1
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Bassan R, Mondal B, Varshney M, Roy S. 1-Naphthylacetic acid appended amino acids-based hydrogels: probing of the supramolecular catalysis of ester hydrolysis reaction. NANOSCALE ADVANCES 2024; 6:3399-3409. [PMID: 38933855 PMCID: PMC11197428 DOI: 10.1039/d4na00268g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2024] [Accepted: 05/07/2024] [Indexed: 06/28/2024]
Abstract
A 1-naphthaleneacetic acid-appended phenylalanine-derivative (Nap-F) forms a stable hydrogel with a minimum gelation concentration (MGC) of 0.7% w/v (21 mM) in phosphate buffer of pH 7.4. Interestingly, Nap-F produces two-component [Nap-F + H = Nap-FH, Nap-F + K = Nap-FK and Nap-F + R = Nap-FR], three-component [Nap-F + H + K = Nap-FH-K, Nap-F + H + R = Nap-FH-R and Nap-F + K + R = Nap-FK-R] and four-component [Nap-F + H + K + R = Nap-FH-K-R] hydrogels in water with all three natural basic amino acids (H = histidine, K = lysine and R = arginine) at various combinations below its MGC. Nap-F-hydrogel forms a nice entangled nanofibrillar network structure as evidenced by field emission scanning electron microscopy (FE-SEM). Interestingly, lysine-based co-assembled two- (Nap-FK), three- (Nap-FH-K and Nap-FK-R) and four-component (Nap-FH-K-R) xerogels exhibit helical nanofibrillar morphology, which was confirmed by circular dichroism spectroscopy, FE-SEM and TEM imaging. However, histidine and arginine-based two-component (Nap-FH and Nap-FR) and three-component (Nap-FH-R) co-assembled xerogels exhibiting straight nanofibrillar morphology. In their co-assembled states, these two-, three- and four-component supramolecular hydrogels show promising esterase-like activity below their MGCs. The enhanced catalytic activity of helical fibers compared to obtained straight fibers (other than lysine-based assembled systems) suggests that the helical fibrillar nanostructure is involved in ordering the esterase-like although all supramolecular assemblies are chemically different from one another.
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Affiliation(s)
- Ruchika Bassan
- Department of Chemistry, Birla Institute of Technology and Science-Pilani K K Birla Goa Campus, NH 17B, Zuarinagar Sancoale Goa 403726 India
| | - Biplab Mondal
- School of Biological Sciences, Indian Association for the Cultivation of Science 2A & 2B, Raja S. C. Mullick Road, Jadavpur Kolkata-700034 West Bengal India
| | - Mayank Varshney
- Senior Application Scientist, Characterization Division, Anton Paar India Pvt. Ltd. 582, Phase V, Udyog Vihar Industrial Area Gurgaon 122016 Haryana India
| | - Subhasish Roy
- Department of Chemistry, Birla Institute of Technology and Science-Pilani K K Birla Goa Campus, NH 17B, Zuarinagar Sancoale Goa 403726 India
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2
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Marshall LR, Korendovych IV. Avoiding common pitfalls in designing kinetic protocols for catalytic amyloid studies. Methods Enzymol 2024; 697:1-13. [PMID: 38816119 DOI: 10.1016/bs.mie.2024.03.029] [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: 06/01/2024]
Abstract
Kinetic characterization of catalytic amyloids arguably presents a most challenging type of kinetic experiment where careful consideration of many factors is required. Here we outline common pitfalls in devising kinetic studies in such systems. Unlike the more specific protocols for various applications described in this volume, this chapter deals with general issues in setting up kinetic experiments that are incredibly important but often go without explicit mention in the specialized literature. The kinetic fundamentals described here can be also be of use to the enzymologists working with more traditional catalysts.
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Affiliation(s)
- Liam R Marshall
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States
| | - Ivan V Korendovych
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, United States.
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3
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Marshall LR, Bhattacharya S, Korendovych IV. Fishing for Catalysis: Experimental Approaches to Narrowing Search Space in Directed Evolution of Enzymes. JACS AU 2023; 3:2402-2412. [PMID: 37772192 PMCID: PMC10523367 DOI: 10.1021/jacsau.3c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/30/2023]
Abstract
Directed evolution has transformed protein engineering offering a path to rapid improvement of protein properties. Yet, in practice it is limited by the hyper-astronomic protein sequence search space, and approaches to identify mutagenic hot spots, i.e., locations where mutations are most likely to have a productive impact, are needed. In this perspective, we categorize and discuss recent progress in the experimental approaches (broadly defined as structural, bioinformatic, and dynamic) to hot spot identification. Recent successes in harnessing protein dynamics and machine learning approaches provide new opportunities for the field and will undoubtedly help directed evolution reach its full potential.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse
University, 111 College Place, Syracuse, New York 13224, United States
| | - Sagar Bhattacharya
- Department of Chemistry, Syracuse
University, 111 College Place, Syracuse, New York 13224, United States
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse
University, 111 College Place, Syracuse, New York 13224, United States
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4
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Casadevall G, Pierce C, Guan B, Iglesias-Fernandez J, Lim HY, Greenberg LR, Walsh ME, Shi K, Gordon W, Aihara H, Evans RL, Kazlauskas R, Osuna S. Designing Efficient Enzymes: Eight Predicted Mutations Convert a Hydroxynitrile Lyase into an Efficient Esterase. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.23.554512. [PMID: 37662272 PMCID: PMC10473745 DOI: 10.1101/2023.08.23.554512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Hydroxynitrile lyase from rubber tree (HbHNL) shares 45% identical amino acid residues with the homologous esterase from tobacco, SABP2, but the two enzymes catalyze different reactions. The x-ray structures reveal a serine-histidine-aspartate catalytic triad in both enzymes along with several differing amino acid residues within the active site. Previous exchange of three amino acid residues in the active site of HbHNL with the corresponding amino acid residue in SABP2 (T11G-E79H-K236M) created variant HNL3, which showed low esterase activity toward p-nitrophenyl acetate. Further structure comparison reveals additional differences surrounding the active site. HbHNL contains an improperly positioned oxyanion hole residue and differing solvation of the catalytic aspartate. We hypothesized that correcting these structural differences would impart good esterase activity on the corresponding HbHNL variant. To predict the amino acid substitutions needed to correct the structure, we calculated shortest path maps for both HbHNL and SABP2, which reveal correlated movements of amino acids in the two enzymes. Replacing four amino acid residues (C81L-N104T-V106F-G176S) whose movements are connected to the movements of the catalytic residues yielded variant HNL7TV (stabilizing substitution H103V was also added), which showed an esterase catalytic efficiency comparable to that of SABP2. The x-ray structure of an intermediate variant, HNL6V, showed an altered solvation of the catalytic aspartate and a partially corrected oxyanion hole. This dramatic increase in catalytic efficiency demonstrates the ability of shortest path maps to predict which residues outside the active site contribute to catalytic activity.
