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Fontecilla-Camps JC. Reflections on the Origin of Coded Protein Biosynthesis. Biomolecules 2024; 14:518. [PMID: 38785925 PMCID: PMC11117964 DOI: 10.3390/biom14050518] [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: 04/09/2024] [Revised: 04/23/2024] [Accepted: 04/24/2024] [Indexed: 05/25/2024] Open
Abstract
The principle of continuity posits that some central features of primordial biocatalytic mechanisms should still be present in the genetically dependent pathway of protein synthesis, a crucial step in the emergence of life. Key bimolecular reactions of this process are catalyzed by DNA-dependent RNA polymerases, aminoacyl-tRNA synthetases, and ribosomes. Remarkably, none of these biocatalysts contribute chemically active groups to their respective reactions. Instead, structural and functional studies have demonstrated that nucleotidic α-phosphate and β-d-ribosyl 2' OH and 3' OH groups can help their own catalysis, a process which, consequently, has been called "substrate-assisted". Furthermore, upon binding, the substrates significantly lower the entropy of activation, exclude water from these catalysts' active sites, and are readily positioned for a reaction. This binding mode has been described as an "entropy trap". The combination of this effect with substrate-assisted catalysis results in reactions that are stereochemically and mechanistically simpler than the ones found in most modern enzymes. This observation is consistent with the way in which primordial catalysts could have operated; it may also explain why, thanks to their complementary reactivities, β-d-ribose and phosphate were naturally selected to be the central components of early coding polymers.
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Yang X, Gao H, Yan J, Zhou J, Shi L. Intramolecular chaperone-assisted dual-anchoring activation (ICDA): a suitable preorganization for electrophilic halocyclization. Chem Sci 2024; 15:6130-6140. [PMID: 38665529 PMCID: PMC11041335 DOI: 10.1039/d4sc00581c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
The halocyclization reaction represents one of the most common methodologies for the synthesis of heterocyclic molecules. Many efforts have been made to balance the relationship between structure, reactivity and selectivity, including the design of new electrophilic halogenation reagents and the utilization of activating strategies. However, discovering universal reagents or activating strategies for electrophilic halocyclization remains challenging due to the case-by-case practice for different substrates or different cyclization models. Here we report an intramolecular chaperone-assisted dual-anchoring activation (ICDA) model for electrophilic halocyclization, taking advantage of the non-covalent dual-anchoring orientation as the driving force. This protocol allows a practical, catalyst-free and rapid approach to access seven types of small-sized, medium-sized, and large-sized heterocyclic units and to realize polyene-like domino halocyclizations, as exemplified by nearly 90 examples, including a risk-reducing flow protocol for gram-scale synthesis. DFT studies verify the crucial role of ICDA in affording a suitable preorganization for transition state stabilization and X+ transfer acceleration. The utilization of the ICDA model allows a spatiotemporal adjustment to straightforwardly obtain fast, selective and high-yielding synthetic transformations.
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Affiliation(s)
- Xihui Yang
- School of Science (Shenzhen), School of Chemistry and Chemical Engineering, Harbin Institute of Technology Shenzhen 518055 China
| | - Haowei Gao
- School of Science (Shenzhen), School of Chemistry and Chemical Engineering, Harbin Institute of Technology Shenzhen 518055 China
| | - Jiale Yan
- School of Science (Shenzhen), School of Chemistry and Chemical Engineering, Harbin Institute of Technology Shenzhen 518055 China
| | - Jia Zhou
- School of Science (Shenzhen), School of Chemistry and Chemical Engineering, Harbin Institute of Technology Shenzhen 518055 China
- Laboratory of Urban Water Resources and Environment, Harbin Institute of Technology (Shenzhen) Shenzhen 518055 China
| | - Lei Shi
- School of Science (Shenzhen), School of Chemistry and Chemical Engineering, Harbin Institute of Technology Shenzhen 518055 China
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Li N, Ma J, Fu H, Yang Z, Xu C, Li H, Zhao Y, Zhao Y, Chen S, Gou L, Zhang X, Zhang S, Li M, Hou X, Zhang L, Lu Y. Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2401150. [PMID: 38582512 DOI: 10.1002/advs.202401150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/08/2024] [Indexed: 04/08/2024]
Abstract
The structural diversity of biological macromolecules in different environments contributes complexity to enzymological processes vital for cellular functions. Fluorescence resonance energy transfer and electron microscopy are used to investigate the enzymatic reaction of T4 DNA ligase catalyzing the ligation of nicked DNA. The data show that both the ligase-AMP complex and the ligase-AMP-DNA complex can have four conformations. This finding suggests the parallel occurrence of four ligation reaction pathways, each characterized by specific conformations of the ligase-AMP complex that persist in the ligase-AMP-DNA complex. Notably, these complexes have DNA bending angles of ≈0°, 20°, 60°, or 100°. The mechanism of parallel reactions challenges the conventional notion of simple sequential reaction steps occurring among multiple conformations. The results provide insights into the dynamic conformational changes and the versatile attributes of T4 DNA ligase and suggest that the parallel multiple reaction pathways may correspond to diverse T4 DNA ligase functions. This mechanism may potentially have evolved as an adaptive strategy across evolutionary history to navigate complex environments.
