1
|
Hilvert D. Spiers Memorial Lecture: Engineering biocatalysts. Faraday Discuss 2024; 252:9-28. [PMID: 39046423 PMCID: PMC11389855 DOI: 10.1039/d4fd00139g] [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: 06/26/2024] [Accepted: 06/26/2024] [Indexed: 07/25/2024]
Abstract
Enzymes are being engineered to catalyze chemical reactions for many practical applications in chemistry and biotechnology. The approaches used are surveyed in this short review, emphasizing methods for accessing reactivities not expressed by native protein scaffolds. The successful generation of completely de novo enzymes that rival the rates and selectivities of their natural counterparts highlights the potential role that designer enzymes may play in the coming years in research, industry, and medicine. Some challenges that need to be addressed to realize this ambitious dream are considered together with possible solutions.
Collapse
Affiliation(s)
- Donald Hilvert
- Laboratory of Organic Chemistry, ETH Zürich, 8093 Zürich, Switzerland.
| |
Collapse
|
2
|
Lauko A, Pellock SJ, Anischanka I, Sumida KH, Juergens D, Ahern W, Shida A, Hunt A, Kalvet I, Norn C, Humphreys IR, Jamieson C, Kang A, Brackenbrough E, Bera AK, Sankaran B, Houk KN, Baker D. Computational design of serine hydrolases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.610411. [PMID: 39257749 PMCID: PMC11384011 DOI: 10.1101/2024.08.29.610411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
Abstract
Enzymes that proceed through multistep reaction mechanisms often utilize complex, polar active sites positioned with sub-angstrom precision to mediate distinct chemical steps, which makes their de novo construction extremely challenging. We sought to overcome this challenge using the classic catalytic triad and oxyanion hole of serine hydrolases as a model system. We used RFdiffusion1 to generate proteins housing catalytic sites of increasing complexity and varying geometry, and a newly developed ensemble generation method called ChemNet to assess active site geometry and preorganization at each step of the reaction. Experimental characterization revealed novel serine hydrolases that catalyze ester hydrolysis with catalytic efficiencies (k cat /K m ) up to 3.8 x 103 M-1 s-1, closely match the design models (Cα RMSDs < 1 Å), and have folds distinct from natural serine hydrolases. In silico selection of designs based on active site preorganization across the reaction coordinate considerably increased success rates, enabling identification of new catalysts in screens of as few as 20 designs. Our de novo buildup approach provides insight into the geometric determinants of catalysis that complements what can be obtained from structural and mutational studies of native enzymes (in which catalytic group geometry and active site makeup cannot be so systematically varied), and provides a roadmap for the design of industrially relevant serine hydrolases and, more generally, for designing complex enzymes that catalyze multi-step transformations.
Collapse
Affiliation(s)
- Anna Lauko
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA, USA
- These authors contributed equally: Anna Lauko, Samuel J. Pellock
| | - Samuel J Pellock
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- These authors contributed equally: Anna Lauko, Samuel J. Pellock
| | - Ivan Anischanka
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Kiera H Sumida
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - David Juergens
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Graduate Program in Molecular Engineering, University of Washington, Seattle, WA, USA
| | - Woody Ahern
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Alex Shida
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Andrew Hunt
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Indrek Kalvet
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Christoffer Norn
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Cooper Jamieson
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - Alex Kang
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Evans Brackenbrough
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Asim K Bera
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Banumathi Sankaran
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| |
Collapse
|
3
|
Birch-Price Z, Hardy FJ, Lister TM, Kohn AR, Green AP. Noncanonical Amino Acids in Biocatalysis. Chem Rev 2024; 124:8740-8786. [PMID: 38959423 PMCID: PMC11273360 DOI: 10.1021/acs.chemrev.4c00120] [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: 02/09/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 07/05/2024]
Abstract
In recent years, powerful genetic code reprogramming methods have emerged that allow new functional components to be embedded into proteins as noncanonical amino acid (ncAA) side chains. In this review, we will illustrate how the availability of an expanded set of amino acid building blocks has opened a wealth of new opportunities in enzymology and biocatalysis research. Genetic code reprogramming has provided new insights into enzyme mechanisms by allowing introduction of new spectroscopic probes and the targeted replacement of individual atoms or functional groups. NcAAs have also been used to develop engineered biocatalysts with improved activity, selectivity, and stability, as well as enzymes with artificial regulatory elements that are responsive to external stimuli. Perhaps most ambitiously, the combination of genetic code reprogramming and laboratory evolution has given rise to new classes of enzymes that use ncAAs as key catalytic elements. With the framework for developing ncAA-containing biocatalysts now firmly established, we are optimistic that genetic code reprogramming will become a progressively more powerful tool in the armory of enzyme designers and engineers in the coming years.
Collapse
Affiliation(s)
| | | | | | | | - Anthony P. Green
- Manchester Institute of Biotechnology,
School of Chemistry, University of Manchester, Manchester M1 7DN, U.K.
| |
Collapse
|
4
|
Huang H, Yan T, Liu C, Lu Y, Wu Z, Wang X, Wang J. Genetically encoded Nδ-vinyl histidine for the evolution of enzyme catalytic center. Nat Commun 2024; 15:5714. [PMID: 38977701 PMCID: PMC11231154 DOI: 10.1038/s41467-024-50005-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024] Open
Abstract
Genetic code expansion has emerged as a powerful tool for precisely introducing unnatural chemical structures into proteins to improve their catalytic functions. Given the high catalytic propensity of histidine in the enzyme pocket, increasing the chemical diversity of catalytic histidine could result in new characteristics of biocatalysts. Herein, we report the genetically encoded Nδ-Vinyl Histidine (δVin-H) and achieve the wild-type-like incorporation efficiency by the evolution of pyrrolysyl tRNA synthetase. As histidine usually acts as the nucleophile or the metal ligand in the catalytic center, we replace these two types of catalytic histidine to δVin-H to improve the performance of the histidine-involved catalytic center. Additionally, we further demonstrate the improvements of the hydrolysis activity of a previously reported organocatalytic esterase (the OE1.3 variant) in the acidic condition and myoglobin (Mb) catalyzed carbene transfer reactions under the aerobic condition. As histidine is one of the most frequently used residues in the enzyme catalytic center, the derivatization of the catalytic histidine by δVin-H holds a great potential to promote the performance of biocatalysts.
Collapse
Affiliation(s)
- Haoran Huang
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Tao Yan
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chang Liu
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuxiang Lu
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Zhigang Wu
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xingchu Wang
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jie Wang
- Department of Chemistry, Research Center for Chemical Biology and Omics Analysis, College of Science, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China.
| |
Collapse
|
5
|
Zhou L, Tao C, Shen X, Sun X, Wang J, Yuan Q. Unlocking the potential of enzyme engineering via rational computational design strategies. Biotechnol Adv 2024; 73:108376. [PMID: 38740355 DOI: 10.1016/j.biotechadv.2024.108376] [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] [Received: 12/27/2023] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/16/2024]
Abstract
Enzymes play a pivotal role in various industries by enabling efficient, eco-friendly, and sustainable chemical processes. However, the low turnover rates and poor substrate selectivity of enzymes limit their large-scale applications. Rational computational enzyme design, facilitated by computational algorithms, offers a more targeted and less labor-intensive approach. There has been notable advancement in employing rational computational protein engineering strategies to overcome these issues, it has not been comprehensively reviewed so far. This article reviews recent developments in rational computational enzyme design, categorizing them into three types: structure-based, sequence-based, and data-driven machine learning computational design. Case studies are presented to demonstrate successful enhancements in catalytic activity, stability, and substrate selectivity. Lastly, the article provides a thorough analysis of these approaches, highlights existing challenges and potential solutions, and offers insights into future development directions.
