried out a theoretical study of the aminolysis reaction of model esters in aqueous solution to gain insights into the corresponding biological processes. We have found that phenolic esters bearing electron-withdrawing groups are particularly reactive. The predicted mechanism involves the formation of a tetrahedral zwitterionic intermediate, which dissociates into an alkoxide and a protonated amide, this charge separation being the driving force for the subsequent proton transfer and final product formation. Structure-reactivity relationships are reported and shown to be a useful tool for evaluating potential inhibitor candidates.
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Affiliation(s)
- Volkan Fındık
- LPCT, UMR 7019, University of Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-les-Nancy, France. .,Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722 Istanbul, Turkey.
| | - Manuel F Ruiz-López
- LPCT, UMR 7019, University of Lorraine, CNRS, BP 70239, 54506 Vandoeuvre-les-Nancy, France.
| | - Safiye Sag Erdem
- Department of Chemistry, Faculty of Arts and Sciences, Marmara University, 34722 Istanbul, Turkey.
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4
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Lin HH, Cheng Y, Huo J, Shanks BH. Selective Ammonolysis of Bioderived Esters for Biobased Amide Synthesis. ACS OMEGA 2021; 6:30040-30049. [PMID: 34778675 PMCID: PMC8582026 DOI: 10.1021/acsomega.1c04750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Amidation is an important reaction for bioderived platform molecules, which can be upgraded for use in applications such as polymers. However, fundamental understanding of the reaction especially in the presence of multiple groups is still lacking. In this study, the amidation of dimethyl fumarate, maleate, and succinate through ester ammonolysis was examined. The reaction networks and significant side reactions, such as conjugate addition and ring closing, were determined. A preliminary kinetic comparison among additional C4 and C6 esters showed a significant correlation between molecular structure and ammonolysis reactivity. Esters with a C=C double bond in the molecule backbone were found to have higher ammonolysis reactivity. To improve the selectivity to unsaturated amides rather than byproducts, the effects of thermal conditions and additives in dimethyl fumarate ammonolysis were examined. Lower temperature and decreasing methoxide ion concentration in the solution relative to the base case conditions increased the fumaramide selectivity from 67.1 to 90.6%.
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Affiliation(s)
- Hsi-Hsin Lin
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
- Center
for Biorenewable Chemicals (CBiRC), Iowa
State University, Ames, Iowa 50011, United
States
| | - Yan Cheng
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
- Center
for Biorenewable Chemicals (CBiRC), Iowa
State University, Ames, Iowa 50011, United
States
| | - Jiajie Huo
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
- Center
for Biorenewable Chemicals (CBiRC), Iowa
State University, Ames, Iowa 50011, United
States
| | - Brent H. Shanks
- Department
of Chemical and Biological Engineering, Iowa State University, Ames, Iowa 50011, United States
- Center
for Biorenewable Chemicals (CBiRC), Iowa
State University, Ames, Iowa 50011, United
States
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5
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Hansen T, Vermeeren P, Bickelhaupt FM, Hamlin TA. Origin of the α‐Effect in S
N
2 Reactions. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202106053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Thomas Hansen
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Leiden Institute of Chemistry Leiden University Einsteinweg 55 2333 CC Leiden The Netherlands
| | - Pascal Vermeeren
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
- Institute for Molecules and Materials Radboud University Heyendaalseweg 135 6525 AJ Nijmegen The Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical Chemistry Amsterdam Institute of Molecular and Life Sciences (AIMMS) Amsterdam Center for Multiscale Modeling (ACMM) Vrije Universiteit Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
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6
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Hansen T, Vermeeren P, Bickelhaupt FM, Hamlin TA. Origin of the α-Effect in S N 2 Reactions. Angew Chem Int Ed Engl 2021; 60:20840-20848. [PMID: 34087047 PMCID: PMC8518820 DOI: 10.1002/anie.202106053] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/27/2021] [Indexed: 11/07/2022]
Abstract
The α-effect is a term used to explain the dramatically enhanced reactivity of α-nucleophiles (R-Y-X:- ) compared to their parent normal nucleophile (R-X:- ) by deviating from the classical Brønsted-type reactivity-basicity relationship. The exact origin of this effect is, however, still heavily under debate. In this work, we have quantum chemically analyzed the α-effect of a set of anionic nucleophiles, including O-, N- and S-based normal and α-nucleophiles, participating in an SN 2 reaction with ethyl chloride using relativistic density functional theory at ZORA-OLYP/QZ4P. Our activation strain and Kohn-Sham molecular orbital analyses identified two criteria an α-nucleophile needs to fulfill in order to show α-effect: (i) a small HOMO lobe on the nucleophilic center, pointing towards the substrate, to reduce the repulsive occupied-occupied orbital overlap and hence (steric) Pauli repulsion with the substrate; and (ii) a sufficiently high energy HOMO to overcome the loss of favorable HOMO-LUMO orbital overlap with the substrate, as a consequence of the first criterion, by reducing the HOMO-LUMO orbital energy gap. If one of these two criteria is not fulfilled, one can expect no α-effect or inverse α-effect.
