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Welborn VV, Head-Gordon T. Fluctuations of Electric Fields in the Active Site of the Enzyme Ketosteroid Isomerase. J Am Chem Soc 2019; 141:12487-12492. [DOI: 10.1021/jacs.9b05323] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Valerie Vaissier Welborn
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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Peng F, Cheng X, Wang H, Song S, Chen T, Li X, He Y, Huang Y, Liu S, Yang F, Su Z. Structure-based reconstruction of a Mycobacterium hypothetical protein into an active Δ 5-3-ketosteroid isomerase. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:821-830. [PMID: 31226491 DOI: 10.1016/j.bbapap.2019.06.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 06/12/2019] [Accepted: 06/14/2019] [Indexed: 11/25/2022]
Abstract
Protein engineering based on structure homology holds the potential to engineer steroid-transforming enzymes on demand. Based on the genome sequencing analysis of industrial Mycobacterium strain HGMS2 to produce 4-androstene-3,17-dione (4-AD), three hypothetical proteins were predicted as putative Δ5-3-ketosteroid isomerases (KSIs) to catalyze an intramolecular proton transfer involving the transformation of 5-androstene-3,17-dione (5-AD) into 4-AD, which were defined as mKSI228, mKSI291 and mKSI753. Activity assays indicated that mKSI228 and mKSI291 exhibited weak activity, as low as 0.7% and 1.5%, respectively, of a well-studied and highly active KSI from Pseudomonas putida KSI (pKSI), while mKSI753 had no activity similar to Mycobacterium tuberculosis KSI (mtKSI). Although the 3D structures of the putative mKSIs were homologous to pKSI, their amino acid sequences were significantly different from those of pKSI and tKSI. Thus, by use of these two KSIs as homology models, we were able to convert the low-active mKSI291 into a high-active active KSI by site-directed mutagenesis. On the other hand, an X-ray crystallographic structure of mKSI291 identified a water molecule in its active site. This unique water molecule might function as a bridge to connect Ser-OH, Tyr57-OH and C3O of the intermediate form a hydrogen-bonding network that was responsible for its weak activity, compared with that of mtKSI. Our results not only demonstrated the use of a protein engineering approach to understanding KSI catalytic mechanism, but also provided an example for engineering the catalytic active sites and gaining a functional enzyme based on homologous structures.
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Affiliation(s)
- Fei Peng
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Xiyao Cheng
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China; Wuhan Amersino Biodevelop Inc, B1-Building, Biolake Park, Wuhan 430075, China
| | - Hongwei Wang
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Shikui Song
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Tian Chen
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Xin Li
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Yijun He
- Hubei Goto Biotech Inc, No. 1 Baiguoshu Road, Shuidu Industrial Park, Danjiangkou, Hubei 442700, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Sen Liu
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China
| | - Fei Yang
- College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), National "111" Center for Cellular Regulation and Molecular Pharmaceutics and Department of Biological and Food Engineering, Hubei University of Technology, Wuhan 430068, China; Wuhan Amersino Biodevelop Inc, B1-Building, Biolake Park, Wuhan 430075, China.
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Samet M, Kass SR. Preorganized Hydrogen Bond Donor Catalysts: Acidities and Reactivities. J Org Chem 2015; 80:7727-31. [DOI: 10.1021/acs.joc.5b01475] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Masoud Samet
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Steven R. Kass
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Schwans JP, Hanoian P, Lengerich BJ, Sunden F, Gonzalez A, Tsai Y, Hammes-Schiffer S, Herschlag D. Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site. Biochemistry 2014; 53:2541-55. [PMID: 24597914 PMCID: PMC4004248 DOI: 10.1021/bi401671t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The
positioning of catalytic groups within proteins plays an important
role in enzyme catalysis, and here we investigate the positioning
of the general base in the enzyme ketosteroid isomerase (KSI). The
oxygen atoms of Asp38, the general base in KSI, were previously shown
to be involved in anion–aromatic interactions with two neighboring
Phe residues. Here we ask whether those interactions are sufficient,
within the overall protein architecture, to position Asp38 for catalysis
or whether the side chains that pack against Asp38 and/or the residues
of the structured loop that is capped by Asp38 are necessary to achieve
optimal positioning for catalysis. To test positioning, we mutated
each of the aforementioned residues, alone and in combinations, in
a background with the native Asp general base and in a D38E mutant
background, as Glu at position 38 was previously shown to be mispositioned
for general base catalysis. These double-mutant cycles reveal positioning
effects as large as 103-fold, indicating that structural
features in addition to the overall protein architecture and the Phe
residues neighboring the carboxylate oxygen atoms play roles in positioning.
X-ray crystallography and molecular dynamics simulations suggest that
the functional effects arise from both restricting dynamic fluctuations
and disfavoring potential mispositioned states. Whereas it may have
been anticipated that multiple interactions would be necessary for
optimal general base positioning, the energetic contributions from
positioning and the nonadditive nature of these interactions are not
revealed by structural inspection and require functional dissection.