Collapse
Affiliation(s)
- Lei Zhou
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chunmeng Tao
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolin Shen
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinxiao Sun
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jia Wang
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| | - Qipeng Yuan
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China.
| |
Collapse
|
6
|
Yi HB, Lee S, Seo K, Kim H, Kim M, Lee HS. Cellular and Biophysical Applications of Genetic Code Expansion. Chem Rev 2024; 124:7465-7530. [PMID: 38753805 DOI: 10.1021/acs.chemrev.4c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Despite their diverse functions, proteins are inherently constructed from a limited set of building blocks. These compositional constraints pose significant challenges to protein research and its practical applications. Strategically manipulating the cellular protein synthesis system to incorporate novel building blocks has emerged as a critical approach for overcoming these constraints in protein research and application. In the past two decades, the field of genetic code expansion (GCE) has achieved significant advancements, enabling the integration of numerous novel functionalities into proteins across a variety of organisms. This technological evolution has paved the way for the extensive application of genetic code expansion across multiple domains, including protein imaging, the introduction of probes for protein research, analysis of protein-protein interactions, spatiotemporal control of protein function, exploration of proteome changes induced by external stimuli, and the synthesis of proteins endowed with novel functions. In this comprehensive Review, we aim to provide an overview of cellular and biophysical applications that have employed GCE technology over the past two decades.
Collapse
Affiliation(s)
- Han Bin Yi
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Seungeun Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Kyungdeok Seo
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyeongjo Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Minah Kim
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| | - Hyun Soo Lee
- Department of Chemistry, Sogang University, 35 Baekbeom-ro, Mapo-gu, Seoul 04107, Republic of Korea
| |
Collapse
|
7
|
Hutton AE, Foster J, Crawshaw R, Hardy FJ, Johannissen LO, Lister TM, Gérard EF, Birch-Price Z, Obexer R, Hay S, Green AP. A non-canonical nucleophile unlocks a new mechanistic pathway in a designed enzyme. Nat Commun 2024; 15:1956. [PMID: 38438341 PMCID: PMC10912507 DOI: 10.1038/s41467-024-46123-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/09/2024] [Indexed: 03/06/2024] Open
Abstract
Directed evolution of computationally designed enzymes has provided new insights into the emergence of sophisticated catalytic sites in proteins. In this regard, we have recently shown that a histidine nucleophile and a flexible arginine can work in synergy to accelerate the Morita-Baylis-Hillman (MBH) reaction with unrivalled efficiency. Here, we show that replacing the catalytic histidine with a non-canonical Nδ-methylhistidine (MeHis23) nucleophile leads to a substantially altered evolutionary outcome in which the catalytic Arg124 has been abandoned. Instead, Glu26 has emerged, which mediates a rate-limiting proton transfer step to deliver an enzyme (BHMeHis1.8) that is more than an order of magnitude more active than our earlier MBHase. Interestingly, although MeHis23 to His substitution in BHMeHis1.8 reduces activity by 4-fold, the resulting His containing variant is still a potent MBH biocatalyst. However, analysis of the BHMeHis1.8 evolutionary trajectory reveals that the MeHis nucleophile was crucial in the early stages of engineering to unlock the new mechanistic pathway. This study demonstrates how even subtle perturbations to key catalytic elements of designed enzymes can lead to vastly different evolutionary outcomes, resulting in new mechanistic solutions to complex chemical transformations.
Collapse
Affiliation(s)
- Amy E Hutton
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Jake Foster
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Rebecca Crawshaw
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Florence J Hardy
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Linus O Johannissen
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Thomas M Lister
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Emilie F Gérard
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Zachary Birch-Price
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Richard Obexer
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Sam Hay
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK
| | - Anthony P Green
- Manchester Institute of Biotechnology, School of Chemistry, The University of Manchester, Manchester, UK.
| |
Collapse
|
8
|
Nam K, Shao Y, Major DT, Wolf-Watz M. Perspectives on Computational Enzyme Modeling: From Mechanisms to Design and Drug Development. ACS OMEGA 2024; 9:7393-7412. [PMID: 38405524 PMCID: PMC10883025 DOI: 10.1021/acsomega.3c09084] [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: 11/14/2023] [Revised: 01/15/2024] [Accepted: 01/19/2024] [Indexed: 02/27/2024]
Abstract
Understanding enzyme mechanisms is essential for unraveling the complex molecular machinery of life. In this review, we survey the field of computational enzymology, highlighting key principles governing enzyme mechanisms and discussing ongoing challenges and promising advances. Over the years, computer simulations have become indispensable in the study of enzyme mechanisms, with the integration of experimental and computational exploration now established as a holistic approach to gain deep insights into enzymatic catalysis. Numerous studies have demonstrated the power of computer simulations in characterizing reaction pathways, transition states, substrate selectivity, product distribution, and dynamic conformational changes for various enzymes. Nevertheless, significant challenges remain in investigating the mechanisms of complex multistep reactions, large-scale conformational changes, and allosteric regulation. Beyond mechanistic studies, computational enzyme modeling has emerged as an essential tool for computer-aided enzyme design and the rational discovery of covalent drugs for targeted therapies. Overall, enzyme design/engineering and covalent drug development can greatly benefit from our understanding of the detailed mechanisms of enzymes, such as protein dynamics, entropy contributions, and allostery, as revealed by computational studies. Such a convergence of different research approaches is expected to continue, creating synergies in enzyme research. This review, by outlining the ever-expanding field of enzyme research, aims to provide guidance for future research directions and facilitate new developments in this important and evolving field.
Collapse
Affiliation(s)
- Kwangho Nam
- Department
of Chemistry and Biochemistry, University
of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department
of Chemistry and Biochemistry, University
of Oklahoma, Norman, Oklahoma 73019-5251, United States
| | - Dan T. Major
- Department
of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | |
Collapse
|
9
|
Yuan X, Wu X, Xiong J, Yan B, Gao R, Liu S, Zong M, Ge J, Lou W. Hydrolase mimic via second coordination sphere engineering in metal-organic frameworks for environmental remediation. Nat Commun 2023; 14:5974. [PMID: 37749093 PMCID: PMC10520056 DOI: 10.1038/s41467-023-41716-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 09/15/2023] [Indexed: 09/27/2023] Open
Abstract
Enzymes achieve high catalytic activity with their elaborate arrangements of amino acid residues in confined optimized spaces. Nevertheless, when exposed to complicated environmental implementation scenarios, including high acidity, organic solvent and high ionic strength, enzymes exhibit low operational stability and poor activity. Here, we report a metal-organic frameworks (MOFs)-based artificial enzyme system via second coordination sphere engineering to achieve high hydrolytic activity under mild conditions. Experiments and theoretical calculations reveal that amide cleavage catalyzed by MOFs follows two distinct catalytic mechanisms, Lewis acid- and hydrogen bonding-mediated hydrolytic processes. The hydrogen bond formed in the secondary coordination sphere exhibits 11-fold higher hydrolytic activity than the Lewis acidic zinc ions. The MOFs exhibit satisfactory degradation performance of toxins and high stability under extreme working conditions, including complicated fermentation broth and high ethanol environments, and display broad substrate specificity. These findings hold great promise for designing artificial enzymes for environmental remediation.