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Affiliation(s)
- Thomas Hansen
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Leiden Institute of ChemistryLeiden UniversityEinsteinweg 552333 CCLeidenThe Netherlands
| | - Pascal Vermeeren
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
| | - F. Matthias Bickelhaupt
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
- Institute for Molecules and MaterialsRadboud UniversityHeyendaalseweg 1356525 AJNijmegenThe Netherlands
| | - Trevor A. Hamlin
- Department of Theoretical ChemistryAmsterdam Institute of Molecular and Life Sciences (AIMMS)Amsterdam Center for Multiscale Modeling (ACMM)Vrije Universiteit AmsterdamDe Boelelaan 10831081 HVAmsterdamThe Netherlands
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7
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Zhou S, Hong Q, Mei W, He Y, Wu C, Sun T. Scale-Up of a Continuous Manufacturing Process of Edaravone. Org Process Res Dev 2021. [DOI: 10.1021/acs.oprd.1c00228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Shuhao Zhou
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
| | - Qingxia Hong
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
| | - Wenliu Mei
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
| | - Yan He
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang 110840, P. R. China
| | - Chengjun Wu
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
| | - Tiemin Sun
- Key Laboratory of Structure-Based Drug Design and Discovery, Shenyang Pharmaceutical University, Ministry of Education, Shenyang 110016, P. R. China
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8
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Tsichla A, Severins C, Gottfried M, Marquardt W. An Experimental Assessment of Model-Based Solvent Selection for Enhancing Reaction Kinetics. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b01040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Angeliki Tsichla
- Aachener Verfahrenstechnik−Process Systems Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
- Bayer Technology Services GmbH, 51368 Leverkusen, Germany
| | | | | | - Wolfgang Marquardt
- Aachener Verfahrenstechnik−Process Systems Engineering, RWTH Aachen University, Forckenbeckstraße 51, 52074 Aachen, Germany
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9
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Castillo GA, Wilson L, Efimenko K, Dickey MD, Gorman CB, Genzer J. Amidation of Polyesters Is Slow in Nonaqueous Solvents: Efficient Amidation of Poly(ethylene terephthalate) with 3-Aminopropyltriethoxysilane in Water for Generating Multifunctional Surfaces. ACS APPLIED MATERIALS & INTERFACES 2016; 8:35641-35649. [PMID: 27977121 DOI: 10.1021/acsami.6b12155] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This paper describes surface functionalization of poly(ethylene terephthalate) (PET) films by transamidation of the ester groups with primary amines. The use of water as a solvent improves tremendously the reaction rate and yield compared to conventionally used alcohols. In this study, PET films were exposed to an aqueous solution of 3-aminopropyltriethoxysilane (APTES), which resulted in ester-to-amide reactions on the surface of the film. Hydrolysis of the resulting ethoxy moieties in APTES creates hydroxyl groups that can be used as anchoring points for further modification of PET films. This scheme offers an alternative approach to modify polyesters using water as the solvent.
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Affiliation(s)
- Gilbert A Castillo
- Department of Chemical & Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695-7905, United States
| | - Lance Wilson
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
| | - Kirill Efimenko
- Department of Chemical & Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695-7905, United States
| | - Michael D Dickey
- Department of Chemical & Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695-7905, United States
| | - Christopher B Gorman
- Department of Chemistry, North Carolina State University , Raleigh, North Carolina 27695-8204, United States
| | - Jan Genzer
- Department of Chemical & Biomolecular Engineering, North Carolina State University , Raleigh, North Carolina 27695-7905, United States
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10
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Merits of online electrochemistry liquid sample desorption electrospray ionization mass spectrometry (EC/LS DESI MS). Anal Bioanal Chem 2016; 408:2227-38. [DOI: 10.1007/s00216-015-9246-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/25/2015] [Accepted: 12/02/2015] [Indexed: 12/11/2022]
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11
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Chen R, Luo X, Liang G. Computational study on the aminolysis mechanism of 4,4-dimethyl-2-vinyl-2-oxazolin-5-one with methylamine. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.09.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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12
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Andrada DM, Zoloff Michoff ME, de Rossi RH, Granados AM. Nucleophilic substitution in ionizable Fischer thiocarbene complexes: steric effect of the alkyl substituent on the heteroatom. Dalton Trans 2015; 44:5520-34. [PMID: 25698135 DOI: 10.1039/c4dt03618b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A detailed kinetic study has been carried out for the aminolysis of ionizable Fischer thiocarbene complexes (CO)5M[double bond, length as m-dash]C(SR)CH3 (M = Cr, W; R = iPr, nBu, cHex, tBu) with five primary amines and one secondary amine in aqueous acetonitrile solutions (50% MeCN-50% water (v/v)). The observed rate constants for the reaction with primary amines showed a first-order dependence on the amine concentration, while with morpholine, the rate constant has second-order dependence. The general base catalysis process was confirmed by the variation of the rate constants with the concentration of an external catalyst and the pH. The results agree with a stepwise mechanism where the nucleophilic addition to the carbene carbon to produce a tetrahedral intermediate (T±) is the first step, followed by a rapid deprotonation of to form the anion T- which leads to the products by general-acid catalysed leaving group (-SR) expulsion. In general, it was found that the chromium complexes are less reactive than the tungsten analogues. The obtained Brønsted parameters for the nucleophilic addition (βnuc) indicate that C-N bond formation has made little progress at the transition state. By using Charton's correlation, the role that the steric factor plays throughout the mechanism has been unraveled. The nucleophilic addition to the thiocarbenes is less sensitive to steric effects than the alkoxycarbenes regardless of the nature of the metal centre. Conversely, the steric effects on the general-base catalysis can be strong depending on the volume of the catalyst and the metal centre. On the basis of the structure-reactivity coefficients β and ψ and comparison with alkoxycarbene complexes, esters and thiolesters, insights into the main factors ruling the reactivity in terms of transition state imbalances are discussed.