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Affiliation(s)
- Na Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Jianbing Ma
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Hang Fu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, Zhejiang, 325011, China
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Chunhua Xu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
| | - Haihong Li
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Shuyu Chen
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Lu Gou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Xinghua Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ming Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
| | - Ximiao Hou
- College of Life Sciences, Northwest A&F University, Yangling, 712100, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an, 710049, China
| | - Ying Lu
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Songshan Lake Materials Laboratory, Dongguan, Guangdong, 523808, China
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Xu W, Wu Y, Gu W, Du D, Lin Y, Zhu C. Atomic-level design of metalloenzyme-like active pockets in metal-organic frameworks for bioinspired catalysis. Chem Soc Rev 2024; 53:137-162. [PMID: 38018371 DOI: 10.1039/d3cs00767g] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Natural metalloenzymes with astonishing reaction activity and specificity underpin essential life transformations. Nevertheless, enzymes only operate under mild conditions to keep sophisticated structures active, limiting their potential applications. Artificial metalloenzymes that recapitulate the catalytic activity of enzymes can not only circumvent the enzymatic fragility but also bring versatile functions into practice. Among them, metal-organic frameworks (MOFs) featuring diverse and site-isolated metal sites and supramolecular structures have emerged as promising candidates for metalloenzymes to move toward unparalleled properties and behaviour of enzymes. In this review, we systematically summarize the significant advances in MOF-based metalloenzyme mimics with a special emphasis on active pocket engineering at the atomic level, including primary catalytic sites and secondary coordination spheres. Then, the deep understanding of catalytic mechanisms and their advanced applications are discussed. Finally, a perspective on this emerging frontier research is provided to advance bioinspired catalysis.
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Affiliation(s)
- Weiqing Xu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Yu Wu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Wenling Gu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
| | - Dan Du
- School of Mechanical and Materials Engineering, Washington State University, 99164, Pullman, USA.
| | - Yuehe Lin
- School of Mechanical and Materials Engineering, Washington State University, 99164, Pullman, USA.
| | - Chengzhou Zhu
- National Key Laboratory of Green Pesticide, International Joint Research Center for Intelligent Biosensing Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, P. R. China.
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Taher M, Dubey KD, Mazumdar S. Computationally guided bioengineering of the active site, substrate access pathway, and water channels of thermostable cytochrome P450, CYP175A1, for catalyzing the alkane hydroxylation reaction. Chem Sci 2023; 14:14316-14326. [PMID: 38098704 PMCID: PMC10718072 DOI: 10.1039/d3sc02857g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 11/10/2023] [Indexed: 12/17/2023] Open
Abstract
Understanding structure-function relationships in proteins is pivotal in their development as industrial biocatalysts. In this regard, rational engineering of protein active site access pathways and various tunnels and channels plays a central role in designing competent enzymes with high stability and enhanced efficiency. Here, we report the rational evolution of a thermostable cytochrome P450, CYP175A1, to catalyze the C-H activation reaction of longer-chain alkanes. A strategy combining computational tools with experiments has shown that the substrate scope and enzymatic activity can be enhanced by rational engineering of certain important channels such as the substrate entry and water channels along with the active site of the enzyme. The evolved enzymes showed an improved catalytic rate for hexadecane hydroxylation with high regioselectivity. The Q67L/Y68F mutation showed binding of the substrate in the active site, water channel mutation L80F/V220T showed improved catalytic activity through the peroxide shunt pathway and substrate entry channel mutation W269F/I270A showed better substrate accessibility to the active pocket. All-atom MD simulations provided the rationale for the inactivity of the wild-type CYP175A1 for hexadecane hydroxylation and predicted the above hot-spot residues to enhance the activity. The reaction mechanism was studied by QM/MM calculations for enzyme-substrate complexes and reaction intermediates. Detailed thermal and thermodynamic stability of all the mutants were analyzed and the results showed that the evolved enzymes were thermally stable. The present strategy showed promising results, and insights gained from this work can be applied to the general enzymatic system to expand substrate scope and improve catalytic activity.