Collapse
Affiliation(s)
- Xin Yuan
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China
| | - Xiaoling Wu
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China.
| | - Jun Xiong
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China
| | - Binhang Yan
- Department of Chemical Engineering, Tsinghua University, 100084, Beijing, China
| | - Ruichen Gao
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China
| | - Shuli Liu
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China
| | - Minhua Zong
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China
| | - Jun Ge
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, 100084, Beijing, China.
| | - Wenyong Lou
- Lab of Applied Biocatalysis, School of Food Science and Technology, South China University of Technology, 510640, Guangzhou, Guangdong, China.
| |
Collapse
|
10
|
Shao Q, Jiang Y, Yang ZJ. EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation. J Chem Inf Model 2023; 63:5650-5659. [PMID: 37611241 PMCID: PMC11211066 DOI: 10.1021/acs.jcim.3c00618] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Directed evolution facilitates enzyme engineering via iterative rounds of mutagenesis. Despite the wide applications of high-throughput screening, building "smart libraries" to effectively identify beneficial variants remains a major challenge in the community. Here, we developed a new computational directed evolution protocol based on EnzyHTP, a software that we have previously reported to automate enzyme modeling. To enhance the throughput efficiency, we implemented an adaptive resource allocation strategy that dynamically allocates different types of computing resources (e.g., GPU/CPU) based on the specific need of an enzyme modeling subtask in the workflow. We implemented the strategy as a Python library and tested the library using fluoroacetate dehalogenase as a model enzyme. The results show that compared to fixed resource allocation where both CPU and GPU are on-call for use during the entire workflow, applying adaptive resource allocation can save 87% CPU hours and 14% GPU hours. Furthermore, we constructed a computational directed evolution protocol under the framework of adaptive resource allocation. The workflow was tested against two rounds of mutational screening in the directed evolution experiments of Kemp eliminase (KE07) with a total of 184 mutants. Using folding stability and electrostatic stabilization energy as computational readout, we identified all four experimentally observed target variants. Enabled by the workflow, the entire computation task (i.e., 18.4 μs MD and 18,400 QM single-point calculations) completes in 3 days of wall-clock time using ∼30 GPUs and ∼1000 CPUs.
Collapse
Affiliation(s)
- Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zhongyue J. Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Grigorenko BL, Polyakov IV, Khrenova MG, Giudetti G, Faraji S, Krylov AI, Nemukhin AV. Multiscale Simulations of the Covalent Inhibition of the SARS-CoV-2 Main Protease: Four Compounds and Three Reaction Mechanisms. J Am Chem Soc 2023; 145:13204-13214. [PMID: 37294056 DOI: 10.1021/jacs.3c02229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We report the results of computational modeling of the reactions of the SARS-CoV-2 main protease (MPro) with four potential covalent inhibitors. Two of them, carmofur and nirmatrelvir, have shown experimentally the ability to inhibit MPro. Two other compounds, X77A and X77C, were designed computationally in this work. They were derived from the structure of X77, a non-covalent inhibitor forming a tight surface complex with MPro. We modified the X77 structure by introducing warheads capable of reacting with the catalytic cysteine residue in the MPro active site. The reaction mechanisms of the four molecules with MPro were investigated by quantum mechanics/molecular mechanics (QM/MM) simulations. The results show that all four compounds form covalent adducts with the catalytic cysteine Cys 145 of MPro. From the chemical perspective, the reactions of these four molecules with MPro follow three distinct mechanisms. The reactions are initiated by a nucleophilic attack of the thiolate group of the deprotonated cysteine residue from the catalytic dyad Cys145-His41 of MPro. In the case of carmofur and X77A, the covalent binding of the thiolate to the ligand is accompanied by the formation of the fluoro-uracil leaving group. The reaction with X77C follows the nucleophilic aromatic substitution SNAr mechanism. The reaction of MPro with nirmatrelvir (which has a reactive nitrile group) leads to the formation of a covalent thioimidate adduct with the thiolate of the Cys145 residue in the enzyme active site. Our results contribute to the ongoing search for efficient inhibitors of the SARS-CoV-2 enzymes.
Collapse
Affiliation(s)
- Bella L Grigorenko
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Igor V Polyakov
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| | - Maria G Khrenova
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Bach Institute of Biochemistry, Federal Research Centre "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow 119071, Russia
| | - Goran Giudetti
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Shirin Faraji
- Zernike Institute for Advanced Materials, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Anna I Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University, Moscow 119991, Russia
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow 119334, Russia
| |
Collapse
|
13
|
Huang J, Xie X, Zheng Z, Ye L, Wang P, Xu L, Wu Y, Yan J, Yang M, Yan Y. De Novo Computational Design of a Lipase with Hydrolysis Activity towards Middle-Chained Fatty Acid Esters. Int J Mol Sci 2023; 24:ijms24108581. [PMID: 37239928 DOI: 10.3390/ijms24108581] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/08/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Innovations in biocatalysts provide great prospects for intolerant environments or novel reactions. Due to the limited catalytic capacity and the long-term and labor-intensive characteristics of mining enzymes with the desired functions, de novo enzyme design was developed to obtain industrial application candidates in a rapid and convenient way. Here, based on the catalytic mechanisms and the known structures of proteins, we proposed a computational protein design strategy combining de novo enzyme design and laboratory-directed evolution. Starting with the theozyme constructed using a quantum-mechanical approach, the theoretical enzyme-skeleton combinations were assembled and optimized via the Rosetta "inside-out" protocol. A small number of designed sequences were experimentally screened using SDS-PAGE, mass spectrometry and a qualitative activity assay in which the designed enzyme 1a8uD1 exhibited a measurable hydrolysis activity of 24.25 ± 0.57 U/g towards p-nitrophenyl octanoate. To improve the activity of the designed enzyme, molecular dynamics simulations and the RosettaDesign application were utilized to further optimize the substrate binding mode and amino acid sequence, thus keeping the residues of theozyme intact. The redesigned lipase 1a8uD1-M8 displayed enhanced hydrolysis activity towards p-nitrophenyl octanoate-3.34 times higher than that of 1a8uD1. Meanwhile, the natural skeleton protein (PDB entry 1a8u) did not display any hydrolysis activity, confirming that the hydrolysis abilities of the designed 1a8uD1 and the redesigned 1a8uD1-M8 were devised from scratch. More importantly, the designed 1a8uD1-M8 was also able to hydrolyze the natural middle-chained substrate (glycerol trioctanoate), for which the activity was 27.67 ± 0.69 U/g. This study indicates that the strategy employed here has great potential to generate novel enzymes exhibiting the desired reactions.