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Affiliation(s)
- Diego M Andrada
- Departamento de Química Orgánica, INFIQC, CONICET and Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria X5000HUA, Córdoba, Argentina.
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13
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Chen R, Luo X, Liang G. Theoretical studies on the aminolysis mechanism of propylene carbonate with ammonia. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1634-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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14
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15
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Katzhendler J, Poles LA, Sard S. Organic Carbonates. Part XIII. Separation of Polar and Steric Effects in the Hydrolyses of Substituted Ethylene and Trimethylene Carbonates. Isr J Chem 2013. [DOI: 10.1002/ijch.197200019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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16
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Theoretical study on the aminolysis of p-substituted phenyl acetates with dimeric ammonia in vacuo and acetonitrile. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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17
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Nigst TA, Antipova A, Mayr H. Nucleophilic Reactivities of Hydrazines and Amines: The Futile Search for the α-Effect in Hydrazine Reactivities. J Org Chem 2012; 77:8142-55. [DOI: 10.1021/jo301497g] [Citation(s) in RCA: 117] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tobias A. Nigst
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13 (Haus F), 81377
München, Germany
| | - Anna Antipova
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13 (Haus F), 81377
München, Germany
| | - Herbert Mayr
- Department Chemie, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13 (Haus F), 81377
München, Germany
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18
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Kingery DA, Strobel SA. Analysis of enzymatic transacylase Brønsted studies with application to the ribosome. Acc Chem Res 2012; 45:495-503. [PMID: 22122380 DOI: 10.1021/ar100162b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Preferential binding of an enzyme to the transition state relative to the ground state is a key strategy for enzyme catalysis. When there is a difference between the ground and transition state charge distributions, enzymes maximize electrostatic interactions to achieve this enhanced transition state binding. Although the transition state is difficult to observe directly by structural methods, the chemical details of this transient species can be characterized by studies of substituent effects (Brønsted, Hammett, Swain-Scott, etc.) and isotope effects. Brønsted analysis can provide an estimate of transition state charges for the nucleophile and leaving group of a reaction. This Account will discuss the theoretical basis of Brønsted analysis and describe its practical application to the study of transacylase enzyme systems including the peptidyl transferase reaction of the ribosome. The Brønsted coefficient is derived from the linear free energy relationship (LFER) that correlates the acidity (pK(a)) of a reactive atom to the log of its rate constant. The Brønsted coefficient establishes the change in atomic charge as the reaction proceeds from the ground state to the transition state. Bonding events alter the electrostatics of atoms and the extent of bonding can be extrapolated from transition state charges. Therefore, well-defined nucleophile and leaving group transition state charges limit the number of mechanisms that are consistent with a particular transition state. Brønsted results are most informative when interpreted in the context of other mechanistic data, especially for enzymatic studies where an active site may promote a transition state that differs significantly from a prediction based on uncatalyzed solution reactions. Here we review Brønsted analyses performed on transacylases to illustrate how these data enhanced the enzymatic mechanistic studies. Through a systematic comparison of five enzymes, we reveal a wide spectrum of Brønsted values that are possible for what otherwise appear to be similar chemical reactions. The variations in the Brønsted coefficients predict different transition states for the various enzymes. This Account explores an overriding theme in the enzymatic mechanisms that catalysis enhances commensurate bond formation and proton abstraction events. The extent of the two bonding events in relationship to each other can be inferred from the Brønsted coefficient. When viewed in the context of recent ribosomal studies, this interpretation provides mechanistic insights into peptide bond formation.
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Affiliation(s)
- David A. Kingery
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, United States
| | - Scott A. Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, United States
- Department of Chemistry, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06520, United States
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19
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Role of bifunctional catalyst 2-pyridone in the aminolysis of p-nitrophenyl acetate with n-butylamine: A computational study. ACTA ACUST UNITED AC 2012. [DOI: 10.1016/j.molcata.2011.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Leung EKY, Suslov N, Tuttle N, Sengupta R, Piccirilli JA. The Mechanism of Peptidyl Transfer Catalysis by the Ribosome. Annu Rev Biochem 2011; 80:527-55. [DOI: 10.1146/annurev-biochem-082108-165150] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Nikolai Suslov
- Department of Biochemistry and Molecular Biology, Chicago, Illinois 60637
| | - Nicole Tuttle
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637;
| | - Raghuvir Sengupta
- Department of Biochemistry, Stanford University, Stanford, California 94305
| | - Joseph Anthony Piccirilli
- Department of Biochemistry and Molecular Biology, Chicago, Illinois 60637
- Department of Chemistry, The University of Chicago, Chicago, Illinois 60637;
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21
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Andrada DM, Jimenez-Halla JOC, Solà M. Mechanism of the aminolysis of Fischer alkoxy and thiocarbene complexes: a DFT study. J Org Chem 2010; 75:5821-36. [PMID: 20704176 DOI: 10.1021/jo100738x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
B3LYP calculations have been carried out to study the reaction mechanism of the aminolysis of Fischer carbene complexes of the type (CO)(5)Cr=C(XMe)R (X = O and S; R = Me and Ph). We have explored different possible reaction mechanisms either through neutral or zwitterionic intermediates as well as a general base catalysis assisted by an ammonia molecule. Our results show that the most favorable pathway for the aminolysis of Fischer carbene complexes is through a stepwise reaction via a zwitterionic intermediate generated by the initial nucleophilic attack. We have found that the ammonia-catalyzed mechanism entails a significantly lower barrier for the rate-determining step than the uncatalyzed one. At lower pressure gas-phase conditions, the rate-determining step corresponds to the concerted proton transfer and MeXH elimination. Thiocarbene complexes show a higher energy barrier for this rate-determining step due to the lower basicity of the MeS(-) substituent. At higher pressure or in solution, the rate-determining step corresponds to the initial nucleophilic attack. Our results indicate that the transition state of the nucleophilic attack is more advanced and has a higher barrier for alkoxycarbene than thiocarbene complexes due to the stronger pi-donor character of the alkoxy group that reduces the electrophilicity of the attacked carbene atom making the nucleophilic attack more difficult.
