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Mahrooz A. Pleiotropic functions and clinical importance of circulating HDL-PON1 complex. Adv Clin Chem 2024; 121:132-171. [PMID: 38797541 DOI: 10.1016/bs.acc.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
High density lipoprotein (HDL) functions are mostly mediated through a complex proteome, particularly its enzymes. HDL can provide a scaffold for the assembly of several proteins that affect each other's function. HDL particles, particularly small, dense HDL3, are rich in paraoxonase 1 (PON1), which is an important enzyme in the functionality of HDL, so the antioxidant and antiatherogenic properties of HDL are largely attributed to this enzyme. There is an increasing need to represent a valid, reproducible, and reliable method to assay HDL function in routine clinical laboratories. In this context, HDL-associated proteins may be key players; notably PON1 activity (its arylesterase activity) may be a proper candidate because its decreased activity can be considered an important risk factor for HDL dysfunctionality. Of note, automated methods have been developed for the measurement of serum PON1 activity that facilitates its assay in large sample numbers. Arylesterase activity is proposed as a preferred activity among the different activities of PON1 for its assay in epidemiological studies. The binding of PON1 to HDL is critical for the maintenance of its activity and it appears apolipoprotein A-I plays an important role in HDL-PON1 interaction as well as in the biochemical and enzymatic properties of PON1. The interrelationships between HDL, PON1, and HDL's other components are complex and incompletely understood. The purpose of this review is to discuss biochemical and clinical evidence considering the interactions of PON1 with HDL and the role of this enzyme as an appropriate biomarker for HDL function as well as a potential therapeutic target.
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Affiliation(s)
- Abdolkarim Mahrooz
- Immunogenetics Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Department of Clinical Biochemistry and Medical Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
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2
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Corbella M, Bravo J, Demkiv AO, Calixto AR, Sompiyachoke K, Bergonzi C, Elias MH, Kamerlin SCL. Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592096. [PMID: 38746346 PMCID: PMC11092605 DOI: 10.1101/2024.05.01.592096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N- acyl-L-homoserine lactones (AHLs). In doing so, they play a role in a microbial communication system, quorum sensing, which contributes to pathogenicity and biofilm formation. There is currently great interest in designing quorum quenching ( QQ ) enzymes that can interfere with this communication and be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific targets requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of the MLL GcL, which is highly proficient, thermostable, and has broad substrate specificity. Strikingly, we show that GcL does not only accept a broad range of substrates but is also capable of utilizing different reaction mechanisms that are differentially used in function of the substrate structure or the remodeling of the active site via mutations. Comparison of GcL to other lactonases such as AiiA and AaL demonstrates similar mechanistic promiscuity, suggesting this is a shared feature across lactonases in this enzyme family. Mechanistic promiscuity has previously been observed in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general-acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and an engineering perspective: in addition to optimizing for specific substrates, it is possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes, but also of other mechanistically promiscuous enzymes.
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3
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Kunachowicz D, Ściskalska M, Kepinska M. Modulatory Effect of Lifestyle-Related, Environmental and Genetic Factors on Paraoxonase-1 Activity: A Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:2813. [PMID: 36833509 PMCID: PMC9957543 DOI: 10.3390/ijerph20042813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Paraoxonase-1 (PON1) is a calcium-dependent, HDL-bound serum hydrolase active toward a wide variety of substrates. PON1 displays three types of activities, among which lactonase, paraoxonase, arylesterase and phosphotriesterase can be distinguished. Not only is this enzyme a major organophosphate compound detoxifier, but it is also an important constituent of the cellular antioxidant system and has anti-inflammatory and antiatherogenic functions. The concentration and activity of PON1 is highly variable among individuals, and these differences can be both of genetic origin and be a subject of epigenetic regulation. Owing to the fact that, in recent decades, the exposure of humans to an increasing number of different xenobiotics has been continuously rising, the issues concerning the role and activity of PON1 shall be reconsidered with particular attention to growing pharmaceuticals intake, dietary habits and environmental awareness. In the following manuscript, the current state of knowledge concerning the influence of certain modifiable and unmodifiable factors, including smoking, alcohol intake, gender, age and genotype variation on PON1 activity, along with pathways through which these could interfere with the enzyme's protective functions, is presented and discussed. Since exposure to certain xenobiotics plays a key role in PON1 activity, the influence of organophosphates, heavy metals and several pharmaceutical agents is also specified.
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Affiliation(s)
| | | | - Marta Kepinska
- Department of Pharmaceutical Biochemistry, Division of Biomedical and Environmental Sciences, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50–556 Wrocław, Poland
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4
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Shen R, Crean RM, Olsen KJ, Corbella M, Calixto AR, Richan T, Brandão TAS, Berry RD, Tolman A, Loria JP, Johnson SJ, Kamerlin SCL, Hengge AC. Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases. Chem Sci 2022; 13:13524-13540. [PMID: 36507179 PMCID: PMC9682893 DOI: 10.1039/d2sc04135a] [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: 07/24/2022] [Accepted: 10/25/2022] [Indexed: 12/15/2022] Open
Abstract
Protein tyrosine phosphatases (PTPs) possess a conserved mobile catalytic loop, the WPD-loop, which brings an aspartic acid into the active site where it acts as an acid/base catalyst. Prior experimental and computational studies, focused on the human enzyme PTP1B and the PTP from Yersinia pestis, YopH, suggested that loop conformational dynamics are important in regulating both catalysis and evolvability. We have generated a chimeric protein in which the WPD-loop of YopH is transposed into PTP1B, and eight chimeras that systematically restored the loop sequence back to native PTP1B. Of these, four chimeras were soluble and were subjected to detailed biochemical and structural characterization, and a computational analysis of their WPD-loop dynamics. The chimeras maintain backbone structural integrity, with somewhat slower rates than either wild-type parent, and show differences in the pH dependency of catalysis, and changes in the effect of Mg2+. The chimeric proteins' WPD-loops differ significantly in their relative stability and rigidity. The time required for interconversion, coupled with electrostatic effects revealed by simulations, likely accounts for the activity differences between chimeras, and relative to the native enzymes. Our results further the understanding of connections between enzyme activity and the dynamics of catalytically important groups, particularly the effects of non-catalytic residues on key conformational equilibria.
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Affiliation(s)
- Ruidan Shen
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Rory M. Crean
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden
| | - Keith J. Olsen
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Marina Corbella
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden
| | - Ana R. Calixto
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden
| | - Teisha Richan
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Tiago A. S. Brandão
- Departamento de Química, ICEX, Universidade Federal de Minas GeraisBelo HorizonteMinas Gerais31270-901Brazil
| | - Ryan D. Berry
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Alex Tolman
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - J. Patrick Loria
- Department of Chemistry, Yale University225 Prospect StreetNew HavenCT 06520USA,Department of Molecular Biophysics and Biochemistry, Yale University266 Whitney AvenueNew HavenCT 06520USA
| | - Sean J. Johnson
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
| | - Shina C. L. Kamerlin
- Science for Life Laboratory, Department of Chemistry – BMC, Uppsala University, BMCBox 576S-751 23 UppsalaSweden,School of Chemistry and Biochemistry, Georgia Institute of Technology901 Atlantic Drive NWAtlanta, GA 30332-0400USA
| | - Alvan C. Hengge
- Department of Chemistry and Biochemistry, Utah State UniversityLoganUtah 84322-0300USA
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5
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Romsuk J, Yasumoto S, Seki H, Fukushima EO, Muranaka T. Identification of key amino acid residues toward improving the catalytic activity and substrate specificity of plant-derived cytochrome P450 monooxygenases CYP716A subfamily enzyme for triterpenoid production in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2022; 10:955650. [PMID: 36061436 PMCID: PMC9437279 DOI: 10.3389/fbioe.2022.955650] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/26/2022] [Indexed: 12/14/2022] Open
Abstract
Triterpenoids constitute a group of specialized plant metabolites with wide structural diversity and high therapeutic value for human health. Cytochrome P450 monooxygenases (CYP) are a family of enzymes important for generating the structural diversity of triterpenoids by catalyzing the site-specific oxidization of the triterpene backbone. The CYP716 enzyme family has been isolated from various plant families as triterpenoid oxidases; however, their experimental crystal structures are not yet available and the detailed catalytic mechanism remains elusive. Here, we address this challenge by integrating bioinformatics approaches with data from other CYP families. Medicago truncatula CYP716A12, the first functionally characterized CYP716A subfamily enzyme, was chosen as the model for this study. We performed homology modeling, structural alignment, in silico site-directed mutagenesis, and molecular docking analysis to search and screen key amino acid residues relevant to the catalytic activity and substrate specificity of the CYP716A subfamily enzyme in triterpenoid biosynthesis. An in vivo functional analysis using engineered yeast that endogenously produced plant-derived triterpenes was performed to elucidate the results. When the amino acids in the signature region and substrate recognition sites (SRSs) were substituted, the product profile of CYP716A12 was modified. We identified amino acid residues that control the substrate contraction of the enzyme (D292) and engineered the enzyme to improve its catalytic activity and substrate specificity (D122, I212, and Q358) for triterpenoid biosynthesis. In addition, we demonstrated the versatility of this strategy by changing the properties of key residues in SRSs to improve the catalytic activity of Arabidopsis thaliana CYP716A1 (S356) and CYP716A2 (M206, F210) at C-28 on the triterpene backbone. This research has the potential to help in the production of desired triterpenoids in engineered yeast by increasing the catalytic activity and substrate specificity of plant CYP716A subfamily enzymes.
