1
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Whitehead J, Leferink NGH, Johannissen LO, Hay S, Scrutton NS. Decoding Catalysis by Terpene Synthases. ACS Catal 2023; 13:12774-12802. [PMID: 37822860 PMCID: PMC10563020 DOI: 10.1021/acscatal.3c03047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/31/2023] [Indexed: 10/13/2023]
Abstract
The review by Christianson, published in 2017 on the twentieth anniversary of the emergence of the field, summarizes the foundational discoveries and key advances in terpene synthase/cyclase (TS) biocatalysis (Christianson, D. W. Chem Rev2017, 117 (17), 11570-11648. DOI: 10.1021/acs.chemrev.7b00287). Here, we review the TS literature published since then, bringing the field up to date and looking forward to what could be the near future of TS rational design. Many revealing discoveries have been made in recent years, building on the knowledge and fundamental principles uncovered during those initial two decades of study. We use these to explore TS reaction chemistry and see how a combined experimental and computational approach helps to decipher the complexities of TS catalysis. Revealed are a suite of catalytic motifs which control product outcome in TSs, some obvious, some more subtle. We examine each in detail, using the most recent papers and insights to illustrate how exactly this fascinating class of enzymes takes a single acyclic substrate and turns it into the many thousands of complex terpenoids found in Nature. We then explore some of the recent strategies for TS engineering, including machine learning and other data-driven approaches. From this, rational and predictive engineering of TSs, "designer terpene synthases", will begin to emerge as a realistic goal.
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Affiliation(s)
- Joshua
N. Whitehead
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nicole G. H. Leferink
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
| | - Linus O. Johannissen
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Sam Hay
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
| | - Nigel S. Scrutton
- Manchester
Institute of Biotechnology, Department of Chemistry, The University of Manchester, Manchester, M1 7DN, United Kingdom
- Future
Biomanufacturing Research Hub (FBRH), Manchester Institute of Biotechnology,
Department of Chemistry, The University
of Manchester, Manchester, M1 7DN, United
Kingdom
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2
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Altunayar-Unsalan C, Unsalan O, Mavromoustakos T. Molecular interactions of hesperidin with DMPC/cholesterol bilayers. Chem Biol Interact 2022; 366:110131. [PMID: 36037876 DOI: 10.1016/j.cbi.2022.110131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/05/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
Abstract
Since cell membranes are complex systems, the use of model lipid bilayers is quite important for the study of their interactions with bioactive molecules. Mammalian cell membranes require cholesterol (CHOL) for their structure and function. For this reason, the mixtures of phospholipid and cholesterol are necessary to use in model membrane studies to better simulate the real systems. In the present study, we investigated the effect of the incorporation of hesperidin in model membranes consisting of dimyristoylphosphatidylcholine (DMPC) and CHOL by using differential scanning calorimetry (DSC), attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, and atomic force microscopy (AFM). ATR-FTIR results demonstrated that hesperidin increases the fluidity of the DMPC/CHOL binary system. DSC findings indicated that the presence of 5 mol% hesperidin induces a broadening of the main phase transition consisting of three overlapping components. AFM experiments showed that hesperidin increases the thickness of DMPC/CHOL lipid bilayer model membranes. In addition to experimental results, molecular docking studies were conducted with hesperidin and human lanosterol synthase (LS), which is an enzyme found in the final step of cholesterol synthesis, to characterize hesperidin's interactions with its surrounding via its hydroxyl and oxygen groups. Then, hesperidin's ADME/Tox (absorption, distribution, metabolism, excretion and toxicity) profile was computed to see the potential impact on living system. In conclusion, considering the data obtained from experimental studies, this work ensures molecular insights in the interaction between a flavonoid, as an antioxidant drug model, and lipids mimicking those found in mammalian membranes. Moreover, computational studies demonstrated that hesperidin may be a great potential for use as a therapeutic agent for hypercholesterolemia due to its antioxidant property.
