1
|
Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024. [PMID: 38959423 DOI: 10.1021/acs.chemrev.4c00120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
Collapse
Affiliation(s)
- Zachary Birch-Price
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Florence J Hardy
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Thomas M Lister
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Anna R Kohn
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester M1 7DN, U.K
| |
Collapse
|
2
|
Khezeli F, Plaisance C. Computational Design of an Electro-Organocatalyst for Conversion of CO 2 into Formaldehyde. J Phys Chem A 2024; 128:1576-1592. [PMID: 38412517 PMCID: PMC10926098 DOI: 10.1021/acs.jpca.3c07806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/02/2024] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
Density functional theory calculations employing a hybrid implicit/explicit solvation method were used to explore a new strategy for electrochemical conversion of CO2 using an electro-organocatalyst. A particular structural motif is identified that consists of an electron-rich vicinal enediamine (>N-C═C-N<) backbone, which is capable of activating CO2 by the formation of a C-C bond while subsequently facilitating the transfer of electrons from a chemically inert cathode to ultimately produce formaldehyde. Unlike transition metal-based electrocatalysts, the electro-organocatalyst is not constrained by scaling relations between the formation energies of activated CO2 and adsorbed CO, nor is it expected to be active for the competing hydrogen evolution reaction. The rate-limiting steps are found to occur during two proton-coupled electron transfer (PCET) sequences and are associated with the transfer of a proton from a proton transfer mediator to a carbon atom on the electro-organocatalyst. The difficulty of this step in the second PCET sequence necessitates an electrode potential of -0.85 V vs RHE to achieve the maximum turnover frequency. In addition, it is postulated that the electro-organocatalyst should also be capable of forming long-chain aldehydes by successively carrying out reductive aldol condensation to grow the alkyl chain one carbon at a time.
Collapse
Affiliation(s)
- Foroogh Khezeli
- Cain Department
of Chemical
Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Craig Plaisance
- Cain Department
of Chemical
Engineering, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| |
Collapse
|
3
|
Juretić D, Bonačić Lošić Ž. Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation. ENTROPY (BASEL, SWITZERLAND) 2024; 26:151. [PMID: 38392406 PMCID: PMC10888251 DOI: 10.3390/e26020151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/18/2024] [Accepted: 02/05/2024] [Indexed: 02/24/2024]
Abstract
Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, kcat, and enzyme efficiency, kcat/KM, of uni-uni enzymes, which convert a single substrate into a single product. We added or multiplied random noise with chosen rate constants to explore the correlation between dissipation and catalytic efficiency for ten enzymes: beta-galactosidase, glucose isomerase, β-lactamases from three bacterial strains, ketosteroid isomerase, triosephosphate isomerase, and carbonic anhydrase I, II, and T200H. Our results highlight the role of biological evolution in accelerating thermodynamic evolution. The catalytic performance of these enzymes is proportional to overall entropy production-the main parameter from irreversible thermodynamics. That parameter is also proportional to the evolutionary distance of β-lactamases PC1, RTEM, and Lac-1 when natural or artificial evolution produces the optimal or maximal possible catalytic efficiency. De novo enzyme design and attempts to speed up the rate-limiting catalytic steps may profit from the described connection between kinetics and thermodynamics.
Collapse
Affiliation(s)
- Davor Juretić
- Mediterranean Institute for Life Sciences, Šetalište Ivana Meštrovića 45, 21000 Split, Croatia
- Faculty of Science, University of Split, Ruđera Boškovića 33, 21000 Split, Croatia
| | | |
Collapse
|
4
|
Musdal Y, Ismail A, Sjödin B, Mannervik B. Potent GST Ketosteroid Isomerase Activity Relevant to Ecdysteroidogenesis in the Malaria Vector Anopheles gambiae. Biomolecules 2023; 13:976. [PMID: 37371556 DOI: 10.3390/biom13060976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/03/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Nobo is a glutathione transferase (GST) crucially contributing to ecdysteroid biosynthesis in insects of the orders Diptera and Lepidoptera. Ecdysone is a vital steroid hormone in insects, which governs larval molting and metamorphosis, and the suppression of its synthesis has potential as a novel approach to insect growth regulation and combatting vectors of disease. In general, GSTs catalyze detoxication, whereas the specific function of Nobo in ecdysteroidogenesis is unknown. We report that Nobo from the malaria-spreading mosquito Anopheles gambiae is a highly efficient ketosteroid isomerase catalyzing double-bond isomerization in the steroids 5-androsten-3,17-dione and 5-pregnen-3,20-dione. These mammalian ketosteroids are unknown in mosquitoes, but the discovered prominent catalytic activity of these compounds suggests that the unknown Nobo substrate in insects has a ketosteroid functionality. Aminoacid residue Asp111 in Nobo is essential for activity with the steroids, but not for conventional GST substrates. Further characterization of Nobo may guide the development of new insecticides to prevent malaria.
Collapse
Affiliation(s)
- Yaman Musdal
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
- Department of Pediatric Genetics, Faculty of Medicine, Hacettepe University, 06230 Ankara, Turkey
| | - Aram Ismail
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Birgitta Sjödin
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Bengt Mannervik
- Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
- Department of Chemistry, Scripps Research, La Jolla, CA 92037, USA
| |
Collapse
|
5
|
Demchenko AP. Proton transfer reactions: from photochemistry to biochemistry and bioenergetics. BBA ADVANCES 2023. [DOI: 10.1016/j.bbadva.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
|
6
|
Yabukarski F, Doukov T, Pinney MM, Biel JT, Fraser JS, Herschlag D. Ensemble-function relationships to dissect mechanisms of enzyme catalysis. SCIENCE ADVANCES 2022; 8:eabn7738. [PMID: 36240280 PMCID: PMC9565801 DOI: 10.1126/sciadv.abn7738] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 08/30/2022] [Indexed: 05/27/2023]
Abstract
Decades of structure-function studies have established our current extensive understanding of enzymes. However, traditional structural models are snapshots of broader conformational ensembles of interchanging states. We demonstrate the need for conformational ensembles to understand function, using the enzyme ketosteroid isomerase (KSI) as an example. Comparison of prior KSI cryogenic x-ray structures suggested deleterious mutational effects from a misaligned oxyanion hole catalytic residue. However, ensemble information from room-temperature x-ray crystallography, combined with functional studies, excluded this model. Ensemble-function analyses can deconvolute effects from altering the probability of occupying a state (P-effects) and changing the reactivity of each state (k-effects); our ensemble-function analyses revealed functional effects arising from weakened oxyanion hole hydrogen bonding and substrate repositioning within the active site. Ensemble-function studies will have an integral role in understanding enzymes and in meeting the future goals of a predictive understanding of enzyme catalysis and engineering new enzymes.
Collapse
Affiliation(s)
- Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Margaux M. Pinney
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Justin T. Biel
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Structural enzymology of cholesterol biosynthesis and storage. Curr Opin Struct Biol 2022; 74:102369. [DOI: 10.1016/j.sbi.2022.102369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/02/2022] [Accepted: 03/01/2022] [Indexed: 11/15/2022]
|
9
|
Weberg AB, Murphy RP, Tomson NC. Oriented internal electrostatic fields: an emerging design element in coordination chemistry and catalysis. Chem Sci 2022; 13:5432-5446. [PMID: 35694353 PMCID: PMC9116365 DOI: 10.1039/d2sc01715f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 11/21/2022] Open
Abstract
The power of oriented electrostatic fields (ESFs) to influence chemical bonding and reactivity is a phenomenon of rapidly growing interest. The presence of strong ESFs has recently been implicated as one of the most significant contributors to the activity of select enzymes, wherein alignment of a substrate's changing dipole moment with a strong, local electrostatic field has been shown to be responsible for the majority of the enzymatic rate enhancement. Outside of enzymology, researchers have studied the impacts of "internal" electrostatic fields via the addition of ionic salts to reactions and the incorporation of charged functional groups into organic molecules (both experimentally and computationally), and "externally" via the implementation of bulk fields between electrode plates. Incorporation of charged moieties into homogeneous inorganic complexes to generate internal ESFs represents an area of high potential for novel catalyst design. This field has only begun to materialize within the past 10 years but could be an area of significant impact moving forward, since it provides a means for tuning the properties of molecular complexes via a method that is orthogonal to traditional strategies, thereby providing possibilities for improved catalytic conditions and novel reactivity. In this perspective, we highlight recent developments in this area and offer insights, obtained from our own research, on the challenges and future directions of this emerging field of research.