Collapse
Affiliation(s)
- Jinsha Huang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaoman Xie
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Zhen Zheng
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Luona Ye
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Pengbo Wang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Li Xu
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Ying Wu
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jinyong Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Min Yang
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yunjun Yan
- Key Laboratory of Molecular Biophysics, Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| |
Collapse
|
14
|
Reed A, Ware T, Li H, Fernando Bazan J, Cravatt BF. TMEM164 is an acyltransferase that forms ferroptotic C20:4 ether phospholipids. Nat Chem Biol 2023; 19:378-388. [PMID: 36782012 PMCID: PMC10362496 DOI: 10.1038/s41589-022-01253-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 12/21/2022] [Indexed: 02/15/2023]
Abstract
Ferroptosis is an iron-dependent form of cell death driven by oxidation of polyunsaturated fatty acid (PUFA) phospholipids. Large-scale genetic screens have uncovered a specialized role for PUFA ether phospholipids (ePLs) in promoting ferroptosis. Understanding of the enzymes involved in PUFA-ePL production, however, remains incomplete. Here we show, using a combination of pathway mining of genetic dependency maps, AlphaFold-guided structure predictions and targeted lipidomics, that the uncharacterized transmembrane protein TMEM164-the genetic ablation of which has been shown to protect cells from ferroptosis-is a cysteine active center enzyme that selectively transfers C20:4 acyl chains from phosphatidylcholine to lyso-ePLs to produce PUFA ePLs. Genetic deletion of TMEM164 across a set of ferroptosis-sensitive cancer cell lines caused selective reductions in C20:4 ePLs with minimal effects on C20:4 diacyl PLs, and this lipid profile produced a variable range of protection from ferroptosis, supportive of an important but contextualized role for C20:4 ePLs in this form of cell death.
Collapse
Affiliation(s)
- Alex Reed
- Department of Chemistry, The Scripps Research Institute, San Diego, CA, USA
| | - Timothy Ware
- Department of Chemistry, The Scripps Research Institute, San Diego, CA, USA
| | - Haoxin Li
- Department of Chemistry, The Scripps Research Institute, San Diego, CA, USA
| | - J Fernando Bazan
- ħ Bioconsulting, LLC, Stillwater, MN, USA.
- Unit for Structural Biology, VIB-UGent Center for Inflammation Research, Ghent, Belgium.
| | - Benjamin F Cravatt
- Department of Chemistry, The Scripps Research Institute, San Diego, CA, USA.
| |
Collapse
|
15
|
Wang X, Xu K, Tan Y, Liu S, Zhou J. Possibilities of Using De Novo Design for Generating Diverse Functional Food Enzymes. Int J Mol Sci 2023; 24:3827. [PMID: 36835238 PMCID: PMC9964944 DOI: 10.3390/ijms24043827] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/17/2023] Open
Abstract
Food enzymes have an important role in the improvement of certain food characteristics, such as texture improvement, elimination of toxins and allergens, production of carbohydrates, enhancing flavor/appearance characteristics. Recently, along with the development of artificial meats, food enzymes have been employed to achieve more diverse functions, especially in converting non-edible biomass to delicious foods. Reported food enzyme modifications for specific applications have highlighted the significance of enzyme engineering. However, using direct evolution or rational design showed inherent limitations due to the mutation rates, which made it difficult to satisfy the stability or specific activity needs for certain applications. Generating functional enzymes using de novo design, which highly assembles naturally existing enzymes, provides potential solutions for screening desired enzymes. Here, we describe the functions and applications of food enzymes to introduce the need for food enzymes engineering. To illustrate the possibilities of using de novo design for generating diverse functional proteins, we reviewed protein modelling and de novo design methods and their implementations. The future directions for adding structural data for de novo design model training, acquiring diversified training data, and investigating the relationship between enzyme-substrate binding and activity were highlighted as challenges to overcome for the de novo design of food enzymes.
Collapse
Affiliation(s)
- Xinglong Wang
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Kangjie Xu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Yameng Tan
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Song Liu
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
| | - Jingwen Zhou
- Engineering Research Center of Ministry of Education on Food Synthetic Biotechnology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi 214122, China
- Jiangsu Province Engineering Research Center of Food Synthetic Biotechnology, Jiangnan University, Wuxi 214122, China
| |
Collapse
|
16
|
Liu N, Li SB, Zheng YZ, Xu SY, Shen JS. Minimalistic Artificial Catalysts with Esterase-Like Activity from Multivalent Nanofibers Formed by the Self-Assembly of Dipeptides. ACS OMEGA 2023; 8:2491-2500. [PMID: 36687071 PMCID: PMC9851029 DOI: 10.1021/acsomega.2c06972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
Imitating and incorporating the multiple key structural features observed in natural enzymes into a minimalistic molecule to develop an artificial catalyst with outstanding catalytic efficiency is an attractive topic for chemists. Herein, we designed and synthesized one class of minimalistic dipeptide molecules containing a terminal -SH group and a terminal His-Phe dipeptide head linked by a hydrophobic alkyl chain with different lengths, marked as HS-C n+1-His-Phe (n = 4, 7, 11, 15, and 17; n + 1 represents the carbon atom number of the alkyl chain). The His (-imidazole), Phe (-CO2 -) moieties, the terminal -SH group, and a long hydrophobic alkyl chain were found to have important contributions to achieve high binding ability leading to outstanding absolute catalytic efficiency (k cat/K M) toward the hydrolysis reactions of carboxylic ester substrates.
Collapse
Affiliation(s)
- Ning Liu
- Xiamen
Key Laboratory of Optoelectronic Materials and Advanced Manufacturing,
College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Shuai-Bing Li
- Xiamen
Key Laboratory of Optoelectronic Materials and Advanced Manufacturing,
College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| | - Yan-Zhen Zheng
- College
of Ocean Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Su-Ying Xu
- State
Key Laboratory of Chemical Resource Engineering, Beijing Key Laboratory
of Environmentally Harmful Chemical Analysis, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jiang-Shan Shen
- Xiamen
Key Laboratory of Optoelectronic Materials and Advanced Manufacturing,
College of Materials Science and Engineering, Huaqiao University, Xiamen 361021, China
| |
Collapse
|
17
|
Babić M, Janković P, Marchesan S, Mauša G, Kalafatovic D. Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs. J Chem Inf Model 2022; 62:6398-6410. [PMID: 36223497 DOI: 10.1021/acs.jcim.2c00977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Ester hydrolysis is of wide biomedical interest, spanning from the green synthesis of pharmaceuticals to biomaterials' development. Existing peptide-based catalysts exhibit low catalytic efficiency compared to natural enzymes, due to the conformational heterogeneity of peptides. Moreover, there is lack of understanding of the correlation between the primary sequence and catalytic function. For this purpose, we statistically analyzed 22 EC 3.1 hydrolases with known catalytic triads, characterized by unique and well-defined mechanisms. The aim was to identify patterns at the sequence level that will better inform the creation of short peptides containing important information for catalysis, based on the catalytic triad, oxyanion holes and the triad residues microenvironments. Moreover, fragmentation schemes of the primary sequence of selected enzymes alongside the study of their amino acid frequencies, composition, and physicochemical properties are proposed. The results showed highly conserved catalytic sites with distinct positional patterns and chemical microenvironments that favor catalysis and revealed variations in catalytic site composition that could be useful for the design of minimalistic catalysts.
