1
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Riuttamäki S, Laczkó G, Madarász Á, Földes T, Pápai I, Bannykh A, Pihko PM. Carboxylate Catalyzed Isomerization of β,γ‐Unsaturated
N
‐Acetylcysteamine Thioesters**. Chemistry 2022; 28:e202201030. [PMID: 35604200 PMCID: PMC9541288 DOI: 10.1002/chem.202201030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Indexed: 11/11/2022]
Abstract
We demonstrate herein the capacity of simple carboxylate salts – tetrametylammonium and tetramethylguanidinium pivalate – to act as catalysts in the isomerization of β,γ‐unsaturated thioesters to α,β‐unsaturated thioesters. The carboxylate catalysts gave reaction rates comparable to those obtained with DBU, but with fewer side reactions. The reaction exhibits a normal secondary kinetic isotope effect (k1H/k1D=1.065±0.026) with a β,γ‐deuterated substrate. Computational analysis of the mechanism provides a similar value (k1H/k1D=1.05) with a mechanism where γ‐reprotonation of the enolate intermediate is rate determining.
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Affiliation(s)
- Saara Riuttamäki
- Department of Chemistry University of Jyväskylä P.O. Box 35 40014 Jyväskylä Finland
| | - Gergely Laczkó
- Institute of Organic Chemistry Research Centre for Natural Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Ádám Madarász
- Institute of Organic Chemistry Research Centre for Natural Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Tamás Földes
- Institute of Organic Chemistry Research Centre for Natural Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Imre Pápai
- Institute of Organic Chemistry Research Centre for Natural Sciences Magyar tudósok körútja 2 1117 Budapest Hungary
| | - Anton Bannykh
- Department of Chemistry University of Jyväskylä P.O. Box 35 40014 Jyväskylä Finland
| | - Petri M. Pihko
- Department of Chemistry University of Jyväskylä P.O. Box 35 40014 Jyväskylä Finland
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2
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Cristobal JR, Richard JP. Glycerol-3-Phosphate Dehydrogenase: The K120 and K204 Side Chains Define an Oxyanion Hole at the Enzyme Active Site. Biochemistry 2022; 61:856-867. [PMID: 35502876 PMCID: PMC9119304 DOI: 10.1021/acs.biochem.2c00053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cationic K120 and K204 side chains lie close to the C-2 carbonyl group of substrate dihydroxyacetone phosphate (DHAP) at the active site of glycerol-3-phosphate dehydrogenase (GPDH), and the K120 side chain is also positioned to form a hydrogen bond to the C-1 hydroxyl of DHAP. The kinetic parameters for unactivated and phosphite dianion-activated GPDH-catalyzed reduction of glycolaldehyde and acetaldehyde (AcA) show that the transition state for the former reaction is stabilized by ca 5 kcal/mole by interactions of the C-1 hydroxyl group with the protein catalyst. The K120A and K204A substitutions at wild-type GPDH result in similar decreases in kcat, but Km is only affected by the K120A substitution. These results are consistent with 3 kcal/mol stabilizing interactions between the K120 or K204 side chains and a negative charge at the C-2 oxygen at the transition state for hydride transfer from NADH to DHAP. This stabilization resembles that observed at oxyanion holes for other enzymes. There is no detectable rescue of the K204A variant by ethylammonium cation (EtNH3+), compared with the efficient rescue of the K120A variant. This is consistent with a difference in the accessibility of the variant enzyme active sites to exogenous EtNH3+. The K120A/K204A substitutions cause a (6 × 106)-fold increase in the promiscuity of wild-type hlGPDH for catalysis of the reduction of AcA compared to DHAP. This may reflect conservation of the active site for an ancestral alcohol dehydrogenase, whose relative activity for catalysis of reduction of AcA increases with substitutions that reduce the activity for reduction of the specific substrate DHAP.