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Affiliation(s)
- Jutapat Romsuk
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
| | - Shuhei Yasumoto
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Hikaru Seki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
| | - Ery Odette Fukushima
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Plant Traslational Research Group, Universidad Regional Amazónica IKIAM, Tena, Ecuador
- *Correspondence: Ery Odette Fukushima, ; Toshiya Muranaka,
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Osaka, Japan
- Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- *Correspondence: Ery Odette Fukushima, ; Toshiya Muranaka,
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6
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Yang Z, Hajlasz N, Kulik HJ. Computational Modeling of Conformer Stability in Benenodin-1, a Thermally Actuated Lasso Peptide Switch. J Phys Chem B 2022; 126:3398-3406. [PMID: 35481742 DOI: 10.1021/acs.jpcb.2c00762] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Benenodin-1 is a thermally actuated lasso peptide rotaxane switch with two primary translational isomers that differ in the relative position of the residue Gln15. The conversion from one conformer to the other involves substantial enthalpy-entropy compensation: one conformer is energetically favored and the other is entropically favored. Here, we take a multi-scale quantum mechanical (QM) and classical molecular dynamic (MD) approach to reveal residue-specific sources of these differences in stability. QM reveals that the two benenodin-1 conformers involve distinct hydrogen bonding networks, with the enthalpically favored conformer having more intra-peptide hydrogen bonds between the Gln15 side chain and nearby residues. The evaluation of configurational entropy over the MD-sampled geometries reveals that the entropically favored conformer has enhanced conformational flexibility. By computing the by-residue-sum entropies, we identify the role of Gln15 and neighboring Glu14 in mediating the entropic variation during the switching process. These computational insights help explain the effects of Glu14Ala and Gln15Ala mutations on the conformational population of benenodin-1 observed experimentally.
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Affiliation(s)
- Zhongyue Yang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Natalia Hajlasz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Heather J Kulik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Romero-Rivera A, Corbella M, Parracino A, Patrick WM, Kamerlin SCL. Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (βα) 8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis. JACS AU 2022; 2:943-960. [PMID: 35557756 PMCID: PMC9088769 DOI: 10.1021/jacsau.2c00063] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 05/16/2023]
Abstract
Enzymes are conformationally dynamic, and their dynamical properties play an important role in regulating their specificity and evolvability. In this context, substantial attention has been paid to the role of ligand-gated conformational changes in enzyme catalysis; however, such studies have focused on tremendously proficient enzymes such as triosephosphate isomerase and orotidine 5'-monophosphate decarboxylase, where the rapid (μs timescale) motion of a single loop dominates the transition between catalytically inactive and active conformations. In contrast, the (βα)8-barrels of tryptophan and histidine biosynthesis, such as the specialist isomerase enzymes HisA and TrpF, and the bifunctional isomerase PriA, are decorated by multiple long loops that undergo conformational transitions on the ms (or slower) timescale. Studying the interdependent motions of multiple slow loops, and their role in catalysis, poses a significant computational challenge. This work combines conventional and enhanced molecular dynamics simulations with empirical valence bond simulations to provide rich details of the conformational behavior of the catalytic loops in HisA, PriA, and TrpF, and the role of their plasticity in facilitating bifunctionality in PriA and evolved HisA variants. In addition, we demonstrate that, similar to other enzymes activated by ligand-gated conformational changes, loops 3 and 4 of HisA and PriA act as gripper loops, facilitating the isomerization of the large bulky substrate ProFAR, albeit now on much slower timescales. This hints at convergent evolution on these different (βα)8-barrel scaffolds. Finally, our work reemphasizes the potential of engineering loop dynamics as a tool to artificially manipulate the catalytic repertoire of TIM-barrel proteins.
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Affiliation(s)
- Adrian Romero-Rivera
- Department
of Chemistry—BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Marina Corbella
- Department
of Chemistry—BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Antonietta Parracino
- Department
of Chemistry—BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Wayne M. Patrick
- Centre
for Biodiscovery, School of Biological Sciences, Victoria University of Wellington, 6012 Wellington, New Zealand
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8
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Abstract
The use of biological enzyme catalysts could have huge ramifications for chemical industries. However, these enzymes are often inactive in nonbiological conditions, such as high temperatures, present in industrial settings. Here, we show that the enzyme PETase (polyethylene terephthalate [PET]), with potential application in plastic recycling, is stabilized at elevated temperature through complexation with random copolymers. We demonstrate this through simulations and experiments on different types of substrates. Our simulations also provide strategies for designing more enzymatically active complexes by altering polymer composition and enzyme charge distribution. Engineered and native enzymes are poised to solve challenges in medicine, bioremediation, and biotechnology. One important goal is the possibility of upcycling polymers using enzymes. However, enzymes are often inactive in industrial, nonbiological conditions. It is particularly difficult to protect water-soluble enzymes at elevated temperatures by methods that preserve their functionality. Through atomistic and coarse-grained molecular dynamics simulations that capture protein conformational change, we show that an enzyme, PETase (polyethylene terephthalate [PET]), can be stabilized at elevated temperatures by complexation with random copolymers into nanoscale aggregates that do not precipitate into macroscopic phases. We demonstrated the efficiency of the method by simulating complexes of random copolymers and the enzyme PETase, which depolymerizes PET, a highly used polymer. These polymers are more industrially viable than peptides and can target specific domains on an enzyme. We design the mean composition of the random copolymers to control the polymer–enzyme surface contacts and the polymer conformation. When positioned on or near the active site, these polymer contacts can further stabilize the conformation of the active site at elevated temperatures. We explore the experimental implications of this active site stabilization method and show that PETase-random copolymer complexes have enhanced activity on both small molecule substrates and solid PET films. These results provide guidelines for engineering enzyme–polymer complexes with enhanced enzyme functionality in nonbiological environments.
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9
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10
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Fu Y, Zhang Y, Fan F, Wang B, Cao Z. Degradation of pesticides diazinon and diazoxon by phosphotriesterase: insight into divergent mechanisms from QM/MM and MD simulations. Phys Chem Chem Phys 2022; 24:687-696. [PMID: 34927643 DOI: 10.1039/d1cp05034f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Enzymatic hydrolysis by phosphotriesterase (PTE) is one of the most effective ways of degrading organophosphorus pesticides, but the catalytic efficiency depends on the structural features of substrates. Here the enzymatic degradation of diazinon (DIN) and diazoxon (DON), characterized by PS and PO, respectively, have been investigated by QM/MM calculations and MM MD simulations. Our calculations demonstrate that the hydrolysis of DON (with PO) is inevitably initiated by the nucleophilic attack of the bridging-OH- on the phosphorus center, while for DIN (with PS), we proposed a new degradation mechanism, initiated by the nucleophilic attack of the Znα-bound water molecule, for its low-energy pathway. For both DIN and DON, the hydrolytic reaction is predicted to be the rate-limiting step, with energy barriers of 18.5 and 17.7 kcal mol-1, respectively. The transportation of substrates to the active site, the release of the leaving group and the degraded product are generally verified to be favorable by MD simulations via umbrella sampling, both thermodynamically and dynamically. The side-chain residues Phe132, Leu271 and Tyr309 play the gate-switching role to manipulate substrate delivery and product release. In comparison with the DON-enzyme system, the degraded product of DIN is more easily released from the active site. These new findings will contribute to the comprehensive understanding of the enzymatic degradation of toxic organophosphorus compounds by PTE.
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Affiliation(s)
- Yuzhuang Fu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Yuwei Zhang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Fangfang Fan
- School of Biological and Chemical Engineering, Zhejiang University of Science and Technology, Hangzhou, 310023, China.
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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Faisal AJ, Said LA, Ali MR. Quorum quenching effect of recombinant Paraoxonase-1 enzyme against quorum sensing genes produced from Pseudomonas aeruginosa. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Singh A, Gao M, Beck MW. Human carboxylesterases and fluorescent probes to image their activity in live cells. RSC Med Chem 2021; 12:1142-1153. [PMID: 34355180 PMCID: PMC8292992 DOI: 10.1039/d1md00073j] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 04/26/2021] [Indexed: 12/12/2022] Open
Abstract
Human carboxylesterases (CESs) are serine hydrolases that are responsible for the phase I metabolism of an assortment of ester, amide, thioester, carbonate, and carbamate containing drugs. CES activity is known to be influenced by a variety of factors including single nucleotide polymorphisms, alternative splicing, and drug-drug interactions. These different factors contribute to interindividual variability of CES activity which has been demonstrated to influence clinical outcomes among people treated with CES-substrate therapeutics. Detailed exploration of the factors that influence CES activity is emerging as an important area of research. The use of fluorescent probes with live cell imaging techniques can selectively visualize the real-time activity of CESs and have the potential to be useful tools to help reveal the impacts of CES activity variations on human health. This review summarizes the properties of the five known human CESs including factors reported to or that could potentially influence their activity before discussing the design aspects and use considerations of CES fluorescent probes in general in addition to highlighting several well-characterized probes.