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Affiliation(s)
- Guillem Casadevall
- Institut de Química Computacional i Catálisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Colin Pierce
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Bo Guan
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Javier Iglesias-Fernandez
- Institut de Química Computacional i Catálisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
| | - Huey-Yee Lim
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Lauren R Greenberg
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Meghan E Walsh
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Ke Shi
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Wendy Gordon
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Hideki Aihara
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Robert L Evans
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Romas Kazlauskas
- Biotechnology Institute and Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 1479 Gortner Avenue, Saint Paul, MN 55108 USA
| | - Sílvia Osuna
- Institut de Química Computacional i Catálisi and Departament de Química, Universitat de Girona, Carrer Maria Aurèlia Capmany 69, 17003 Girona, Spain
- ICREA, Barcelona, Spain
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5
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Platero-Rochart D, Krivobokova T, Gastegger M, Reibnegger G, Sánchez-Murcia PA. Prediction of Enzyme Catalysis by Computing Reaction Energy Barriers via Steered QM/MM Molecular Dynamics Simulations and Machine Learning. J Chem Inf Model 2023; 63:4623-4632. [PMID: 37479222 PMCID: PMC10430765 DOI: 10.1021/acs.jcim.3c00772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Indexed: 07/23/2023]
Abstract
The prediction of enzyme activity is one of the main challenges in catalysis. With computer-aided methods, it is possible to simulate the reaction mechanism at the atomic level. However, these methods are usually expensive if they are to be used on a large scale, as they are needed for protein engineering campaigns. To alleviate this situation, machine learning methods can help in the generation of predictive-decision models. Herein, we test different regression algorithms for the prediction of the reaction energy barrier of the rate-limiting step of the hydrolysis of mono-(2-hydroxyethyl)terephthalic acid by the MHETase ofIdeonella sakaiensis. As a training data set, we use steered quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulation snapshots and their corresponding pulling work values. We have explored three algorithms together with three chemical representations. As an outcome, our trained models are able to predict pulling works along the steered QM/MM MD simulations with a mean absolute error below 3 kcal mol-1 and a score value above 0.90. More challenging is the prediction of the energy maximum with a single geometry. Whereas the use of the initial snapshot of the QM/MM MD trajectory as input geometry yields a very poor prediction of the reaction energy barrier, the use of an intermediate snapshot of the former trajectory brings the score value above 0.40 with a low mean absolute error (ca. 3 kcal mol-1). Altogether, we have faced in this work some initial challenges of the final goal of getting an efficient workflow for the semiautomatic prediction of enzyme-catalyzed energy barriers and catalytic efficiencies.
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Affiliation(s)
- Daniel Platero-Rochart
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
| | - Tatyana Krivobokova
- Department
of Statistics and Operations Research, University
of Vienna, Oskar-Morgenstern-Platz 1, A-1090 Vienna, Austria
| | - Michael Gastegger
- Institute
of Software Engineering and Theoretical Computer Science, Machine
Learning Group, Technische Universität, 10587 Berlin, Germany
| | - Gilbert Reibnegger
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
| | - Pedro A. Sánchez-Murcia
- Laboratory
of Computer-Aided Molecular Design, Division of Medicinal Chemistry,
Otto-Loewi Research Center, Medical University
of Graz, Neue Stiftingtalstraße 6/III, A-8010 Graz, Austria
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6
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Belinskaia DA, Voronina PA, Popova PI, Voitenko NG, Shmurak VI, Vovk MA, Baranova TI, Batalova AA, Korf EA, Avdonin PV, Jenkins RO, Goncharov NV. Albumin Is a Component of the Esterase Status of Human Blood Plasma. Int J Mol Sci 2023; 24:10383. [PMID: 37373530 DOI: 10.3390/ijms241210383] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/13/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The esterase status of blood plasma can claim to be one of the universal markers of various diseases; therefore, it deserves attention when searching for markers of the severity of COVID-19 and other infectious and non-infectious pathologies. When analyzing the esterase status of blood plasma, the esterase activity of serum albumin, which is the major protein in the blood of mammals, should not be ignored. The purpose of this study is to expand understanding of the esterase status of blood plasma and to evaluate the relationship of the esterase status, which includes information on the amount and enzymatic activity of human serum albumin (HSA), with other biochemical parameters of human blood, using the example of surviving and deceased patients with confirmed COVID-19. In experiments in vitro and in silico, the activity of human plasma and pure HSA towards various substrates was studied, and the effect of various inhibitors on this activity was tested. Then, a comparative analysis of the esterase status and a number of basic biochemical parameters of the blood plasma of healthy subjects and patients with confirmed COVID-19 was performed. Statistically significant differences have been found in esterase status and biochemical indices (including albumin levels) between healthy subjects and patients with COVID-19, as well as between surviving and deceased patients. Additional evidence has been obtained for the importance of albumin as a diagnostic marker. Of particular interest is a new index, [Urea] × [MDA] × 1000/(BChEb × [ALB]), which in the group of deceased patients was 10 times higher than in the group of survivors and 26 times higher than the value in the group of apparently healthy elderly subjects.
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Affiliation(s)
- Daria A Belinskaia
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Polina A Voronina
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Polina I Popova
- City Polyclinic No. 112, 25 Academician Baykov Str., 195427 St. Petersburg, Russia
| | - Natalia G Voitenko
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Vladimir I Shmurak
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Mikhail A Vovk
- Centre for Magnetic Resonance, St. Petersburg State University, Universitetskij pr., 26, Peterhof, 198504 St. Petersburg, Russia
| | - Tatiana I Baranova
- Faculty of Biology, St. Petersburg State University, 7-9 Universitetskaya Emb., 199034 St. Petersburg, Russia
| | - Anastasia A Batalova
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Ekaterina A Korf
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
| | - Pavel V Avdonin
- Koltsov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilova Str., 119334 Moscow, Russia
| | - Richard O Jenkins
- Leicester School of Allied Health Sciences, De Montfort University, The Gateway, Leicester LE1 9BH, UK
| | - Nikolay V Goncharov
- Sechenov Institute of Evolutionary Physiology and Biochemistry, Russian Academy of Sciences, pr. Torez 44, 194223 St. Petersburg, Russia
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7
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Ożga K, Berlicki Ł. Miniprotein-Based Artificial Retroaldolase. ACS Catal 2022. [DOI: 10.1021/acscatal.2c04311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Katarzyna Ożga
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
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8
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Fernandez-Lopez L, Roda S, Gonzalez-Alfonso JL, Plou FJ, Guallar V, Ferrer M. Design and Characterization of In-One Protease-Esterase PluriZyme. Int J Mol Sci 2022; 23:13337. [PMID: 36362119 PMCID: PMC9655419 DOI: 10.3390/ijms232113337] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 10/14/2023] Open
Abstract
Proteases are abundant in prokaryotic genomes (~10 per genome), but their recovery encounters expression problems, as only 1% can be produced at high levels; this value differs from that of similarly abundant esterases (1-15 per genome), 50% of which can be expressed at good levels. Here, we design a catalytically efficient artificial protease that can be easily produced. The PluriZyme EH1AB1 with two active sites supporting the esterase activity was employed. A Leu24Cys mutation in EH1AB1, remodelled one of the esterase sites into a proteolytic one through the incorporation of a catalytic dyad (Cys24 and His214). The resulting artificial enzyme, EH1AB1C, efficiently hydrolysed (azo)casein at pH 6.5-8.0 and 60-70 °C. The presence of both esterase and protease activities in the same scaffold allowed the one-pot cascade synthesis (55.0 ± 0.6% conversion, 24 h) of L-histidine methyl ester from the dipeptide L-carnosine in the presence of methanol. This study demonstrates that active sites supporting proteolytic activity can be artificially introduced into an esterase scaffold to design easy-to-produce in-one protease-esterase PluriZymes for cascade reactions, namely, the synthesis of amino acid esters from dipeptides. It is also possible to design artificial proteases with good production yields, in contrast to natural proteases that are difficult to express.