Recognizing the extent, type, and energetic interconnectivity of interactions
that contribute to positioning catalytic groups has implications for
enzyme evolution and may help reveal the nature and extent of interactions
required to design enzymes that rival those found in biology.
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Affiliation(s)
- Jason P Schwans
- Department of Biochemistry, Stanford University , B400 Beckman Center, 279 Campus Drive, Stanford, California 94305, United States
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Thermodynamic framework for identifying free energy inventories of enzyme catalytic cycles. Proc Natl Acad Sci U S A 2013; 110:12271-6. [PMID: 23840058 DOI: 10.1073/pnas.1310964110] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Pauling's suggestion that enzymes are complementary in structure to the activated complexes of the reactions they catalyze has provided the conceptual basis to explain how enzymes obtain their fantastic catalytic prowess, and has served as a guiding principle in drug design for over 50 y. However, this model by itself fails to predict the magnitude of enzymes' rate accelerations. We construct a thermodynamic framework that begins with the classic concept of differential binding but invokes additional terms that are needed to account for subtle effects in the catalytic cycle's proton inventory. Although the model presented can be applied generally, this analysis focuses on ketosteroid isomerase (KSI) as an example, where recent experiments along with a large body of kinetic and thermodynamic data have provided strong support for the noncanonical thermodynamic contribution described. The resulting analysis precisely predicts the free energy barrier of KSI's reaction as determined from transition-state theory using only empirical thermodynamic data. This agreement is suggestive that a complete free energy inventory of the KSI catalytic cycle has been identified.
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Layfield JP, Hammes-Schiffer S. Calculation of vibrational shifts of nitrile probes in the active site of ketosteroid isomerase upon ligand binding. J Am Chem Soc 2012; 135:717-25. [PMID: 23210919 DOI: 10.1021/ja3084384] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The vibrational Stark effect provides insight into the roles of hydrogen bonding, electrostatics, and conformational motions in enzyme catalysis. In a recent application of this approach to the enzyme ketosteroid isomerase (KSI), thiocyanate probes were introduced in site-specific positions throughout the active site. This paper implements a quantum mechanical/molecular mechanical (QM/MM) approach for calculating the vibrational shifts of nitrile (CN) probes in proteins. This methodology is shown to reproduce the experimentally measured vibrational shifts upon binding of the intermediate analogue equilinen to KSI for two different nitrile probe positions. Analysis of the molecular dynamics simulations provides atomistic insight into the roles that key residues play in determining the electrostatic environment and hydrogen-bonding interactions experienced by the nitrile probe. For the M116C-CN probe, equilinen binding reorients an active-site water molecule that is directly hydrogen-bonded to the nitrile probe, resulting in a more linear C≡N--H angle and increasing the CN frequency upon binding. For the F86C-CN probe, equilinen binding orients the Asp103 residue, decreasing the hydrogen-bonding distance between the Asp103 backbone and the nitrile probe and slightly increasing the CN frequency. This QM/MM methodology is applicable to a wide range of biological systems and has the potential to assist in the elucidation of the fundamental principles underlying enzyme catalysis.
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Affiliation(s)
- Joshua P Layfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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Jha SK, Ji M, Gaffney KJ, Boxer SG. Site-specific measurement of water dynamics in the substrate pocket of ketosteroid isomerase using time-resolved vibrational spectroscopy. J Phys Chem B 2012; 116:11414-21. [PMID: 22931297 DOI: 10.1021/jp305225r] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Little is known about the reorganization capacity of water molecules at the active sites of enzymes and how this couples to the catalytic reaction. Here, we study the dynamics of water molecules at the active site of a highly proficient enzyme, Δ(5)-3-ketosteroid isomerase (KSI), during a light-activated mimic of its catalytic cycle. Photoexcitation of a nitrile-containing photoacid, coumarin183 (C183), mimics the change in charge density that occurs at the active site of KSI during the first step of the catalytic reaction. The nitrile of C183 is exposed to water when bound to the KSI active site, and we used time-resolved vibrational spectroscopy as a site-specific probe to study the solvation dynamics of water molecules in the vicinity of the nitrile. We observed that water molecules at the active site of KSI are highly rigid, during the light-activated catalytic cycle, compared to the solvation dynamics observed in bulk water. On the basis of this result, we hypothesize that rigid water dipoles at the active site might help in the maintenance of the preorganized electrostatic environment required for efficient catalysis. The results also demonstrate the utility of nitrile probes in measuring the dynamics of local (H-bonded) water molecules in contrast to the commonly used fluorescence methods which measure the average behavior of primary and subsequent spheres of solvation.
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Affiliation(s)
- Santosh Kumar Jha
- Department of Chemistry, Stanford University, Stanford, California 94305-5012, USA
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