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Affiliation(s)
- Anchal Singh
- Department of Chemistry and Biochemistry, Eastern Illinois University Charleston IL 61920 USA +1 217 581 6227
| | - Mingze Gao
- Department of Biological Sciences, Eastern Illinois University Charleston IL 61920 USA
| | - Michael W Beck
- Department of Chemistry and Biochemistry, Eastern Illinois University Charleston IL 61920 USA +1 217 581 6227
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Xu W, Zhao S, Zhang W, Wu H, Guang C, Mu W. Recent advances and future prospective of organophosphorus-degrading enzymes: identification, modification, and application. Crit Rev Biotechnol 2021; 41:1096-1113. [PMID: 33906533 DOI: 10.1080/07388551.2021.1898331] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The organophosphorus-based OPs) nerve agents and pesticides have been applied in the agriculture industry for a long time. However, they were found to have a persistent effect on the environment and threaten human health. Traditional methods, including incineration and landfilling, could not thoroughly remove these organophosphorus compounds (OPs). Meanwhile, chemical hydrolysis for decontamination was also inhibited due to the presence of corrosive materials and high costs. Biological remediation for OPs employing microorganisms and organophosphorus-degrading enzymes is promising due to a mild and controllable procedure, environmental-friendly reactions, and high efficacy. A wide variety of enzymes have shown latent ability in degrading OPs hazards like organophosphorus hydrolase (OPH), organophosphorus acid anhydrolase (OPAA), the diisopropylfluorophosphatase (DFPase), and mammalian paraoxonase 1 (PON 1). To this end, increasing efforts have been made on these intriguing enzymes to increase their expression level, enhance the catalytic activity, modify the optimal substrate, and expand the practical application. In this review, the enzyme resource, crystal structure, molecular modification, and industry application were compared and discussed in detail. Moreover, the proposed ideas and positive results could be useful for the other relevant OPs-degrading enzymes.
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Affiliation(s)
- Wei Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Sumao Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Hao Wu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Cuie Guang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
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14
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Singh A, Saini S, Mayank, Kaur N, Singh A, Singh N, Jang DO. Paraoxonase Mimic by a Nanoreactor Aggregate Containing Benzimidazolium Calix and l-Histidine: Demonstration of the Acetylcholine Esterase Activity. Chemistry 2021; 27:5737-5744. [PMID: 33350530 DOI: 10.1002/chem.202004944] [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: 11/13/2020] [Indexed: 11/09/2022]
Abstract
An anion-mediated preorganization approach was used to design and synthesize the benzimidazolium-based calix compound R1⋅2 ClO4 - . X-ray crystallography analysis revealed that the hydrogen-bonding interactions between the benzimidazolium cations and N,N-dimethylformamide (DMF) helped R1⋅2 ClO4 - encapsulate DMF molecule(s). A nanoreactor, with R1⋅2 ClO4 - and l-histidine (l-His) as the components, was fabricated by using a neutralization method. The nanoreactor could detoxify paraoxon in 30 min. l-His played a vital role in this process. Paraoxonase is a well-known enzyme used for pesticide degradation. The Ellman's reagent was used to determine the percentage inhibition of the acetylcholinesterase (AChE) activity in the presence of the nanoreactor. The results indicated that the nanoreactor inhibited AChE inhibition.
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Affiliation(s)
- Amanpreet Singh
- Department of Chemistry, Indian Institute of Technology Ropar, Roopnagar, Punjab, 140001, India
| | - Sanjeev Saini
- Department of Chemistry, Indian Institute of Technology Ropar, Roopnagar, Punjab, 140001, India
| | - Mayank
- Department of Chemistry, Indian Institute of Technology Ropar, Roopnagar, Punjab, 140001, India
| | - Navneet Kaur
- Department of Chemistry, Panjab University, Chandigarh, 160014, India
| | - Ajnesh Singh
- Department of Applied Sciences & Humanities, Jawaharlal Nehru Govt. Eng. College, Sundernagar, 175018, India
| | - Narinder Singh
- Department of Chemistry, Indian Institute of Technology Ropar, Roopnagar, Punjab, 140001, India
| | - Doo Ok Jang
- Department of Chemistry, Yonsei University, Wonju, 26493, Republic of Korea
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15
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Crean RM, Biler M, van der Kamp MW, Hengge AC, Kamerlin SCL. Loop Dynamics and Enzyme Catalysis in Protein Tyrosine Phosphatases. J Am Chem Soc 2021; 143:3830-3845. [PMID: 33661624 PMCID: PMC8031367 DOI: 10.1021/jacs.0c11806] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Indexed: 12/16/2022]
Abstract
Protein tyrosine phosphatases (PTPs) play an important role in cellular signaling and have been implicated in human cancers, diabetes, and obesity. Despite shared catalytic mechanisms and transition states for the chemical steps of catalysis, catalytic rates within the PTP family vary over several orders of magnitude. These rate differences have been implied to arise from differing conformational dynamics of the closure of a protein loop, the WPD-loop, which carries a catalytically critical residue. The present work reports computational studies of the human protein tyrosine phosphatase 1B (PTP1B) and YopH from Yersinia pestis, for which NMR has demonstrated a link between their respective rates of WPD-loop motion and catalysis rates, which differ by an order of magnitude. We have performed detailed structural analysis, both conventional and enhanced sampling simulations of their loop dynamics, as well as empirical valence bond simulations of the chemical step of catalysis. These analyses revealed the key residues and structural features responsible for these differences, as well as the residues and pathways that facilitate allosteric communication in these enzymes. Curiously, our wild-type YopH simulations also identify a catalytically incompetent hyper-open conformation of its WPD-loop, sampled as a rare event, previously only experimentally observed in YopH-based chimeras. The effect of differences within the WPD-loop and its neighboring loops on the modulation of loop dynamics, as revealed in this work, may provide a facile means for the family of PTP enzymes to respond to environmental changes and regulate their catalytic activities.
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Affiliation(s)
- Rory M. Crean
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| | - Michal Biler
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
| | - Marc W. van der Kamp
- School
of Biochemistry, University of Bristol, Biomedical Sciences Building, University
Walk, Bristol BS8 1TD, United Kingdom
| | - Alvan C. Hengge
- Department
of Chemistry and Biochemistry, Utah State
University, Logan, Utah 84322-0300, United States
| | - Shina C. L. Kamerlin
- Science
for Life Laboratory, Department of Chemistry − BMC, Uppsala University, Box 576, S-751 23 Uppsala, Sweden
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16
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Rational protein engineering of α-L-arabinofuranosidase from Aspergillus niger for improved catalytic hydrolysis efficiency on kenaf hemicellulose. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.12.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Mhashal AR, Major DT. Temperature-Dependent Kinetic Isotope Effects in R67 Dihydrofolate Reductase from Path-Integral Simulations. J Phys Chem B 2021; 125:1369-1377. [PMID: 33522797 PMCID: PMC7883348 DOI: 10.1021/acs.jpcb.0c10318] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/05/2021] [Indexed: 11/28/2022]
Abstract
Calculation of temperature-dependent kinetic isotope effects (KIE) in enzymes presents a significant theoretical challenge. Additionally, it is not trivial to identify enzymes with available experimental accurate intrinsic KIEs in a range of temperatures. In the current work, we present a theoretical study of KIEs in the primitive R67 dihydrofolate reductase (DHFR) enzyme and compare with experimental work. The advantage of R67 DHFR is its significantly lower kinetic complexity compared to more evolved DHFR isoforms. We employ mass-perturbation-based path-integral simulations in conjunction with umbrella sampling and a hybrid quantum mechanics-molecular mechanics Hamiltonian. We obtain temperature-dependent KIEs in good agreement with experiments and ascribe the temperature-dependent KIEs primarily to zero-point energy effects. The active site in the primitive enzyme is found to be poorly preorganized, which allows excessive water access to the active site and results in loosely bound reacting ligands.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Dan Thomas Major
- Department of Chemistry and Institute
for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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18
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From Ru-bda to Ru-bds: a step forward to highly efficient molecular water oxidation electrocatalysts under acidic and neutral conditions. Nat Commun 2021; 12:373. [PMID: 33446649 PMCID: PMC7809030 DOI: 10.1038/s41467-020-20637-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 12/14/2020] [Indexed: 11/09/2022] Open
Abstract
Significant advances during the past decades in the design and studies of Ru complexes with polypyridine ligands have led to the great development of molecular water oxidation catalysts and understanding on the O−O bond formation mechanisms. Here we report a Ru-based molecular water oxidation catalyst [Ru(bds)(pic)2] (Ru-bds; bds2− = 2,2′-bipyridine-6,6′-disulfonate) containing a tetradentate, dianionic sulfonate ligand at the equatorial position and two 4-picoline ligands at the axial positions. This Ru-bds catalyst electrochemically catalyzes water oxidation with turnover frequencies (TOF) of 160 and 12,900 s−1 under acidic and neutral conditions respectively, showing much better performance than the state-of-art Ru-bda catalyst. Density functional theory calculations reveal that (i) under acidic conditions, the high valent Ru intermediate RuV=O featuring the 7-coordination configuration is involved in the O−O bond formation step; (ii) under neutral conditions, the seven-coordinate RuIV=O triggers the O−O bond formation; (iii) in both cases, the I2M (interaction of two M−O units) pathway is dominant over the WNA (water nucleophilic attack) pathway. Developing efficient molecular water oxidation catalysts for artificial photosynthesis is a challenging task. Here the authors introduce a ruthenium based complex with negatively charged sulfonate groups to effectively drive water oxidation under both acidic and neutral conditions.