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Affiliation(s)
- Diego M Andrada
- Instituto de Investigaciones en Fisicoquímica de Córdoba, Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5016 Córdoba, Argentina
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Rangelov MA, Petrova GP, Yomtova VM, Vayssilov GN. Hierarchical approach to conformational search and selection of computational method in modeling the mechanism of ester ammonolysis. J Mol Graph Model 2010; 29:246-55. [DOI: 10.1016/j.jmgm.2010.07.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2010] [Revised: 07/17/2010] [Accepted: 07/20/2010] [Indexed: 02/02/2023]
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23
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24
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Hiller DA, Zhong M, Singh V, Strobel SA. Transition states of uncatalyzed hydrolysis and aminolysis reactions of a ribosomal P-site substrate determined by kinetic isotope effects. Biochemistry 2010; 49:3868-78. [PMID: 20359191 PMCID: PMC2864349 DOI: 10.1021/bi901458x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The ester bond of peptidyl-tRNA undergoes nucleophilic attack in solution and when catalyzed by the ribosome. To characterize the uncatalyzed hydrolysis reaction, a model of peptide release, the transition state structure for hydrolysis of a peptidyl-tRNA mimic was determined. Kinetic isotope effects were measured at several atoms that potentially undergo a change in bonding in the transition state. Large kinetic isotope effects of carbonyl (18)O and alpha-deuterium substitutions on uncatalyzed hydrolysis indicate the transition state is nearly tetrahedral. Kinetic isotope effects were also measured for aminolysis by hydroxylamine to study a reaction similar to the formation of a peptide bond. In contrast to hydrolysis, the large leaving group (18)O isotope effect indicates the C-O3' bond has undergone significant scission in the transition state. The smaller carbonyl (18)O and alpha-deuterium effects are consistent with a later transition state. The assay developed here can also be used to measure isotope effects for the ribosome-catalyzed reactions. These uncatalyzed reactions serve as a basis for determining what aspects of the transition states are stabilized by the ribosome to achieve a rate enhancement.
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Affiliation(s)
- David A Hiller
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven CT 06511 USA
| | | | - Vipender Singh
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven CT 06511 USA
| | - Scott A Strobel
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven CT 06511 USA
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25
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Vána J, Sedlák M, Hanusek J. Kinetic Evidence for the Coexistence of Zwitterionic (T±), Neutral (T0) and Anionic (T−) Intermediates during Rearrangement of S-(2-Oxotetrahydrofuran-3-yl)-N-(4-methoxyphenyl)isothiuronium Bromide to 5-(2-Hydroxyethyl)-2-(4-methoxyphenylimino)-1,3-thiazolidin-4-one. J Org Chem 2010; 75:3729-36. [DOI: 10.1021/jo1004873] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jirí Vána
- Faculty of Chemical Technology, Institute of Organic Chemistry and Technology, University of Pardubice, CZ-532 10 Pardubice, The Czech Republic
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26
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Xia X, Zhang C, Xue Y, Kim CK, Yan G. DFT Study and Monte Carlo Simulation on the Aminolysis of XC(O)OCH3 (X = NH2, H, and CF3) with Monomeric and Dimeric Ammonias. J Chem Theory Comput 2008; 4:1643-53. [DOI: 10.1021/ct800099a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xuefei Xia
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, P. R. China, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, P. R. China, and Department of Chemistry, Inha University, Inchon 402-751, Korea
| | - Chenghua Zhang
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, P. R. China, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, P. R. China, and Department of Chemistry, Inha University, Inchon 402-751, Korea
| | - Ying Xue
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, P. R. China, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, P. R. China, and Department of Chemistry, Inha University, Inchon 402-751, Korea
| | - Chan Kyung Kim
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, P. R. China, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, P. R. China, and Department of Chemistry, Inha University, Inchon 402-751, Korea
| | - Guosen Yan
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, P. R. China, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, P. R. China, and Department of Chemistry, Inha University, Inchon 402-751, Korea
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27
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An uncharged amine in the transition state of the ribosomal peptidyl transfer reaction. ACTA ACUST UNITED AC 2008; 15:493-500. [PMID: 18482701 DOI: 10.1016/j.chembiol.2008.04.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2008] [Revised: 04/11/2008] [Accepted: 04/14/2008] [Indexed: 11/20/2022]
Abstract
The ribosome has an active site comprised of RNA that catalyzes peptide bond formation. To understand how RNA promotes this reaction requires a detailed understanding of the chemical transition state. Here, we report the Brønsted coefficient of the alpha-amino nucleophile with a series of puromycin derivatives. Both 50S subunit- and 70S ribosome-catalyzed reactions displayed linear free-energy relationships with slopes close to zero under conditions where chemistry is rate limiting. These results indicate that, at the transition state, the nucleophile is neutral in the ribosome-catalyzed reaction, in contrast to the substantial positive charge reported for typical uncatalyzed aminolysis reactions. This suggests that the ribosomal transition state involves deprotonation to a degree commensurate with nitrogen-carbon bond formation. Such a transition state is significantly different from that of uncatalyzed aminolysis reactions in solution.