Collapse
Affiliation(s)
- Alexander B Weberg
- R, oy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia Pennsylvania 19104 USA
| | - Ryan P Murphy
- R, oy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia Pennsylvania 19104 USA
| | - Neil C Tomson
- R, oy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania 231 S. 34th Street Philadelphia Pennsylvania 19104 USA
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Selvaraj C, Rudhra O, Alothaim AS, Alkhanani M, Singh SK. Structure and chemistry of enzymatic active sites that play a role in the switch and conformation mechanism. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2022; 130:59-83. [PMID: 35534116 DOI: 10.1016/bs.apcsb.2022.02.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Enzymes, which are biological molecules, are constructed from polypeptide chains, and these molecules are activated through reaction mechanisms. It is the role of enzymes to speed up chemical reactions that are used to build or break down cell structures. Activation energy is reduced by the enzymes' selective binding of substrates in a protected environment. In enzyme tertiary structures, the active sites are commonly situated in a "cleft," which necessitates the diffusion of substrates and products. The amino acid residues of the active site may be far apart in the primary structure owing to the folding required for tertiary structure. Due to their critical role in substrate binding and attraction, changes in amino acid structure at or near the enzyme's active site usually alter enzyme activity. At the enzyme's active site, or where the chemical reactions occur, the substrate is bound. Enzyme substrates are the primary targets of the enzyme's active site, which is designed to assist in the chemical reaction. This chapter elucidates the summary of structure and chemistry of enzymes, their active site features, charges and role of water in the structures to clarify the biochemistry of the enzymes in the depth of atomic features.
Collapse
Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| | - Ondipilliraja Rudhra
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India
| | - Abdulaziz S Alothaim
- Department of Biology, College of Science in Zulfi, Majmaah University, Majmaah, Saudi Arabia
| | - Mustfa Alkhanani
- Emergency Service Department, College of Applied Sciences, Al Maarefa University, Riyadh, Saudi Arabia
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modelling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi, Tamil Nadu, India.
| |
Collapse
|
12
|
Mannervik B, Ismail A, Lindström H, Sjödin B, Ing NH. Glutathione Transferases as Efficient Ketosteroid Isomerases. Front Mol Biosci 2021; 8:765970. [PMID: 34881290 PMCID: PMC8645602 DOI: 10.3389/fmolb.2021.765970] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 11/01/2021] [Indexed: 01/01/2023] Open
Abstract
In addition to their well-established role in detoxication, glutathione transferases (GSTs) have other biological functions. We are focusing on the ketosteroid isomerase activity, which appears to contribute to steroid hormone biosynthesis in mammalian tissues. A highly efficient GST A3-3 is present in some, but not all, mammals. The alpha class enzyme GST A3-3 in humans and the horse shows the highest catalytic efficiency with kcat/Km values of approximately 107 M-1s-1, ranking close to the most active enzymes known. The expression of GST A3-3 in steroidogenic tissues suggests that the enzyme has evolved to support the activity of 3β-hydroxysteroid dehydrogenase, which catalyzes the formation of 5-androsten-3,17-dione and 5-pregnen-3,20-dione that are substrates for the double-bond isomerization catalyzed by GST A3-3. The dehydrogenase also catalyzes the isomerization, but its kcat of approximately 1 s-1 is 200-fold lower than the kcat values of human and equine GST A3-3. Inhibition of GST A3-3 in progesterone-producing human cells suppress the formation of the hormone. Glutathione serves as a coenzyme contributing a thiolate as a base in the isomerase mechanism, which also involves the active-site Tyr9 and Arg15. These conserved residues are necessary but not sufficient for the ketosteroid isomerase activity. A proper assortment of H-site residues is crucial to efficient catalysis by forming the cavity binding the hydrophobic substrate. It remains to elucidate why some mammals, such as rats and mice, lack GSTs with the prominent ketosteroid isomerase activity found in certain other species. Remarkably, the fruit fly Drosophila melanogaster, expresses a GSTE14 with notable steroid isomerase activity, even though Ser14 has evolved as the active-site residue corresponding to Tyr9 in the mammalian alpha class.
Collapse
Affiliation(s)
- Bengt Mannervik
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Aram Ismail
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Helena Lindström
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Birgitta Sjödin
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Nancy H. Ing
- Department of Animal Science, Texas A&M AgriLife Research, Texas A&M University, College Station, TX, United States
| |
Collapse
|
13
|
KHARSHIING GAYLE, CHRUNGOO NIKHILK. Wx alleles in rice: relationship with apparent amylose content of starch and a possible role in rice domestication. J Genet 2021. [DOI: 10.1007/s12041-021-01311-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
14
|
Behrens DM, Hartke B. Globally Optimized Molecular Embeddings for Dynamic Reaction Solvate Shell Optimization and Active Site Design. Top Catal 2021. [DOI: 10.1007/s11244-021-01486-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
AbstractWe demonstrate how a full QM/MM derivatization of the recently developed GOCAT model can be utilized in the global optimization of molecular embeddings. To this end, we provide two distinct examples: An $$\text {S}_\text {N}2$$
S
N
2
reaction, and one enzymatic example of recent interest, the ketosteroid isomerase. These serve us to highlight the advantages of such an approach and sketch the roadmap for further improvements.
Collapse
|
15
|
Liang Y, Li W, Liang H, Lou X, Liu R, Zhang Q, Bartlam M. Structural characterization and Kemp eliminase activity of the Mycobacterium smegmatis Ketosteroid Isomerase. Biochem Biophys Res Commun 2021; 560:159-164. [PMID: 33992958 DOI: 10.1016/j.bbrc.2021.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 11/26/2022]
Abstract
The Kemp elimination reaction, involving the ring-opening of benzoxazole and its derivatives under the action of natural enzymes or chemical catalysts, has been of interest to researchers since its discovery. Because this reaction does not exist in all currently known metabolic pathways, the computational design of Kemp eliminases has provided valuable insights into principles of enzymatic catalysis. However, it was discovered that the naturally occurring promiscuous enzymes ydbC, xapA and ketosteroid isomerase also can catalyze Kemp elimination. Here, we report the crystal structure of ketosteroid isomerase (KSI) from Mycobacterium smegmatis MC2 155. MsKSI crystallizes in the P212121 space group with two molecules in an asymmetric unit, and ultracentrifugation data confirms that it forms a stable dimer in solution, consistent with the 1.9 Å-resolution structure. Our assays confirm that MsKSI accelerates the Kemp elimination of 5-nitrobenzoxazole (5NBI) with an optimal pH of 5.5. A 2.35 Å resolution crystal structure of the MsKSI-5NBI complex reveals that the substrate 5NBI is bound in the active pocket of the enzyme composed of hydrophobic residues. In addition, the Glu127 residue is proposed to play an important role as a general base in proton transfer and breaking weak O-N bonds to open the five-membered ring. This work provides a starting point for exploring the artificial modification of MsKSI using the natural enzyme as the backbone.