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19
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Development of metallosupramolecular phosphatases based on the combinatorial self-assembly of metal complexes and organic building blocks for the catalytic hydrolysis of phosphate monoesters. RESULTS IN CHEMISTRY 2021. [DOI: 10.1016/j.rechem.2021.100133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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20
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Biler M, Crean RM, Schweiger AK, Kourist R, Kamerlin SCL. Ground-State Destabilization by Active-Site Hydrophobicity Controls the Selectivity of a Cofactor-Free Decarboxylase. J Am Chem Soc 2020; 142:20216-20231. [PMID: 33180505 PMCID: PMC7735706 DOI: 10.1021/jacs.0c10701] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Indexed: 01/11/2023]
Abstract
Bacterial arylmalonate decarboxylase (AMDase) and evolved variants have become a valuable tool with which to access both enantiomers of a broad range of chiral arylaliphatic acids with high optical purity. Yet, the molecular principles responsible for the substrate scope, activity, and selectivity of this enzyme are only poorly understood to date, greatly hampering the predictability and design of improved enzyme variants for specific applications. In this work, empirical valence bond and metadynamics simulations were performed on wild-type AMDase and variants thereof to obtain a better understanding of the underlying molecular processes determining reaction outcome. Our results clearly reproduce the experimentally observed substrate scope and support a mechanism driven by ground-state destabilization of the carboxylate group being cleaved by the enzyme. In addition, our results indicate that, in the case of the nonconverted or poorly converted substrates studied in this work, increased solvent exposure of the active site upon binding of these substrates can disturb the vulnerable network of interactions responsible for facilitating the AMDase-catalyzed cleavage of CO2. Finally, our results indicate a switch from preferential cleavage of the pro-(R) to the pro-(S) carboxylate group in the CLG-IPL variant of AMDase for all substrates studied. This appears to be due to the emergence of a new hydrophobic pocket generated by the insertion of the six amino acid substitutions, into which the pro-(S) carboxylate binds. Our results allow insight into the tight interaction network determining AMDase selectivity, which in turn provides guidance for the identification of target residues for future enzyme engineering.
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Affiliation(s)
- Michal Biler
- Department
of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Rory M. Crean
- Department
of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Anna K. Schweiger
- Institute
of Molecular Biotechnology, Graz University
of Technology, NAWI Graz,
Petersgasse 14, 8010 Graz, Austria
| | - Robert Kourist
- Institute
of Molecular Biotechnology, Graz University
of Technology, NAWI Graz,
Petersgasse 14, 8010 Graz, Austria
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21
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Mhashal AR, Romero-Rivera A, Mydy LS, Cristobal JR, Gulick AM, Richard JP, Kamerlin SCL. Modeling the Role of a Flexible Loop and Active Site Side Chains in Hydride Transfer Catalyzed by Glycerol-3-phosphate Dehydrogenase. ACS Catal 2020; 10:11253-11267. [PMID: 33042609 PMCID: PMC7536716 DOI: 10.1021/acscatal.0c02757] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/31/2020] [Indexed: 11/30/2022]
Abstract
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Glycerol-3-phosphate
dehydrogenase is a biomedically important
enzyme that plays a crucial role in lipid biosynthesis. It is activated
by a ligand-gated conformational change that is necessary for the
enzyme to reach a catalytically competent conformation capable of
efficient transition-state stabilization. While the human form (hlGPDH) has been the subject of extensive structural and
biochemical studies, corresponding computational studies to support
and extend experimental observations have been lacking. We perform
here detailed empirical valence bond and Hamiltonian replica exchange
molecular dynamics simulations of wild-type hlGPDH
and its variants, as well as providing a crystal structure of the
binary hlGPDH·NAD R269A variant where the enzyme
is present in the open conformation. We estimated the activation free
energies for the hydride transfer reaction in wild-type and substituted hlGPDH and investigated the effect of mutations on catalysis
from a detailed structural study. In particular, the K120A and R269A
variants increase both the volume and solvent exposure of the active
site, with concomitant loss of catalytic activity. In addition, the
R269 side chain interacts with both the Q295 side chain on the catalytic
loop, and the substrate phosphodianion. Our structural data and simulations
illustrate the critical role of this side chain in facilitating the
closure of hlGPDH into a catalytically competent
conformation, through modulating the flexibility of a key catalytic
loop (292-LNGQKL-297). This, in turn, rationalizes a tremendous 41,000
fold decrease experimentally in the turnover number, kcat, upon truncating this residue, as loop closure is
essential for both correct positioning of key catalytic residues in
the active site, as well as sequestering the active site from the
solvent. Taken together, our data highlight the importance of this
ligand-gated conformational change in catalysis, a feature that can
be exploited both for protein engineering and for the design of allosteric
inhibitors targeting this biomedically important enzyme.
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Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Adrian Romero-Rivera
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
| | - Lisa S. Mydy
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1121, United States
| | - Judith R. Cristobal
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Andrew M. Gulick
- Department of Structural Biology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203-1121, United States
| | - John P. Richard
- Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States
| | - Shina C. L. Kamerlin
- Department of Chemistry—BMC, Uppsala University, Box 576, Uppsala SE-751 23, Sweden
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22
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Sierra-Campos E, Valdez-Solana M, Avitia-Domínguez C, Campos-Almazán M, Flores-Molina I, García-Arenas G, Téllez-Valencia A. Effects of Moringa oleifera Leaf Extract on Diabetes-Induced Alterations in Paraoxonase 1 and Catalase in Rats Analyzed through Progress Kinetic and Blind Docking. Antioxidants (Basel) 2020; 9:antiox9090840. [PMID: 32911700 PMCID: PMC7555439 DOI: 10.3390/antiox9090840] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 08/18/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023] Open
Abstract
In our study, we aimed to evaluate the effects of Moringa oleifera leaves extract on rat paraoxonase 1 (rPON1) and catalase (rCAT) activities in alloxan-induced diabetic rats. Our study included three groups; group C (control, n = 5); group D (diabetic, n = 5); and group DM (M. oleifera extract-supplemented diabetic rats, n = 5). Daily oral administration of M. oleifera extract at 200 mg/kg doses produced an increase in endogenous antioxidants. Serum rPON1 (lactonase) and liver cytosol catalase activities were determined by a spectrophotometric assay using progress curve analysis. We found a decrease in the Vm value of rPON1 in diabetic rats, but dihydrocoumarin (DHC) affinity (Km) was slightly increased. The value of Vm for the DM group was found to be reduced approximately by a factor of 3 compared with those obtained for group C, whereas Km was largely changed (96 times). Catalase activity was significantly higher in the DM group. These data suggest that the activation of rPON1 and rCAT activities by M. oleifera extracts may be mediated via the effect of the specific flavonoids on the enzyme structure. In addition, through molecular blind docking analysis, rPON1 was found to have two binding sites for flavonoids. In contrast, flavonoids bound at four sites in rCAT. In conclusion, the data suggest that compounds from M. oleifera leaves extract were able to influence the catalytic activities of both enzymes to compensate for the changes provoked by diabetes in rats.
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Affiliation(s)
- Erick Sierra-Campos
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango Campus Gómez Palacio, Avenida Artículo 123 S/N, Fracc, Filadelfia, Gómez Palacio 35010, Mexico; (M.V.-S.); (I.F.-M.)
- Correspondence: (E.S.-C.); (A.T.-V.)
| | - Mónica Valdez-Solana
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango Campus Gómez Palacio, Avenida Artículo 123 S/N, Fracc, Filadelfia, Gómez Palacio 35010, Mexico; (M.V.-S.); (I.F.-M.)
| | - Claudia Avitia-Domínguez
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Avenida Universidad y Fanny Anitúa S/N, Durango 34000, Mexico; (C.A.-D.); (M.C.-A.)
| | - Mara Campos-Almazán
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Avenida Universidad y Fanny Anitúa S/N, Durango 34000, Mexico; (C.A.-D.); (M.C.-A.)
| | - Ismael Flores-Molina
- Facultad de Ciencias Químicas, Universidad Juárez del Estado de Durango Campus Gómez Palacio, Avenida Artículo 123 S/N, Fracc, Filadelfia, Gómez Palacio 35010, Mexico; (M.V.-S.); (I.F.-M.)
| | - Guadalupe García-Arenas
- Facultad de Ciencias de la Salud, Universidad Juárez del Estado de Durango Campus, Gómez Palacio 35010, Mexico;
| | - Alfredo Téllez-Valencia
- Facultad de Medicina y Nutrición, Universidad Juárez del Estado de Durango, Avenida Universidad y Fanny Anitúa S/N, Durango 34000, Mexico; (C.A.-D.); (M.C.-A.)
- Correspondence: (E.S.-C.); (A.T.-V.)
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23
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Prag HA, Kula-Alwar D, Pala L, Caldwell ST, Beach TE, James AM, Saeb-Parsy K, Krieg T, Hartley RC, Murphy MP. Selective Delivery of Dicarboxylates to Mitochondria by Conjugation to a Lipophilic Cation via a Cleavable Linker. Mol Pharm 2020; 17:3526-3540. [PMID: 32692564 PMCID: PMC7482397 DOI: 10.1021/acs.molpharmaceut.0c00533] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
![]()
Many
mitochondrial metabolites and bioactive molecules contain
two carboxylic acid moieties that make them unable to cross biological
membranes. Hence, there is considerable interest in facilitating the
uptake of these molecules into cells and mitochondria to modify or
report on their function. Conjugation to the triphenylphosphonium
(TPP) lipophilic cation is widely used to deliver molecules selectively
to mitochondria in response to the membrane potential. However, permanent
attachment to the cation can disrupt the biological function of small
dicarboxylates. Here, we have developed a strategy using TPP to release
dicarboxylates selectively within mitochondria. For this, the dicarboxylate
is attached to a TPP compound via a single ester bond, which is then
cleaved by intramitochondrial esterase activity, releasing the dicarboxylate
within the organelle. Leaving the second carboxylic acid free also
means mitochondrial uptake is dependent on the pH gradient across
the inner membrane. To assess this strategy, we synthesized a range
of TPP monoesters of the model dicarboxylate, malonate. We then tested
their mitochondrial accumulation and ability to deliver malonate to
isolated mitochondria and to cells, in vitro and in vivo. A TPP–malonate monoester compound, TPP11–malonate, in which the dicarboxylate group was attached
to the TPP compound via a hydrophobic undecyl link, was most effective
at releasing malonate within mitochondria in cells and in
vivo. Therefore, we have developed a TPP–monoester
platform that enables the selective release of bioactive dicarboxylates
within mitochondria.