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28
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Galabov B, Ilieva S, Hadjieva B, Atanasov Y, Schaefer HF. Predicting Reactivities of Organic Molecules. Theoretical and Experimental Studies on the Aminolysis of Phenyl Acetates. J Phys Chem A 2008; 112:6700-7. [DOI: 10.1021/jp8007514] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Boris Galabov
- Department of Chemistry, University of Sofia, Sofia 1126, Bulgaria, and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
| | - Sonia Ilieva
- Department of Chemistry, University of Sofia, Sofia 1126, Bulgaria, and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
| | - Boriana Hadjieva
- Department of Chemistry, University of Sofia, Sofia 1126, Bulgaria, and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
| | - Yasen Atanasov
- Department of Chemistry, University of Sofia, Sofia 1126, Bulgaria, and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
| | - Henry F. Schaefer
- Department of Chemistry, University of Sofia, Sofia 1126, Bulgaria, and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602
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29
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Petrova T, Okovytyy S, Gorb L, Leszczynski J. Computational Study of the Aminolysis of Anhydrides: Effect of the Catalysis to the Reaction of Succinic Anhydride with Methylamine in Gas Phase and Nonpolar Solution. J Phys Chem A 2008; 112:5224-35. [DOI: 10.1021/jp7102897] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tetyana Petrova
- Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217-0510, and Department of Organic Chemistry, Dnepropetrovsk National University, Dnepropetrovsk 49625, Ukraine
| | - Sergiy Okovytyy
- Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217-0510, and Department of Organic Chemistry, Dnepropetrovsk National University, Dnepropetrovsk 49625, Ukraine
| | - Leonid Gorb
- Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217-0510, and Department of Organic Chemistry, Dnepropetrovsk National University, Dnepropetrovsk 49625, Ukraine
| | - Jerzy Leszczynski
- Department of Chemistry, Computational Center for Molecular Structure and Interactions, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, Mississippi 39217-0510, and Department of Organic Chemistry, Dnepropetrovsk National University, Dnepropetrovsk 49625, Ukraine
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30
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Yi GQ, Zeng Y, Xia XF, Xue Y, Kim CK, Yan GS. The substituent effects of the leaving groups on the aminolysis of phenyl acetates: DFT studies. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.01.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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31
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Ren Y, Yamataka H. The alpha-effect in gas-phase SN2 reactions: existence and the origin of the effect. J Org Chem 2007; 72:5660-7. [PMID: 17590049 DOI: 10.1021/jo070650m] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The origin of enhanced reactivity of alpha-nucleophiles in SN2 reactions was examined on the basis of computational results at the high level G2(+) method for 22 gas-phase reactions: Nu- + RCl --> RNu + Cl- [R = Et and i-Pr; Nu- = HO-, CH3O-, HS-, Cl-, Br-, NH2O-, HOO-, FO-, HSO-, ClO-, and BrO-]. The results clearly indicate the existence of the alpha-effect, whose size varies depending on the R group and the identity of the alpha-atom. The alpha-effect is larger for i-PrCl than EtCl, and for an alpha-nucleophile with a harder alpha-atom. Analyses of the present results, together with previously reported ones for MeF and MeCl reactions, reveal that several rationales so far presented to explain the alpha-effect, such as thermodynamic product stability, transition state (TS) tightness, electrostatic interaction, ET rationale, and polarizability, cannot explain the observed size of the alpha-effect. The importance of deformation energy on going from the reactant to the TS is presented.
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Affiliation(s)
- Yi Ren
- Faculty of Chemistry, and Key State Laboratory of Biotherapy, Sichuan University, Chengdu 610064, China
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32
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Klinman JP. Kinetic isotope effects in enzymology. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 46:415-94. [PMID: 345770 DOI: 10.1002/9780470122914.ch7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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33
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Abstract
[reaction: see text] CCA-pcb (cytidylyl-(3'5')-cytidylyl-(3'5')-3'(2')-O-(N-(6-D-(+)-biotinoylaminohexanoyl)-L-phenylalanyl)adenosine), a ribosomal P-site substrate, was synthesized by phosphoramidite chemistry in 26 steps with an overall yield of 18%, starting from biotin. The synthesis relies on the judicious selection of orthogonal silyl protecting groups for the 5'-hydroxyls and acid-labile protecting groups (DMTr, AcE, and MeE) at other reactive sites to ensure the intactness of the labile ester. Both 3'-esterification and nucleotide coupling were accomplished by in situ activation with imidazolium ions.