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Affiliation(s)
- Judith R Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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3
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Kries H, Bloch JS, Bunzel HA, Pinkas DM, Hilvert D. Contribution of Oxyanion Stabilization to Kemp Eliminase Efficiency. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00575] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Hajo Kries
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Joël S. Bloch
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - H. Adrian Bunzel
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Daniel M. Pinkas
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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4
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Zhong M, Lynch A, Muellers SN, Jehle S, Luo L, Hall DR, Iwase R, Carolan JP, Egbert M, Wakefield A, Streu K, Harvey CM, Ortet PC, Kozakov D, Vajda S, Allen KN, Whitty A. Interaction Energetics and Druggability of the Protein-Protein Interaction between Kelch-like ECH-Associated Protein 1 (KEAP1) and Nuclear Factor Erythroid 2 Like 2 (Nrf2). Biochemistry 2020; 59:563-581. [PMID: 31851823 PMCID: PMC8177486 DOI: 10.1021/acs.biochem.9b00943] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Development of small molecule inhibitors of protein-protein interactions (PPIs) is hampered by our poor understanding of the druggability of PPI target sites. Here, we describe the combined application of alanine-scanning mutagenesis, fragment screening, and FTMap computational hot spot mapping to evaluate the energetics and druggability of the highly charged PPI interface between Kelch-like ECH-associated protein 1 (KEAP1) and nuclear factor erythroid 2 like 2 (Nrf2), an important drug target. FTMap identifies four binding energy hot spots at the active site. Only two of these are exploited by Nrf2, which alanine scanning of both proteins shows to bind primarily through E79 and E82 interacting with KEAP1 residues S363, R380, R415, R483, and S508. We identify fragment hits and obtain X-ray complex structures for three fragments via crystal soaking using a new crystal form of KEAP1. Combining these results provides a comprehensive and quantitative picture of the origins of binding energy at the interface. Our findings additionally reveal non-native interactions that might be exploited in the design of uncharged synthetic ligands to occupy the same site on KEAP1 that has evolved to bind the highly charged DEETGE binding loop of Nrf2. These include π-stacking with KEAP1 Y525 and interactions at an FTMap-identified hot spot deep in the binding site. Finally, we discuss how the complementary information provided by alanine-scanning mutagenesis, fragment screening, and computational hot spot mapping can be integrated to more comprehensively evaluate PPI druggability.
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Affiliation(s)
| | | | | | | | | | - David R Hall
- Acpharis, Inc. , 160 North Mill Street , Holliston , Massachusetts 01746 , United States
| | | | | | | | | | | | | | | | - Dima Kozakov
- Department of Applied Mathematics , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Sandor Vajda
- Biomolecular Engineering Research Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Karen N Allen
- Biomolecular Engineering Research Center , Boston University , Boston , Massachusetts 02215 , United States
| | - Adrian Whitty
- Biomolecular Engineering Research Center , Boston University , Boston , Massachusetts 02215 , United States
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5
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Cuesta SA, Mora JR, Zambrano CH, Torres FJ, Rincón L. Comparative study of the nucleophilic attack step in the proteases catalytic activity: A theoretical study. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1705412] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sebastián A. Cuesta
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - José R. Mora
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Cesar H. Zambrano
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - F. Javier Torres
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
| | - Luis Rincón
- Instituto de Simulación Computacional (ISM), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
- Departamento de Ingeniería Química – Grupo de Química Computacional y Teórica (QCT), Universidad San Francisco de Quito (USFQ), Quito, Ecuador
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6
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Abstract
What happens inside an enzyme's active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists' attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme's active site. These experiments have provided compelling evidence supporting a major electrostatic contribution to enzymatic catalysis. Here, we review these results and develop a simple model for electrostatic catalysis that enables us to incorporate disparate concepts introduced by many investigators to describe how enzymes work into a more unified framework stressing the importance of electric fields at the active site.
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Affiliation(s)
- Stephen D Fried
- Proteins and Nucleic Acid Chemistry Division, Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305;
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7
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Zhai X, Amyes TL, Richard JP. Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase. J Am Chem Soc 2015; 137:15185-97. [PMID: 26570983 PMCID: PMC4694050 DOI: 10.1021/jacs.5b09328] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The side chains of
Y208 and S211 from loop 7 of triosephosphate
isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls
from loop 6 to stabilize the caged enzyme–substrate complex.
The effect of seven mutations [Y208T, Y208S, Y208A, Y208F, S211G,
S211A, Y208T/S211G] on the kinetic parameters for TIM catalyzed reactions
of the whole substrates dihydroxyacetone phosphate and d-glyceraldehyde
3-phosphate [(kcat/Km)GAP and (kcat/Km)DHAP] and of the substrate pieces
glycolaldehyde and phosphite dianion (kcat/KHPiKGA)
are reported. The linear logarithmic correlation between these kinetic
parameters, with slope of 1.04 ± 0.03, shows that most mutations
of TIM result in an identical change in the activation barriers for
the catalyzed reactions of whole substrate and substrate pieces, so
that the transition states for these reactions are stabilized by similar
interactions with the protein catalyst. The second linear logarithmic
correlation [slope = 0.53 ± 0.16] between kcat for isomerization of GAP and Kd⧧ for phosphite dianion binding to the transition
state for wildtype and many mutant TIM-catalyzed reactions of substrate
pieces shows that ca. 50% of the wildtype TIM dianion binding energy,
eliminated by these mutations, is expressed at the wildtype Michaelis
complex, and ca. 50% is only expressed at the wildtype transition
state. Negative deviations from this correlation are observed when
the mutation results in a decrease in enzyme reactivity at the catalytic
site. The main effect of Y208T, Y208S, and Y208A mutations is to cause
a reduction in the total intrinsic dianion binding energy, but the
effect of Y208F extends to the catalytic site.