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Affiliation(s)
- Cisem Altunayar-Unsalan
- Ege University Central Research Testing and Analysis Laboratory Research and Application Center, 35100, Bornova, Izmir, Turkey.
| | - Ozan Unsalan
- Ege University, Faculty of Science, Department of Physics, 35100, Bornova, Izmir, Turkey.
| | - Thomas Mavromoustakos
- Section of Organic Chemistry, Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15771, Greece.
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3
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Raz K, Driller R, Dimos N, Ringel M, Brück T, Loll B, Major DT. The Impression of a Nonexisting Catalytic Effect: The Role of CotB2 in Guiding the Complex Biosynthesis of Cyclooctat-9-en-7-ol. J Am Chem Soc 2020; 142:21562-21574. [PMID: 33289561 DOI: 10.1021/jacs.0c11348] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Terpene synthases generate terpenes employing diversified carbocation chemistry, including highly specific ring formations, proton and hydride transfers, and methyl as well as methylene migrations, followed by reaction quenching. In this enzyme family, the main catalytic challenge is not rate enhancement, but rather structural and reactive control of intrinsically unstable carbocations in order to guide the resulting product distribution. Here we employ multiscale modeling within classical and quantum dynamics frameworks to investigate the reaction mechanism in the diterpene synthase CotB2, commencing with the substrate geranyl geranyl diphosphate and terminating with the carbocation precursor to the final product cyclooctat-9-en-7-ol. The 11-step in-enzyme carbocation cascade is compared with the same reaction in the absence of the enzyme. Remarkably, the free energy profiles in gas phase and in CotB2 are surprisingly similar. This similarity contrasts the multitude of strong π-cation, dipole-cation, and ion-pair interactions between all intermediates in the reaction cascade and the enzyme, suggesting a remarkable balance of interactions in CotB2. We ascribe this balance to the similar magnitude of the interactions between the carbocations along the reaction coordinate and the enzyme environment. The effect of CotB2 mutations is studied using multiscale mechanistic docking, machine learning, and X-ray crystallography, pointing the way for future terpene synthase design.
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Affiliation(s)
- Keren Raz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Ronja Driller
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Nicole Dimos
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Marion Ringel
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748 Garching, Germany
| | - Thomas Brück
- Werner Siemens Chair of Synthetic Biotechnology, Department of Chemistry, Technical University of Munich (TUM), Lichtenbergstr. 4, 85748 Garching, Germany
| | - Bernhard Loll
- Institut für Chemie und Biochemie, Strukturbiochemie, Freie Universität Berlin, Takustr. 6, 14195 Berlin, Germany
| | - Dan Thomas Major
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
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4
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Raz K, Levi S, Gupta PK, Major DT. Enzymatic control of product distribution in terpene synthases: insights from multiscale simulations. Curr Opin Biotechnol 2020; 65:248-258. [PMID: 32679412 DOI: 10.1016/j.copbio.2020.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/03/2020] [Accepted: 06/07/2020] [Indexed: 11/25/2022]
Abstract
In this opinion, we review some recent work on terpene biosynthesis using multiscale simulation approaches, with special focus on contributions from our group. Terpene synthases generate terpenes employing rich carbocation chemistry, including highly specific ring formations, proton, hydride, methyl, and methylene migrations, followed by reaction quenching. In these enzymes, the main catalytic challenge is not rate enhancement, but rather control of intrinsically reactive carbocations and the resulting product distribution. Herein, we review multiscale simulations of selected mono-, sesqui-, and diterpene synthases. We point to the many tools adopted by terpene synthases to achieve correct substrate fold, carbocation formation, carbocation reaction environment, and reaction quenching. A better understanding of the toolbox employed by terpene synthases is expected to aid in the search for new enzymatic and biomimetic synthetic routes to natural and unnatural terpenes.