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Affiliation(s)
- Hiran A Prag
- Molecular Research Center, Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Duvaraka Kula-Alwar
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Laura Pala
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Stuart T Caldwell
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Timothy E Beach
- Department of Surgery, Cambridge National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Andrew M James
- Molecular Research Center, Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, United Kingdom
| | - Kourosh Saeb-Parsy
- Department of Surgery, Cambridge National Institute for Health Research Biomedical Research Centre, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Thomas Krieg
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
| | - Richard C Hartley
- School of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Michael P Murphy
- Molecular Research Center, Mitochondrial Biology Unit, Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, United Kingdom.,Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, United Kingdom
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24
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Crean RM, Gardner JM, Kamerlin SCL. Harnessing Conformational Plasticity to Generate Designer Enzymes. J Am Chem Soc 2020; 142:11324-11342. [PMID: 32496764 PMCID: PMC7467679 DOI: 10.1021/jacs.0c04924] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Indexed: 02/08/2023]
Abstract
Recent years have witnessed an explosion of interest in understanding the role of conformational dynamics both in the evolution of new enzymatic activities from existing enzymes and in facilitating the emergence of enzymatic activity de novo on scaffolds that were previously non-catalytic. There are also an increasing number of examples in the literature of targeted engineering of conformational dynamics being successfully used to alter enzyme selectivity and activity. Despite the obvious importance of conformational dynamics to both enzyme function and evolvability, many (although not all) computational design approaches still focus either on pure sequence-based approaches or on using structures with limited flexibility to guide the design. However, there exist a wide variety of computational approaches that can be (re)purposed to introduce conformational dynamics as a key consideration in the design process. Coupled with laboratory evolution and more conventional existing sequence- and structure-based approaches, these techniques provide powerful tools for greatly expanding the protein engineering toolkit. This Perspective provides an overview of evolutionary studies that have dissected the role of conformational dynamics in facilitating the emergence of novel enzymes, as well as advances in computational approaches that allow one to target conformational dynamics as part of enzyme design. Harnessing conformational dynamics in engineering studies is a powerful paradigm with which to engineer the next generation of designer biocatalysts.
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Affiliation(s)
- Rory M. Crean
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Jasmine M. Gardner
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Department of Chemistry -
BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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25
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Risso VA, Romero-Rivera A, Gutierrez-Rus LI, Ortega-Muñoz M, Santoyo-Gonzalez F, Gavira JA, Sanchez-Ruiz JM, Kamerlin SCL. Enhancing a de novo enzyme activity by computationally-focused ultra-low-throughput screening. Chem Sci 2020; 11:6134-6148. [PMID: 32832059 PMCID: PMC7407621 DOI: 10.1039/d0sc01935f] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 05/18/2020] [Indexed: 01/02/2023] Open
Abstract
Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains sluggish, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib is a novel approach which uses phylogenetic analysis and Rosetta design to rank enzyme variants with multiple mutations, on the basis of predicted stability. Here, we use it to target the active site region of a minimalist-designed, de novo Kemp eliminase. The similarity between the Michaelis complex and transition state for the enzymatic reaction makes this system particularly challenging to optimize. Yet, experimental screening of a small number of active-site variants at the top of the predicted stability ranking leads to catalytic efficiencies and turnover numbers (∼2 × 104 M-1 s-1 and ∼102 s-1) for this anthropogenic reaction that compare favorably to those of modern natural enzymes. This result illustrates the promise of FuncLib as a powerful tool with which to speed up directed evolution, even on scaffolds that were not originally evolved for those functions, by guiding screening to regions of the sequence space that encode stable and catalytically diverse enzymes. Empirical valence bond calculations reproduce the experimental activation energies for the optimized eliminases to within ∼2 kcal mol-1 and indicate that the enhanced activity is linked to better geometric preorganization of the active site. This raises the possibility of further enhancing the stability-guidance of FuncLib by computational predictions of catalytic activity, as a generalized approach for computational enzyme design.
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Affiliation(s)
- Valeria A Risso
- Departamento de Química Física, Facultad de Ciencias , Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , Universidad de Granada , 18071 Granada , Spain .
| | - Adrian Romero-Rivera
- Science for Life Laboratory , Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden .
| | - Luis I Gutierrez-Rus
- Departamento de Química Física, Facultad de Ciencias , Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , Universidad de Granada , 18071 Granada , Spain .
| | - Mariano Ortega-Muñoz
- Departamento de Química Orgánica , Facultad de Ciencias , Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , Universidad de Granada , 18071 Granada , Spain
| | - Francisco Santoyo-Gonzalez
- Departamento de Química Orgánica , Facultad de Ciencias , Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , Universidad de Granada , 18071 Granada , Spain
| | - Jose A Gavira
- Laboratorio de Estudios Cristalográficos , Instituto Andaluz de Ciencias de la Tierra , CSIC, Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , University of Granada , Avenida de las Palmeras 4 , 18100 Armilla , Granada , Spain
| | - Jose M Sanchez-Ruiz
- Departamento de Química Física, Facultad de Ciencias , Unidad de Excelencia de Química aplicada a Biomedicina y Medioambiente (UEQ) , Universidad de Granada , 18071 Granada , Spain .
| | - Shina C L Kamerlin
- Science for Life Laboratory , Department of Chemistry-BMC , Uppsala University , BMC Box 576 , S-751 23 Uppsala , Sweden .
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26
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Gardner JM, Biler M, Risso VA, Sanchez-Ruiz JM, Kamerlin SCL. Manipulating Conformational Dynamics To Repurpose Ancient Proteins for Modern Catalytic Functions. ACS Catal 2020. [DOI: 10.1021/acscatal.0c00722] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jasmine M. Gardner
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Michal Biler
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Valeria A. Risso
- Departamento de Quı́mica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quı́mica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quı́mica Fisica, Facultad de Ciencias, Unidad de Excelencia de Quı́mica Aplicada a Biomedicina y Medioambiente (UEQ), Universidad de Granada, 18071 Granada, Spain
| | - Shina C. L. Kamerlin
- Department of Chemistry - BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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27
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Sriramulu DK, Lee SG. Combinatorial Effect of Ligand and Ligand-Binding Site Hydrophobicities on Binding Affinity. J Chem Inf Model 2020; 60:1678-1684. [PMID: 32108477 DOI: 10.1021/acs.jcim.9b01143] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Computational methods to study protein-ligand interactions at a molecular level have been successful to a certain extent in predicting the pose, atomic interactions, and so forth, but poor efficiency in estimating a protein-ligand binding affinity is still a crucial problem to be solved. Analyzing the protein-ligand interactions quantitatively is one primary concern for understanding. Qualitative analysis of these interactions may lead to better insights about protein-ligand interactions. To perform such an analysis, the macroscopic molecular properties of the protein and ligand can be studied in detail and should be correlated with the ligand-binding affinity. This detailed study can be helpful in designing the ligands and the ligand-binding site as well. In this study, we attempted to identify the hydrophobic/hydrophilic features of a ligand and ligand-binding site and check their correlation with the experimental affinity of the protein-ligand complexes. This combinatorial analysis of ligand log P and binding site hydrophobicity on data set distribution and binding affinity suggested two critical findings. The hydrophobic ligands bind to hydrophilic and hydrophobic pockets equally, whereas hydrophilic ligands are specific to hydrophilic pockets. The combination of the hydrophobic ligand-hydrophobic pocket prefers high-affinity values compared to other combinations. Although these results cannot be used for atomic-level design of ligands or binding sites, they are expected to be used as a reference for screening the ligands for a given target binding site.
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Affiliation(s)
- Dinesh Kumar Sriramulu
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan 609-735, Republic of Korea
| | - Sun-Gu Lee
- Department of Polymer Science and Chemical Engineering, Pusan National University, Busan 609-735, Republic of Korea
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Shokri Y, Variji A, Nosrati M, Khonakdar-Tarsi A, Kianmehr A, Kashi Z, Bahar A, Bagheri A, Mahrooz A. Importance of paraoxonase 1 (PON1) as an antioxidant and antiatherogenic enzyme in the cardiovascular complications of type 2 diabetes: Genotypic and phenotypic evaluation. Diabetes Res Clin Pract 2020; 161:108067. [PMID: 32044348 DOI: 10.1016/j.diabres.2020.108067] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/13/2020] [Accepted: 02/06/2020] [Indexed: 12/12/2022]
Abstract
Oxidant-antioxidant imbalance is involved in the etiology of different diseases, including cardiovascular diseases (CVDs), liver disorders, kidney diseases, cancers and diabetes mellitus. Antioxidant enzymes play a key role in striking an oxidant-antioxidant balance. Moreover, paraoxonase 1 (PON1) is an antioxidant enzyme that binds with high-density lipoprotein (HDL) in the circulation, and antioxidant and antiaterogenic properties of this lipoprotein are significantly associated with PON1. Research suggests PON1 contributes to the pathogenesis of certain human diseases such as type 2 diabetes (T2D). The association between PON1 and T2D appear to be reciprocal so that the disease significantly decreases PON1 levels and in turn, the genetics of PON1 may have a role the risk of susceptibility to T2D. Several factors that reduce the activity and concentration of PON1 in patients with T2D include increased glycation and loss-of-function polymorphisms. The genotypic and phenotypic evaluations of PON1 are therefore crucial for assessing the risk of cardiovascular complications in these patients, and strategies for increasing or restoring PON1 levels are useful for reducing or preventing their cardiovascular complications as their main cause of mortality. The present review aimed at discussing and emphasizing the key role of PON1 in T2D as a silent and dangerous disease.