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Affiliation(s)
- Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY , Buffalo, New York 14260-3000, United States
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8
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Sigala PA, Ruben EA, Liu CW, Piccoli PMB, Hohenstein EG, Martínez TJ, Schultz AJ, Herschlag D. Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability. J Am Chem Soc 2015; 137:5730-40. [PMID: 25871450 DOI: 10.1021/ja512980h] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hydrogen bonds profoundly influence the architecture and activity of biological macromolecules. Deep appreciation of hydrogen bond contributions to biomolecular function thus requires a detailed understanding of hydrogen bond structure and energetics and the relationship between these properties. Hydrogen bond formation energies (ΔGf) are enormously more favorable in aprotic solvents than in water, and two classes of contributing factors have been proposed to explain this energetic difference, focusing respectively on the isolated and hydrogen-bonded species: (I) water stabilizes the dissociated donor and acceptor groups much better than aprotic solvents, thereby reducing the driving force for hydrogen bond formation; and (II) water lengthens hydrogen bonds compared to aprotic environments, thereby decreasing the potential energy within the hydrogen bond. Each model has been proposed to provide a dominant contribution to ΔGf, but incisive tests that distinguish the importance of these contributions are lacking. Here we directly test the structural basis of model II. Neutron crystallography, NMR spectroscopy, and quantum mechanical calculations demonstrate that O-H···O hydrogen bonds in crystals, chloroform, acetone, and water have nearly identical lengths and very similar potential energy surfaces despite ΔGf differences >8 kcal/mol across these solvents. These results rule out a substantial contribution from solvent-dependent differences in hydrogen bond structure and potential energy after association (model II) and thus support the conclusion that differences in hydrogen bond ΔGf are predominantly determined by solvent interactions with the dissociated groups (model I). These findings advance our understanding of universal hydrogen-bonding interactions and have important implications for biology and engineering.
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Affiliation(s)
| | | | | | - Paula M B Piccoli
- §Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | | | | | - Arthur J Schultz
- §Intense Pulsed Neutron Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
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9
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Sunden F, Peck A, Salzman J, Ressl S, Herschlag D. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site. eLife 2015; 4. [PMID: 25902402 PMCID: PMC4438272 DOI: 10.7554/elife.06181] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 04/22/2015] [Indexed: 01/30/2023] Open
Abstract
Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.
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Affiliation(s)
- Fanny Sunden
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
| | - Ariana Peck
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
| | - Julia Salzman
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
| | - Susanne Ressl
- Molecular and Cellular Biochemistry Department, Indiana University Bloomington, Bloomington, United States
| | - Daniel Herschlag
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
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10
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Hanoian P, Liu CT, Hammes-Schiffer S, Benkovic S. Perspectives on electrostatics and conformational motions in enzyme catalysis. Acc Chem Res 2015; 48:482-9. [PMID: 25565178 PMCID: PMC4334233 DOI: 10.1021/ar500390e] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
![]()
Enzymes
are essential for all living organisms, and their effectiveness as
chemical catalysts has driven more than a half century of research
seeking to understand the enormous rate enhancements they provide.