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Affiliation(s)
- Keren Raz
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Shani Levi
- Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Prashant Kumar Gupta
- 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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5
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Tantillo DJ. Interrogating chemical mechanisms in natural products biosynthesis using quantum chemical calculations. WIREs Comput Mol Sci 2020. [DOI: 10.1002/wcms.1453] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Dean J. Tantillo
- Department of Chemistry University of California–Davis Davis California
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6
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Das S, Shimshi M, Raz K, Nitoker Eliaz N, Mhashal AR, Ansbacher T, Major DT. EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes. J Chem Theory Comput 2019; 15:5116-5134. [DOI: 10.1021/acs.jctc.9b00366] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Susanta Das
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Mor Shimshi
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Keren Raz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | - Anil Ranu Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Tamar Ansbacher
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
- Hadassah Academic College, 7 Hanevi’im Street, Jerusalem 9101001, Israel
| | - Dan T. Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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7
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Berni R, Hoque MZ, Legay S, Cai G, Siddiqui KS, Hausman JF, Andre CM, Guerriero G. Tuscan Varieties of Sweet Cherry Are Rich Sources of Ursolic and Oleanolic Acid: Protein Modeling Coupled to Targeted Gene Expression and Metabolite Analyses. Molecules 2019; 24:E1590. [PMID: 31013661 PMCID: PMC6515059 DOI: 10.3390/molecules24081590] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Revised: 04/20/2019] [Accepted: 04/20/2019] [Indexed: 11/16/2022] Open
Abstract
The potential of six ancient Tuscan sweet cherry (Prunus avium L.) varieties as a source of health-promoting pentacyclic triterpenes is here evaluated by means of a targeted gene expression and metabolite analysis. By using a sequence homology criterion, we identify five oxidosqualene cyclase genes (OSCs) and three cytochrome P450s (CYP85s) that are putatively involved in the triterpene production pathway in sweet cherries. We performed 3D structure prediction and induced-fit docking using cation intermediates and reaction products for some OSCs to predict their function. We show that the Tuscan varieties have different amounts of ursolic and oleanolic acids and that these variations are related to different gene expression profiles. This study stresses the interest of valorizing ancient fruits as alternative sources of functional molecules with nutraceutical value. It also provides information on sweet cherry triterpene biosynthetic genes, which could be the object of follow-up functional studies.
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Affiliation(s)
- Roberto Berni
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, 53100 Siena, Italy.
- Trees and Timber Institute, National Research Council of Italy (CNR-IVALSA), via Aurelia 49, 58022 Follonica (GR), Italy.
| | - Mubasher Zahir Hoque
- Bio-Bio-1 Research Foundation, Sangskriti Bikash Kendra Bhaban, 1/E/1 Poribagh, Dhaka 1000, Bangladesh.
- Life Sciences Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.
| | - Sylvain Legay
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Giampiero Cai
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, 53100 Siena, Italy.
| | - Khawar Sohail Siddiqui
- Life Sciences Department, King Fahd University of Petroleum and Minerals (KFUPM), Dhahran 31261, Saudi Arabia.
| | - Jean-Francois Hausman
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Christelle M Andre
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
| | - Gea Guerriero
- Environmental Research and Innovation Department, Luxembourg Institute of Science and Technology, 5 avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
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8
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Copp JN, Anderson DW, Akiva E, Babbitt PC, Tokuriki N. Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions. Methods Enzymol 2019; 620:315-47. [PMID: 31072492 DOI: 10.1016/bs.mie.2019.03.015] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions by enabling the observation and investigation of complex sequence-structure-function and evolutionary relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) and phylogenetic reconstructions to map the functional divergence and evolutionary history of protein superfamilies. We exemplify this approach using the nitroreductase (NTR) flavoenzyme superfamily, demonstrating that SSN investigations can provide a rapid and effective means to classify groups of proteins, expose sequence similarity relationships across the global scale of a protein superfamily, and efficiently support detailed phylogenetic analyses. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes, their evolution, and their associated physiological roles.