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Affiliation(s)
- Yasaman Shokri
- Department of Clinical Biochemistry and Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Atena Variji
- Department of Clinical Biochemistry and Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mani Nosrati
- Department of Clinical Biochemistry and Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Abbas Khonakdar-Tarsi
- Department of Clinical Biochemistry and Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Anvarsadat Kianmehr
- Golestan Research Center of Gastroenterology and Hepatology, Golestan University of Medical Sciences, Gorgan, Iran; Department of Medical Biotechnology, Faculty of Advanced Madical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Zahra Kashi
- Diabetes Research Center, Imam Teaching Hospital, Mazandaran University of Medical Sciences, Sari, Iran
| | - Adele Bahar
- Diabetes Research Center, Imam Teaching Hospital, Mazandaran University of Medical Sciences, Sari, Iran
| | - Abouzar Bagheri
- Department of Clinical Biochemistry and Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Abdolkarim Mahrooz
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; Diabetes Research Center, Imam Teaching Hospital, Mazandaran University of Medical Sciences, Sari, Iran.
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29
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Ben-David M, Soskine M, Dubovetskyi A, Cherukuri KP, Dym O, Sussman JL, Liao Q, Szeler K, Kamerlin SCL, Tawfik DS. Enzyme Evolution: An Epistatic Ratchet versus a Smooth Reversible Transition. Mol Biol Evol 2019; 37:1133-1147. [DOI: 10.1093/molbev/msz298] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Evolutionary trajectories are deemed largely irreversible. In a newly diverged protein, reversion of mutations that led to the functional switch typically results in loss of both the new and the ancestral functions. Nonetheless, evolutionary transitions where reversions are viable have also been described. The structural and mechanistic causes of reversion compatibility versus incompatibility therefore remain unclear. We examined two laboratory evolution trajectories of mammalian paraoxonase-1, a lactonase with promiscuous organophosphate hydrolase (OPH) activity. Both trajectories began with the same active-site mutant, His115Trp, which lost the native lactonase activity and acquired higher OPH activity. A neo-functionalization trajectory amplified the promiscuous OPH activity, whereas the re-functionalization trajectory restored the native activity, thus generating a new lactonase that lacks His115. The His115 revertants of these trajectories indicated opposite trends. Revertants of the neo-functionalization trajectory lost both the evolved OPH and the original lactonase activity. Revertants of the trajectory that restored the original lactonase function were, however, fully active. Crystal structures and molecular simulations show that in the newly diverged OPH, the reverted His115 and other catalytic residues are displaced, thus causing loss of both the original and the new activity. In contrast, in the re-functionalization trajectory, reversion compatibility of the original lactonase activity derives from mechanistic versatility whereby multiple residues can fulfill the same task. This versatility enables unique sequence-reversible compositions that are inaccessible when the active site was repurposed toward a new function.
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Affiliation(s)
- Moshe Ben-David
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Misha Soskine
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Artem Dubovetskyi
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| | | | - Orly Dym
- Department of Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Joel L Sussman
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Qinghua Liao
- Department of Chemistry – BMC, Uppsala University, Uppsala, Sweden
| | - Klaudia Szeler
- Department of Chemistry – BMC, Uppsala University, Uppsala, Sweden
| | | | - Dan S Tawfik
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
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30
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Mahrooz A, Mackness M, Bagheri A, Ghaffari-Cherati M, Masoumi P. The epigenetic regulation of paraoxonase 1 (PON1) as an important enzyme in HDL function: The missing link between environmental and genetic regulation. Clin Biochem 2019; 73:1-10. [PMID: 31351988 DOI: 10.1016/j.clinbiochem.2019.07.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Paraoxonase 1 (PON1) is an important antiatherogenic and antioxidant enzyme in the circulation that has been associated with adverse health outcomes particularly cardiovascular disease (CVD) and other metabolic disorders. PON1 is a highly promiscuous enzyme and can hydrolyse a large variety of substrates, however, detailed structure/function studies have concluded that the natural substrates for PON1 are lipophilic lactones. The interindividual variability in PON1 activity has been mainly attributed to genetic determinants; however, it appears that the contribution of epigenetics has been ignored as a result of the lack of adequate research. CONTENT Epigenetic processes, including the histone modifications in the PON1 gene, the methylation of CpG sites in the promoter region of the PON1 gene and the microRNA modulation of PON1 expression can be responsible for the under researched gap between the environmental and genetic regulation of PON1. Environmental factors, including diet, pollution and lifestyle-related factors widely differ between individuals and populations and can cause large differences in the distribution of PON1 and it is important to note that their effects may be exerted through the epigenetic processes. This review discusses and emphasizes the importance of the epigenetic regulation of PON1 as a less-studied subject to highlight future research landscapes. SUMMARY Epigenetic regulation is known as an important contributor to the pathogenesis of human diseases, particularly multifactorial diseases such as CVD, which is life-threatening. Due to the importance of PON1 in the functionality of high-density lipoprotein (HDL) and its association with CVD, further explorations of its epigenetic regulation using advanced methods such as Methyl-Seq may lead to the identification of new epigenetic contributors that in turn may lead to targeted therapies.
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Affiliation(s)
- Abdolkarim Mahrooz
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Mike Mackness
- Division of Cardiovascular Sciences, University of Manchester, Manchester, UK
| | - Abouzar Bagheri
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Maryam Ghaffari-Cherati
- Department of Clinical Biochemistry and Genetics, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Parisa Masoumi
- Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
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Calixto AR, Moreira C, Pabis A, Kötting C, Gerwert K, Rudack T, Kamerlin SCL. GTP Hydrolysis Without an Active Site Base: A Unifying Mechanism for Ras and Related GTPases. J Am Chem Soc 2019; 141:10684-10701. [PMID: 31199130 DOI: 10.1021/jacs.9b03193] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
GTP hydrolysis is a biologically crucial reaction, being involved in regulating almost all cellular processes. As a result, the enzymes that catalyze this reaction are among the most important drug targets. Despite their vital importance and decades of substantial research effort, the fundamental mechanism of enzyme-catalyzed GTP hydrolysis by GTPases remains highly controversial. Specifically, how do these regulatory proteins hydrolyze GTP without an obvious general base in the active site to activate the water molecule for nucleophilic attack? To answer this question, we perform empirical valence bond simulations of GTPase-catalyzed GTP hydrolysis, comparing solvent- and substrate-assisted pathways in three distinct GTPases, Ras, Rab, and the Gαi subunit of a heterotrimeric G-protein, both in the presence and in the absence of the corresponding GTPase activating proteins. Our results demonstrate that a general base is not needed in the active site, as the preferred mechanism for GTP hydrolysis is a conserved solvent-assisted pathway. This pathway involves the rate-limiting nucleophilic attack of a water molecule, leading to a short-lived intermediate that tautomerizes to form H2PO4- and GDP as the final products. Our fundamental biochemical insight into the enzymatic regulation of GTP hydrolysis not only resolves a decades-old mechanistic controversy but also has high relevance for drug discovery efforts. That is, revisiting the role of oncogenic mutants with respect to our mechanistic findings would pave the way for a new starting point to discover drugs for (so far) "undruggable" GTPases like Ras.
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Affiliation(s)
- Ana R Calixto
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Cátia Moreira
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
| | - Anna Pabis
- Department of Cell and Molecular Biology , Uppsala University , BMC Box 596, S-751 24 , Uppsala , Sweden
| | - Carsten Kötting
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Klaus Gerwert
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Till Rudack
- Department of Biophysics , Ruhr University Bochum , 44801 Bochum , Germany
| | - Shina C L Kamerlin
- Department of Chemistry-BMC , Uppsala University , Box 576, S-751 23 Uppsala , Sweden
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32
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Claverie M, Cioci G, Guionnet M, Schörghuber J, Lichtenecker R, Moulis C, Remaud-Simeon M, Lippens G. Futile Encounter Engineering of the DSR-M Dextransucrase Modifies the Resulting Polymer Length. Biochemistry 2019; 58:2853-2859. [DOI: 10.1021/acs.biochem.9b00373] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Marion Claverie
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France
| | - Gianluca Cioci
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France
| | - Matthieu Guionnet
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France
| | - Julia Schörghuber
- Institute of Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Roman Lichtenecker
- Institute of Organic Chemistry, University of Vienna, 1090 Vienna, Austria
| | - Claire Moulis
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France
| | | | - Guy Lippens
- LISBP, Université de Toulouse, CNRS, INRA, INSA, 31400 Toulouse, France
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33
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Samir A, Ohura K, Bodor N, Imai T. Identification of Major Esterase Involved in Hydrolysis of Soft Anticholinergic (2R3'R-SGM) Designed From Glycopyrrolate in Human and Rat Tissues. J Pharm Sci 2019; 108:2791-2797. [PMID: 30954525 DOI: 10.1016/j.xphs.2019.03.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/19/2019] [Accepted: 03/28/2019] [Indexed: 10/27/2022]
Abstract
The glycopyrrolate soft analog, SGM, designed to be easily hydrolyzed into the significantly less active zwitterionic metabolite, SGa, typifies soft drug that reduces systemic side effects (a problem often seen with traditional anticholinergics) following local administration. In this study, hydrolysis of 2R3'R-SGM, the highest pharmacologically active stereoisomer of SGM, was investigated in human and rat tissues. In both species, 2R3'R-SGM was metabolized to 2R3'R-SGa in plasma but was stable in liver and intestine. The half-life of 2R3'R-SGM was found to be 16.9 min and 9.8 min in human and rat plasma, respectively. The enzyme inhibition and stimulation experiments showed that plasma paraoxonase 1 (PON1) is responsible for the hydrolysis of 2R3'R-SGM in humans and rats. The PON1-mediated hydrolysis of 2R3'R-SGM was confirmed in the lipoprotein-rich fractions of human plasma. As PON1 is naturally attached to high-density lipoprotein, it might be absent in topical tissues where 2R3'R-SGM is applied, supporting its local stability and efficacy. The metabolic behavior of 2R3'R-SGM indicates that it is an ideal soft drug to be detoxified as soon as it moves into systemic circulation. Furthermore, the similarity of 2R3'R-SGM metabolism in humans and rats showed that the rat is a suitable animal for preclinical study.