Nevertheless, a complete understanding of the factors that govern
the rate enhancements and selectivities of enzymes remains elusive,
due to the extraordinary complexity and cooperativity that are the
hallmarks of these biomolecules. We have used a combination of site-directed
mutagenesis, pre-steady-state kinetics, X-ray crystallography, nuclear
magnetic resonance (NMR), vibrational and fluorescence spectroscopies,
resonance energy transfer, and computer simulations to study the implications
of conformational motions and electrostatic interactions on enzyme
catalysis in the enzyme dihydrofolate reductase (DHFR). We have
demonstrated that modest equilibrium conformational changes are functionally
related to the hydride transfer reaction. Results obtained for mutant
DHFRs illustrated that reductions in hydride transfer rates are correlated
with altered conformational motions, and analysis of the evolutionary
history of DHFR indicated that mutations appear to have occurred to
preserve both the hydride transfer rate and the associated conformational
changes. More recent results suggested that differences in local electrostatic
environments contribute to finely tuning the substrate pKa in the initial protonation step. Using a combination
of primary and solvent kinetic isotope effects, we demonstrated that
the reaction mechanism is consistent across a broad pH range, and
computer simulations suggested that deprotonation of the active site
Tyr100 may play a crucial role in substrate protonation at high pH. Site-specific incorporation of vibrational thiocyanate probes into
the ecDHFR active site provided an experimental tool
for interrogating these microenvironments and for investigating changes
in electrostatics along the DHFR catalytic cycle. Complementary molecular
dynamics simulations in conjunction with mixed quantum mechanical/molecular
mechanical calculations accurately reproduced the vibrational frequency
shifts in these probes and provided atomic-level insight into the
residues influencing these changes. Our findings indicate that conformational
and electrostatic changes are intimately related and functionally
essential. This approach can be readily extended to the study of other
enzyme systems to identify more general trends in the relationship
between conformational fluctuations and electrostatic interactions.
These results are relevant to researchers seeking to design novel
enzymes as well as those seeking to develop therapeutic agents that
function as enzyme inhibitors.
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Affiliation(s)
- Philip Hanoian
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - C. Tony Liu
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department
of Chemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Stephen Benkovic
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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11
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Ito M, Brinck T. Novel Approach for Identifying Key Residues in Enzymatic Reactions: Proton Abstraction in Ketosteroid Isomerase. J Phys Chem B 2014; 118:13050-8. [DOI: 10.1021/jp508423s] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mika Ito
- Applied
Physical Chemistry, KTH Royal Institute of Technology, Teknikringen
30, 100 44 Stockholm, Sweden
| | - Tore Brinck
- Applied
Physical Chemistry, KTH Royal Institute of Technology, Teknikringen
30, 100 44 Stockholm, Sweden
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12
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Goldman L, Amyes TL, Goryanova B, Gerlt JA, Richard JP. Enzyme architecture: deconstruction of the enzyme-activating phosphodianion interactions of orotidine 5'-monophosphate decarboxylase. J Am Chem Soc 2014; 136:10156-65. [PMID: 24958125 PMCID: PMC4227808 DOI: 10.1021/ja505037v] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Indexed: 12/12/2022]
Abstract
The mechanism for activation of orotidine 5'-monophosphate decarboxylase (OMPDC) by interactions of side chains from Gln215 and Try217 at a gripper loop and R235, adjacent to this loop, with the phosphodianion of OMP was probed by determining the kinetic parameters k(cat) and K(m) for all combinations of single, double, and triple Q215A, Y217F, and R235A mutations. The 12 kcal/mol intrinsic binding energy of the phosphodianion is shown to be equal to the sum of the binding energies of the side chains of R235 (6 kcal/mol), Q215 (2 kcal/mol), Y217 (2 kcal/mol), and hydrogen bonds to the G234 and R235 backbone amides (2 kcal/mol). Analysis of a triple mutant cube shows small (ca. 1 kcal/mol) interactions between phosphodianion gripper side chains, which are consistent with steric crowding of the side chains around the phosphodianion at wild-type OMPDC. These mutations result in the same change in the activation barrier to the OMPDC-catalyzed reactions of the whole substrate OMP and the substrate pieces (1-β-D-erythrofuranosyl)orotic acid (EO) and phosphite dianion. This shows that the transition states for these reactions are stabilized by similar interactions with the protein catalyst. The 12 kcal/mol intrinsic phosphodianion binding energy of OMP is divided between the 8 kcal/mol of binding energy, which is utilized to drive a thermodynamically unfavorable conformational change of the free enzyme, resulting in an increase in (k(cat))(obs) for OMPDC-catalyzed decarboxylation of OMP, and the 4 kcal/mol of binding energy, which is utilized to stabilize the Michaelis complex, resulting in a decrease in (K(m))(obs).