Collapse
Affiliation(s)
- Yakun Liang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Weiping Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Han Liang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xiaorui Lou
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ruihua Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Qionglin Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Mark Bartlam
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Science and College of Life Sciences, Nankai University, Tianjin, 300071, China
| |
Collapse
|
16
|
Pinney MM, Mokhtari DA, Akiva E, Yabukarski F, Sanchez DM, Liang R, Doukov T, Martinez TJ, Babbitt PC, Herschlag D. Parallel molecular mechanisms for enzyme temperature adaptation. Science 2021; 371:371/6533/eaay2784. [PMID: 33674467 DOI: 10.1126/science.aay2784] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 08/23/2020] [Accepted: 01/04/2021] [Indexed: 12/13/2022]
Abstract
The mechanisms that underly the adaptation of enzyme activities and stabilities to temperature are fundamental to our understanding of molecular evolution and how enzymes work. Here, we investigate the molecular and evolutionary mechanisms of enzyme temperature adaption, combining deep mechanistic studies with comprehensive sequence analyses of thousands of enzymes. We show that temperature adaptation in ketosteroid isomerase (KSI) arises primarily from one residue change with limited, local epistasis, and we establish the underlying physical mechanisms. This residue change occurs in diverse KSI backgrounds, suggesting parallel adaptation to temperature. We identify residues associated with organismal growth temperature across 1005 diverse bacterial enzyme families, suggesting widespread parallel adaptation to temperature. We assess the residue properties, molecular interactions, and interaction networks that appear to underly temperature adaptation.
Collapse
Affiliation(s)
- Margaux M Pinney
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.
| | - Daniel A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Filip Yabukarski
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94110, USA
| | - David M Sanchez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Ruibin Liang
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Tzanko Doukov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Todd J Martinez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA.,Department of Photon Sciences, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences and Quantitative Biosciences Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA. .,Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA.,Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
17
|
Li WL, Head-Gordon T. Catalytic Principles from Natural Enzymes and Translational Design Strategies for Synthetic Catalysts. ACS CENTRAL SCIENCE 2021; 7:72-80. [PMID: 33532570 PMCID: PMC7844850 DOI: 10.1021/acscentsci.0c01556] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Indexed: 05/19/2023]
Abstract
As biocatalysts, enzymes are characterized by their high catalytic efficiency and strong specificity but are relatively fragile by requiring narrow and specific reactive conditions for activity. Synthetic catalysts offer an opportunity for more chemical versatility operating over a wider range of conditions but currently do not reach the remarkable performance of natural enzymes. Here we consider some new design strategies based on the contributions of nonlocal electric fields and thermodynamic fluctuations to both improve the catalytic step and turnover for rate acceleration in arbitrary synthetic catalysts through bioinspired studies of natural enzymes. With a focus on the enzyme as a whole catalytic construct, we illustrate the translational impact of natural enzyme principles to synthetic enzymes, supramolecular capsules, and electrocatalytic surfaces.
Collapse
Affiliation(s)
- Wan-Lu Li
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California Berkeley, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Chemical
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Kenneth
S. Pitzer Center for Theoretical Chemistry, University of California Berkeley, Berkeley, California 94720, United States
- Department of Chemistry, Department of Chemical and Biomolecular Engineering, and Department of
Bioengineering, University of California
Berkeley, Berkeley, California 94720, United States
| |
Collapse
|
18
|
Zhang Z, Tamura Y, Tang M, Qiao T, Sato M, Otsu Y, Sasamura S, Taniguchi M, Watanabe K, Tang Y. Biosynthesis of the Immunosuppressant (-)-FR901483. J Am Chem Soc 2021; 143:132-136. [PMID: 33372776 DOI: 10.1021/jacs.0c12352] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report characterization of the biosynthetic pathway of the potent immunosuppressant (-)-FR901483 (1) through heterologous expression and enzymatic assays. The biosynthetic logic to form the azatricyclic alkaloid is consistent with those proposed in biomimetic syntheses and involves aza-spiro annulation of dityrosyl-piperazine to form a ketoaldehyde intermediate, followed by regioselective aldol condensation, stereoselective ketoreduction, and phosphorylation. A possible target of 1 is proposed based on the biosynthetic studies.
Collapse
Affiliation(s)
| | - Yui Tamura
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | | | | | - Michio Sato
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | - Yoshihiro Otsu
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki 300-2611, Japan
| | - Satoshi Sasamura
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki 300-2611, Japan
| | - Masatoshi Taniguchi
- Discovery and Preclinical Research Division, Taiho Pharmaceutical Co., Ltd., Tsukuba, Ibaraki 300-2611, Japan
| | - Kenji Watanabe
- Department of Pharmaceutical Sciences, University of Shizuoka, Shizuoka 422-8526, Japan
| | | |
Collapse
|
19
|
Golec JC, Carter EM, Ward JW, Whittingham WG, Simón L, Paton RS, Dixon DJ. BIMP-Catalyzed 1,3-Prototropic Shift for the Highly Enantioselective Synthesis of Conjugated Cyclohexenones. Angew Chem Int Ed Engl 2020; 59:17417-17422. [PMID: 32558981 PMCID: PMC7540019 DOI: 10.1002/anie.202006202] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/03/2020] [Indexed: 12/18/2022]
Abstract
A bifunctional iminophosphorane (BIMP)-catalysed enantioselective synthesis of α,β-unsaturated cyclohexenones through a facially selective 1,3-prototropic shift of β,γ-unsaturated prochiral isomers, under mild reaction conditions and in short reaction times, on a range of structurally diverse substrates, is reported. α,β-Unsaturated cyclohexenone products primed for downstream derivatisation were obtained in high yields (up to 99 %) and consistently high enantioselectivity (up to 99 % ee). Computational studies into the reaction mechanism and origins of enantioselectivity, including multivariate linear regression of TS energy, were carried out and the obtained data were found to be in good agreement with experimental findings.
Collapse
Affiliation(s)
- Jonathan C. Golec
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Eve M. Carter
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - John W. Ward
- Leverhulme Research Centre for Functional Materials DesignThe Materials Innovation FactoryDepartment of ChemistryUniversity of LiverpoolLiverpoolL7 3NYUK
| | | | - Luis Simón
- Facultad de Ciencias QuímicasUniversidad de SalamancaPlaza de los Caídos 1–537008SalamancaSpain
| | - Robert S. Paton
- Department of ChemistryColorado State University1301 Center AveFt. CollinsCO80523-1872USA
| | - Darren J. Dixon
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| |
Collapse
|
20
|
Morris JS, Caldo KMP, Liang S, Facchini PJ. PR10/Bet v1-like Proteins as Novel Contributors to Plant Biochemical Diversity. Chembiochem 2020; 22:264-287. [PMID: 32700448 DOI: 10.1002/cbic.202000354] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/16/2020] [Indexed: 02/06/2023]
Abstract
Pathogenesis-related (PR) proteins constitute a broad class of plant proteins with analogues found throughout nature from bacteria to higher eukaryotes. PR proteins were first noted in plants as part of the hypersensitive response, but have since been assigned an array of biological roles. The PR10/Bet v1-like proteins are a subset of PR proteins characterized by an ability to bind a wide range of lipophilic ligands, uniquely positioning them as contributors to specialized biosynthetic pathways. PR10/Bet v1-like proteins participate in the production of plant alkaloids and phenolics including flavonoids, both as general binding proteins and in special cases as catalysts. Owing initially to the perceived allergenic properties of PR10/Bet v1-like proteins, many were studied at the structural level to elucidate the basis for ligand binding. These studies provided a foundation for more recent efforts to understand higher-level structural order and how PR10/Bet v1-like proteins catalyse key reactions in plant pathways. Synthetic biology aimed at reconstituting plant-specialized metabolism in microorganisms uses knowledge of these proteins to fine-tune performance in new systems.