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Affiliation(s)
- Minghong Zhong
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520-8114, USA
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34
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Morin M, Rivard C, Keillor JW. γ-Glutamyl transpeptidase acylation with peptidic substrates: free energy relationships measured by an HPLC kinetic assay. Org Biomol Chem 2006; 4:3790-801. [PMID: 17024286 DOI: 10.1039/b606914b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
gamma-Glutamyl transpeptidase (GGT, EC 2.3.2.2) is a highly glycosylated heterodimeric enzyme linked to the external cellular membrane that catalyzes the hydrolysis of glutathione as well as the transfer of its gamma-glutamyl group to amino acids and dipeptides in a transpeptidation reaction. The measurement of both the hydrolytic and transpeptidation activity of this important enzyme is a challenge, since its native substrates are not highly chromogenic. We have developed an HPLC-based method for the quantitative photometric detection of numerous enzyme substrates and products, after their pre-column derivation with dabsyl chloride. The broad applicability of this method was demonstrated in the kinetic investigation of transpeptidation reactions of rat kidney GGT with glutathione, its native substrate, as well as a series of pertinent glutathione analogues. The pH-rate profile constructed for glutathione confirmed the dependence on the ionisation state of at least two residues. Analysis of the free-energy relationships in the series of synthetic peptidic substrate analogues revealed the importance of enzyme-substrate interactions unrelated to amine leaving group basicity during the acylation step. These results are further interpreted in the context of the recently published structure for a similar GGT.
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Affiliation(s)
- Mylène Morin
- Département de Chimie, Université de Montréal, C.P. 6128, Succ. Centre-ville, Montréal, QC H3C 3J7, Canada
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35
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Galabov B, Atanasov Y, Ilieva S, Schaefer HF. Mechanism of the Aminolysis of Methyl Benzoate: A Computational Study†. J Phys Chem A 2005; 109:11470-4. [PMID: 16354037 DOI: 10.1021/jp0536403] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional and ab initio methods were applied in examining the possible mechanistic pathways for the reaction of methyl benzoate with ammonia. Transition state structures and energies were determined for concerted and neutral stepwise mechanisms. The theoretical results show that the two possible pathways have similar activation energies. The general base catalysis of the process was also examined. The predictions reveal that the catalytic process results in considerable energy savings and the most favorable pathway of the reaction is through a general-base-catalyzed neutral stepwise mechanism. The structure and transition vectors of the transition states indicate that the catalytic role of ammonia is realized by facilitating the proton-transfer processes. Comparison of the energetics of the aminolysis for methyl benzoate and methyl formate shows the more favorable process to be that for the aliphatic ester. The differing reactivity of the two esters is explained in terms of the electrostatic potential values at the atoms of the ester functionality.
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Affiliation(s)
- Boris Galabov
- Department of Chemistry, University of Sofia, Sofia 1164, Bulgaria
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36
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Seila AC, Okuda K, Núñez S, Seila AF, Strobel SA. Kinetic isotope effect analysis of the ribosomal peptidyl transferase reaction. Biochemistry 2005; 44:4018-27. [PMID: 15751978 DOI: 10.1021/bi047742f] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ribosome is the macromolecular machine responsible for protein synthesis in all cells. Here, we establish a kinetic framework for the 50S modified fragment reaction that makes it possible to measure the kinetic effects that result from isotopic substitution in either the A or P site of the ribosome. This simplified peptidyl transferase assay follows a rapid equilibrium random mechanism in which the reverse reaction is nonexistent and the forward commitment is negligible. A normal effect (1.009) is observed for (15)N substitution of the incoming nucleophile at both low and high pH. This suggests that the first irreversible step is the formation of the tetrahedral intermediate. The observation of a normal isotope effect that does not change as a function of pH suggests that the ribosome promotes peptide bond formation by a mechanism that differs in its details from an uncatalyzed aminolysis reaction in solution. This implies that the ribosome contributes chemically to catalysis of peptide bond formation.
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Affiliation(s)
- Amy C Seila
- Department of Molecular Biophysics, Yale University, New Haven, Connecticut 06520-8114, USA
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37
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Adler M, Adler S, Boche G. Tetrahedral intermediates in reactions of carboxylic acid derivatives with nucleophiles. J PHYS ORG CHEM 2005. [DOI: 10.1002/poc.807] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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38
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Croll TI, O'Connor AJ, Stevens GW, Cooper-White JJ. Controllable surface modification of poly(lactic-co-glycolic acid) (PLGA) by hydrolysis or aminolysis I: physical, chemical, and theoretical aspects. Biomacromolecules 2004; 5:463-73. [PMID: 15003007 DOI: 10.1021/bm0343040] [Citation(s) in RCA: 262] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While biodegradable, biocompatible polyesters such as poly (lactic-co-glycolic acid) (PLGA) are popular materials for the manufacture of tissue engineering scaffolds, their surface properties are not particularly suitable for directed tissue growth. Although a number of approaches to chemically modify the PLGA surface have been reported, their applicability to soft tissue scaffolds, which combine large volumes, complex shapes, and extremely fine structures, is questionable. In this paper, we describe two wet-chemical methods, base hydrolysis and aminolysis, to introduce useful levels of carboxylic acid or primary and secondary amine groups, respectively, onto the surface of PLGA with minimal degradation. The effects of temperature, concentration, pH, and solvent type on the kinetics of these reactions are studied by following changes in the wettability of the PLGA using contact angle measurements. In addition, the treated surfaces are studied using X-ray photoelectron spectroscopy (XPS) to determine the effect on the surface chemical structure. Furthermore, we show using XPS analysis that these carboxyl and amine groups are readily activated to allow the covalent attachment of biological macromolecules.