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Affiliation(s)
- Lawrence
M. Goldman
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Bogdana Goryanova
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - John A. Gerlt
- Departments
of Biochemistry and Chemistry, University
of Illinois, Urbana, Illinois 61801, United
States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
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13
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Natarajan A, Schwans JP, Herschlag D. Using unnatural amino acids to probe the energetics of oxyanion hole hydrogen bonds in the ketosteroid isomerase active site. J Am Chem Soc 2014; 136:7643-54. [PMID: 24787954 PMCID: PMC4046884 DOI: 10.1021/ja413174b] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Indexed: 02/04/2023]
Abstract
Hydrogen bonds are ubiquitous in enzyme active sites, providing binding interactions and stabilizing charge rearrangements on substrate groups over the course of a reaction. But understanding the origin and magnitude of their catalytic contributions relative to hydrogen bonds made in aqueous solution remains difficult, in part because of complexities encountered in energetic interpretation of traditional site-directed mutagenesis experiments. It has been proposed for ketosteroid isomerase and other enzymes that active site hydrogen bonding groups provide energetic stabilization via "short, strong" or "low-barrier" hydrogen bonds that are formed due to matching of their pKa or proton affinity to that of the transition state. It has also been proposed that the ketosteroid isomerase and other enzyme active sites provide electrostatic environments that result in larger energetic responses (i.e., greater "sensitivity") to ground-state to transition-state charge rearrangement, relative to aqueous solution, thereby providing catalysis relative to the corresponding reaction in water. To test these models, we substituted tyrosine with fluorotyrosines (F-Tyr's) in the ketosteroid isomerase (KSI) oxyanion hole to systematically vary the proton affinity of an active site hydrogen bond donor while minimizing steric or structural effects. We found that a 40-fold increase in intrinsic F-Tyr acidity caused no significant change in activity for reactions with three different substrates. F-Tyr substitution did not change the solvent or primary kinetic isotope effect for proton abstraction, consistent with no change in mechanism arising from these substitutions. The observed shallow dependence of activity on the pKa of the substituted Tyr residues suggests that the KSI oxyanion hole does not provide catalysis by forming an energetically exceptional pKa-matched hydrogen bond. In addition, the shallow dependence provides no indication of an active site electrostatic environment that greatly enhances the energetic response to charge accumulation, consistent with prior experimental results.
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Affiliation(s)
- Aditya Natarajan
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine, Stanford, California 94305, United States
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14
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Rajagopalan S, Wang C, Yu K, Kuzin AP, Richter F, Lew S, Miklos AE, Matthews ML, Seetharaman J, Su M, Hunt JF, Cravatt BF, Baker D. Design of activated serine-containing catalytic triads with atomic-level accuracy. Nat Chem Biol 2014; 10:386-91. [PMID: 24705591 PMCID: PMC4048123 DOI: 10.1038/nchembio.1498] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 03/10/2014] [Indexed: 01/07/2023]
Abstract
A challenge in the computational design of enzymes is that multiple properties, including substrate binding, transition state stabilization and product release, must be simultaneously optimized, and this has limited the absolute activity of successful designs. Here, we focus on a single critical property of many enzymes: the nucleophilicity of an active site residue that initiates catalysis. We design proteins with idealized serine-containing catalytic triads and assess their nucleophilicity directly in native biological systems using activity-based organophosphate probes. Crystal structures of the most successful designs show unprecedented agreement with computational models, including extensive hydrogen bonding networks between the catalytic triad (or quartet) residues, and mutagenesis experiments demonstrate that these networks are critical for serine activation and organophosphate reactivity. Following optimization by yeast display, the designs react with organophosphate probes at rates comparable to natural serine hydrolases. Co-crystal structures with diisopropyl fluorophosphate bound to the serine nucleophile suggest that the designs could provide the basis for a new class of organophosphate capture agents.
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Affiliation(s)
- Sridharan Rajagopalan
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Chu Wang
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kai Yu
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Alexandre P. Kuzin
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Florian Richter
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Graduate program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington 98195, USA
| | - Scott Lew
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | | | - Megan L. Matthews
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jayaraman Seetharaman
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Min Su
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - John. F. Hunt
- Northeast Structural Genomics Consortium, Department of Biological Sciences, Columbia University, New York, New York 10027
| | - Benjamin F. Cravatt
- The Skaggs Institute for Chemical Biology and Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States,Graduate program in Biological Physics, Structure and Design, University of Washington, Seattle, Washington 98195, USA,Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, United States
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15
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Schwans JP, Hanoian P, Lengerich BJ, Sunden F, Gonzalez A, Tsai Y, Hammes-Schiffer S, Herschlag D. Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site. Biochemistry 2014; 53:2541-55. [PMID: 24597914 PMCID: PMC4004248 DOI: 10.1021/bi401671t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The
positioning of catalytic groups within proteins plays an important
role in enzyme catalysis, and here we investigate the positioning
of the general base in the enzyme ketosteroid isomerase (KSI). The
oxygen atoms of Asp38, the general base in KSI, were previously shown
to be involved in anion–aromatic interactions with two neighboring
Phe residues. Here we ask whether those interactions are sufficient,
within the overall protein architecture, to position Asp38 for catalysis
or whether the side chains that pack against Asp38 and/or the residues
of the structured loop that is capped by Asp38 are necessary to achieve
optimal positioning for catalysis. To test positioning, we mutated
each of the aforementioned residues, alone and in combinations, in
a background with the native Asp general base and in a D38E mutant
background, as Glu at position 38 was previously shown to be mispositioned
for general base catalysis. These double-mutant cycles reveal positioning
effects as large as 103-fold, indicating that structural
features in addition to the overall protein architecture and the Phe
residues neighboring the carboxylate oxygen atoms play roles in positioning.