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Affiliation(s)
- Ahmed Samir
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan
| | - Kayoko Ohura
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan; Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto, Japan
| | - Nicholas Bodor
- Bodor Laboratories, Miami, Florida 33137; College of Pharmacy, University of Florida, Gainesville, Florida 32611
| | - Teruko Imai
- Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan.
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34
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Kulkarni Y, Kamerlin SCL. Computational physical organic chemistry using the empirical valence bond approach. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2019. [DOI: 10.1016/bs.apoc.2019.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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35
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Liao Q, Kulkarni Y, Sengupta U, Petrović D, Mulholland AJ, van der Kamp MW, Strodel B, Kamerlin SCL. Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case. J Am Chem Soc 2018; 140:15889-15903. [PMID: 30362343 DOI: 10.1021/jacs.8b09378] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Conformational changes are crucial for the catalytic action of many enzymes. A prototypical and well-studied example is loop opening and closure in triosephosphate isomerase (TIM), which is thought to determine the rate of catalytic turnover in many circumstances. Specifically, TIM loop 6 "grips" the phosphodianion of the substrate and, together with a change in loop 7, sets up the TIM active site for efficient catalysis. Crystal structures of TIM typically show an open or a closed conformation of loop 6, with the tip of the loop moving ∼7 Å between conformations. Many studies have interpreted this motion as a two-state, rigid-body transition. Here, we use extensive molecular dynamics simulations, with both conventional and enhanced sampling techniques, to analyze loop motion in apo and substrate-bound TIM in detail, using five crystal structures of the dimeric TIM from Saccharomyces cerevisiae. We find that loop 6 is highly flexible and samples multiple conformational states. Empirical valence bond simulations of the first reaction step show that slight displacements away from the fully closed-loop conformation can be sufficient to abolish most of the catalytic activity; full closure is required for efficient reaction. The conformational change of the loops in TIM is thus not a simple "open and shut" case and is crucial for its catalytic action. Our detailed analysis of loop motion in a highly efficient enzyme highlights the complexity of loop conformational changes and their role in biological catalysis.
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Affiliation(s)
- Qinghua Liao
- Department of Chemistry - BMC , Uppsala University , BMC Box 576, 751 23 Uppsala , Sweden
| | - Yashraj Kulkarni
- Department of Chemistry - BMC , Uppsala University , BMC Box 576, 751 23 Uppsala , Sweden
| | - Ushnish Sengupta
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich , 52425 Jülich , Germany.,German Research School for Simulation Sciences , RWTH Aachen University , 52062 Aachen , Germany
| | - Dušan Petrović
- Department of Chemistry - BMC , Uppsala University , BMC Box 576, 751 23 Uppsala , Sweden.,Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich , 52425 Jülich , Germany
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Cantock's Close , BS8 1TS Bristol , United Kingdom
| | - Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry , University of Bristol , Cantock's Close , BS8 1TS Bristol , United Kingdom.,School of Biochemistry , University of Bristol , University Walk , BS8 1TD Bristol , United Kingdom
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , 40225 Düsseldorf , Germany
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36
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Mhashal AR, Pshetitsky Y, Cheatum CM, Kohen A, Major DT. Evolutionary Effects on Bound Substrate pKa in Dihydrofolate Reductase. J Am Chem Soc 2018; 140:16650-16660. [DOI: 10.1021/jacs.8b09089] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Anil R. Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | - Yaron Pshetitsky
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
| | | | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Dan Thomas Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 5290002, Israel
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37
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Affiliation(s)
- Valerie Vaissier Welborn
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Teresa Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry and Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Department of Chemical and Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, California 94720, United States
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38
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Saez DA, Zinovjev K, Tuñón I, Vöhringer-Martinez E. Catalytic Reaction Mechanism in Native and Mutant Catechol-O-methyltransferase from the Adaptive String Method and Mean Reaction Force Analysis. J Phys Chem B 2018; 122:8861-8871. [DOI: 10.1021/acs.jpcb.8b07339] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- David Adrian Saez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
| | - Kirill Zinovjev
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepcion, Chile
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39
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Kokkonen P, Bednar D, Dockalova V, Prokop Z, Damborsky J. Conformational changes allow processing of bulky substrates by a haloalkane dehalogenase with a small and buried active site. J Biol Chem 2018; 293:11505-11512. [PMID: 29858243 PMCID: PMC6065182 DOI: 10.1074/jbc.ra117.000328] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 05/28/2018] [Indexed: 12/21/2022] Open
Abstract
Haloalkane dehalogenases catalyze the hydrolysis of halogen-carbon bonds in organic halogenated compounds and as such are of great utility as biocatalysts. The crystal structures of the haloalkane dehalogenase DhlA from the bacterium from Xanthobacter autotrophicus GJ10, specifically adapted for the conversion of the small 1,2-dichloroethane (DCE) molecule, display the smallest catalytic site (110 Å3) within this enzyme family. However, during a substrate-specificity screening, we noted that DhlA can catalyze the conversion of far bulkier substrates, such as the 4-(bromomethyl)-6,7-dimethoxy-coumarin (220 Å3). This large substrate cannot bind to DhlA without conformational alterations. These conformational changes have been previously inferred from kinetic analysis, but their structural basis has not been understood. Using molecular dynamic simulations, we demonstrate here the intrinsic flexibility of part of the cap domain that allows DhlA to accommodate bulky substrates. The simulations displayed two routes for transport of substrates to the active site, one of which requires the conformational change and is likely the route for bulky substrates. These results provide insights into the structure-dynamics function relationships in enzymes with deeply buried active sites. Moreover, understanding the structural basis for the molecular adaptation of DhlA to 1,2-dichloroethane introduced into the biosphere during the industrial revolution provides a valuable lesson in enzyme design by nature.
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Affiliation(s)
- Piia Kokkonen
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Veronika Dockalova
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology, Research Centre for Toxic Compounds in the Environment (RECETOX), Masaryk University, Kamenice 5/A13, 625 00 Brno, Czech Republic; International Centre for Clinical Research, St. Anne's University Hospital, Pekarska 53, 656 91 Brno, Czech Republic.
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40
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Maurer D, Enugala TR, Hamnevik E, Bauer P, Lüking M, Petrović D, Hillier H, Kamerlin SCL, Dobritzsch D, Widersten M. Stereo- and Regioselectivity in Catalyzed Transformation of a 1,2-Disubstituted Vicinal Diol and the Corresponding Diketone by Wild Type and Laboratory Evolved Alcohol Dehydrogenases. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01762] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Dirk Maurer
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Thilak Reddy Enugala
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Emil Hamnevik
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Paul Bauer
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
- Biophysics, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden
| | - Malin Lüking
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Dušan Petrović
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Heidi Hillier
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
- Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry − BMC, Uppsala University, Box 576, SE-751 23 Uppsala, Sweden
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41
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Petrović D, Risso VA, Kamerlin SCL, Sanchez-Ruiz JM. Conformational dynamics and enzyme evolution. J R Soc Interface 2018; 15:20180330. [PMID: 30021929 PMCID: PMC6073641 DOI: 10.1098/rsif.2018.0330] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/27/2018] [Indexed: 12/21/2022] Open
Abstract
Enzymes are dynamic entities, and their dynamic properties are clearly linked to their biological function. It follows that dynamics ought to play an essential role in enzyme evolution. Indeed, a link between conformational diversity and the emergence of new enzyme functionalities has been recognized for many years. However, it is only recently that state-of-the-art computational and experimental approaches are revealing the crucial molecular details of this link. Specifically, evolutionary trajectories leading to functional optimization for a given host environment or to the emergence of a new function typically involve enriching catalytically competent conformations and/or the freezing out of non-competent conformations of an enzyme. In some cases, these evolutionary changes are achieved through distant mutations that shift the protein ensemble towards productive conformations. Multifunctional intermediates in evolutionary trajectories are probably multi-conformational, i.e. able to switch between different overall conformations, each competent for a given function. Conformational diversity can assist the emergence of a completely new active site through a single mutation by facilitating transition-state binding. We propose that this mechanism may have played a role in the emergence of enzymes at the primordial, progenote stage, where it was plausibly promoted by high environmental temperatures and the possibility of additional phenotypic mutations.
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Affiliation(s)
- Dušan Petrović
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Valeria A Risso
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071 Granada, Spain
| | | | - Jose M Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias, University of Granada, 18071 Granada, Spain
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42
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Shunmoogam N, Naidoo P, Chilton R. Paraoxonase (PON)-1: a brief overview on genetics, structure, polymorphisms and clinical relevance. Vasc Health Risk Manag 2018; 14:137-143. [PMID: 29950852 PMCID: PMC6014389 DOI: 10.2147/vhrm.s165173] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Paraoxonase-1 (PON1) is a high-density lipoprotein-associated esterase and is speculated to play a role in several human diseases including diabetes mellitus and atherosclerosis. Low PON1 activity has been associated with increased risk of major cardiovascular events, therefore a variety of studies have been conducted to establish the cardioprotective properties and clinical relevance of PON1. The major aim of this review was to highlight the important studies and to subsequently assess if PON1 has clinical relevance. A review of the literature showed that there is currently insufficient data to suggest that PON1 has clinical relevance. It is our opinion that robust studies are required to clarify the clinical relevance of PON1.