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Affiliation(s)
- Tristan I Croll
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Victoria 3010 Australia
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39
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Ilieva S, Atanasov Y, Kalcheva V, Galabov B. Computational study of the general base catalysed aminolysis of 2-benzoxazolinone. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0166-1280(03)00310-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Ilieva S, Galabov B, Musaev DG, Morokuma K. Computational study of the aminolysis of 2-benzoxazolinone. J Org Chem 2003; 68:3406-12. [PMID: 12713338 DOI: 10.1021/jo026682l] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three possible mechanisms (zwitterionic, neutral stepwise, and neutral concerted) of the ring-opening reaction of 2-benzoxazolinone (BO) upon aminolysis with methylamine were studied at the B3LYP/6-31G* level. In the gas phase, the neutral concerted mechanism is shown to be most favorable, which proceeds via a rate-determining barrier of 28-29 kcal/mol. The transition state, CTS, associated with this barrier is a four-centered one, where 1,2-addition of the N[bond]H of methylamine to the C[bond]O of BO ring occurs. The rate-determining barrier of the neutral stepwise pathway is found to be ca. 42 kcal/mol. The inclusion of solvent effects by a polarizable continuum model (PCM) does not change the conclusions based on the gas-phase study; the barrier at CTS is reduced to 20, 20, and 22 kcal/mol in water, ethanol, and acetonitrile, respectively.
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Affiliation(s)
- Sonia Ilieva
- Department of Chemistry, University of Sofia, Sofia 1164, Bulgaria.
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41
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Ilieva S, Galabov B, Musaev DG, Morokuma K, Schaefer HF. Computational study of the aminolysis of esters. The reaction of methylformate with ammonia. J Org Chem 2003; 68:1496-502. [PMID: 12585894 DOI: 10.1021/jo0263723] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The aminolysis of esters is a basic organic reaction considered as a model for the interaction of carbonyl group with nucleophiles. In the present computational study the different possible mechanistic pathways of the reaction are reinvestigated by applying higher level electronic structure theory, examining the general base catalysis by the nucleophile, and a more comprehensive study the solvent effect. Both the ab initio QCISD/6-31(d,p) method and density functional theory at the B3LYP/6-31G(d) level were employed to calculate the reaction pathways for the simplest model aminolysis reaction between methylformate and ammonia. Solvent effects were assessed by the PCM method. The results show that in the case of noncatalyzed aminolysis the addition/elimination stepwise mechanism involving two transition states and the concerted mechanism have very similar activation energies. However, in the case of catalyzed aminolysis by a second ammonia molecule the stepwise mechanism has a distinctly lower activation energy. All transition states in the catalyzed aminolysis are 10-17 kcal/mol lower than those for the uncatalyzed process.
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Affiliation(s)
- Sonia Ilieva
- Department of Chemistry, University of Sofia, Sofia 1164, Bulgaria
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42
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Di Loreto HE, Czarnowski J, dos Santos Afonso M. Kinetics of hydrolysis and cyclization of ethyl 2-(aminosulfonyl)benzoate to saccharin. CHEMOSPHERE 2002; 49:353-361. [PMID: 12363315 DOI: 10.1016/s0045-6535(02)00279-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The cyclization of ethyl 2-(aminosulfonyl)benzoate (ASB) to give saccharin was investigated in aqueous solutions at pH between 5.2 and 9.5 and in the temperature range of 296.2-334.2 K. The initial concentration of the reactant was varied between 1.45 x 10(-5) and 3.86 x 10(-4) M. Ultraviolet spectroscopy was used to obtain the kinetic data. The reaction is acid catalyzed and follows pseudo-first-order kinetics. The experimental rate constant, k(obs), increases with temperature and pH. Its dependence on the temperature and pH is well described by: k(obs) = k1 [OH-] = [(2.52 +/- 0.9) x 10(16) exp(-20.2 +/- 1 kcalmol(-1)/RT) s(-1)][OH-] A mechanism is proposed and the half-life of ethyl ASB is calculated.
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Affiliation(s)
- H E Di Loreto
- Laboratorio de Compuestos Orgánicos-LADECOM, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Argentina
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43
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Marchal S, Branlant G. Engineered nonphosphorylating glyceraldehyde 3-phosphate dehydrogenase at position 268 binds hydroxylamine and hydrazine as acyl acceptors. EUROPEAN JOURNAL OF BIOCHEMISTRY 2001; 268:5764-70. [PMID: 11722561 DOI: 10.1046/j.0014-2956.2001.02517.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Nonphosphorylating nicotinamide adenine dinucleotide (phosphate)-dependent aldehyde dehydrogenases (ALDHs) catalyze the oxidation of aldehydes into either nonactivated acids or CoA-activated acids. The NADP-dependent nonphosphorylating glyceraldehyde 3-phosphate dehydrogenase (GAPN) belongs to the first subclass. It catalyzes the irreversible oxidation of glyceraldehyde 3-phosphate into 3-phosphoglycerate via a two step mechanism in which deacylation is rate-limiting. Recent studies on GAPN from Streptococcus mutans have shown that residue Glu268 plays an essential role only in the deacylation step [Marchal, S., Rahuel-Clermont, S. & Branlant, G. (2000) Biochemistry 39, 3327-3335]. The substitution of Glu268 by alanine or glutamine leads to mutants in which the attacking water molecule involved in the hydrolytic process is poorly activated. Activity can be restored by the presence of hydroxylamine and hydrazine. Neutral and protonated forms of both nucleophiles are recognized by the deacylating subsite of both mutants. pH rate profiles of deacylation show pK(a) values of 6.3 and 8.1 with hydroxylamine and hydrazine, respectively, which are those of the nucleophiles in solution. The increase in enzymatic rate is probably due to a high local concentration and not to a change of the chemical reactivity of both nucleophiles upon their binding within the active site of both mutants. The deacylation subsite of the wild-type also binds hydroxylamine and hydrazine but as inhibitors of the hydrolytic process and not as acyl acceptors. Altogether, the results point out the crucial role of the carboxyl group of Glu268 in preventing nucleophiles, other than water, from binding as efficient acyl acceptors. This may also explain why CoA-dependent ALDHs never possesses a glutamate residue at position 268.