X-ray crystallography and molecular dynamics simulations suggest that
the functional effects arise from both restricting dynamic fluctuations
and disfavoring potential mispositioned states. Whereas it may have
been anticipated that multiple interactions would be necessary for
optimal general base positioning, the energetic contributions from
positioning and the nonadditive nature of these interactions are not
revealed by structural inspection and require functional dissection.
Recognizing the extent, type, and energetic interconnectivity of interactions
that contribute to positioning catalytic groups has implications for
enzyme evolution and may help reveal the nature and extent of interactions
required to design enzymes that rival those found in biology.
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Affiliation(s)
- Jason P Schwans
- Department of Biochemistry, Stanford University , B400 Beckman Center, 279 Campus Drive, Stanford, California 94305, United States
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16
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Zhai X, Malabanan MM, Amyes TL, Richard JP. Mechanistic Imperatives for Deprotonation of Carbon Catalyzed by Triosephosphate Isomerase: Enzyme-Activation by Phosphite Dianion. J PHYS ORG CHEM 2014; 27:269-276. [PMID: 24729658 PMCID: PMC3979633 DOI: 10.1002/poc.3195] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The mechanistic imperatives for catalysis of deprotonation of α-carbonyl carbon by triosephosphate isomerase (TIM) are discussed. There is a strong imperative to reduce the large thermodynamic barrier for deprotonation of carbon to form an enediolate reaction intermediate; and, a strong imperative for specificity in the expression of the intrinsic phosphodianion binding energy at the transition state for the enzyme-catalyzed reaction. Binding energies of 2 and 6 kcal/mol, respectively, have been determined for formation of phosphite dianion complexes to TIM and to the transition state for TIM-catalyzed deprotonation of the truncated substrate glycolaldehyde [T. L. Amyes, J. P. Richard, Biochemistry2007, 46, 5841]. We propose that the phosphite dianion binding energy, which is specifically expressed at the transition state complex, is utilized to stabilize a rare catalytically active loop-closed form of TIM. The results of experiments to probe the role of the side chains of Ile172 and Leu232 in activating the loop-closed form of TIM for catalysis of substrate deprotonation are discussed. Evidence is presented that the hydrophobic side chain of Ile172 assists in activating TIM for catalysis of substrate deprotonation through an enhancement of the basicity of the carboxylate side-chain of Glu167. Our experiments link the two imperatives for TIM-catalyzed deprotonation of carbon by providing evidence that the phosphodianion binding energy is utilized to drive an enzyme conformational change, which results in a reduction in the thermodynamic barrier to deprotonation of the carbon acid substrate at TIM compared with the barrier for deprotonation in water. The effects of a P168A mutation on the kinetic parameters for the reactions of whole and truncated substrates are discussed.
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Affiliation(s)
- Xiang Zhai
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
| | - M Merced Malabanan
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
| | - Tina L Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
| | - John P Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, NY 14260, USA
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17
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Parker ML, Osuna S, Bollot G, Vaddypally S, Zdilla MJ, Houk KN, Schafmeister CE. Acceleration of an aromatic Claisen rearrangement via a designed spiroligozyme catalyst that mimics the ketosteroid isomerase catalytic dyad. J Am Chem Soc 2014; 136:3817-27. [PMID: 24456160 PMCID: PMC4004270 DOI: 10.1021/ja409214c] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Indexed: 01/03/2023]
Abstract
A series of hydrogen-bonding catalysts have been designed for the aromatic Claisen rearrangement of a 1,1-dimethylallyl coumarin. These catalysts were designed as mimics of the two-point hydrogen-bonding interaction present in ketosteroid isomerase that has been proposed to stabilize a developing negative charge on the ether oxygen in the migration of the double bond.1 Two hydrogen bond donating groups, a phenol alcohol and a carboxylic acid, were grafted onto a conformationally restrained spirocyclic scaffold, and together they enhance the rate of the Claisen rearrangement by a factor of 58 over the background reaction. Theoretical calculations correctly predict the most active catalyst and suggest that both preorganization and favorable interactions with the transition state of the reaction are responsible for the observed rate enhancement.