Collapse
Affiliation(s)
- Jeremy S Morris
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N N4, Canada
| | - Kristian Mark P Caldo
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N N4, Canada
| | - Siyu Liang
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, 2500 University Drive N.W., Calgary, Alberta, T2N N4, Canada
| |
Collapse
|
21
|
Golec JC, Carter EM, Ward JW, Whittingham WG, Simón L, Paton RS, Dixon DJ. BIMP‐Catalyzed 1,3‐Prototropic Shift for the Highly Enantioselective Synthesis of Conjugated Cyclohexenones. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006202] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jonathan C. Golec
- Department of Chemistry Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Eve M. Carter
- Department of Chemistry Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| | - John W. Ward
- Leverhulme Research Centre for Functional Materials Design The Materials Innovation Factory Department of Chemistry University of Liverpool Liverpool L7 3NY UK
| | | | - Luis Simón
- Facultad de Ciencias Químicas Universidad de Salamanca Plaza de los Caídos 1–5 37008 Salamanca Spain
| | - Robert S. Paton
- Department of Chemistry Colorado State University 1301 Center Ave Ft. Collins CO 80523-1872 USA
| | - Darren J. Dixon
- Department of Chemistry Chemistry Research Laboratory University of Oxford Mansfield Road Oxford OX1 3TA UK
| |
Collapse
|
22
|
Hennefarth MR, Alexandrova AN. Direct Look at the Electric Field in Ketosteroid Isomerase and Its Variants. ACS Catal 2020. [DOI: 10.1021/acscatal.0c02795] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Matthew R. Hennefarth
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
| | - Anastassia N. Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E. Young Drive East, Los Angeles, California 90095-1569, United States
- California NanoSystems Institute, University of California, Los Angeles, 570 Westwood Plaza, Los Angeles, California 90095-1569, United Sates
| |
Collapse
|
23
|
Wu Y, Fried SD, Boxer SG. A Preorganized Electric Field Leads to Minimal Geometrical Reorientation in the Catalytic Reaction of Ketosteroid Isomerase. J Am Chem Soc 2020; 142:9993-9998. [PMID: 32378409 DOI: 10.1021/jacs.0c00383] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Electrostatic interactions play a pivotal role in enzymatic catalysis and are increasingly modeled explicitly in computational enzyme design; nevertheless, they are challenging to measure experimentally. Using vibrational Stark effect (VSE) spectroscopy, we have measured electric fields inside the active site of the enzyme ketosteroid isomerase (KSI). These studies have shown that these fields can be unusually large, but it has been unclear to what extent they specifically stabilize the transition state (TS) relative to a ground state (GS). In the following, we use crystallography and computational modeling to show that KSI's intrinsic electric field is nearly perfectly oriented to stabilize the geometry of its reaction's TS. Moreover, we find that this electric field adjusts the orientation of its substrate in the ground state so that the substrate needs to only undergo minimal structural changes upon activation to its TS. This work provides evidence that the active site electric field in KSI is preorganized to facilitate catalysis and provides a template for how electrostatic preorganization can be measured in enzymatic systems.
Collapse
Affiliation(s)
- Yufan Wu
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Stephen D Fried
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, United States
| |
Collapse
|
24
|
Škerlová J, Lindström H, Gonis E, Sjödin B, Neiers F, Stenmark P, Mannervik B. Structure and steroid isomerase activity of
Drosophila
glutathione transferase E14 essential for ecdysteroid biosynthesis. FEBS Lett 2020; 594:1187-1195. [DOI: 10.1002/1873-3468.13718] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 11/25/2019] [Accepted: 12/11/2019] [Indexed: 11/10/2022]
Affiliation(s)
- Jana Škerlová
- Department of Biochemistry and Biophysics Stockholm University Sweden
| | - Helena Lindström
- Department of Biochemistry and Biophysics Stockholm University Sweden
| | - Elodie Gonis
- CSGA Laboratory of Taste and Olfaction University Bourgogne Franche‐Comté Dijon France
| | - Birgitta Sjödin
- Department of Biochemistry and Biophysics Stockholm University Sweden
| | - Fabrice Neiers
- CSGA Laboratory of Taste and Olfaction University Bourgogne Franche‐Comté Dijon France
| | - Pål Stenmark
- Department of Biochemistry and Biophysics Stockholm University Sweden
- Department of Experimental Medical Science Lund University Sweden
| | - Bengt Mannervik
- Department of Biochemistry and Biophysics Stockholm University Sweden
| |
Collapse
|
25
|
Saa JM, Frontera A. On the Role of Water as a Catalyst in Prebiotic Chemistry. Chemphyschem 2020; 21:313-320. [PMID: 31904135 DOI: 10.1002/cphc.201901069] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/17/2019] [Indexed: 12/20/2022]
Abstract
In this manuscript we provide computational support to the catalytic role of water in all kinds of pseudopericyclic reactions operating in the reductive acid cycle, as well as in other metabolic processes. Water catalysis is not limited to those reactions where simple translocation of hydrogen atoms occurs, such as those represented by NuH+E→Nu-EH general equation. Indeed, water catalysis is more general and extremely important in tautomerization reactions of the type HX-Y=Z→X=Y-ZH, which operate in the reductive citric acid cycle and metabolic processes. Moreover, the comprehensive theoretical study reported herein illustrates that these reactions appear to behave as authentic enzyme-catalyzed reactions showing Michaelis-Menten behavior, however with the abnormal singularity that the concentration of the catalytic "water clusters" of different length and nature must be taken as a huge number. Overall, the results presented are suggestive of the workability of the so-called "metabolism first" proposal in a hot water world, as water catalysis eliminates the dilution problem frequently associated to this proposal.
Collapse
Affiliation(s)
- José M Saa
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), SPAIN
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca (Baleares), SPAIN
| |
Collapse
|
26
|
Bearne SL. The role of Brønsted base basicity in estimating carbon acidity at enzyme active sites: a caveat. Org Biomol Chem 2019; 17:7161-7165. [PMID: 31317156 DOI: 10.1039/c9ob00863b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many enzymes catalyze the abstraction of a proton from a carbon acid substrate to initiate a variety of reactions; however, the development of a complete quantitative description of enzyme-catalyzed heterolytic cleavage of a C-H bond remains a challenge to enzymologists. To determine the pK value for such substrates bound at the active site, recent studies have estimated the equilibrium for formation of the deprotonated intermediate at the active site, however, accurate knowledge of the pK of the conjugate acid of the Brønsted base catalyst (BH+) is also required. Herein, it is shown that using the value of pK of the enzyme-substrate complex can underestimate the value of pK by an amount between zero and pδ, where pδ is the change in basicity of BH+ upon going from the enzyme-substrate complex to the enzyme-intermediate complex.
Collapse
Affiliation(s)
- Stephen L Bearne
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada. and Department of Chemistry, Dalhousie University, Halifax, NS B3H 4R2, Canada
| |
Collapse
|
27
|
Long T, Hassan A, Thompson BM, McDonald JG, Wang J, Li X. Structural basis for human sterol isomerase in cholesterol biosynthesis and multidrug recognition. Nat Commun 2019; 10:2452. [PMID: 31165728 PMCID: PMC6549186 DOI: 10.1038/s41467-019-10279-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 04/30/2019] [Indexed: 12/28/2022] Open
Abstract
3-β-hydroxysteroid-Δ8, Δ7-isomerase, known as Emopamil-Binding Protein (EBP), is an endoplasmic reticulum membrane protein involved in cholesterol biosynthesis, autophagy, oligodendrocyte formation. The mutation on EBP can cause Conradi-Hunermann syndrome, an inborn error. Interestingly, EBP binds an abundance of structurally diverse pharmacologically active compounds, causing drug resistance. Here, we report two crystal structures of human EBP, one in complex with the anti-breast cancer drug tamoxifen and the other in complex with the cholesterol biosynthesis inhibitor U18666A. EBP adopts an unreported fold involving five transmembrane-helices (TMs) that creates a membrane cavity presenting a pharmacological binding site that accommodates multiple different ligands. The compounds exploit their positively-charged amine group to mimic the carbocationic sterol intermediate. Mutagenesis studies on specific residues abolish the isomerase activity and decrease the multidrug binding capacity. This work reveals the catalytic mechanism of EBP-mediated isomerization in cholesterol biosynthesis and how this protein may act as a multi-drug binder.