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Affiliation(s)
- S Marchal
- Laboratoire de Maturation des ARN et Enzymologie Moléculaire, Université Henri Poincaré Nancy 1, Faculté des Sciences, Vandoeuvre-lès-Nancy, France
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44
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Heidary DK, O'Neill JC, Roy M, Jennings PA. An essential intermediate in the folding of dihydrofolate reductase. Proc Natl Acad Sci U S A 2000; 97:5866-70. [PMID: 10811909 PMCID: PMC18525 DOI: 10.1073/pnas.100547697] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The folding of Escherichia coli dihydrofolate reductase was examined at pH 7.8 and 15 degrees C by using stopped-flow fluorescence and absorbance spectroscopies. The formation of a highly fluorescent intermediate occurs with relaxation times ranging between 142 and 343 msec, whereas stopped-flow absorbance spectroscopy using methotrexate binding assays shows a distinct lag phase during these time frames for the native state. The lag in absorbance kinetics and the lack of fast-track folding events indicate that the formation of this ensemble of intermediates is an obligatory step in the folding reaction.
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Affiliation(s)
- D K Heidary
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, USA
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45
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Štrajbl M, Florián J, Warshel A. Ab Initio Evaluation of the Potential Surface for General Base- Catalyzed Methanolysis of Formamide: A Reference Solution Reaction for Studies of Serine Proteases. J Am Chem Soc 2000. [DOI: 10.1021/ja992441s] [Citation(s) in RCA: 106] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marek Štrajbl
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Jan Florián
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-1062
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Kirby AJ, Komarov IV, Feeder N. Spontaneous, Millisecond Formation of a Twisted Amide from the Amino Acid, and the Crystal Structure of a Tetrahedral Intermediate. J Am Chem Soc 1998. [DOI: 10.1021/ja980700s] [Citation(s) in RCA: 64] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Anthony J. Kirby
- University Chemical Laboratory Cambridge University Cambridge CB2 1EW, UK
| | - Igor V. Komarov
- University Chemical Laboratory Cambridge University Cambridge CB2 1EW, UK
| | - Neil Feeder
- University Chemical Laboratory Cambridge University Cambridge CB2 1EW, UK
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47
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Rojas CM, Rebek J. Convergent Functional Groups: Intramolecular Acyl Transfer through a 34-Membered Ring. J Am Chem Soc 1998. [DOI: 10.1021/ja9733806] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian M. Rojas
- The Skaggs Institute for Chemical Biology and The Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, California 92037
| | - Julius Rebek
- The Skaggs Institute for Chemical Biology and The Department of Chemistry, The Scripps Research Institute 10550 North Torrey Pines Road La Jolla, California 92037
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Adalsteinsson H, Bruice TC. What Is the Mechanism of Catalysis of Ester Aminolysis by Weak Amine Bases? Comparison of Experimental Studies and Theoretical Investigation of the Aminolysis of Substituted Phenyl Esters of Quinoline-6- and -8-Carboxylic Acids. J Am Chem Soc 1998. [DOI: 10.1021/ja972162+] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Marlier JF, Haptonstall BA, Johnson AJ, Sacksteder KA. Heavy-Atom Isotope Effects on the Hydrazinolysis of Methyl Formate. J Am Chem Soc 1997. [DOI: 10.1021/ja970993+] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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Mock WL, Liu Y. Hydrolysis of picolinylprolines by prolidase. A general mechanism for the dual-metal ion containing aminopeptidases. J Biol Chem 1995; 270:18437-46. [PMID: 7629169 DOI: 10.1074/jbc.270.31.18437] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The velocity of enzymic cleavage of 4-substituted picolinylprolines by swine kidney prolidase approaches that of physiological dipeptides, but depends substantially upon the nature of the pyridine-ring substituent. The pH dependence of kcat/Km for picolinylproline is sigmoidal, with optimum activity on the acidic limb and a delimiting enzymic pKa of 6.6, unlike glycylproline (bell-shaped pH profile, maximum at pH 7.7). Productive chelation to an active site metal ion by the N terminus of substrates is indicated, with a water molecule ligated to that hyper(Lewis)acidic center prior to substrate binding supplying the pKa of 6.6. The rate-governing catalytic step differs according to the 4-substituent on the picolinyl residue; productive binding is slow in the case of electron-withdrawing groups, but subsequent nucleophilic addition to the metal ion-activated scissile linkage becomes controlling with more basic pyridine rings. Rate constants yield a Brønsted-type correlation with substrate pKa, providing a gauge of active-site Lewis acidity. A mechanism is suggested involving the cooperative participation of two especially acidic metal ions positioned adjacently within the active site (situated as in an homologous and structurally characterized aminopeptidase), with both serving to stabilize a bridging carboxamide-hydrate intermediate.
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Affiliation(s)
- W L Mock
- Department of Chemistry, University of Illinois, Chicago 60607-7061, USA
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