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Affiliation(s)
| | - Sergi Roda
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | | | | | - Víctor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
| | - Manuel Ferrer
- Department of Applied Biocatalysis, ICP, CSIC, 28049 Madrid, Spain
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9
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Koebke KJ, Pinter TBJ, Pitts WC, Pecoraro VL. Catalysis and Electron Transfer in De Novo Designed Metalloproteins. Chem Rev 2022; 122:12046-12109. [PMID: 35763791 PMCID: PMC10735231 DOI: 10.1021/acs.chemrev.1c01025] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the hallmark advances in our understanding of metalloprotein function is showcased in our ability to design new, non-native, catalytically active protein scaffolds. This review highlights progress and milestone achievements in the field of de novo metalloprotein design focused on reports from the past decade with special emphasis on de novo designs couched within common subfields of bioinorganic study: heme binding proteins, monometal- and dimetal-containing catalytic sites, and metal-containing electron transfer sites. Within each subfield, we highlight several of what we have identified as significant and important contributions to either our understanding of that subfield or de novo metalloprotein design as a discipline. These reports are placed in context both historically and scientifically. General suggestions for future directions that we feel will be important to advance our understanding or accelerate discovery are discussed.
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Affiliation(s)
- Karl J. Koebke
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
| | | | - Winston C. Pitts
- Department of Chemistry, University of Michigan Ann Arbor, MI 48109 USA
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10
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Abstract
The ability to design efficient enzymes from scratch would have a profound effect on chemistry, biotechnology and medicine. Rapid progress in protein engineering over the past decade makes us optimistic that this ambition is within reach. The development of artificial enzymes containing metal cofactors and noncanonical organocatalytic groups shows how protein structure can be optimized to harness the reactivity of nonproteinogenic elements. In parallel, computational methods have been used to design protein catalysts for diverse reactions on the basis of fundamental principles of transition state stabilization. Although the activities of designed catalysts have been quite low, extensive laboratory evolution has been used to generate efficient enzymes. Structural analysis of these systems has revealed the high degree of precision that will be needed to design catalysts with greater activity. To this end, emerging protein design methods, including deep learning, hold particular promise for improving model accuracy. Here we take stock of key developments in the field and highlight new opportunities for innovation that should allow us to transition beyond the current state of the art and enable the robust design of biocatalysts to address societal needs.
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11
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Green biomanufacturing promoted by automatic retrobiosynthesis planning and computational enzyme design. Chin J Chem Eng 2022. [DOI: 10.1016/j.cjche.2021.08.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Mariz BDP, Carvalho S, Batalha IL, Pina AS. Artificial enzymes bringing together computational design and directed evolution. Org Biomol Chem 2021; 19:1915-1925. [PMID: 33443278 DOI: 10.1039/d0ob02143a] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Enzymes are proteins that catalyse chemical reactions and, as such, have been widely used to facilitate a variety of natural and industrial processes, dating back to ancient times. In fact, the global enzymes market is projected to reach $10.5 billion in 2024. The development of computational and DNA editing tools boosted the creation of artificial enzymes (de novo enzymes) - synthetic or organic molecules created to present abiological catalytic functions. These novel catalysts seek to expand the catalytic power offered by nature through new functions and properties. In this manuscript, we discuss the advantages of combining computational design with directed evolution for the development of artificial enzymes and how this strategy allows to fill in the gaps that these methods present individually by providing key insights about the sequence-function relationship. We also review examples, and respective strategies, where this approach has enabled the creation of artificial enzymes with promising catalytic activity. Such key enabling technologies are opening new windows of opportunity in a variety of industries, including pharmaceutical, chemical, biofuels, and food, contributing towards a more sustainable development.
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Affiliation(s)
- Beatriz de Pina Mariz
- UCIBIO, Chemistry Department, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal.
| | - Sara Carvalho
- UCIBIO, Chemistry Department, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal.
| | - Iris L Batalha
- Nanoscience Centre, Department of Engineering, University of Cambridge, 11 J.J. Thomson Avenue, Cambridge, CB3 0FF, UK
| | - Ana Sofia Pina
- UCIBIO, Chemistry Department, School of Science and Technology, NOVA University of Lisbon, 2829-516 Caparica, Portugal.
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13
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Roda S, Robles-Martín A, Xiang R, Kazemi M, Guallar V. Structural-Based Modeling in Protein Engineering. A Must Do. J Phys Chem B 2021; 125:6491-6500. [PMID: 34106727 DOI: 10.1021/acs.jpcb.1c02545] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Biotechnological solutions will be a key aspect in our immediate future society, where optimized enzymatic processes through enzyme engineering might be an important solution for waste transformation, clean energy production, biodegradable materials, and green chemistry, for example. Here we advocate the importance of structural-based bioinformatics and molecular modeling tools in such developments. We summarize our recent experiences indicating a great prediction/success ratio, and we suggest that an early in silico phase should be performed in enzyme engineering studies. Moreover, we demonstrate the potential of a new technique combining Rosetta and PELE, which could provide a faster and more automated procedure, an essential aspect for a broader use.
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Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | | | - Ruite Xiang
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Masoud Kazemi
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Spain
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14
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Hamley IW. Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures. Biomacromolecules 2021; 22:1835-1855. [PMID: 33843196 PMCID: PMC8154259 DOI: 10.1021/acs.biomac.1c00240] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/31/2021] [Indexed: 12/15/2022]
Abstract
Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.
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Affiliation(s)
- Ian W. Hamley
- Department of Chemistry, University of Reading, RG6 6AD Reading, United Kingdom
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15
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Pereira JM, Vieira M, Santos SM. Step-by-step design of proteins for small molecule interaction: A review on recent milestones. Protein Sci 2021; 30:1502-1520. [PMID: 33934427 DOI: 10.1002/pro.4098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 04/21/2021] [Accepted: 04/23/2021] [Indexed: 01/01/2023]
Abstract
Protein design is the field of synthetic biology that aims at developing de novo custom-made proteins and peptides for specific applications. Despite exploring an ambitious goal, recent computational advances in both hardware and software technologies have paved the way to high-throughput screening and detailed design of novel folds and improved functionalities. Modern advances in the field of protein design for small molecule targeting are described in this review, organized in a step-by-step fashion: from the conception of a new or upgraded active binding site, to scaffold design, sequence optimization, and experimental expression of the custom protein. In each step, contemporary examples are described, and state-of-the-art software is briefly explored.