Collapse
Affiliation(s)
- Tao Long
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Abdirahman Hassan
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Bonne M Thompson
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jeffrey G McDonald
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Center for Human Nutrition, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jiawei Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| |
Collapse
|
28
|
Viljanto MJ, Kicman AT, Walker CJ, Parkin MC, Wolff K, Pearce CM, Scarth J. Elucidation of the biosynthetic pathways of boldenone in the equine testis. Steroids 2019; 146:79-91. [PMID: 30951760 DOI: 10.1016/j.steroids.2019.03.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 03/20/2019] [Accepted: 03/26/2019] [Indexed: 11/28/2022]
Abstract
Boldenone is an anabolic-androgenic steroid that is prohibited in equine sports. Urine from the uncastrated male horse contains boldenone that is thought to be of endogenous origin and thus a threshold ('cut-off') concentration has been adopted internationally for free and conjugated boldenone to help distinguish cases of doping from its natural production. The testis is likely to be a source of boldenone. Qualitative analysis was performed on extracts of equine testicular homogenates (n = 3 horses) incubated non-spiked and in the presence of its potential precursors using liquid chromatography tandem mass spectrometry (LC-MS/MS) and LC high resolution mass spectrometry (LC-HRMS). Samples were analysed both underivatised and derivatised to increase the certainty of identification. In addition to previously reported endogenous steroids, analysis of non-spiked testicular tissue samples demonstrated the presence of boldenone and boldienone at trace levels in the equine testis. Incubation of homogenates with deuterium or carbon isotope labelled testosterone and androstenedione resulted in the matching stable isotope analogues of boldenone and boldienone being formed. Additionally, deuterium and carbon labelled 2-hydroxyandrostenedione was detected, raising the possibility that this steroid is a biosynthetic intermediate. In conclusion, boldenone and boldienone are naturally present in the equine testis, with the biosynthesis of these steroids arising from the conversion of testosterone and androstenedione. However, additional work employing larger numbers of animals, further enzyme kinetic experiments and pure reference standards for 2-OH androstenedione isomers would be required to better characterize the pathways involved in these transformations.
Collapse
Affiliation(s)
- Marjaana J Viljanto
- LGC, Fordham, Cambridgeshire, UK; Drug Control Centre, Department of Analytical, Environmental and Forensic Sciences, King's College London, UK.
| | - Andrew T Kicman
- Drug Control Centre, Department of Analytical, Environmental and Forensic Sciences, King's College London, UK
| | - Christopher J Walker
- Drug Control Centre, Department of Analytical, Environmental and Forensic Sciences, King's College London, UK
| | - Mark C Parkin
- Drug Control Centre, Department of Analytical, Environmental and Forensic Sciences, King's College London, UK; Eurofins Forensic Services, Teddington, London, UK
| | - Kim Wolff
- Drug Control Centre, Department of Analytical, Environmental and Forensic Sciences, King's College London, UK
| | | | | |
Collapse
|
29
|
Dastmalchi M, Chen X, Hagel JM, Chang L, Chen R, Ramasamy S, Yeaman S, Facchini PJ. Neopinone isomerase is involved in codeine and morphine biosynthesis in opium poppy. Nat Chem Biol 2019; 15:384-390. [DOI: 10.1038/s41589-019-0247-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 02/11/2019] [Indexed: 11/09/2022]
|
30
|
Abstract
![]()
The enormous rate accelerations observed
for many enzyme catalysts
are due to strong stabilizing interactions between the protein and
reaction transition state. The defining property of these catalysts
is their specificity for binding the transition state with a much
higher affinity than substrate. Experimental results are presented
which show that the phosphodianion-binding energy of phosphate monoester
substrates is used to drive conversion of their protein catalysts
from flexible and entropically rich ground states to stiff and catalytically
active Michaelis complexes. These results are generalized to other
enzyme-catalyzed reactions. The existence of many enzymes in flexible,
entropically rich, and inactive ground states provides a mechanism
for utilization of ligand-binding energy to mold these catalysts into
stiff and active forms. This reduces the substrate-binding energy
expressed at the Michaelis complex, while enabling the full and specific
expression of large transition-state binding energies. Evidence is
presented that the complexity of enzyme conformational changes increases
with increases in the enzymatic rate acceleration. The requirement
that a large fraction of the total substrate-binding energy be utilized
to drive conformational changes of floppy enzymes is proposed to favor
the selection and evolution of protein folds with multiple flexible
unstructured loops, such as the TIM-barrel fold. The effect of protein
motions on the kinetic parameters for enzymes that undergo ligand-driven
conformational changes is considered. The results of computational
studies to model the complex ligand-driven conformational change in
catalysis by triosephosphate isomerase are presented.
Collapse
Affiliation(s)
- John P Richard
- Department of Chemistry , SUNY, University at Buffalo , Buffalo , New York 14260-3000 , United States
| |
Collapse
|
31
|
An Ab Initio QM/MM Study of the Electrostatic Contribution to Catalysis in the Active Site of Ketosteroid Isomerase. Molecules 2018; 23:molecules23102410. [PMID: 30241317 PMCID: PMC6222312 DOI: 10.3390/molecules23102410] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 01/28/2023] Open
Abstract
The electric field in the hydrogen-bond network of the active site of ketosteroid isomerase (KSI) has been experimentally measured using vibrational Stark effect (VSE) spectroscopy, and utilized to study the electrostatic contribution to catalysis. A large gap was found in the electric field between the computational simulation based on the Amber force field and the experimental measurement. In this work, quantum mechanical (QM) calculations of the electric field were performed using an ab initio QM/MM molecular dynamics (MD) simulation and electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. Our results demonstrate that the QM-derived electric field based on the snapshots from QM/MM MD simulation could give quantitative agreement with the experiment. The accurate calculation of the electric field inside the protein requires both the rigorous sampling of configurations, and a QM description of the electrostatic field. Based on the direct QM calculation of the electric field, we theoretically confirmed that there is a linear correlation relationship between the activation free energy and the electric field in the active site of wild-type KSI and its mutants (namely, D103N, Y16S, and D103L). Our study presents a computational protocol for the accurate simulation of the electric field in the active site of the protein, and provides a theoretical foundation that supports the link between electric fields and enzyme catalysis.
Collapse
|
32
|
|
33
|
Viljanto M, Hincks P, Hillyer L, Cawley A, Suann C, Noble G, Walker CJ, Parkin MC, Kicman AT, Scarth J. Monitoring dehydroepiandrosterone (DHEA) in the urine of Thoroughbred geldings for doping control purposes. Drug Test Anal 2018; 10:1518-1527. [PMID: 29797687 DOI: 10.1002/dta.2411] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 05/12/2018] [Accepted: 05/12/2018] [Indexed: 01/01/2023]
Abstract
The use of testosterone and its pro-drugs, such as dehydroepiandrosterone (DHEA), is currently regulated in horseracing by the application of international testosterone thresholds. However, additional steroidomic approaches, such as steroid ratios, to distinguish overall adrenal stimulation from drug administrations and an equine biological passport for longitudinal steroid profiling of individual animals could be advantageous in equine doping testing. Thus, DHEA concentrations and related ratios (testosterone [T] to DHEA and DHEA to epitestosterone [E]) were assessed in the reference population by quantitative analysis of 200 post-race gelding urine samples using liquid chromatography-tandem mass spectrometry. DHEA concentrations ranged between 0.9 and 136.6 ng/mL (mean 12.8 ng/mL), T:DHEA ratios between 0.06 and 1.85 (mean 0.43), and DHEA:E ratios between 0.21 and 13.56 (mean 2.20). Based on the reference population statistical upper limits of 5.4 for T:DHEA ratio and 48.1 for DHEA:E ratio are proposed with a risk of 1 in 10 000 for a normal outlier exceeding the value. Analysis of post-administration urine samples collected following administrations of DHEA, Equi-Bolic® (a mix of DHEA and pregnenolone) and testosterone propionate to geldings showed that the upper limit for T:DHEA ratio was exceeded following testosterone propionate administration and DHEA:E ratio following DHEA administrations and thus these ratios could be used as additional biomarkers when determining the cause of an atypical testosterone concentration. Additionally, DHEA concentrations and ratios can be used as a starting point to establish reference ranges for an equine biological passport.
