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Kang MJ, Reyes-De-Corcuera JI. Stabilization of galactose oxidase by high hydrostatic pressure: Insights on the role of cavities size. Biotechnol Bioeng 2024; 121:2057-2066. [PMID: 38650386 DOI: 10.1002/bit.28715] [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: 12/06/2023] [Revised: 03/24/2024] [Accepted: 04/07/2024] [Indexed: 04/25/2024]
Abstract
High hydrostatic pressure stabilized galactose oxidase (GaOx) at 70.0-80.0°C against thermal inactivation. The pseudo-first-order rate constant of inactivation kinact decreased by a factor of 8 at 80°C and by a factor of 44 at 72.5°C. The most pronounced effect of pressure was at the lowest studied temperature of 70.0°C with an activation volume of inactivation ΔV‡ of 78.8 cm3 mol-1. The optimal pressure against thermal inactivation was between 200 and 300 MPa. Unlike other enzymes, as temperature increased the ΔV‡ of inactivation decreased, and as pressure increased the activation energy of inactivation Eai increased. Combining the results for GaOx with earlier research on the pressure-induced stabilization of other enzymes suggests that ΔV‡ of inactivation correlates with the total molar volume of cavities larger than ~100 Å3 in enzyme monomers for enzymes near the optimal pH and whose thermal unfolding is not accompanied by oligomer dissociation.
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Affiliation(s)
- Min J Kang
- Department of Food Science and Technology, University of Georgia, Athens, Georgia, USA
| | - José I Reyes-De-Corcuera
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida, USA
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2
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Liu MH, Zhou X, Zhang MM, Wang YJ, Zhou B, Ding N, Wu QF, Lei CR, Dong ZY, Ren JL, Zhao JR, Jia CL, Liu J, Lu D, Zhong HY. Integration of food raw materials, food microbiology, and food additives: systematic research and comprehensive insights into sweet sorghum juice, Clostridium tyrobutyricum TGL-A236 and bio-butyric acid. Front Microbiol 2024; 15:1410968. [PMID: 38873149 PMCID: PMC11169884 DOI: 10.3389/fmicb.2024.1410968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/01/2024] [Indexed: 06/15/2024] Open
Abstract
Introduction Sweet sorghum juice is a typical production feedstock for natural, eco-friendly sweeteners and beverages. Clostridium tyrobutyricum is one of the widely used microorganisms in the food industry, and its principal product, bio-butyric acid is an important food additive. There are no published reports of Clostridium tyrobutyricum producing butyric acid using SSJ as the sole substrate without adding exogenous substances, which could reach a food-additive grade. This study focuses on tailoring a cost-effective, safe, and sustainable process and strategy for their production and application. Methods This study modeled the enzymolysis of non-reducing sugars via the first/second-order kinetics and added food-grade diatomite to the hydrolysate. Qualitative and quantitative analysis were performed using high-performance liquid chromatography, gas chromatography-mass spectrometer, full-scale laser diffraction method, ultra-performance liquid chromatography-tandem mass spectrometry, the cell double-staining assay, transmission electron microscopy, and Oxford nanopore technology sequencing. Quantitative real-time polymerase chain reaction, pathway and process enrichment analysis, and homology modeling were conducted for mutant genes. Results The treated sweet sorghum juice showed promising results, containing 70.60 g/L glucose and 63.09 g/L fructose, with a sucrose hydrolysis rate of 98.29% and a minimal sucrose loss rate of 0.87%. Furthermore, 99.62% of the colloidal particles and 82.13% of the starch particles were removed, and the concentrations of hazardous substances were effectively reduced. A food microorganism Clostridium tyrobutyricum TGL-A236 with deep utilization value was developed, which showed superior performance by converting 30.65% glucose and 37.22% fructose to 24.1364 g/L bio-butyric acid in a treated sweet sorghum juice (1:1 dilution) fermentation broth. This titer was 2.12 times higher than that of the original strain, with a butyric acid selectivity of 86.36%. Finally, the Genome atlas view, Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and evolutionary genealogy of genes: Non-supervised Orthologous (eggNOG) functional annotations, three-dimensional structure and protein cavity prediction of five non-synonymous variant genes were obtained. Conclusion This study not only includes a systematic process flow and in-depth elucidation of relevant mechanisms but also provides a new strategy for green processing of food raw materials, improving food microbial performance, and ensuring the safe production of food additives.