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9
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Karunanithi PS, Zerbe P. Terpene Synthases as Metabolic Gatekeepers in the Evolution of Plant Terpenoid Chemical Diversity. Front Plant Sci 2019; 10:1166. [PMID: 31632418 PMCID: PMC6779861 DOI: 10.3389/fpls.2019.01166] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/26/2019] [Indexed: 05/18/2023]
Abstract
Terpenoids comprise tens of thousands of small molecule natural products that are widely distributed across all domains of life. Plants produce by far the largest array of terpenoids with various roles in development and chemical ecology. Driven by selective pressure to adapt to their specific ecological niche, individual species form only a fraction of the myriad plant terpenoids, typically representing unique metabolite blends. Terpene synthase (TPS) enzymes are the gatekeepers in generating terpenoid diversity by catalyzing complex carbocation-driven cyclization, rearrangement, and elimination reactions that enable the transformation of a few acyclic prenyl diphosphate substrates into a vast chemical library of hydrocarbon and, for a few enzymes, oxygenated terpene scaffolds. The seven currently defined clades (a-h) forming the plant TPS family evolved from ancestral triterpene synthase- and prenyl transferase-type enzymes through repeated events of gene duplication and subsequent loss, gain, or fusion of protein domains and further functional diversification. Lineage-specific expansion of these TPS clades led to variable family sizes that may range from a single TPS gene to families of more than 100 members that may further function as part of modular metabolic networks to maximize the number of possible products. Accompanying gene family expansion, the TPS family shows a profound functional plasticity, where minor active site alterations can dramatically impact product outcome, thus enabling the emergence of new functions with minimal investment in evolving new enzymes. This article reviews current knowledge on the functional diversity and molecular evolution of the plant TPS family that underlies the chemical diversity of bioactive terpenoids across the plant kingdom.
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Affiliation(s)
- Prema S Karunanithi
- Department of Plant Biology, University of California Davis, Davis, CA, United States
| | - Philipp Zerbe
- Department of Plant Biology, University of California Davis, Davis, CA, United States
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10
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Blank PN, Pemberton TA, Chow JY, Poulter CD, Christianson DW. Crystal Structure of Cucumene Synthase, a Terpenoid Cyclase That Generates a Linear Triquinane Sesquiterpene. Biochemistry 2018; 57:6326-6335. [PMID: 30346736 DOI: 10.1021/acs.biochem.8b00899] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Linear triquinanes are sesquiterpene natural products with hydrocarbon skeletons consisting of three fused five-membered rings. Importantly, several of these compounds exhibit useful anticancer, anti-inflammatory, and antibiotic properties. However, linear triquinanes pose significant challenges to organic synthesis because of the structural and stereochemical complexity of their hydrocarbon skeletons. To illuminate nature's solution to the generation of linear triquinanes, we now describe the crystal structure of Streptomyces clavuligerus cucumene synthase. This sesquiterpene cyclase catalyzes the stereospecific cyclization of farnesyl diphosphate to form a linear triquinane product, (5 S,7 S,10 R,11 S)-cucumene. Specifically, we report the structure of the wild-type enzyme at 3.05 Å resolution and the structure of the T181N variant at 1.96 Å resolution, both in the open active site conformations without any bound ligands. The high-resolution structure of T181N cucumene synthase enables inspection of the active site contour, which adopts a three-dimensional shape complementary to a linear triquinane. Several aromatic residues outline the active site contour and are believed to facilitate cation-π interactions that would stabilize carbocation intermediates in catalysis. Thus, aromatic residues in the active site not only define the template for catalysis but also play a role in reducing activation barriers in the multistep cyclization cascade.
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Affiliation(s)
- Patrick N Blank
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Travis A Pemberton
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
| | - Jeng-Yeong Chow
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - C Dale Poulter
- Department of Chemistry , University of Utah , 315 South 1400 East , Salt Lake City , Utah 84112 , United States
| | - David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry , University of Pennsylvania , 231 South 34th Street , Philadelphia , Pennsylvania 19104-6323 , United States
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11
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Abstract
The rapidly expanding number of protein sequences found in public databases can improve our understanding of how protein functions evolve. However, our current knowledge of protein function likely represents a small fraction of the diverse repertoire that exists in nature. Integrative computational methods can facilitate the discovery of new protein functions and enzymatic reactions through the observation and investigation of the complex sequence-structure-function relationships within protein superfamilies. Here, we highlight the use of sequence similarity networks (SSNs) to identify previously unexplored sequence and function space. We exemplify this approach using the nitroreductase (NTR) superfamily. We demonstrate that SSN investigations can provide a rapid and effective means to classify groups of proteins, therefore exposing experimentally unexplored sequences that may exhibit novel functionality. Integration of such approaches with systematic experimental characterization will expand our understanding of the functional diversity of enzymes and their associated physiological roles.