Collapse
Affiliation(s)
- Marjaana Viljanto
- LGC, Fordham, Cambridgeshire, UK.,Drug Control Centre, Analytical and Environmental Sciences Research Divisions, King's College London, UK
| | | | - Lynn Hillyer
- The Turf Club, The Curragh, Kildare, Co Kildare, Ireland
| | | | | | - Glenys Noble
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - Christopher J Walker
- Drug Control Centre, Analytical and Environmental Sciences Research Divisions, King's College London, UK
| | - Mark C Parkin
- Drug Control Centre, Analytical and Environmental Sciences Research Divisions, King's College London, UK
| | - Andrew T Kicman
- Drug Control Centre, Analytical and Environmental Sciences Research Divisions, King's College London, UK
| | | |
Collapse
|
34
|
Currin A, Dunstan MS, Johannissen LO, Hollywood KA, Vinaixa M, Jervis AJ, Swainston N, Rattray NJW, Gardiner JM, Kell DB, Takano E, Toogood HS, Scrutton NS. Engineering the "Missing Link" in Biosynthetic (-)-Menthol Production: Bacterial Isopulegone Isomerase. ACS Catal 2018; 8:2012-2020. [PMID: 29750129 PMCID: PMC5937688 DOI: 10.1021/acscatal.7b04115] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/15/2018] [Indexed: 12/28/2022]
Abstract
![]()
The
realization of a synthetic biology approach to microbial (1R,2S,5R)-(−)-menthol (1) production relies on the identification
of a gene encoding an isopulegone isomerase (IPGI), the only enzyme
in the Mentha piperita biosynthetic
pathway as yet unidentified. We demonstrate that Δ5-3-ketosteroid
isomerase (KSI) from Pseudomonas putida can act as an IPGI, producing (R)-(+)-pulegone
((R)-2) from (+)-cis-isopulegone (3). Using a robotics-driven semirational
design strategy, we identified a key KSI variant encoding four active
site mutations, which confer a 4.3-fold increase in activity over
the wild-type enzyme. This was assisted by the generation of crystal
structures of four KSI variants, combined with molecular modeling
of 3 binding to identify key active site residue targets.
The KSI variant was demonstrated to function efficiently within cascade
biocatalytic reactions with downstream Mentha enzymes pulegone reductase and (−)-menthone:(−)-menthol
reductase to generate 1 from 3. This study
introduces the use of a recombinant IPGI, engineered to function efficiently
within a biosynthetic pathway for the production of 1 in microorganisms.
Collapse
|
35
|
Abstract
In recent years, there has been much discussion regarding the origin of enzymatic catalysis and whether including protein dynamics is necessary for understanding catalytic enhancement. An important contribution in this debate was made with the application of the vibrational Stark effect spectroscopy to measure electric fields in the active site. This provided a window on electric fields at the transition state in enzymatic reactions. We performed computational studies on two enzymes where we have shown that fast dynamics is part of the reaction mechanism and calculated the electric field near the bond-breaking event. We found that the fast motions that we had identified lead to an increase of the electric field, thus preparing an enzymatic configuration that is electrostatically favorable for the catalytic chemical step. We also studied the enzyme that has been the subject of Stark spectroscopy, ketosteroid isomerase, and found electric fields of a similar magnitude to the two previous examples.
Collapse
|
36
|
Wang L, Fried SD, Markland TE. Proton Network Flexibility Enables Robustness and Large Electric Fields in the Ketosteroid Isomerase Active Site. J Phys Chem B 2017; 121:9807-9815. [DOI: 10.1021/acs.jpcb.7b06985] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Lu Wang
- Department
of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Stephen D. Fried
- Medical Research
Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Thomas E. Markland
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| |
Collapse
|
37
|
Wu CH, Ito K, Buytendyk AM, Bowen KH, Wu JI. Enormous Hydrogen Bond Strength Enhancement through π-Conjugation Gain: Implications for Enzyme Catalysis. Biochemistry 2017. [PMID: 28635262 DOI: 10.1021/acs.biochem.7b00395] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Surprisingly large resonance-assistance effects may explain how some enzymes form extremely short, strong hydrogen bonds to stabilize reactive oxyanion intermediates and facilitate catalysis. Computational models for several enzymic residue-substrate interactions reveal that when a π-conjugated, hydrogen bond donor (XH) forms a hydrogen bond to a charged substrate (Y-), XH can become significantly more π-electron delocalized, and this "extra" stabilization may boost the [XH···Y-] hydrogen bond strength by ≥15 kcal/mol. This reciprocal relationship departs from the widespread pKa concept (i.e., the idea that short, strong hydrogen bonds form when the interacting moieties have matching pKa values), which has been the rationale for enzymic acid-base reactions. The findings presented here provide new insight into how short, strong hydrogen bonds could form in enzymes.
Collapse
Affiliation(s)
- Chia-Hua Wu
- Department of Chemistry, University of Houston , Houston, Texas 77204, United States
| | | | - Allyson M Buytendyk
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - K H Bowen
- Department of Chemistry, Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Judy I Wu
- Department of Chemistry, University of Houston , Houston, Texas 77204, United States
| |
Collapse
|
38
|
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.
Collapse
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;
| |
Collapse
|
39
|
Mota SF, Oliveira DF, Heleno VCG, Soares ACF, Midiwo JO, Souza EA. Methyl and p-Bromobenzyl Esters of Hydrogenated Kaurenoic Acid for Controlling Anthracnose in Common Bean Plants. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:1489-1495. [PMID: 28161946 DOI: 10.1021/acs.jafc.6b05159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Kaurenoic acid derivatives were prepared and submitted to in vitro assays with the fungus Colletotrichum lindemuthianum, which causes anthracnose disease in the common bean. The most active substances were found to be methyl and p-bromobenzylesters, 7 and 9, respectively, of the hydrogenated kaurenoic acid, which presented a minimum inhibitory concentration (MIC) of 0.097 and 0.131 mM, respectively, while the commercial fungicide methyl thiophanate (MT) presented a MIC of 0.143 mM. Substances 7 (1.401 mM) and 9 (1.886 mM) reduced the severity of anthracnose in common bean to values statistically comparable to MT (2.044 mM). According to an in silico study, both compounds 7 and 9 are inhibitors of the ketosteroid isomerase (KSI) enzyme produced by other organisms, the amino acid sequence of which could be detected in fungal genomes. These substances appeared to act against C. lindemuthianum by inhibiting its KSI. Therefore, substances 7 and 9 are promising for the development of new fungicides.