Collapse
Affiliation(s)
- Marko Babić
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia
| | - Patrizia Janković
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127Trieste, Italy
| | - Goran Mauša
- Faculty of Engineering, University of Rijeka, 51000Rijeka, Croatia
| | - Daniela Kalafatovic
- Department of Biotechnology, University of Rijeka, 51000Rijeka, Croatia.,Center for Advanced Computing and Modeling, University of Rijeka, 51000Rijeka, Croatia
| |
Collapse
|
18
|
Birch-Price Z, Taylor CJ, Ortmayer M, Green AP. Engineering enzyme activity using an expanded amino acid alphabet. Protein Eng Des Sel 2022; 36:6825271. [PMID: 36370045 PMCID: PMC9863031 DOI: 10.1093/protein/gzac013] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/01/2022] [Accepted: 11/07/2022] [Indexed: 11/14/2022] Open
Abstract
Enzyme design and engineering strategies are typically constrained by the limited size of nature's genetic alphabet, comprised of only 20 canonical amino acids. In recent years, site-selective incorporation of non-canonical amino acids (ncAAs) via an expanded genetic code has emerged as a powerful means of inserting new functional components into proteins, with hundreds of structurally diverse ncAAs now available. Here, we highlight how the emergence of an expanded repertoire of amino acids has opened new avenues in enzyme design and engineering. ncAAs have been used to probe complex biological mechanisms, augment enzyme function and, most ambitiously, embed new catalytic mechanisms into protein active sites that would be challenging to access within the constraints of nature's genetic code. We predict that the studies reviewed in this article, along with further advances in genetic code expansion technology, will establish ncAA incorporation as an increasingly important tool for biocatalysis in the coming years.
Collapse
Affiliation(s)
- Zachary Birch-Price
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Christopher J Taylor
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | - Mary Ortmayer
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, Manchester, M1 7DN, UK
| | | |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
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: 25] [Impact Index Per Article: 12.5] [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.
Collapse
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
| | | |
Collapse
|
21
|
Zhang S, Zhang J, Luo W, Wang P, Zhu Y. A preorganization oriented computational method for de novo design of Kemp elimination enzymes. Enzyme Microb Technol 2022; 160:110093. [DOI: 10.1016/j.enzmictec.2022.110093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/13/2022] [Accepted: 06/30/2022] [Indexed: 11/26/2022]
|
22
|
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.
Collapse
|
23
|
Ferreira JC, Fadl S, Rabeh WM. Key dimer interface residues impact the catalytic activity of 3CLpro, the main protease of SARS-CoV-2. J Biol Chem 2022; 298:102023. [PMID: 35568197 PMCID: PMC9091064 DOI: 10.1016/j.jbc.2022.102023] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 02/07/2023] Open
Abstract
3C-like protease (3CLpro) is one of two proteases that process and liberate functional viral proteins essential for the maturation and infectivity of severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19. It has been suggested that 3CLpro is catalytically active as a dimer, making the dimerization interface a target for antiviral development. Guided by structural analysis, here we introduced single amino acid substitutions at nine residues at three key sites of the dimer interface to assess their impact on dimerization and activity. We show that at site 1, alanine substitution of S1 or E166 increased by 2-fold or reduced relative activity, respectively. At site 2, alanine substitution of S10 or E14 eliminated activity, whereas K12A exhibited ∼60% relative activity. At site 3, alanine substitution of R4, E290, or Q299 eliminated activity, whereas S139A exhibited 46% relative activity. We further found the oligomerization states of the dimer interface mutants varied; the inactive mutants R4A, R4Q, S10A/C, E14A/D/Q/S, E290A, and Q299A/E were present as dimers, demonstrating that dimerization is not an indication of catalytically active 3CLpro. In addition, present mostly as monomers, K12A displayed residual activity, which could be attributed to the conspicuous amount of dimer present. Finally, differential scanning calorimetry did not reveal a direct relationship between the thermodynamic stability of mutants with oligomerization or catalytic activity. These results provide insights on two allosteric sites, R4/E290 and S10/E14, that may promote the design of antiviral compounds that target the dimer interface rather than the active site of SARS-CoV-2 3CLpro.
Collapse
Affiliation(s)
- Juliana C Ferreira
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Samar Fadl
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates
| | - Wael M Rabeh
- Science Division, New York University Abu Dhabi, PO Box 129188, Abu Dhabi, United Arab Emirates.
| |
Collapse
|
24
|
Khersonsky O, Fleishman SJ. What Have We Learned from Design of Function in Large Proteins? BIODESIGN RESEARCH 2022; 2022:9787581. [PMID: 37850148 PMCID: PMC10521758 DOI: 10.34133/2022/9787581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 02/21/2022] [Indexed: 10/19/2023] Open
Abstract
The overarching goal of computational protein design is to gain complete control over protein structure and function. The majority of sophisticated binders and enzymes, however, are large and exhibit diverse and complex folds that defy atomistic design calculations. Encouragingly, recent strategies that combine evolutionary constraints from natural homologs with atomistic calculations have significantly improved design accuracy. In these approaches, evolutionary constraints mitigate the risk from misfolding and aggregation, focusing atomistic design calculations on a small but highly enriched sequence subspace. Such methods have dramatically optimized diverse proteins, including vaccine immunogens, enzymes for sustainable chemistry, and proteins with therapeutic potential. The new generation of deep learning-based ab initio structure predictors can be combined with these methods to extend the scope of protein design, in principle, to any natural protein of known sequence. We envision that protein engineering will come to rely on completely computational methods to efficiently discover and optimize biomolecular activities.
Collapse
Affiliation(s)
- Olga Khersonsky
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sarel J. Fleishman
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot 7610001, Israel
| |
Collapse
|
25
|
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]
|
26
|
Evolutionary Aspects of the Oxido-Reductive Network of Methylglyoxal. J Mol Evol 2021; 89:618-638. [PMID: 34718825 DOI: 10.1007/s00239-021-10031-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 10/08/2021] [Indexed: 10/19/2022]
Abstract
In the chemoautotrophic theory for the origin of life, offered as an alternative to broth theory, the archaic reductive citric acid cycle operating without enzymes is in the center. The non-enzymatic (methyl)glyoxalase pathway has been suggested to be the anaplerotic route for the reductive citric acid cycle. In the recent years, much has been learned about methylglyoxal, but its importance in the metabolic machinery is still uncovered. If methylglyoxal had been essential participant of the early stage of evolution, then it is a legitimate question whether it might have played a role in the early oxido-reduction network, too. Therefore, an oxido-reduction network of methylglyoxal that might have functioned under ancient circumstances without enzymes was constructed and analyzed by virtue of group contribution method. Taking methylglyoxal as input material, it turned out that the evolutionary value of reactions and biomolecules were not similar. Glycerol, glycerate, and tartonate, the output components, were conserved to different degrees. Although the tartonate route was similarly favorable from energetic point of view, its intermediates are almost not present in extant biochemistry. The presence of two carboxyl or aldehyde groups, or their combination in tricarbons of the constructed network seemed disadvantageous for selection, and the inductive effect, resulting in an asymmetry in electron cloud of chemicals, might have been important. The evolutionary role for cysteine, H2S, and formaldehyde in the emergence of high-energy bonds in the form of thioesters and in Fe-S cluster formation as well as in imidazole synthesis was shown to bridge the gap between prebiotic chemistry and contemporary biochemistry. Overall, the ideas developed here represent an approach fitting to chemoautotrophic origin of life and implying to the role of methylglyoxal in triose formation. The proposed network is expected to have an impact upon how one may think of prebiological chemical processes on methylglyoxal, too. Finally, along the evolutionary time line, the network functioning without enzymes is situated between the formation of simple organic compounds and primeval cells, being closer to the former and well preceding the last common metabolic ancestor developed after primitive cells emerged.