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Affiliation(s)
- Janine N Copp
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
| | - Eyal Akiva
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Patricia C Babbitt
- Department of Bioengineering and Therapeutic Sciences , University of California , San Francisco , California 94158 , United States.,Quantitative Biosciences Institute , University of California , San Francisco , California 94143 , United States
| | - Nobuhiko Tokuriki
- Michael Smith Laboratories , University of British Columbia , 2185 East Mall , Vancouver , British Columbia V6T 1Z4 , Canada
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12
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Affiliation(s)
- Jacquelyn S. Fetrow
- Office of the President, Albright College, Reading, Pennsylvania, United States of America
- * E-mail:
| | - Patricia C. Babbitt
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, California, United States of America
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13
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Abstract
![]()
The exponentially increasing number
of protein and nucleic acid
sequences provides opportunities to discover novel enzymes, metabolic
pathways, and metabolites/natural products, thereby adding to our
knowledge of biochemistry and biology. The challenge has evolved from
generating sequence information to mining the databases to integrating
and leveraging the available information, i.e., the availability of
“genomic enzymology” web tools. Web tools that allow
identification of biosynthetic gene clusters are widely used by the
natural products/synthetic biology community, thereby facilitating
the discovery of novel natural products and the enzymes responsible
for their biosynthesis. However, many novel enzymes with interesting
mechanisms participate in uncharacterized small-molecule metabolic
pathways; their discovery and functional characterization also can
be accomplished by leveraging information in protein and nucleic acid
databases. This Perspective focuses on two genomic enzymology web
tools that assist the discovery novel metabolic pathways: (1) Enzyme
Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating
sequence similarity networks to visualize and analyze sequence–function
space in protein families and (2) Enzyme Function Initiative-Genome
Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks
to visualize and analyze the genome context in microbial and fungal
genomes. Both tools have been adapted to other applications to facilitate
target selection for enzyme discovery and functional characterization.
As the natural products community has demonstrated, the enzymology
community needs to embrace the essential role of web tools that allow
the protein and genome sequence databases to be leveraged for novel
insights into enzymological problems.
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Affiliation(s)
- John A Gerlt
- Departments of Biochemistry and Chemistry, Institute for Genomic Biology, University of Illinois , Urbana-Champaign Urbana, Illinois 61801, United States
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14
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Abstract
![]()
The
year 2017 marks the twentieth anniversary of terpenoid cyclase
structural biology: a trio of terpenoid cyclase structures reported
together in 1997 were the first to set the foundation for understanding
the enzymes largely responsible for the exquisite chemodiversity of
more than 80000 terpenoid natural products. Terpenoid cyclases catalyze
the most complex chemical reactions in biology, in that more than
half of the substrate carbon atoms undergo changes in bonding and
hybridization during a single enzyme-catalyzed cyclization reaction.
The past two decades have witnessed structural, functional, and computational
studies illuminating the modes of substrate activation that initiate
the cyclization cascade, the management and manipulation of high-energy
carbocation intermediates that propagate the cyclization cascade,
and the chemical strategies that terminate the cyclization cascade.
The role of the terpenoid cyclase as a template for catalysis is paramount
to its function, and protein engineering can be used to reprogram
the cyclization cascade to generate alternative and commercially important
products. Here, I review key advances in terpenoid cyclase structural
and chemical biology, focusing mainly on terpenoid cyclases and related
prenyltransferases for which X-ray crystal structures have informed
and advanced our understanding of enzyme structure and function.