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Affiliation(s)
- Matthew
F. L. Parker
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sílvia Osuna
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | - Guillaume Bollot
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | - Shivaiah Vaddypally
- Department
of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania, 19122, United States
| | - Michael J. Zdilla
- Department
of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania, 19122, United States
| | - K. N. Houk
- Department
of Chemistry and Biochemistry, University
of California, Los Angeles, California 90095-1569, United States
| | - Christian E. Schafmeister
- Department
of Chemistry, Temple University, 1901 North 13th Street, Philadelphia, Pennsylvania, 19122, United States
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18
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Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. Uncovering the determinants of a highly perturbed tyrosine pKa in the active site of ketosteroid isomerase. Biochemistry 2013; 52:7840-55. [PMID: 24151972 PMCID: PMC3890242 DOI: 10.1021/bi401083b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Within the idiosyncratic enzyme active-site environment, side chain and ligand pKa values can be profoundly perturbed relative to their values in aqueous solution. Whereas structural inspection of systems has often attributed perturbed pKa values to dominant contributions from placement near charged groups or within hydrophobic pockets, Tyr57 of a Pseudomonas putida ketosteroid isomerase (KSI) mutant, suggested to have a pKa perturbed by nearly 4 units to 6.3, is situated within a solvent-exposed active site devoid of cationic side chains, metal ions, or cofactors. Extensive comparisons among 45 variants with mutations in and around the KSI active site, along with protein semisynthesis, (13)C NMR spectroscopy, absorbance spectroscopy, and X-ray crystallography, was used to unravel the basis for this perturbed Tyr pKa. The results suggest that the origin of large energetic perturbations are more complex than suggested by visual inspection. For example, the introduction of positively charged residues near Tyr57 raises its pKa rather than lowers it; this effect, and part of the increase in the Tyr pKa from the introduction of nearby anionic groups, arises from accompanying active-site structural rearrangements. Other mutations with large effects also cause structural perturbations or appear to displace a structured water molecule that is part of a stabilizing hydrogen-bond network. Our results lead to a model in which three hydrogen bonds are donated to the stabilized ionized Tyr, with these hydrogen-bond donors, two Tyr side chains, and a water molecule positioned by other side chains and by a water-mediated hydrogen-bond network. These results support the notion that large energetic effects are often the consequence of multiple stabilizing interactions rather than a single dominant interaction. Most generally, this work provides a case study for how extensive and comprehensive comparisons via site-directed mutagenesis in a tight feedback loop with structural analysis can greatly facilitate our understanding of enzyme active-site energetics. The extensive data set provided may also be a valuable resource for those wishing to extensively test computational approaches for determining enzymatic pKa values and energetic effects.
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Affiliation(s)
- Jason P. Schwans
- Department of Biochemistry, Stanford University, Stanford, California 94305
| | - Fanny Sunden
- Department of Biochemistry, Stanford University, Stanford, California 94305
| | - Ana Gonzalez
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Yingssu Tsai
- Department of Chemistry, Stanford University, Stanford, California 94305
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, California 94305
- Department of Chemistry, Stanford University, Stanford, California 94305
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19
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Abstract
Linus Pauling proposed that the large rate accelerations for enzymes are caused by the high specificity of the protein catalyst for binding the reaction transition state. The observation that stable analogues of the transition states for enzymatic reactions often act as tight-binding inhibitors provided early support for this simple and elegant proposal. We review experimental results that support the proposal that Pauling's model provides a satisfactory explanation for the rate accelerations for many heterolytic enzymatic reactions through high-energy reaction intermediates, such as proton transfer and decarboxylation. Specificity in transition state binding is obtained when the total intrinsic binding energy of the substrate is significantly larger than the binding energy observed at the Michaelis complex. The results of recent studies that aimed to characterize the specificity in binding of the enolate oxygen at the transition state for the 1,3-isomerization reaction catalyzed by ketosteroid isomerase are reviewed. Interactions between pig heart succinyl-coenzyme A:3-oxoacid coenzyme A transferase (SCOT) and the nonreacting portions of coenzyme A (CoA) are responsible for a rate increase of 3 × 10(12)-fold, which is close to the estimated total 5 × 10(13)-fold enzymatic rate acceleration. Studies that partition the interactions between SCOT and CoA into their contributing parts are reviewed. Interactions of the protein with the substrate phosphodianion group provide an ~12 kcal/mol stabilization of the transition state for the reactions catalyzed by triosephosphate isomerase, orotidine 5'-monophosphate decarboxylase, and α-glycerol phosphate dehydrogenase. The interactions of these enzymes with the substrate piece phosphite dianion provide a 6-8 kcal/mol stabilization of the transition state for reaction of the appropriate truncated substrate. Enzyme activation by phosphite dianion reflects the higher dianion affinity for binding to the enzyme-transition state complex compared with that of the free enzyme. Evidence is presented that supports a model in which the binding energy of the phosphite dianion piece, or the phosphodianion group of the whole substrate, is utilized to drive an enzyme conformational change from an inactive open form E(O) to an active closed form E(C), by closure of a phosphodianion gripper loop. Members of the enolase and haloalkanoic acid dehalogenase superfamilies use variable capping domains to interact with nonreacting portions of the substrate and sequester the substrate from interaction with bulk solvent. Interactions of this capping domain with the phenyl group of mandelate have been shown to activate mandelate racemase for catalysis of deprotonation of α-carbonyl carbon. We propose that an important function of these capping domains is to utilize the binding interactions with nonreacting portions of the substrate to activate the enzyme for catalysis.