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Affiliation(s)
- José M Pereira
- CICECO & Departamento de Química, Universidade de Aveiro, Aveiro, Portugal
| | - Maria Vieira
- CICECO & Departamento de Química, Universidade de Aveiro, Aveiro, Portugal
| | - Sérgio M Santos
- CICECO & Departamento de Química, Universidade de Aveiro, Aveiro, Portugal
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16
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Bhaskaran A, Aitken HM, Xiao Z, Blyth M, Nothling MD, Kamdar S, O'Mara ML, Connal LA. Enzyme inspired polymer functionalized with an artificial catalytic triad. POLYMER 2021. [DOI: 10.1016/j.polymer.2021.123735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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17
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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18
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Naudin EA, McEwen AG, Tan SK, Poussin-Courmontagne P, Schmitt JL, Birck C, DeGrado WF, Torbeev V. Acyl Transfer Catalytic Activity in De Novo Designed Protein with N-Terminus of α-Helix As Oxyanion-Binding Site. J Am Chem Soc 2021; 143:3330-3339. [PMID: 33635059 PMCID: PMC8012002 DOI: 10.1021/jacs.0c10053] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The design of catalytic proteins with functional sites capable of specific chemistry is gaining momentum and a number of artificial enzymes have recently been reported, including hydrolases, oxidoreductases, retro-aldolases, and others. Our goal is to develop a peptide ligase for robust catalysis of amide bond formation that possesses no stringent restrictions to the amino acid composition at the ligation junction. We report here the successful completion of the first step in this long-term project by building a completely de novo protein with predefined acyl transfer catalytic activity. We applied a minimalist approach to rationally design an oxyanion hole within a small cavity that contains an adjacent thiol nucleophile. The N-terminus of the α-helix with unpaired hydrogen-bond donors was exploited as a structural motif to stabilize negatively charged tetrahedral intermediates in nucleophilic addition-elimination reactions at the acyl group. Cysteine acting as a principal catalytic residue was introduced at the second residue position of the α-helix N-terminus in a designed three-α-helix protein based on structural informatics prediction. We showed that this minimal set of functional elements is sufficient for the emergence of catalytic activity in a de novo protein. Using peptide-αthioesters as acyl-donors, we demonstrated their catalyzed amidation concomitant with hydrolysis and proved that the environment at the catalytic site critically influences the reaction outcome. These results represent a promising starting point for the development of efficient catalysts for protein labeling, conjugation, and peptide ligation.
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Affiliation(s)
- Elise A Naudin
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Alastair G McEwen
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Sophia K Tan
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Pierre Poussin-Courmontagne
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - Jean-Louis Schmitt
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
| | - Catherine Birck
- Integrated Structural Biology Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS (UMR 7104), INSERM (U1258), University of Strasbourg, Illkirch 67404, France
| | - William F DeGrado
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California San Francisco, San Francisco, California 94158-9001, United States
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS), International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg, CNRS (UMR 7006), Strasbourg 67000, France
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Pollastrini M, Marafon G, Clayden J, Moretto A. Light-mediated control of activity in a photosensitive foldamer that mimics an esterase. Chem Commun (Camb) 2021; 57:2269-2272. [PMID: 33533349 DOI: 10.1039/d0cc08309g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a catalytic foldamer in which a fumaramide chromophore links a Ser residue to a helical domain that contains within its sequence the residues His and Asp. Photoisomerization of the fumaramide chromophore (with E geometry) to the corresponding maleamide (with Z geometry) brings together a 'catalytic triad' of Ser, His, and Asp, triggering esterase activity that is absent in the fumaramide isomer. The fumaramide/maleamide linker thus acts as a light-sensitive switchable cofactor for activation of catalytic activity in short foldamers.
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Affiliation(s)
- Matteo Pollastrini
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy.
| | - Giulia Marafon
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy.
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Alessandro Moretto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy.
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20
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Mikolajczak DJ, Berger AA, Koksch B. Catalytically Active Peptide-Gold Nanoparticle Conjugates: Prospecting for Artificial Enzymes. Angew Chem Int Ed Engl 2020; 59:8776-8785. [PMID: 31905254 PMCID: PMC7318681 DOI: 10.1002/anie.201908625] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 11/27/2019] [Indexed: 12/12/2022]
Abstract
The self-assembly of peptides onto the surface of gold nanoparticles has emerged as a promising strategy towards the creation of artificial enzymes. The resulting high local peptide density surrounding the nanoparticle leads to cooperative and synergistic effects, which result in rate accelerations and distinct catalytic properties compared to the unconjugated peptide. This Minireview summarizes contributions to and progress made in the field of catalytically active peptide-gold nanoparticle conjugates. The origin of distinct properties, as well as potential applications, are also discussed.
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Affiliation(s)
- Dorian J. Mikolajczak
- Department of Biology, Chemistry and PharmacyFreie Universität BerlinTakustraße 314195BerlinGermany
| | - Allison A. Berger
- Department of Biology, Chemistry and PharmacyFreie Universität BerlinTakustraße 314195BerlinGermany
| | - Beate Koksch
- Department of Biology, Chemistry and PharmacyFreie Universität BerlinTakustraße 314195BerlinGermany
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21
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Enzymes with noncanonical amino acids. Curr Opin Chem Biol 2020; 55:136-144. [DOI: 10.1016/j.cbpa.2020.01.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/10/2019] [Accepted: 01/15/2020] [Indexed: 12/19/2022]
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22
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Mikolajczak DJ, Berger AA, Koksch B. Catalytically Active Peptide–Gold Nanoparticle Conjugates: Prospecting for Artificial Enzymes. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201908625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Dorian J. Mikolajczak
- Department of Biology, Chemistry and Pharmacy Freie Universität Berlin Takustraße 3 14195 Berlin Germany
| | - Allison A. Berger
- Department of Biology, Chemistry and Pharmacy Freie Universität Berlin Takustraße 3 14195 Berlin Germany
| | - Beate Koksch
- Department of Biology, Chemistry and Pharmacy Freie Universität Berlin Takustraße 3 14195 Berlin Germany
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23
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Wang H, Lin X, Li S, Lin J, Xie C, Liu D, Yao D. Rational molecular design for improving digestive enzyme resistance of beta-glucosidase from Trichoderma viride based on inhibition of bound state formation. Enzyme Microb Technol 2019; 133:109465. [PMID: 31874695 DOI: 10.1016/j.enzmictec.2019.109465] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 11/18/2022]
Abstract
Beta-glucosidase (BGL1) is widely used in animal feed industries. However, degradation caused by digestive enzymes in the intestine hampers its application. Improving the resistance of feed enzymes against proteases is crucial in livestock farming. To improve the resistance of beta-glucosidase against pepsin and trypsin, a rational molecular design based on the inhibition of bound-state formation and secondary design was developed. The strategy includes: (1) prediction of the interaction surface of the pepsin-BGL1 complex structure, (2) prediction of key amino acids affecting the formation of the complex, (3) optimization of pepsin-resistant mutants by structural evaluation, (4) secondary molecular design based on pepsin-resistant mutants, and optimization of pepsin and trypsin-resistant mutants. Two BGL1 protein mutants (BGL1Q627C and BGL1Q627C/R543H/R646W) were constructed, and then mutated and wild-type BGL1s were expressed in Pichia pastoris. The half-life of BGL1Q627C and BGL1Q627C/R543H/R646W were 1.36 and 1.51 times that of the wild type upon pepsin exposure, respectively. For trypsin resistance, the half-life were 0.93 and 1.53 times that of the wild type, respectively. Compare to those of the wild type, most of the basic enzymatic properties of both mutants were not significantly changed except for increased Michaelis constants. The rational design method can be used as a guide for modifying other feed enzymes.