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Affiliation(s)
| | | | - Robert Chilton
- Department of Medicine, Division of Cardiology and Interventional Cardiology, University of Texas Health Science Center at San Antonia, San Antonia, TX, USA
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43
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Janfalk Carlsson Å, Bauer P, Dobritzsch D, Kamerlin SCL, Widersten M. Epoxide hydrolysis as a model system for understanding flux through a branched reaction scheme. IUCRJ 2018; 5:269-282. [PMID: 29755743 PMCID: PMC5929373 DOI: 10.1107/s2052252518003573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/01/2018] [Indexed: 06/08/2023]
Abstract
The epoxide hydrolase StEH1 catalyzes the hydrolysis of trans-methylstyrene oxide to 1-phenyl-propane-1,2-diol. The (S,S)-epoxide is exclusively transformed into the (1R,2S)-diol, while hydrolysis of the (R,R)-epoxide results in a mixture of product enantiomers. In order to understand the differences in the stereoconfigurations of the products, the reactions were studied kinetically during both the pre-steady-state and steady-state phases. A number of closely related StEH1 variants were analyzed in parallel, and the results were rationalized by structure-activity analysis using the available crystal structures of all tested enzyme variants. Finally, empirical valence-bond simulations were performed in order to provide additional insight into the observed kinetic behaviour and ratios of the diol product enantiomers. These combined data allow us to present a model for the flux through the catalyzed reactions. With the (R,R)-epoxide, ring opening may occur at either C atom and with similar energy barriers for hydrolysis, resulting in a mixture of diol enantiomer products. However, with the (S,S)-epoxide, although either epoxide C atom may react to form the covalent enzyme intermediate, only the pro-(R,S) alkylenzyme is amenable to subsequent hydrolysis. Previously contradictory observations from kinetics experiments as well as product ratios can therefore now be explained for this biocatalytically relevant enzyme.
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Affiliation(s)
- Åsa Janfalk Carlsson
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Paul Bauer
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, 751 24 Uppsala, Sweden
| | - Doreen Dobritzsch
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
| | - Shina C. L. Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, 751 24 Uppsala, Sweden
| | - Mikael Widersten
- Department of Chemistry, BMC, Uppsala University, Box 576, 751 23 Uppsala, Sweden
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44
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Petrović D, Szeler K, Kamerlin SCL. Challenges and advances in the computational modeling of biological phosphate hydrolysis. Chem Commun (Camb) 2018; 54:3077-3089. [PMID: 29412205 DOI: 10.1039/c7cc09504j] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.
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Affiliation(s)
- Dušan Petrović
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
| | - Klaudia Szeler
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden.
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45
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Cooperativity and flexibility in enzyme evolution. Curr Opin Struct Biol 2018; 48:83-92. [DOI: 10.1016/j.sbi.2017.10.020] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/24/2017] [Indexed: 11/23/2022]
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46
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Purg M, Kamerlin SCL. Empirical Valence Bond Simulations of Organophosphate Hydrolysis: Theory and Practice. Methods Enzymol 2018; 607:3-51. [DOI: 10.1016/bs.mie.2018.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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47
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Purg M, Elias M, Kamerlin SCL. Similar Active Sites and Mechanisms Do Not Lead to Cross-Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering. J Am Chem Soc 2017; 139:17533-17546. [PMID: 29113434 PMCID: PMC5724027 DOI: 10.1021/jacs.7b09384] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2017] [Indexed: 01/27/2023]
Abstract
Organophosphate hydrolases are proficient catalysts of the breakdown of neurotoxic organophosphates and have great potential as both biotherapeutics for treating acute organophosphate toxicity and as bioremediation agents. However, proficient organophosphatases such as serum paraoxonase 1 (PON1) and the organophosphate-hydrolyzing lactonase SsoPox are unable to hydrolyze bulkyorganophosphates with challenging leaving groups such as diisopropyl fluorophosphate (DFP) or venomous agent X, creating a major challenge for enzyme design. Curiously, despite their mutually exclusive substrate specificities, PON1 and diisopropyl fluorophosphatase (DFPase) have essentially identical active sites and tertiary structures. In the present work, we use empirical valence bond simulations to probe the catalytic mechanism of DFPase as well as temperature, pH, and mutational effects, demonstrating that DFPase and PON1 also likely utilize identical catalytic mechanisms to hydrolyze their respective substrates. However, detailed examination of both static structures and dynamical simulations demonstrates subtle but significant differences in the electrostatic properties and solvent penetration of the two active sites and, most critically, the role of residues that make no direct contact with either substrate in acting as "specificity switches" between the two enzymes. Specifically, we demonstrate that key residues that are structurally and functionally critical for the paraoxonase activity of PON1 prevent it from being able to hydrolyze DFP with its fluoride leaving group. These insights expand our understanding of the drivers of the evolution of divergent substrate specificity in enzymes with identical active sites and guide the future design of organophosphate hydrolases that hydrolyze compounds with challenging leaving groups.
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Affiliation(s)
- Miha Purg
- Science for Life
Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Mikael Elias
- Department of Biochemistry, Molecular Biology and Biophysics &
Biotechnology Institute, University of Minnesota, 1479 Gortner Avenue, St. Paul, Minnesota 55108, United States
| | - Shina Caroline Lynn Kamerlin
- Science for Life
Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
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48
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Kulkarni YS, Liao Q, Petrović D, Krüger DM, Strodel B, Amyes TL, Richard JP, Kamerlin SCL. Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase. J Am Chem Soc 2017; 139:10514-10525. [PMID: 28683550 PMCID: PMC5543394 DOI: 10.1021/jacs.7b05576] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Triosephosphate isomerase (TIM) is a proficient catalyst of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to d-glyceraldehyde phosphate (GAP), via general base catalysis by E165. Historically, this enzyme has been an extremely important model system for understanding the fundamentals of biological catalysis. TIM is activated through an energetically demanding conformational change, which helps position the side chains of two key hydrophobic residues (I170 and L230), over the carboxylate side chain of E165. This is critical both for creating a hydrophobic pocket for the catalytic base and for maintaining correct active site architecture. Truncation of these residues to alanine causes significant falloffs in TIM's catalytic activity, but experiments have failed to provide a full description of the action of this clamp in promoting substrate deprotonation. We perform here detailed empirical valence bond calculations of the TIM-catalyzed deprotonation of DHAP and GAP by both wild-type TIM and its I170A, L230A, and I170A/L230A mutants, obtaining exceptional quantitative agreement with experiment. Our calculations provide a linear free energy relationship, with slope 0.8, between the activation barriers and Gibbs free energies for these TIM-catalyzed reactions. We conclude that these clamping side chains minimize the Gibbs free energy for substrate deprotonation, and that the effects on reaction driving force are largely expressed at the transition state for proton transfer. Our combined analysis of previous experimental and current computational results allows us to provide an overview of the breakdown of ground-state and transition state effects in enzyme catalysis in unprecedented detail, providing a molecular description of the operation of a hydrophobic clamp in triosephosphate isomerase.
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Affiliation(s)
- Yashraj S Kulkarni
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, Uppsala S-751 24, Sweden
| | - Qinghua Liao
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, Uppsala S-751 24, Sweden
| | - Dušan Petrović
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich , Jülich 52425, Germany
| | - Dennis M Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, Uppsala S-751 24, Sweden
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry, Forschungszentrum Jülich , Jülich 52425, Germany.,Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf , Universitätsstrasse 1, Düsseldorf 40225, Germany
| | - 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
| | - Shina C L Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University , BMC Box 596, Uppsala S-751 24, Sweden
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49
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Zhan S, Mårtensson D, Purg M, Kamerlin SCL, Ahlquist MSG. Capturing the Role of Explicit Solvent in the Dimerization of RuV
(bda) Water Oxidation Catalysts. Angew Chem Int Ed Engl 2017; 56:6962-6965. [DOI: 10.1002/anie.201701488] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/23/2017] [Indexed: 11/06/2022]
Affiliation(s)
- Shaoqi Zhan
- Division of Theoretical Chemistry & Biology; School of Biotechnology; KTH Royal Institute of Technology; 10691 Stockholm Sweden
| | - Daniel Mårtensson
- Division of Theoretical Chemistry & Biology; School of Biotechnology; KTH Royal Institute of Technology; 10691 Stockholm Sweden
| | - Miha Purg
- Department of Cell and Molecular Biology; Uppsala University; 75124 Uppsala Sweden
| | - Shina C. L. Kamerlin
- Department of Cell and Molecular Biology; Uppsala University; 75124 Uppsala Sweden
| | - Mårten S. G. Ahlquist
- Division of Theoretical Chemistry & Biology; School of Biotechnology; KTH Royal Institute of Technology; 10691 Stockholm Sweden
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50
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Zhan S, Mårtensson D, Purg M, Kamerlin SCL, Ahlquist MSG. Capturing the Role of Explicit Solvent in the Dimerization of RuV
(bda) Water Oxidation Catalysts. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Shaoqi Zhan
- Division of Theoretical Chemistry & Biology; School of Biotechnology; KTH Royal Institute of Technology; 10691 Stockholm Sweden
| | - Daniel Mårtensson
- Division of Theoretical Chemistry & Biology; School of Biotechnology; KTH Royal Institute of Technology; 10691 Stockholm Sweden
| | - Miha Purg
- Department of Cell and Molecular Biology; Uppsala University; 75124 Uppsala Sweden
| | - Shina C. L. Kamerlin
- Department of Cell and Molecular Biology; Uppsala University; 75124 Uppsala Sweden
| | - Mårten S. G. Ahlquist
- Division of Theoretical Chemistry & Biology; School of Biotechnology; KTH Royal Institute of Technology; 10691 Stockholm Sweden
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