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Affiliation(s)
- Tina L. Amyes
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000
| | - John P. Richard
- To whom correspondence should be addressed: Tel: (716) 645 4232; Fax: (716) 645 6963;
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20
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Herschlag D, Natarajan A. Fundamental challenges in mechanistic enzymology: progress toward understanding the rate enhancements of enzymes. Biochemistry 2013; 52:2050-67. [PMID: 23488725 DOI: 10.1021/bi4000113] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes are remarkable catalysts that lie at the heart of biology, accelerating chemical reactions to an astounding extent with extraordinary specificity. Enormous progress in understanding the chemical basis of enzymatic transformations and the basic mechanisms underlying rate enhancements over the past decades is apparent. Nevertheless, it has been difficult to achieve a quantitative understanding of how the underlying mechanisms account for the energetics of catalysis, because of the complexity of enzyme systems and the absence of underlying energetic additivity. We review case studies from our own work that illustrate the power of precisely defined and clearly articulated questions when dealing with such complex and multifaceted systems, and we also use this approach to evaluate our current ability to design enzymes. We close by highlighting a series of questions that help frame some of what remains to be understood, and we encourage the reader to define additional questions and directions that will deepen and broaden our understanding of enzymes and their catalysis.
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Affiliation(s)
- Daniel Herschlag
- Department of Biochemistry, Stanford University School of Medicine , Stanford, California 94305, United States
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21
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Ruben EA, Schwans JP, Sonnett M, Natarajan A, Gonzalez A, Tsai Y, Herschlag D. Ground state destabilization from a positioned general base in the ketosteroid isomerase active site. Biochemistry 2013; 52:1074-81. [PMID: 23311398 DOI: 10.1021/bi301348x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We compared the binding affinities of ground state analogues for bacterial ketosteroid isomerase (KSI) with a wild-type anionic Asp general base and with uncharged Asn and Ala in the general base position to provide a measure of potential ground state destabilization that could arise from the close juxtaposition of the anionic Asp and hydrophobic steroid in the reaction's Michaelis complex. The analogue binding affinity increased ~1 order of magnitude for the Asp38Asn mutation and ~2 orders of magnitude for the Asp38Ala mutation, relative to the affinity with Asp38, for KSI from two sources. The increased level of binding suggests that the abutment of a charged general base and a hydrophobic steroid is modestly destabilizing, relative to a standard state in water, and that this destabilization is relieved in the transition state and intermediate in which the charge on the general base has been neutralized because of proton abstraction. Stronger binding also arose from mutation of Pro39, the residue adjacent to the Asp general base, consistent with an ability of the Asp general base to now reorient to avoid the destabilizing interaction. Consistent with this model, the Pro mutants reduced or eliminated the increased level of binding upon replacement of Asp38 with Asn or Ala. These results, supported by additional structural observations, suggest that ground state destabilization from the negatively charged Asp38 general base provides a modest contribution to KSI catalysis. They also provide a clear illustration of the well-recognized concept that enzymes evolve for catalytic function and not, in general, to maximize ground state binding. This ground state destabilization mechanism may be common to the many enzymes with anionic side chains that deprotonate carbon acids.
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Affiliation(s)
- Eliza A Ruben
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
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