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Affiliation(s)
- Hao Wang
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; Department of Bioengineering, Jinan University, Guangzhou City, Guangdong Province, 510632, China
| | - Xiangna Lin
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou City, Guangdong Province, 510632, China
| | - Shuang Li
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; Department of Bioengineering, Jinan University, Guangzhou City, Guangdong Province, 510632, China
| | - Jianlin Lin
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China
| | - Chunfang Xie
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; Department of Bioengineering, Jinan University, Guangzhou City, Guangdong Province, 510632, China
| | - Daling Liu
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; Department of Bioengineering, Jinan University, Guangzhou City, Guangdong Province, 510632, China.
| | - Dongsheng Yao
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou City, Guangdong Province, 510632, China.
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24
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Rodon Fores J, Criado‐Gonzalez M, Chaumont A, Carvalho A, Blanck C, Schmutz M, Serra CA, Boulmedais F, Schaaf P, Jierry L. Supported Catalytically Active Supramolecular Hydrogels for Continuous Flow Chemistry. Angew Chem Int Ed Engl 2019; 58:18817-18822. [DOI: 10.1002/anie.201909424] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 09/18/2019] [Indexed: 11/09/2022]
Affiliation(s)
- Jennifer Rodon Fores
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Miryam Criado‐Gonzalez
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche MédicaleINSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de StrasbourgFaculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Alain Chaumont
- Université de StrasbourgFaculté de Chimie, UMR7140 1 rue Blaise Pascal 67008 Strasbourg Cedex France
| | - Alain Carvalho
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christian Blanck
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Marc Schmutz
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christophe A. Serra
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - F. Boulmedais
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Pierre Schaaf
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche MédicaleINSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de StrasbourgFaculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Loïc Jierry
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
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25
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Alonso S, Santiago G, Cea-Rama I, Fernandez-Lopez L, Coscolín C, Modregger J, Ressmann AK, Martínez-Martínez M, Marrero H, Bargiela R, Pita M, Gonzalez-Alfonso JL, Briand ML, Rojo D, Barbas C, Plou FJ, Golyshin PN, Shahgaldian P, Sanz-Aparicio J, Guallar V, Ferrer M. Genetically engineered proteins with two active sites for enhanced biocatalysis and synergistic chemo- and biocatalysis. Nat Catal 2019. [DOI: 10.1038/s41929-019-0394-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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26
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Rivilla I, Odriozola-Gimeno M, Aires A, Gimeno A, Jiménez-Barbero J, Torrent-Sucarrat M, Cortajarena AL, Cossío FP. Discovering Biomolecules with Huisgenase Activity: Designed Repeat Proteins as Biocatalysts for (3 + 2) Cycloadditions. J Am Chem Soc 2019; 142:762-776. [DOI: 10.1021/jacs.9b06823] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Iván Rivilla
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
| | - Mikel Odriozola-Gimeno
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
| | - Antonio Aires
- Parque Tecnológico de San Sebastián, CIC biomaGUNE, Paseo Miramón 182, 20014 Donostia/San Sebastián, Spain
| | - Ana Gimeno
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
| | - Jesús Jiménez-Barbero
- Molecular Recognition & Host−Pathogen Interactions Unit, CIC bioGUNE, Bizkaia Technology Park, Building 801A, 48170 Derio, Spain
- Department of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa 48940, Bizkaia, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Aitziber L. Cortajarena
- Parque Tecnológico de San Sebastián, CIC biomaGUNE, Paseo Miramón 182, 20014 Donostia/San Sebastián, Spain
- Ikerbasque, Basque Foundation for Science, Ma Diaz de Haro 3, Bilbao 48013, Spain
| | - Fernando P. Cossío
- Department of Organic Chemistry I, Centro de Innovación en Química Avanzada (ORFEO−CINQA), Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU) and Donostia International Physics Center (DIPC), P° Manuel Lardizabal 3, E-20018 Donostia/San Sebastián, Spain
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27
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Rodon Fores J, Criado‐Gonzalez M, Chaumont A, Carvalho A, Blanck C, Schmutz M, Serra CA, Boulmedais F, Schaaf P, Jierry L. Supported Catalytically Active Supramolecular Hydrogels for Continuous Flow Chemistry. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201909424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jennifer Rodon Fores
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Miryam Criado‐Gonzalez
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche MédicaleINSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de StrasbourgFaculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Alain Chaumont
- Université de StrasbourgFaculté de Chimie, UMR7140 1 rue Blaise Pascal 67008 Strasbourg Cedex France
| | - Alain Carvalho
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christian Blanck
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Marc Schmutz
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Christophe A. Serra
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - F. Boulmedais
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
| | - Pierre Schaaf
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
- Institut National de la Santé et de la Recherche MédicaleINSERM Unité 1121 11 rue Humann 67085 Strasbourg Cedex France
- Université de StrasbourgFaculté de Chirurgie Dentaire 8 rue Sainte Elisabeth 67000 Strasbourg France
| | - Loïc Jierry
- Université de StrasbourgCNRSInstitut Charles Sadron (UPR22) 23 rue du Loess, BP 84047 67034 Strasbourg Cedex 2 France
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28
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Marshall LR, Zozulia O, Lengyel-Zhand Z, Korendovych IV. Minimalist de novo Design of Protein Catalysts. ACS Catal 2019; 9:9265-9275. [PMID: 34094654 PMCID: PMC8174531 DOI: 10.1021/acscatal.9b02509] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of protein design has grown enormously in the past few decades. In this review we discuss the minimalist approach to design of artificial enzymes, in which protein sequences are created with the minimum number of elements for folding and function. This method relies on identifying starting points in catalytically inert scaffolds for active site installation. The progress of the field from the original helical assemblies of the 1980s to the more complex structures of the present day is discussed, highlighting the variety of catalytic reactions which have been achieved using these methods. We outline the strengths and weaknesses of the minimalist approaches, describe representative design cases and put it in the general context of the de novo design of proteins.
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Affiliation(s)
- Liam R. Marshall
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Zsofia Lengyel-Zhand
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
| | - Ivan V. Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA
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29
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Burke AJ, Lovelock SL, Frese A, Crawshaw R, Ortmayer M, Dunstan M, Levy C, Green AP. Design and evolution of an enzyme with a non-canonical organocatalytic mechanism. Nature 2019; 570:219-223. [PMID: 31132786 DOI: 10.1038/s41586-019-1262-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/13/2019] [Indexed: 11/09/2022]
Abstract
The combination of computational design and laboratory evolution is a powerful and potentially versatile strategy for the development of enzymes with new functions1-4. However, the limited functionality presented by the genetic code restricts the range of catalytic mechanisms that are accessible in designed active sites. Inspired by mechanistic strategies from small-molecule organocatalysis5, here we report the generation of a hydrolytic enzyme that uses Nδ-methylhistidine as a non-canonical catalytic nucleophile. Histidine methylation is essential for catalytic function because it prevents the formation of unreactive acyl-enzyme intermediates, which has been a long-standing challenge when using canonical nucleophiles in enzyme design6-10. Enzyme performance was optimized using directed evolution protocols adapted to an expanded genetic code, affording a biocatalyst capable of accelerating ester hydrolysis with greater than 9,000-fold increased efficiency over free Nδ-methylhistidine in solution. Crystallographic snapshots along the evolutionary trajectory highlight the catalytic devices that are responsible for this increase in efficiency. Nδ-methylhistidine can be considered to be a genetically encodable surrogate of the widely employed nucleophilic catalyst dimethylaminopyridine11, and its use will create opportunities to design and engineer enzymes for a wealth of valuable chemical transformations.