Collapse
|
27
|
Yan B, Ran X, Jiang Y, Torrence SK, Yuan L, Shao Q, Yang ZJ. Rate-Perturbing Single Amino Acid Mutation for Hydrolases: A Statistical Profiling. J Phys Chem B 2021; 125:10682-10691. [PMID: 34524819 DOI: 10.1021/acs.jpcb.1c05901] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrolases are a critical component for modern chemical, pharmaceutical, and environmental sciences. Identifying mutations that enhance catalytic efficiency presents a roadblock to design and to discover new hydrolases for broad academic and industrial uses. Here, we report the statistical profiling for rate-perturbing mutant hydrolases with a single amino acid substitution. We constructed an integrated structure-kinetics database for hydrolases, IntEnzyDB, which contains 3907 kcats, 4175 KMs, and 2715 Protein Data Bank IDs. IntEnzyDB adopts a relational architecture with a flattened data structure, enabling facile and efficient access to clean and tabulated data for machine learning uses. We conducted statistical analyses on how single amino acids mutations influence the turnover number (i.e., kcat) and efficiency (i.e., kcat/KM), with a particular emphasis on profiling the features for rate-enhancing mutations. The results show that mutation to bulky nonpolar residues with a hydrocarbon chain involves a higher likelihood for rate acceleration than to other types of residues. Linear regression models reveal geometric descriptors of substrate and mutation residues that mediate rate-perturbing outcomes for hydrolases with bulky nonpolar mutations. On the basis of the analyses of the structure-kinetics relationship, we observe that the propensity for rate enhancement is independent of protein sizes. In addition, we observe that distal mutations (i.e., >10 Å from the active site) in hydrolases are significantly more prone to induce efficiency neutrality and avoid efficiency deletion but involve similar propensity for rate enhancement. The studies reveal the statistical features for identifying rate-enhancing mutations in hydrolases, which will potentially guide hydrolase discovery in biocatalysis.
Collapse
Affiliation(s)
- Bailu Yan
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Department of Biostatistics, Vanderbilt University, Nashville, Tennessee 37203, United States
| | - Xinchun Ran
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Sarah K Torrence
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Li Yuan
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zhongyue J Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States.,Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.,Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States.,Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
| |
Collapse
|
28
|
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.
Collapse
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.
| |
Collapse
|
29
|
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.
Collapse
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
| |
Collapse
|
30
|
Revolutionizing enzyme engineering through artificial intelligence and machine learning. Emerg Top Life Sci 2021; 5:113-125. [PMID: 33835131 DOI: 10.1042/etls20200257] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 12/20/2022]
Abstract
The combinatorial space of an enzyme sequence has astronomical possibilities and exploring it with contemporary experimental techniques is arduous and often ineffective. Multi-target objectives such as concomitantly achieving improved selectivity, solubility and activity of an enzyme have narrow plausibility under approaches of restricted mutagenesis and combinatorial search. Traditional enzyme engineering approaches have a limited scope for complex optimization due to the requirement of a priori knowledge or experimental burden of screening huge protein libraries. The recent surge in high-throughput experimental methods including Next Generation Sequencing and automated screening has flooded the field of molecular biology with big-data, which requires us to re-think our concurrent approaches towards enzyme engineering. Artificial Intelligence (AI) and Machine Learning (ML) have great potential to revolutionize smart enzyme engineering without the explicit need for a complete understanding of the underlying molecular system. Here, we portray the role and position of AI techniques in the field of enzyme engineering along with their scope and limitations. In addition, we explain how the traditional approaches of directed evolution and rational design can be extended through AI tools. Recent successful examples of AI-assisted enzyme engineering projects and their deviation from traditional approaches are highlighted. A comprehensive picture of current challenges and future avenues for AI in enzyme engineering are also discussed.
Collapse
|
31
|
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]
|
32
|
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: 58] [Impact Index Per Article: 19.3] [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.
Collapse
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
| |
Collapse
|
33
|
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: 9] [Impact Index Per Article: 3.0] [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.
Collapse
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
| |
Collapse
|
34
|
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.
Collapse
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.
| |
Collapse
|
35
|
Metrano AJ, Chinn AJ, Shugrue CR, Stone EA, Kim B, Miller SJ. Asymmetric Catalysis Mediated by Synthetic Peptides, Version 2.0: Expansion of Scope and Mechanisms. Chem Rev 2020; 120:11479-11615. [PMID: 32969640 PMCID: PMC8006536 DOI: 10.1021/acs.chemrev.0c00523] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Low molecular weight synthetic peptides have been demonstrated to be effective catalysts for an increasingly wide array of asymmetric transformations. In many cases, these peptide-based catalysts have enabled novel multifunctional substrate activation modes and unprecedented selectivity manifolds. These features, along with their ease of preparation, modular and tunable structures, and often biomimetic attributes make peptides well-suited as chiral catalysts and of broad interest. Many examples of peptide-catalyzed asymmetric reactions have appeared in the literature since the last survey of this broad field in Chemical Reviews (Chem. Rev. 2007, 107, 5759-5812). The overarching goal of this new Review is to provide a comprehensive account of the numerous advances in the field. As a corollary to this goal, we survey the many different types of catalytic reactions, ranging from acylation to C-C bond formation, in which peptides have been successfully employed. In so doing, we devote significant discussion to the structural and mechanistic aspects of these reactions that are perhaps specific to peptide-based catalysts and their interactions with substrates and/or reagents.
Collapse
Affiliation(s)
- Anthony J. Metrano
- AstraZeneca Oncology R&D, 35 Gatehouse Dr., Waltham, MA 02451, United States
| | - Alex J. Chinn
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Christopher R. Shugrue
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Elizabeth A. Stone
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, United States
| | - Byoungmoo Kim
- Department of Chemistry, Clemson University, Clemson, SC 29634, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, United States
| |
Collapse
|
36
|
A De Novo Designed Esterase with p-Nitrophenyl Acetate Hydrolysis Activity. Molecules 2020; 25:molecules25204658. [PMID: 33066055 PMCID: PMC7587395 DOI: 10.3390/molecules25204658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/04/2020] [Accepted: 10/10/2020] [Indexed: 11/18/2022] Open
Abstract
Esterases are a large family of enzymes with wide applications in the industry. However, all esterases originated from natural sources, limiting their use in harsh environments or newly- emerged reactions. In this study, we designed a new esterase to develop a new protocol to satisfy the needs for better biocatalysts. The ideal spatial conformation of the serine catalytic triad and the oxygen anion hole at the substrate-binding site was constructed by quantum mechanical calculation. The catalytic triad and oxygen anion holes were then embedded in the protein scaffold using the new enzyme protocol in Rosetta 3. The design results were subsequently evaluated, and optimized designs were used for expression and purification. The designed esterase had significant lytic activities towards p-nitrophenyl acetate, which was confirmed by point mutations. Thus, this study developed a new protocol to obtain novel enzymes that may be useful in unforgiving environments or novel reactions.