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Affiliation(s)
- Mohd Taher
- Department of Chemical Sciences, Tata Institute of Fundamental Research Homi Bhabha Road, Colaba Mumbai 400005 India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar Institution of Eminence Delhi-NCR NH91, Tehsil Dadri Greater Noida Uttar Pradesh 201314 India
| | - Shyamalava Mazumdar
- Department of Chemical Sciences, Tata Institute of Fundamental Research Homi Bhabha Road, Colaba Mumbai 400005 India
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Yang G, Shi W, Qian Y, Zheng X, Meng Z, Jiang HL. Turning on Asymmetric Catalysis of Achiral Metal-Organic Frameworks by Imparting Chiral Microenvironment. Angew Chem Int Ed Engl 2023; 62:e202308089. [PMID: 37551837 DOI: 10.1002/anie.202308089] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/09/2023]
Abstract
The development of heterogeneous asymmetric catalysts has attracted increasing interest in synthetic chemistry but mostly relies on the immobilization of homogeneous chiral catalysts. Herein, a series of chiral metal-organic frameworks (MOFs) have been fabricated by anchoring similar chiral hydroxylated molecules (catalytically inactive) with different lengths onto Zr-oxo clusters in achiral PCN-222(Cu). The resulting chiral MOFs exhibit regulated enantioselectivity up to 83 % ee in the asymmetric ring-opening of cyclohexene oxide. The chiral molecules furnished onto the catalytic Lewis sites in the MOF create multilevel microenvironment, including the hydrogen interaction between the substrate and the chiral -OH group, the steric hindrance endowed by the benzene ring on the chiral molecules, and the proximity between the catalytic sites and chiral molecules confined in the MOF pores, which play crucial roles and synergistically promote chiral catalysis. This work nicely achieves heterogeneous enantioselective catalysis by chiral microenvironment modulation around Lewis acid sites.
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Affiliation(s)
- Ge Yang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemistry, University of Science and Technology of China, 230026, Hefei, Anhui, P. R. China
| | - Wenwen Shi
- CAS Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, 230026, Hefei, Anhui, P. R. China
| | - Yunyang Qian
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemistry, University of Science and Technology of China, 230026, Hefei, Anhui, P. R. China
| | - Xiao Zheng
- CAS Key Laboratory of Precision and Intelligent Chemistry, University of Science and Technology of China, 230026, Hefei, Anhui, P. R. China
- Department of Chemistry, Fudan University, 200433, Shanghai, P. R. China
| | - Zheng Meng
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemistry, University of Science and Technology of China, 230026, Hefei, Anhui, P. R. China
| | - Hai-Long Jiang
- Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemistry, University of Science and Technology of China, 230026, Hefei, Anhui, P. R. China
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Fontecilla-Camps JC. Reflections on the Origin and Early Evolution of the Genetic Code. Chembiochem 2023; 24:e202300048. [PMID: 37052530 DOI: 10.1002/cbic.202300048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/01/2023] [Indexed: 04/14/2023]
Abstract
Examination of the genetic code (GeCo) reveals that amino acids coded by (A/U) codons display a large functional spectrum and bind RNA whereas, except for Arg, those coded by (G/C) codons do not. From a stereochemical viewpoint, the clear preference for (A/U)-rich codons to be located at the GeCo half blocks suggests they were specifically determined. Conversely, the overall lower affinity of cognate amino acids for their (G/C)-rich anticodons points to their late arrival to the GeCo. It is proposed that i) initially the code was composed of the eight (A/U) codons; ii) these codons were duplicated when G/C nucleotides were added to their wobble positions, and three new codons with G/C in their first position were incorporated; and iii) a combination of A/U and G/C nucleotides progressively generated the remaining codons.
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Taut J, Chambron J, Kersting B. Fifty Years of Inorganic Biomimetic Chemistry: From the Complexation of Single Metal Cations to Polynuclear Metal Complexes by Multidentate Thiolate Ligands. Eur J Inorg Chem 2023. [DOI: 10.1002/ejic.202200739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Affiliation(s)
- Josef Taut
- Institut für Anorganische Chemie Universität Leipzig Johannisallee 29 04103 Leipzig Germany
- Institut de Chimie de Strasbourg UMR 7177 CNRS-Université de Strasbourg 1, rue Blaise Pascal 67008 Strasbourg France
| | - Jean‐Claude Chambron
- Institut de Chimie de Strasbourg UMR 7177 CNRS-Université de Strasbourg 1, rue Blaise Pascal 67008 Strasbourg France
| | - Berthold Kersting
- Institut für Anorganische Chemie Universität Leipzig Johannisallee 29 04103 Leipzig Germany
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