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Affiliation(s)
- Ashleigh J Burke
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Sarah L Lovelock
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Amina Frese
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Rebecca Crawshaw
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Mary Ortmayer
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Mark Dunstan
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Colin Levy
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, University of Manchester, Manchester, UK.
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30
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Carvalho HF, Branco RJF, Leite FAS, Matzapetakis M, Roque ACA, Iranzo O. Hydrolytic zinc metallopeptides using a computational multi-state design approach. Catal Sci Technol 2019. [DOI: 10.1039/c9cy01364d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combination of multi-state design and long-timescale conformational dynamics as a powerful strategy to obtain metalloenzymes.
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Affiliation(s)
- Henrique F. Carvalho
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Ricardo J. F. Branco
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Fábio A. S. Leite
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
| | - Manolis Matzapetakis
- Instituto de Tecnologia Química e Biológica António Xavier
- Universidade Nova de Lisboa
- 2780-157 Oeiras
- Portugal
| | - A. Cecília A. Roque
- UCIBIO
- Departamento de Química
- Faculdade de Ciências e Tecnologia
- Universidade Nova de Lisboa
- 2829-516 Caparica
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31
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Studer S, Hansen DA, Pianowski ZL, Mittl PRE, Debon A, Guffy SL, Der BS, Kuhlman B, Hilvert D. Evolution of a highly active and enantiospecific metalloenzyme from short peptides. Science 2018; 362:1285-1288. [DOI: 10.1126/science.aau3744] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022]
Abstract
Primordial sequence signatures in modern proteins imply ancestral origins tracing back to simple peptides. Although short peptides seldom adopt unique folds, metal ions might have templated their assembly into higher-order structures in early evolution and imparted useful chemical reactivity. Recapitulating such a biogenetic scenario, we have combined design and laboratory evolution to transform a zinc-binding peptide into a globular enzyme capable of accelerating ester cleavage with exacting enantiospecificity and high catalytic efficiency (kcat/KM~ 106M−1s−1). The simultaneous optimization of structure and function in a naïve peptide scaffold not only illustrates a plausible enzyme evolutionary pathway from the distant past to the present but also proffers exciting future opportunities for enzyme design and engineering.
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32
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Lechner H, Ferruz N, Höcker B. Strategies for designing non-natural enzymes and binders. Curr Opin Chem Biol 2018; 47:67-76. [PMID: 30248579 DOI: 10.1016/j.cbpa.2018.07.022] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 07/16/2018] [Accepted: 07/17/2018] [Indexed: 12/20/2022]
Abstract
The design of tailor-made enzymes is a major goal in biochemical research that can result in wide-range applications and will lead to a better understanding of how proteins fold and function. In this review we highlight recent advances in enzyme and small molecule binder design. A focus is placed on novel strategies for the design of scaffolds, developments in computational methods, and recent applications of these techniques on receptors, sensors, and enzymes. Further, the integration of computational and experimental methodologies is discussed. The outlined examples of designed enzymes and binders for various purposes highlight the importance of this topic and underline the need for tailor-made proteins.
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Affiliation(s)
- Horst Lechner
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Noelia Ferruz
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany
| | - Birte Höcker
- Department of Biochemistry, University of Bayreuth, 95447 Bayreuth, Germany.
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33
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Affiliation(s)
- Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244, USA
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244, USA
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34
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Gosavi PM, Jayachandran M, Rempillo JJL, Zozulia O, Makhlynets OV, Korendovych IV. A Designed Enzyme Promotes Selective Post-translational Acylation. Chembiochem 2018; 19:1605-1608. [PMID: 29756279 DOI: 10.1002/cbic.201800196] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Indexed: 11/10/2022]
Abstract
A computationally designed, allosterically regulated catalyst (CaM M144H) produced by substituting a single residue in calmodulin, a non-enzymatic protein, is capable of efficient and site selective post-translational acylation of lysines in peptides with highly diverse sequences. Calmodulin's binding partners are involved in regulating a large number of cellular processes; this new chemical-biology tool will help to identify them and provide structural insight into their interactions with calmodulin.
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Affiliation(s)
- Pallavi M Gosavi
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Megha Jayachandran
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Joel J L Rempillo
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Oleksii Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Olga V Makhlynets
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA
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35
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Drewniak M, Węglarz-Tomczak E, Ożga K, Rudzińska-Szostak E, Macegoniuk K, Tomczak JM, Bejger M, Rypniewski W, Berlicki Ł. Helix-loop-helix peptide foldamers and their use in the construction of hydrolase mimetics. Bioorg Chem 2018; 81:356-361. [PMID: 30195249 DOI: 10.1016/j.bioorg.2018.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 01/18/2023]
Abstract
De novo designed helix-loop-helix peptide foldamers containing cis-2-aminocyclopentanecarboxylic acid residues were evaluated for their conformational stability and possible use in enzyme mimetic development. The correlation between hydrogen bond network size and conformational stability was demonstrated through CD and NMR spectroscopies. Molecules incorporating a Cys/His/Glu triad exhibited enzyme-like hydrolytic activity.
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Affiliation(s)
- Magda Drewniak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ewelina Węglarz-Tomczak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Macegoniuk
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jakub M Tomczak
- Amsterdam Machine Learning Lab, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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36
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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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37
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Abstract
Self-assembly of molecules often results in new emerging properties. Even very short peptides can self-assemble into structures with a variety of physical and structural characteristics. Remarkably, many peptide assemblies show high catalytic activity in model reactions reaching efficiencies comparable to those found in natural enzymes by weight. In this review, we discuss different strategies used to rationally develop self-assembled peptide catalysts with natural and unnatural backbones as well as with metal-containing cofactors.
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Affiliation(s)
- O Zozulia
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY 13244, USA.
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38
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Li R, Wijma HJ, Song L, Cui Y, Otzen M, Tian Y, Du J, Li T, Niu D, Chen Y, Feng J, Han J, Chen H, Tao Y, Janssen DB, Wu B. Computational redesign of enzymes for regio- and enantioselective hydroamination. Nat Chem Biol 2018; 14:664-670. [PMID: 29785057 DOI: 10.1038/s41589-018-0053-0] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 03/09/2018] [Indexed: 12/29/2022]
Abstract
Introduction of innovative biocatalytic processes offers great promise for applications in green chemistry. However, owing to limited catalytic performance, the enzymes harvested from nature's biodiversity often need to be improved for their desired functions by time-consuming iterative rounds of laboratory evolution. Here we describe the use of structure-based computational enzyme design to convert Bacillus sp. YM55-1 aspartase, an enzyme with a very narrow substrate scope, to a set of complementary hydroamination biocatalysts. The redesigned enzymes catalyze asymmetric addition of ammonia to substituted acrylates, affording enantiopure aliphatic, polar and aromatic β-amino acids that are valuable building blocks for the synthesis of pharmaceuticals and bioactive compounds. Without a requirement for further optimization by laboratory evolution, the redesigned enzymes exhibit substrate tolerance up to a concentration of 300 g/L, conversion up to 99%, β-regioselectivity >99% and product enantiomeric excess >99%. The results highlight the use of computational design to rapidly adapt an enzyme to industrially viable reactions.