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Affiliation(s)
- David W Christianson
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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15
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Abstract
Terpenoid synthases create diverse carbon skeletons by catalyzing complex carbocation rearrangements, making them particularly challenging for enzyme function prediction. To begin to address this challenge, we have developed a computational approach for the systematic enumeration of terpenoid carbocations. Application of this approach allows us to systematically define a nearly complete chemical space for the potential carbon skeletons of products from monoterpenoid synthases. Specifically, 18758 carbocations were generated, which we cluster into 74 cyclic skeletons. Five of the 74 skeletons are found in known natural products; some of the others are plausible for new functions, either in nature or engineered. This work systematizes the description of function for this class of enzymes, and provides a basis for predicting functions of uncharacterized enzymes. To our knowledge, this is the first computational study to explore the complete product chemical space of this important class of enzymes. Terpenoids, as one of the largest classes of natural products, provide complex carbocycle structures for many drugs (e.g. taxol) and prodrugs. The diverse carbocycle structures arise from complex carbocation rearrangements catalyzed by terpenoid synthases. Many putative terpene synthase enzymes identified in genome sequencing efforts remain functionally uncharacterized, and some of these will undoubtedly have novel products, potentially including previously undiscovered carbocycles. In this work, we present a computational approach that systematically enumerates all plausible carbocations of monoterpenoid synthases in order to define and organize the potentially large product chemical space of this important class of enzymes.
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Affiliation(s)
- Boxue Tian
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
| | - C. Dale Poulter
- Department of Chemistry, University of Utah, Salt Lake City, Utah, United States of America
| | - Matthew P. Jacobson
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, San Francisco, California, United States of America
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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16
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O'Brien TE, Bertolani SJ, Tantillo DJ, Siegel JB. Mechanistically informed predictions of binding modes for carbocation intermediates of a sesquiterpene synthase reaction. Chem Sci 2016; 7:4009-4015. [PMID: 30155043 PMCID: PMC6013805 DOI: 10.1039/c6sc00635c] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 03/18/2016] [Indexed: 11/21/2022] Open
Abstract
Sesquiterpenoids comprise a class of terpenoid natural products with thousands of compounds that are highly diverse in structure, generally containing a polycyclic carbon backbone that is constructed by a sesquiterpene synthase. Decades of experimental and computational studies have demonstrated that these enzymes generate a carbocation in the active site, which undergoes a series of structural rearrangements until a product is formed via deprotonation or nucleophile attack. However, for the vast majority of these enzymes the productive binding orientation of the intermediate carbocations has remained unclear. In this work, a method that combines quantum mechanics and computational docking is used to generate an all-atom model of every putative intermediate formed in the context of the enzyme active site for tobacco epi-aristolochene synthase (TEAS). This method identifies a single pathway that links the first intermediate to the last, enabling us to propose the first high-resolution model for the reaction intermediates in the active site of TEAS, and providing testable predictions.
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Affiliation(s)
- T E O'Brien
- Department of Chemistry , University of California Davis , Davis , California , USA . ;
| | - S J Bertolani
- Department of Chemistry , University of California Davis , Davis , California , USA . ;
| | - D J Tantillo
- Department of Chemistry , University of California Davis , Davis , California , USA . ;
| | - J B Siegel
- Department of Chemistry , University of California Davis , Davis , California , USA . ; .,Department of Biochemistry and Molecular Medicine , University of California Davis , Davis , California , USA.,Genome Center , University of California Davis , Davis , California , USA
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17
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Hong YJ, Tantillo DJ. Tension between Internal and External Modes of Stabilization in Carbocations Relevant to Terpene Biosynthesis: Modulating Minima Depth via C–H···π Interactions. Org Lett 2015; 17:5388-91. [DOI: 10.1021/acs.orglett.5b02740] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Young J. Hong
- Department
of Chemistry, Univeristy of California—Davis, Davis, California 95616, United States
| | - Dean J. Tantillo
- Department
of Chemistry, Univeristy of California—Davis, Davis, California 95616, United States
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18
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Chow JY, Tian BX, Ramamoorthy G, Hillerich BS, Seidel RD, Almo SC, Jacobson MP, Poulter CD. Computational-guided discovery and characterization of a sesquiterpene synthase from Streptomyces clavuligerus. Proc Natl Acad Sci U S A 2015; 112:5661-6. [PMID: 25901324 DOI: 10.1073/pnas.1505127112] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Terpenoids are a large structurally diverse group of natural products with an array of functions in their hosts. The large amount of genomic information from recent sequencing efforts provides opportunities and challenges for the functional assignment of terpene synthases that construct the carbon skeletons of these compounds. Inferring function from the sequence and/or structure of these enzymes is not trivial because of the large number of possible reaction channels and products. We tackle this problem by developing an algorithm to enumerate possible carbocations derived from the farnesyl cation, the first reactive intermediate of the substrate, and evaluating their steric and electrostatic compatibility with the active site. The homology model of a putative pentalenene synthase (Uniprot: B5GLM7) from Streptomyces clavuligerus was used in an automated computational workflow for product prediction. Surprisingly, the workflow predicted a linear triquinane scaffold as the top product skeleton for B5GLM7. Biochemical characterization of B5GLM7 reveals the major product as (5S,7S,10R,11S)-cucumene, a sesquiterpene with a linear triquinane scaffold. To our knowledge, this is the first documentation of a terpene synthase involved in the synthesis of a linear triquinane. The success of our prediction for B5GLM7 suggests that this approach can be used to facilitate the functional assignment of novel terpene synthases.