Collapse
Affiliation(s)
- Suellen F Mota
- Departamento de Biologia, Universidade Federal de Lavras , Lavras, MG CEP 37.200-000, Brazil
| | - Denilson F Oliveira
- Departamento de Química, Universidade Federal de Lavras , Lavras, MG CEP 37.200-000, Brazil
| | - Vladimir C G Heleno
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca , Franca, SP CEP 14.404-600, Brazil
| | - Ana Carolina F Soares
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca , Franca, SP CEP 14.404-600, Brazil
| | - Jacob O Midiwo
- Department of Chemistry, University of Nairobi , Nairobi 00100, Kenya
| | - Elaine A Souza
- Departamento de Biologia, Universidade Federal de Lavras , Lavras, MG CEP 37.200-000, Brazil
| |
Collapse
|
40
|
Lamba V, Sanchez E, Fanning LR, Howe K, Alvarez MA, Herschlag D, Forconi M. Kemp Eliminase Activity of Ketosteroid Isomerase. Biochemistry 2017; 56:582-591. [PMID: 28045505 DOI: 10.1021/acs.biochem.6b00762] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Kemp eliminases represent the most successful class of computationally designed enzymes, with rate accelerations of up to 109-fold relative to the rate of the same reaction in aqueous solution. Nevertheless, several other systems such as micelles, catalytic antibodies, and cavitands are known to accelerate the Kemp elimination by several orders of magnitude. We found that the naturally occurring enzyme ketosteroid isomerase (KSI) also catalyzes the Kemp elimination. Surprisingly, mutations of D38, the residue that acts as a general base for its natural substrate, produced variants that catalyze the Kemp elimination up to 7000-fold better than wild-type KSI does, and some of these variants accelerate the Kemp elimination more than the computationally designed Kemp eliminases. Analysis of the D38N general base KSI variant suggests that a different active site carboxylate residue, D99, performs the proton abstraction. Docking simulations and analysis of inhibition by active site binders suggest that the Kemp elimination takes place in the active site of KSI and that KSI uses the same catalytic strategies of the computationally designed enzymes. In agreement with prior observations, our results strengthen the conclusion that significant rate accelerations of the Kemp elimination can be achieved with very few, nonspecific interactions with the substrate if a suitable catalytic base is present in a hydrophobic environment. Computational design can fulfill these requirements, and the design of more complex and precise environments represents the next level of challenges for protein design.
Collapse
Affiliation(s)
- Vandana Lamba
- Department of Biochemistry, Stanford University , Stanford, California 94305, United States
| | - Enis Sanchez
- Department of Chemistry and Biochemistry, College of Charleston , Charleston, South Carolina 29424, United States
| | - Lauren Rose Fanning
- Department of Chemistry and Biochemistry, College of Charleston , Charleston, South Carolina 29424, United States
| | - Kathryn Howe
- Palmetto Homeschool Association , Rock Hill, South Carolina 29730, United States
| | | | - Daniel Herschlag
- Department of Biochemistry, Stanford University , Stanford, California 94305, United States.,Department of Chemistry, Department of Chemical Engineering, and Stanford ChEM-H, Stanford University , Stanford, California 94305, United States
| | - Marcello Forconi
- Department of Chemistry and Biochemistry, College of Charleston , Charleston, South Carolina 29424, United States
| |
Collapse
|
41
|
Welsch R, Driscoll E, Dawlaty JM, Miller TF. Molecular Seesaw: How Increased Hydrogen Bonding Can Hinder Excited-State Proton Transfer. J Phys Chem Lett 2016; 7:3616-3620. [PMID: 27556887 DOI: 10.1021/acs.jpclett.6b01391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A previously unexplained effect in the relative rate of excited-state intramolecular proton transfer (ESIPT) in related indole derivatives is investigated using both theory and experiment. Ultrafast spectroscopy [ J. Phys. Chem. A, 2015, 119, 5618-5625 ] found that although the diol 1,3-bis(2-pyridylimino)-4,7-dihydroxyisoindole exhibits two equivalent intramolecular hydrogen bonds, the ESIPT rate associated with tautomerization of either hydrogen bond is a factor of 2 slower than that of the single intramolecular hydrogen bond in the ethoxy-ol 1,3-bis(2-pyridylimino)-4-ethoxy-7-hydroxyisoindole. Excited-state electronic structure calculations suggest a resolution to this puzzle by revealing a seesaw effect in which the two hydrogen bonds of the diol are both longer than the single hydrogen bond in the ethoxy-ol. Semiclassical rate theory recovers the previously unexplained trends and leads to clear predictions regarding the relative H/D kinetic isotope effect (KIE) for ESIPT in the two systems. The theoretical KIE predictions are tested using ultrafast spectroscopy, confirming the seesaw effect.
Collapse
Affiliation(s)
- Ralph Welsch
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| | - Eric Driscoll
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-1062, United States
| | - Jahan M Dawlaty
- Department of Chemistry, University of Southern California , Los Angeles, California 90089-1062, United States
| | - Thomas F Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology , 1200 East California Blvd., Pasadena, California 91125, United States
| |
Collapse
|
42
|
Wu Y, Boxer SG. A Critical Test of the Electrostatic Contribution to Catalysis with Noncanonical Amino Acids in Ketosteroid Isomerase. J Am Chem Soc 2016; 138:11890-5. [PMID: 27545569 PMCID: PMC5063566 DOI: 10.1021/jacs.6b06843] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The vibrational Stark effect (VSE) has been used to measure the electric field in the active site of ketosteroid isomerase (KSI). These measured fields correlate with ΔG(⧧) in a series of conventional mutants, yielding an estimate for the electrostatic contribution to catalysis (Fried et al. Science 2014, 346, 1510-1513). In this work we test this result with much more conservative variants in which individual Tyr residues in the active site are replaced by 3-chlorotyrosine via amber suppression. The electric fields sensed at the position of the carbonyl bond involved in charge displacement during catalysis were characterized using the VSE, where the field sensitivity has been calibrated by vibrational Stark spectroscopy, solvatochromism, and MD simulations. A linear relationship is observed between the electric field and ΔG(⧧) that interpolates between wild-type and more drastic conventional mutations, reinforcing the evaluation of the electrostatic contribution to catalysis in KSI. A simplified model and calculation are developed to estimate changes in the electric field accompanying changes in the extended hydrogen-bond network in the active site. The results are consistent with a model in which the O-H group of a key active site tyrosine functions by imposing a static electrostatic potential onto the carbonyl bond. The model suggests that the contribution to catalysis from the active site hydrogen bonds is of similar weight to the distal interactions from the rest of the protein. A similar linear correlation was also observed between the proton affinity of KSI's active site and the catalytic rate, suggesting a direct connection between the strength of the H-bond and the electric field it exerts.