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Affiliation(s)
- Ruifeng Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Transducer Technology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Hein J Wijma
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Lu Song
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yinglu Cui
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Transducer Technology, Chinese Academy of Sciences, Beijing, China
| | - Marleen Otzen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
| | - Yu'e Tian
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jiawei Du
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Tao Li
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Dingding Niu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanchun Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jing Feng
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jian Han
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Hao Chen
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yong Tao
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Dick B Janssen
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands.
| | - Bian Wu
- CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
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39
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Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein. Nat Chem Biol 2018; 14:542-547. [PMID: 29686357 DOI: 10.1038/s41589-018-0043-2] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 03/01/2018] [Indexed: 11/09/2022]
Abstract
The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase. We show how the intrinsic reactivity of a desolvated general acid was harnessed by a series of mutations radiating from the active site, which optimized enzyme-substrate complementarity and transition-state stabilization and minimized sampling of noncatalytic conformations. Our work reveals the molecular evolutionary processes that underlie the emergence of enzymes de novo, which are notably mirrored by recent examples of computational enzyme design and directed evolution.
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40
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Santiago G, Martínez-Martínez M, Alonso S, Bargiela R, Coscolín C, Golyshin PN, Guallar V, Ferrer M. Rational Engineering of Multiple Active Sites in an Ester Hydrolase. Biochemistry 2018; 57:2245-2255. [DOI: 10.1021/acs.biochem.8b00274] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gerard Santiago
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | | | - Sandra Alonso
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Rafael Bargiela
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | - Cristina Coscolín
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
| | | | - Víctor Guallar
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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41
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Getting Momentum: From Biocatalysis to Advanced Synthetic Biology. Trends Biochem Sci 2018; 43:180-198. [DOI: 10.1016/j.tibs.2018.01.003] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 11/20/2022]
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42
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A de novo enzyme catalyzes a life-sustaining reaction in Escherichia coli. Nat Chem Biol 2018; 14:253-255. [PMID: 29334382 DOI: 10.1038/nchembio.2550] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 11/27/2017] [Indexed: 01/30/2023]
Abstract
Producing novel enzymes that are catalytically active in vitro and biologically functional in vivo is a key goal of synthetic biology. Here we describe Syn-F4, the first de novo protein that meets both criteria. Purified Syn-F4 hydrolyzes the siderophore ferric enterobactin, and expression of Syn-F4 allows an inviable strain of Escherichia coli to grow in iron-limited medium. These findings demonstrate that entirely new sequences can provide life-sustaining enzymatic functions in living organisms.
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43
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Abstract
This mini review gives an overview over different design approaches and methodologies applied in rational and semirational enzyme engineering. The underlying principles for engineering novel activities, enantioselectivity, substrate specificity, stability, and pH optimum are summarized.
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Affiliation(s)
- Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, NY, 13244, USA.
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44
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Hung PY, Chen YH, Huang KY, Yu CC, Horng JC. Design of Polyproline-Based Catalysts for Ester Hydrolysis. ACS OMEGA 2017; 2:5574-5581. [PMID: 31457823 PMCID: PMC6644415 DOI: 10.1021/acsomega.7b00928] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 08/24/2017] [Indexed: 05/21/2023]
Abstract
A number of simple oligopeptides have been recently developed as minimalistic catalysts for mimicking the activity and selectivity of natural proteases. Although the arrangement of amino acid residues in natural enzymes provides a strategy for designing artificial enzymes, creating catalysts with efficient binding and catalytic activity is still challenging. In this study, we used the polyproline scaffold and designed a series of 13-residue peptides with a catalytic dyad or triad incorporated to serve as artificial enzymes. Their catalytic efficiency on ester hydrolysis was evaluated by ultraviolet-visible spectroscopy using the p-nitrophenyl acetate assay, and their secondary structures were also characterized by circular dichroism spectroscopy. The results indicate that a well-formed polyproline II structure may result in a much higher catalytic efficiency. This is the first report to show that a functional dyad or triad engineered into a polyproline helix framework can enhance the catalytic activity on ester hydrolysis. Our study has also revealed the necessity of maintaining an ordered structure and a well-organized catalytic site for effective biocatalysts.
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Affiliation(s)
- Pei-Yu Hung
- Department
of Chemistry and Frontier Research Center on Fundamental and
Applied Science of Matters, National Tsing
Hua University, 101 Sec. 2 Kuang-Fu Rd., Hsinchu, Taiwan 30013, ROC
| | - Yu-Han Chen
- Department
of Chemistry and Frontier Research Center on Fundamental and
Applied Science of Matters, National Tsing
Hua University, 101 Sec. 2 Kuang-Fu Rd., Hsinchu, Taiwan 30013, ROC
| | - Kuei-Yen Huang
- Department
of Chemistry and Frontier Research Center on Fundamental and
Applied Science of Matters, National Tsing
Hua University, 101 Sec. 2 Kuang-Fu Rd., Hsinchu, Taiwan 30013, ROC
| | - Chi-Ching Yu
- Department
of Chemistry and Frontier Research Center on Fundamental and
Applied Science of Matters, National Tsing
Hua University, 101 Sec. 2 Kuang-Fu Rd., Hsinchu, Taiwan 30013, ROC
| | - Jia-Cherng Horng
- Department
of Chemistry and Frontier Research Center on Fundamental and
Applied Science of Matters, National Tsing
Hua University, 101 Sec. 2 Kuang-Fu Rd., Hsinchu, Taiwan 30013, ROC
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45
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Risso VA, Martinez-Rodriguez S, Candel AM, Krüger DM, Pantoja-Uceda D, Ortega-Muñoz M, Santoyo-Gonzalez F, Gaucher EA, Kamerlin SCL, Bruix M, Gavira JA, Sanchez-Ruiz JM. De novo active sites for resurrected Precambrian enzymes. Nat Commun 2017; 8:16113. [PMID: 28719578 PMCID: PMC5520109 DOI: 10.1038/ncomms16113] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 05/30/2017] [Indexed: 11/22/2022] Open
Abstract
Protein engineering studies often suggest the emergence of completely new enzyme functionalities to be highly improbable. However, enzymes likely catalysed many different reactions already in the last universal common ancestor. Mechanisms for the emergence of completely new active sites must therefore either plausibly exist or at least have existed at the primordial protein stage. Here, we use resurrected Precambrian proteins as scaffolds for protein engineering and demonstrate that a new active site can be generated through a single hydrophobic-to-ionizable amino acid replacement that generates a partially buried group with perturbed physico-chemical properties. We provide experimental and computational evidence that conformational flexibility can assist the emergence and subsequent evolution of new active sites by improving substrate and transition-state binding, through the sampling of many potentially productive conformations. Our results suggest a mechanism for the emergence of primordial enzymes and highlight the potential of ancestral reconstruction as a tool for protein engineering.