Collapse
|
37
|
Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico. Nat Commun 2020; 11:4808. [PMID: 32968058 PMCID: PMC7511930 DOI: 10.1038/s41467-020-18619-x] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/25/2020] [Indexed: 01/30/2023] Open
Abstract
The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (kcat/KM 146 M−1s−1). We observe that catalytic residues are increasingly rigidified, the active site becomes better pre-organized, and its entrance is widened. Based on these observations, we engineer HG4, an efficient biocatalyst (kcat/KM 103,000 M−1s−1) containing key first and second-shell mutations found during evolution. HG4 structures reveal that its active site is pre-organized and rigidified for efficient catalysis. Our results show how directed evolution circumvents challenges inherent to enzyme design by shifting conformational ensembles to favor catalytically-productive sub-states, and suggest improvements to the design methodology that incorporate ensemble modeling of crystallographic data. Kemp eliminases are artificial enzymes that catalyze the concerted deprotonation and ring-opening of benzisoxazoles. Here, the authors use room-temperature X-ray crystallography to investigate changes to the conformational ensemble of the Kemp eliminase HG3 along a directed evolutionary trajectory, and develop an experimentally guided, ensemble-based computational enzyme design procedure.
Collapse
|
38
|
Roda S, Santiago G, Guallar V. Mapping enzyme-substrate interactions: its potential to study the mechanism of enzymes. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:1-31. [PMID: 32951809 DOI: 10.1016/bs.apcsb.2020.06.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
With the increase of the need to use more sustainable processes for the industry in our society, the modeling of enzymes has become crucial to fully comprehend their mechanism of action and use this knowledge to enhance and design their properties. A lot of methods to study enzymes computationally exist and they have been classified on sequence-based, structure-based, and the more new artificial intelligence-based ones. Albeit the abundance of methods to help predict the function of an enzyme, molecular modeling is crucial when trying to understand the enzyme mechanism, as they aim to correlate atomistic information with experimental data. Among them, methods that simulate the system dynamics at a molecular mechanics level of theory (classical force fields) have shown to offer a comprehensive study. In this book chapter, we will analyze these techniques, emphasizing the importance of precise modeling of enzyme-substrate interactions. In the end, a brief explanation of the transference of the information from research studies to the industry is given accompanied with two examples of family enzymes where their modeling has helped their exploitation.
Collapse
Affiliation(s)
- Sergi Roda
- Barcelona Supercomputing Center (BSC), Barcelona, Spain
| | | | - Victor Guallar
- Barcelona Supercomputing Center (BSC), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| |
Collapse
|
39
|
Basanta B, Bick MJ, Bera AK, Norn C, Chow CM, Carter LP, Goreshnik I, Dimaio F, Baker D. An enumerative algorithm for de novo design of proteins with diverse pocket structures. Proc Natl Acad Sci U S A 2020; 117:22135-22145. [PMID: 32839327 PMCID: PMC7486743 DOI: 10.1073/pnas.2005412117] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To create new enzymes and biosensors from scratch, precise control over the structure of small-molecule binding sites is of paramount importance, but systematically designing arbitrary protein pocket shapes and sizes remains an outstanding challenge. Using the NTF2-like structural superfamily as a model system, we developed an enumerative algorithm for creating a virtually unlimited number of de novo proteins supporting diverse pocket structures. The enumerative algorithm was tested and refined through feedback from two rounds of large-scale experimental testing, involving in total the assembly of synthetic genes encoding 7,896 designs and assessment of their stability on yeast cell surface, detailed biophysical characterization of 64 designs, and crystal structures of 5 designs. The refined algorithm generates proteins that remain folded at high temperatures and exhibit more pocket diversity than naturally occurring NTF2-like proteins. We expect this approach to transform the design of small-molecule sensors and enzymes by enabling the creation of binding and active site geometries much more optimal for specific design challenges than is accessible by repurposing the limited number of naturally occurring NTF2-like proteins.
Collapse
Affiliation(s)
- Benjamin Basanta
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Matthew J Bick
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Christoffer Norn
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Cameron M Chow
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Lauren P Carter
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Inna Goreshnik
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - Frank Dimaio
- Institute for Protein Design, University of Washington, Seattle, WA 98195
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
| | - David Baker
- Institute for Protein Design, University of Washington, Seattle, WA 98195;
- Biochemistry Department, School of Medicine, University of Washington, Seattle, WA 98195
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195
| |
Collapse
|
40
|
|
41
|
Xiao F, Dong S, Liu Y, Feng Y, Li H, Yun CH, Cui Q, Li W. Structural Basis of Specificity for Carboxyl-Terminated Acyl Donors in a Bacterial Acyltransferase. J Am Chem Soc 2020; 142:16031-16038. [PMID: 32803979 DOI: 10.1021/jacs.0c07331] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Macrolactins (MLNs) are a class of important antimacular degeneration and antitumor agents. Malonylated/succinylated MLNs are even more important due to their efficacy in overcoming multi-drug-resistant bacteria. However, which enzyme catalyzes this reaction remains enigmatic. Herein, we deciphered a β-lactamase homologue BmmI to be responsible for this step. BmmI could specifically attach C3-C5 alkyl acid thioesters onto 7-OH of MLN A and also exhibits substrate promiscuity toward acyl acceptors with different scaffolds. The crystal structure of BmmI covalently linked to the succinyl group and systematic mutagenesis highlighted the role of oxyanion holelike geometry in the recognition of carboxyl-terminated acyl donors. The engineering of this geometry expanded its substrate scope, with the R166A/G/Q variants recognizing up to C12 alkyl acid thioester. The structure of BmmI with acyl acceptor MLN A revealed the importance of Arg292 in the recognition of macrolide substrates. Moreover, the mechanism of the BmmI-catalyzed acyltransfer reaction was established, unmasking the deft role of Lys76 in governing acyl donors as well as catalysis. Our studies uncover the delicate mechanism underlying the substrate selectivity of acyltransferases, which would guide rational enzyme engineering for drug development.