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19
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Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL. Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. Biochim Biophys Acta 2015; 1854:1019-37. [PMID: 25900361 DOI: 10.1016/j.bbapap.2015.04.015] [Citation(s) in RCA: 550] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 03/30/2015] [Accepted: 04/14/2015] [Indexed: 11/19/2022]
Abstract
The Enzyme Function Initiative, an NIH/NIGMS-supported Large-Scale Collaborative Project (EFI; U54GM093342; http://enzymefunction.org/), is focused on devising and disseminating bioinformatics and computational tools as well as experimental strategies for the prediction and assignment of functions (in vitro activities and in vivo physiological/metabolic roles) to uncharacterized enzymes discovered in genome projects. Protein sequence similarity networks (SSNs) are visually powerful tools for analyzing sequence relationships in protein families (H.J. Atkinson, J.H. Morris, T.E. Ferrin, and P.C. Babbitt, PLoS One 2009, 4, e4345). However, the members of the biological/biomedical community have not had access to the capability to generate SSNs for their "favorite" protein families. In this article we announce the EFI-EST (Enzyme Function Initiative-Enzyme Similarity Tool) web tool (http://efi.igb.illinois.edu/efi-est/) that is available without cost for the automated generation of SSNs by the community. The tool can create SSNs for the "closest neighbors" of a user-supplied protein sequence from the UniProt database (Option A) or of members of any user-supplied Pfam and/or InterPro family (Option B). We provide an introduction to SSNs, a description of EFI-EST, and a demonstration of the use of EFI-EST to explore sequence-function space in the OMP decarboxylase superfamily (PF00215). This article is designed as a tutorial that will allow members of the community to use the EFI-EST web tool for exploring sequence/function space in protein families.
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Affiliation(s)
- John A Gerlt
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Chemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA.
| | - Jason T Bouvier
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA; Department of Biochemistry, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Daniel B Davidson
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Heidi J Imker
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Boris Sadkhin
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - David R Slater
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
| | - Katie L Whalen
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL 61801 USA
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20
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Pemberton RP, Ho KC, Tantillo DJ. Modulation of inherent dynamical tendencies of the bisabolyl cation via preorganization in epi-isozizaene synthase. Chem Sci 2015; 6:2347-2353. [PMID: 29308148 PMCID: PMC5645776 DOI: 10.1039/c4sc03782k] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2014] [Accepted: 01/30/2015] [Indexed: 01/09/2023] Open
Abstract
The relative importance of preorganization, selective transition state stabilization and inherent reactivity are assessed through quantum chemical and docking calculations for a sesquiterpene synthase (epi-isozizaene synthase, EIZS). Inherent reactivity of the bisabolyl cation, both static and dynamic, appears to determine the pathway to product, although preorganization and selective binding of the final transition state structure in the multi-step carbocation cascade that forms epi-isozizaene appear to play important roles.
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Affiliation(s)
- Ryan P Pemberton
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , CA 95616 , USA .
| | - Krystina C Ho
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , CA 95616 , USA .
| | - Dean J Tantillo
- Department of Chemistry , University of California, Davis , One Shields Avenue , Davis , CA 95616 , USA .
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