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Affiliation(s)
- Valeria A. Risso
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | | | - Adela M. Candel
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | - Dennis M. Krüger
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - David Pantoja-Uceda
- Departamento de Quimica Fisica Biologica, Instituto de Quimica Fisica Rocasolano, CSIC, c/Serrano 119, 28006-Madrid, Spain
| | - Mariano Ortega-Muñoz
- Departamento de Quimica Organica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
| | | | - Eric A. Gaucher
- School of Biology, School of Chemistry and Biochemistry, Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30322, USA
| | - Shina C. L. Kamerlin
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Marta Bruix
- Departamento de Quimica Fisica Biologica, Instituto de Quimica Fisica Rocasolano, CSIC, c/Serrano 119, 28006-Madrid, Spain
| | - Jose A. Gavira
- Laboratorio de Estudios Cristalograficos, Instituto Andaluz de Ciencias de la Tierra, CSIC-University of Granada Avenida de la Palmeras 4, Granada, 18100 Armilla, Spain
| | - Jose M. Sanchez-Ruiz
- Departamento de Quimica Fisica, Facultad de Ciencias University of Granada, 18071 Granada, Spain
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46
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Hiebler K, Lengyel Z, Castañeda CA, Makhlynets OV. Functional tuning of the catalytic residue p
K
a
in a
de novo
designed esterase. Proteins 2017; 85:1656-1665. [DOI: 10.1002/prot.25321] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 04/20/2017] [Accepted: 05/17/2017] [Indexed: 11/05/2022]
Affiliation(s)
| | - Zsófia Lengyel
- Department of ChemistrySyracuse UniversitySyracuse New York13244
| | - Carlos A. Castañeda
- Department of ChemistrySyracuse UniversitySyracuse New York13244
- Department of BiologySyracuse UniversitySyracuse New York13244
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47
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Paladino A, Marchetti F, Rinaldi S, Colombo G. Protein design: from computer models to artificial intelligence. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1318] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Antonella Paladino
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Filippo Marchetti
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Silvia Rinaldi
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
| | - Giorgio Colombo
- Biomolecular Simulations & Computational Chemistry Group; Istituto Istituto di Chimica del Riconoscimento Molecolare, CNR; Milano Italy
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48
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Li A, Wang B, Ilie A, Dubey KD, Bange G, Korendovych IV, Shaik S, Reetz MT. A redox-mediated Kemp eliminase. Nat Commun 2017; 8:14876. [PMID: 28348375 PMCID: PMC5379065 DOI: 10.1038/ncomms14876] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/08/2017] [Indexed: 01/27/2023] Open
Abstract
The acid/base-catalysed Kemp elimination of 5-nitro-benzisoxazole forming 2-cyano-4-nitrophenol has long served as a design platform of enzymes with non-natural reactions, providing new mechanistic insights in protein science. Here we describe an alternative concept based on redox catalysis by P450-BM3, leading to the same Kemp product via a fundamentally different mechanism. QM/MM computations show that it involves coordination of the substrate's N-atom to haem-Fe(II) with electron transfer and concomitant N-O heterolysis liberating an intermediate having a nitrogen radical moiety Fe(III)-N· and a phenoxyl anion. Product formation occurs by bond rotation and H-transfer. Two rationally chosen point mutations cause a notable increase in activity. The results shed light on the prevailing mechanistic uncertainties in human P450-catalysed metabolism of the immunomodulatory drug leflunomide, which likewise undergoes redox-mediated Kemp elimination by P450-BM3. Other isoxazole-based pharmaceuticals are probably also metabolized by a redox mechanism. Our work provides a basis for designing future artificial enzymes.
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Affiliation(s)
- Aitao Li
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany.,Department of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Binju Wang
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Adriana Ilie
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany.,Department of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Kshatresh D Dubey
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Gert Bange
- LOEWE Center for Synthetic Microbiology (SYNMIKRO) and Department of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, 111 College Place, Syracuse, New York 13244, USA
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Manfred T Reetz
- Department of Biocatalysis, Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mülheim an der Ruhr 45470, Germany.,Department of Chemistry, Philipps-Universität Marburg, Marburg 35032, Germany
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49
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Khersonsky O, Fleishman SJ. Incorporating an allosteric regulatory site in an antibody through backbone design. Protein Sci 2017; 26:807-813. [PMID: 28142198 DOI: 10.1002/pro.3126] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 12/17/2022]
Abstract
Allosteric regulation underlies living cells' ability to sense changes in nutrient and signaling-molecule concentrations, but the ability to computationally design allosteric regulation into non-allosteric proteins has been elusive. Allosteric-site design is complicated by the requirement to encode the relative stabilities of active and inactive conformations of the same protein in the presence and absence of both ligand and effector. To address this challenge, we used Rosetta to design the backbone of the flexible heavy-chain complementarity-determining region 3 (HCDR3), and used geometric matching and sequence optimization to place a Zn2+ -coordination site in a fluorescein-binding antibody. We predicted that due to HCDR3's flexibility, the fluorescein-binding pocket would configure properly only upon Zn2+ application. We found that regulation by Zn2+ was reversible and sensitive to the divalent ion's identity, and came at the cost of reduced antibody stability and fluorescein-binding affinity. Fluorescein bound at an order of magnitude higher affinity in the presence of Zn2+ than in its absence, and the increase in fluorescein affinity was due almost entirely to faster fluorescein on-rate, suggesting that Zn2+ preorganized the antibody for fluorescein binding. Mutation analysis demonstrated the extreme sensitivity of Zn2+ regulation on the atomic details in and around the metal-coordination site. The designed antibody could serve to study how allosteric regulation evolved from non-allosteric binding proteins, and suggests a way to designing molecular sensors for environmental and biomedical targets.
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Affiliation(s)
- Olga Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Sarel J Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, 76100, Israel
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50
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Pan T, Liu Y, Si C, Bai Y, Qiao S, Zhao L, Xu J, Dong Z, Luo Q, Liu J. Construction of ATP-Switched Allosteric Antioxidant Selenoenzyme. ACS Catal 2017. [DOI: 10.1021/acscatal.6b03274] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Tiezheng Pan
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, 2699
Qianjin Road, Changchun 130012, China
| | - Yao Liu
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, 2699
Qianjin Road, Changchun 130012, China
| | - Chengye Si
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, 2699
Qianjin Road, Changchun 130012, China
| | - Yushi Bai
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, 2699
Qianjin Road, Changchun 130012, China
| | - Shanpeng Qiao
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, 2699
Qianjin Road, Changchun 130012, China
| | - Linlu Zhao
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, 2699
Qianjin Road, Changchun 130012, China
| | - Jiayun Xu
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, 2699
Qianjin Road, Changchun 130012, China
| | - Zeyuan Dong
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, 2699
Qianjin Road, Changchun 130012, China
| | - Quan Luo
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, 2699
Qianjin Road, Changchun 130012, China
| | - Junqiu Liu
- State Key Laboratory of Supramolecular
Structure and Materials, College of Chemistry, Jilin University, 2699
Qianjin Road, Changchun 130012, China
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