Collapse
Affiliation(s)
- Fei Xiao
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | | | - Yang Liu
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China
| | | | - Huayue Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Cai-Hong Yun
- Department of Biochemistry and Biophysics & Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, Peking University, 38 Xueyuan Road, 100191 Beijing, China
| | | | - Wenli Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 266003 Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| |
Collapse
|
42
|
Lin M, Wang F, Zhu Y. Modeled structure-based computational redesign of a glycosyltransferase for the synthesis of rebaudioside D from rebaudioside A. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107626] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
43
|
Prejanò M, Romeo I, Russo N, Marino T. On the Catalytic Activity of the Engineered Coiled-Coil Heptamer Mimicking the Hydrolase Enzymes: Insights from a Computational Study. Int J Mol Sci 2020; 21:E4551. [PMID: 32604744 PMCID: PMC7352413 DOI: 10.3390/ijms21124551] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 06/22/2020] [Accepted: 06/24/2020] [Indexed: 01/22/2023] Open
Abstract
Recently major advances were gained on the designed proteins aimed to generate biomolecular mimics of proteases. Although such enzyme-like catalysts must still suffer refinements for improving the catalytic activity, at the moment, they represent a good example of artificial enzymes to be tested in different fields. Herein, a de novo designed homo-heptameric peptide assembly (CC-Hept) where the esterase activity towards p-nitro-phenylacetate was obtained for introduction of the catalytic triad (Cys-His-Glu) into the hydrophobic matrix, is the object of the present combined molecular dynamics and quantum mechanics/molecular mechanics investigation. Constant pH Molecular Dynamics simulations on the apoform of CC-Hept suggested that the Cys residues are present in the protonated form. Molecular dynamics (MD) simulations of the enzyme-substrate complex evidenced the attitude of the enzyme-like system to retain water molecules, necessary in the hydrolytic reaction, in correspondence of the active site, represented by the Cys-His-Glu triad on each of the seven chains, without significant structural perturbations. A detailed reaction mechanism of esterase activity of CC-Hept-Cys-His-Glu was investigated on the basis of the quantum mechanics/molecular mechanics calculations employing a large quantum mechanical (QM) region of the active site. The proposed mechanism is consistent with available esterases kinetics and structural data. The roles of the active site residues were also evaluated. The deacylation phase emerged as the rate-determining step, in agreement with esterase activity of other natural proteases.
Collapse
Affiliation(s)
| | | | - Nino Russo
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy; (M.P.); (I.R.)
| | - Tiziana Marino
- Department of Chemistry and Chemical Technologies, University of Calabria, 87036 Arcavacata di Rende, Cosenza, Italy; (M.P.); (I.R.)
| |
Collapse
|
44
|
Mazmanian K, Sargsyan K, Lim C. How the Local Environment of Functional Sites Regulates Protein Function. J Am Chem Soc 2020; 142:9861-9871. [PMID: 32407086 DOI: 10.1021/jacs.0c02430] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteins form complex biological machineries whose functions in the cell are highly regulated at both the cellular and molecular levels. Cellular regulation of protein functions involves differential gene expressions, post-translation modifications, and signaling cascades. Molecular regulation, on the other hand, involves tuning an optimal local protein environment for the functional site. Precisely how a protein achieves such an optimal environment around a given functional site is not well understood. Herein, by surveying the literature, we first summarize the various reported strategies used by certain proteins to ensure their correct functioning. We then formulate three key physicochemical factors for regulating a protein's functional site, namely, (i) its immediate interactions, (ii) its solvent accessibility, and (iii) its conformational flexibility. We illustrate how these factors are applied to regulate the functions of free/metal-bound Cys and Zn sites in proteins.
Collapse
Affiliation(s)
- Karine Mazmanian
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Karen Sargsyan
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Carmay Lim
- Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu 300, Taiwan
| |
Collapse
|
45
|
Nothling MD, Xiao Z, Hill NS, Blyth MT, Bhaskaran A, Sani MA, Espinosa-Gomez A, Ngov K, White J, Buscher T, Separovic F, O’Mara ML, Coote ML, Connal LA. A multifunctional surfactant catalyst inspired by hydrolases. SCIENCE ADVANCES 2020; 6:eaaz0404. [PMID: 32270041 PMCID: PMC7112759 DOI: 10.1126/sciadv.aaz0404] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 01/08/2020] [Indexed: 05/04/2023]
Abstract
The remarkable power of enzymes to undertake catalysis frequently stems from their grouping of multiple, complementary chemical units within close proximity around the enzyme active site. Motivated by this, we report here a bioinspired surfactant catalyst that incorporates a variety of chemical functionalities common to hydrolytic enzymes. The textbook hydrolase active site, the catalytic triad, is modeled by positioning the three groups of the triad (-OH, -imidazole, and -CO2H) on a single, trifunctional surfactant molecule. To support this, we recreate the hydrogen bond donating arrangement of the oxyanion hole by imparting surfactant functionality to a guanidinium headgroup. Self-assembly of these amphiphiles in solution drives the collection of functional headgroups into close proximity around a hydrophobic nano-environment, affording hydrolysis of a model ester at rates that challenge α-chymotrypsin. Structural assessment via NMR and XRD, paired with MD simulation and QM calculation, reveals marked similarities of the co-micelle catalyst to native enzymes.
Collapse
Affiliation(s)
- Mitchell D. Nothling
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Zeyun Xiao
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China
| | - Nicholas S. Hill
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Mitchell T. Blyth
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Ayana Bhaskaran
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Marc-Antoine Sani
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Andrea Espinosa-Gomez
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kevin Ngov
- Department of Chemical and Biomolecular Engineering, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jonathan White
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Tim Buscher
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Frances Separovic
- School of Chemistry, Bio21 Institute, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Megan L. O’Mara
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Michelle L. Coote
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
| | - Luke A. Connal
- Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia
- Corresponding author.
| |
Collapse
|
46
|
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]
|
47
|
Huang KY, Yu CC, Horng JC. Conjugating Catalytic Polyproline Fragments with a Self-Assembling Peptide Produces Efficient Artificial Hydrolases. Biomacromolecules 2020; 21:1195-1201. [PMID: 31951389 DOI: 10.1021/acs.biomac.9b01620] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A polyproline fragment containing a catalytic dyad of His-His or Ser-His was coupled with a self-assembling peptide MAX1 to design new hydrolases (H2H5 and H2S5) for catalyzing ester hydrolysis. Circular dichroism measurements indicated that the peptides change their conformation from random coils to β-sheets when pH increases from 5 to 10. IR spectra also displayed the vibration modes corresponding to their β-structures at pH 9.0. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) measurements showed that in solution, the designed peptides self-assemble into network fibrils having a significantly increased catalytic efficiency on ester hydrolysis. On p-nitrophenyl acetate (p-NPA) substrate, the designed peptides exhibit high catalytic efficiency at pH 9.0 (kcat/KM = 12.1 M-1 s-1 for H2H5, 13.3 M-1 s-1 for H2S5), and their efficiency is even better at pH 10.0 (kcat/KM = 24.3 M-1 s-1 for H2H5, 99.4 M-1 s-1 for H2S5). Additionally, H2H5 and H2S5 also display good activity on catalyzing the hydrolysis of p-nitrophenyl-(2-phenyl)-propanoate (p-NPP) and p-nitrophenyl methoxyacetate (p-NPMA). Combining the polyproline-based catalytic scaffold with a self-assembling peptide generates an efficient hydrolase, providing a new design for effective artificial enzymes.
Collapse
Affiliation(s)
- Kuei-Yen Huang
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, R.O.C
| | - Chi-Ching Yu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, R.O.C
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan, R.O.C.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan, R.O.C
| |
Collapse
|
48
|
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]
|
49
|
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.
Collapse
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
| |
Collapse
|
50
|
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: 90] [Impact Index Per Article: 18.0] [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.
Collapse
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.
| |
Collapse
|