Collapse
Affiliation(s)
- Yufan Wu
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University , Stanford, California 94305-5012, United States
| |
Collapse
|
43
|
Fryszkowska A, Peterson J, Davies NL, Dewar C, Evans G, Bycroft M, Triggs N, Fleming T, Gorantla SSC, Hoge G, Quirmbach M, Timmanna U, Reddy Poreddy S, Kumar Reddy DN, Dahanukar V, Holt-Tiffin KE. Development of a Chemoenzymatic Process for Dehydroepiandrosterone Acetate Synthesis. Org Process Res Dev 2016. [DOI: 10.1021/acs.oprd.6b00215] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anna Fryszkowska
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Justine Peterson
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Nichola L. Davies
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Colin Dewar
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - George Evans
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Matthew Bycroft
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Neil Triggs
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Toni Fleming
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | | | - Garrett Hoge
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| | - Michael Quirmbach
- Dr. Reddy’s Laboratories SA Elisabethenanlage, 11CH-4051 Basel, Switzerland
| | - Upadhya Timmanna
- Custom
Pharmaceutical Services, Dr. Reddy’s Laboratories Ltd, Bollaram
Road, Miyapur, Hyderabad 500049, India
| | - Srinivas Reddy Poreddy
- Custom
Pharmaceutical Services, Dr. Reddy’s Laboratories Ltd, Bollaram
Road, Miyapur, Hyderabad 500049, India
| | - D. Naresh Kumar Reddy
- Custom
Pharmaceutical Services, Dr. Reddy’s Laboratories Ltd, Bollaram
Road, Miyapur, Hyderabad 500049, India
| | - Vilas Dahanukar
- Custom
Pharmaceutical Services, Dr. Reddy’s Laboratories Ltd, Bollaram
Road, Miyapur, Hyderabad 500049, India
| | - Karen E. Holt-Tiffin
- Chirotech
Technology Centre, Dr. Reddy’s Laboratories EU Ltd., 410 Cambridge
Science Park, Cambridge CB4 0PE, United Kingdom
| |
Collapse
|
44
|
Cha HJ, Jang DS, Jeong JH, Hong BH, Yun YS, Shin EJ, Choi KY. Role of conserved Met112 residue in the catalytic activity and stability of ketosteroid isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:1322-7. [PMID: 27375051 DOI: 10.1016/j.bbapap.2016.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2016] [Revised: 06/11/2016] [Accepted: 06/29/2016] [Indexed: 10/21/2022]
Abstract
Ketosteroid isomerase (3-oxosteroid Δ(5)-Δ(4)-isomerase, KSI) from Pseudomonas putida catalyzes allylic rearrangement of the 5,6-double bond of Δ(5)-3-ketosteroid to 4,5-position by stereospecific intramolecular transfer of a proton. The active site of KSI is formed by several hydrophobic residues and three catalytic residues (Tyr14, Asp38, and Asp99). In this study, we investigated the role of a hydrophobic Met112 residue near the active site in the catalysis, steroid binding, and stability of KSI. Replacing Met112 with alanine (yields M112A) or leucine (M112L) decreased the kcat by 20- and 4-fold, respectively. Compared with the wild type (WT), M112A and M112L KSIs showed increased KD values for equilenin, an intermediate analogue; these changes suggest that loss of packing at position 112 might lead to unfavorable steroid binding, thereby resulting in decreased catalytic activity. Furthermore, M112A and M112L mutations reduced melting temperature (Tm) by 6.4°C and 2.5°C, respectively. These changes suggest that favorable packing in the core is important for the maintenance of stability in KSI. The M112K mutation decreased kcat by 2000-fold, compared with the WT. In M112K KSI structure, a new salt bridge was formed between Asp38 and Lys112. This bridge could change the electrostatic potential of Asp38, and thereby contribute to the decreased catalytic activity. The M112K mutation also decreased the stability by reducing Tm by 4.1°C. Our data suggest that the Met112 residue may contribute to the catalytic activity and stability of KSI by providing favorable hydrophobic environments and compact packing in the catalytic core.
Collapse
Affiliation(s)
- Hyung Jin Cha
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Do Soo Jang
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Jae-Hee Jeong
- Pohang Accelerator Laboratory, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Bee Hak Hong
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Young Sung Yun
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea
| | - Eun Ju Shin
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea
| | - Kwan Yong Choi
- Department of Life Sciences, POSTECH, Pohang, Republic of Korea.
| |
Collapse
|
45
|
Pupo G, Properzi R, List B. Asymmetric Catalysis with CO2 : The Direct α-Allylation of Ketones. Angew Chem Int Ed Engl 2016; 55:6099-102. [PMID: 27071633 DOI: 10.1002/anie.201601545] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Indexed: 11/10/2022]
Abstract
Quaternary stereocenters are found in numerous bioactive molecules. The Tsuji-Trost reaction has proven to be a powerful C-C bond forming process, and, at least in principle, should be well suited to access quaternary stereocenters via the α-allylation of ketones. However, while indirect approaches are known, the direct, catalytic asymmetric α-allylation of branched ketones has been elusive until today. By combining "enol catalysis" with the use of CO2 as a formal catalyst for asymmetric catalysis, we have now developed a solution to this problem: we report a direct, highly enantioselective and highly atom-economic Tsuji-Trost allylation of branched ketones with allylic alcohol. Our reaction delivers products bearing quaternary stereocenters with high enantioselectivity and water as the sole by-product. We expect our methodology to be of utility in asymmetric catalysis and inspire the design of other highly atom-economic transformations.
Collapse
Affiliation(s)
- Gabriele Pupo
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Roberta Properzi
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany
| | - Benjamin List
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470, Mülheim an der Ruhr, Germany.
| |
Collapse
|
46
|
Pupo G, Properzi R, List B. Asymmetrische Katalyse mit CO
2
: Die direkte α‐Allylierung von Ketonen. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201601545] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Gabriele Pupo
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - Roberta Properzi
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| | - Benjamin List
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr Deutschland
| |
Collapse
|
47
|
Meitinger N, Munkert J, Maia de Pádua R, de Souza Filho JD, Maid H, Bauer W, Braga FC, Kreis W. The catalytic mechanism of the 3-ketosteroid isomerase of Digitalis lanata involves an intramolecular proton transfer and the activity is not associated with the 3β-hydroxysteroid dehydrogenase activity. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.02.099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
48
|
Tolosa S, Hidalgo A, Sansón JA. Theoretical study of enzymatically catalyzed tautomerization of carbon acids in aqueous solution: quantum calculations and steered molecular dynamics simulations. J Mol Model 2016; 22:44. [PMID: 26815031 DOI: 10.1007/s00894-016-2914-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 01/11/2016] [Indexed: 10/22/2022]
Abstract
The thermodynamics and kinetics of enzymatically assisted reactions of carbon acids were studied theoretically in this work. Quantum electronic (QE) structure calculations and steered molecular dynamics (SMD) simulations were carried out. Three 3-butenal tautomerization reactions that proceed from the β,γ-unsaturated reactant (R) to the α,β-unsaturated carbon acid product (P) and occur in two elementary steps through an intermediate (I) were studied, ignoring or including the surrounding aqueous medium in the calculations. The Gibbs free energies of activation of the R ⇆ I enolization and I ⇆ P ketonization steps were found to decrease considerably when residues simulating enzymes were introduced into these processes. Although the processes became slightly more favorable thermodynamically when the solution was included in the simulations, they became less favorable kinetically. The results from SMD simulations of these reactions were qualitatively consistent with the values we obtained using QE as well as those found by other authors in similar studies. Our simulations also allowed us to perform a detailed study of these reactions in solution.
Collapse
Affiliation(s)
- Santiago Tolosa
- Departamento de Ingeniería Química y Química Física, Universidad de Extremadura, Avda. Elvas s/n, 06071, Badajoz, Spain.
| | - Antonio Hidalgo
- Departamento de Ingeniería Química y Química Física, Universidad de Extremadura, Avda. Elvas s/n, 06071, Badajoz, Spain
| | - Jorge A Sansón
- Departamento de Ingeniería Química y Química Física, Universidad de Extremadura, Avda. Elvas s/n, 06071, Badajoz, Spain
| |
Collapse
|
49
|
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.
Collapse
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
| |
Collapse
|
50
|
Lindemann P. Steroidogenesis in plants--Biosynthesis and conversions of progesterone and other pregnane derivatives. Steroids 2015; 103:145-52. [PMID: 26282543 DOI: 10.1016/j.steroids.2015.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 07/03/2015] [Accepted: 08/06/2015] [Indexed: 01/23/2023]
Abstract
In plants androstanes, estranes, pregnanes and corticoids have been described. Sometimes 17β-estradiol, androsterone, testosterone or progesterone were summarized as sex hormones. These steroids influence plant development: cell divisions, root and shoot growth, embryo growth, flowering, pollen tube growth and callus proliferation. First reports on the effect of applicated substances and of their endogenous occurrence date from the early twenties of the last century. This caused later on doubts on the identity of the compounds. Best investigated is the effect of progesterone. Main steps of the progesterone biosynthetic pathway have been analyzed in Digitalis. Cholesterol-side-chain-cleavage, pregnenolone and progesterone formation as well as the stereospecific reduction of progesterone are described and the corresponding enzymes are presented. Biosynthesis of androstanes, estranes and corticoids is discussed. Possible progesterone receptors and physiological reactions on progesterone application are reviewed.
Collapse
Affiliation(s)
- Peter Lindemann
- Institut für Pharmazie, Martin-Luther Universität Halle/Wittenberg, Hoher Weg 8, 06120 Halle, Germany.
| |
Collapse
|