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Affiliation(s)
- Mei-Han Liu
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Xiang Zhou
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, China
- Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin, China
| | - Miao-Miao Zhang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, China
- Gansu Key Laboratory of Microbial Resources Exploitation and Application, Lanzhou, China
| | - Ya-Juan Wang
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, China
| | - Bo Zhou
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
- Hunan Key Laboratory of Forestry Edible Resources Safety and Processing, Changsha, Hunan, China
| | - Nan Ding
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, China
| | - Qing-Feng Wu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
| | - Cai-Rong Lei
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, China
| | - Zi-Yi Dong
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, China
| | - Jun-Le Ren
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, China
| | - Jing-Ru Zhao
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, China
| | - Cheng-Lin Jia
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, China
| | - Jun Liu
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
| | - Dong Lu
- Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- University of Chinese Academy of Sciences, Chinese Academy of Science, Beijing, China
- Kejin Innovation Institute of Heavy Ion Beam Biological Industry, Baiyin, China
- Gansu Key Laboratory of Microbial Resources Exploitation and Application, Lanzhou, China
| | - Hai-Yan Zhong
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha, China
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Zhang Z, Cai Y, Zheng N, Deng Y, Gao L, Wang Q, Xia X. Diverse models of cavity engineering in enzyme modification: Creation, filling, and reshaping. Biotechnol Adv 2024; 72:108346. [PMID: 38518963 DOI: 10.1016/j.biotechadv.2024.108346] [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: 09/08/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Most enzyme modification strategies focus on designing the active sites or their surrounding structures. Interestingly, a large portion of the enzymes (60%) feature active sites located within spacious cavities. Despite recent discoveries, cavity-mediated enzyme engineering remains crucial for enhancing enzyme properties and unraveling folding-unfolding mechanisms. Cavity engineering influences enzyme stability, catalytic activity, specificity, substrate recognition, and docking. This article provides a comprehensive review of various cavity engineering models for enzyme modification, including cavity creation, filling, and reshaping. Additionally, it also discusses feasible tools for geometric analysis, functional assessment, and modification of cavities, and explores potential future research directions in this field. Furthermore, a promising universal modification strategy for cavity engineering that leverages state-of-the-art technologies and methodologies to tailor cavities according to the specific requirements of industrial production conditions is proposed.
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Affiliation(s)
- Zehua Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yongchao Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Nan Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yu Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Qiong Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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Zhao H, Du H, Zhao S, Chen Z, Li Y, Xu K, Liu B, Cheng X, Wen W, Li G, Chen G, Zhao Z, Qiu G, Liu P, Zhang TJ, Wu Z, Wu N. SIGMA leverages protein structural information to predict the pathogenicity of missense variants. CELL REPORTS METHODS 2024; 4:100687. [PMID: 38211594 PMCID: PMC10831939 DOI: 10.1016/j.crmeth.2023.100687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 08/15/2023] [Accepted: 12/14/2023] [Indexed: 01/13/2024]
Abstract
Leveraging protein structural information to evaluate pathogenicity has been hindered by the scarcity of experimentally determined 3D protein. With the aid of AlphaFold2 predictions, we developed the structure-informed genetic missense mutation assessor (SIGMA) to predict missense variant pathogenicity. In comparison with existing predictors across labeled variant datasets and experimental datasets, SIGMA demonstrates superior performance in predicting missense variant pathogenicity (AUC = 0.933). We found that the relative solvent accessibility of the mutated residue contributed greatly to the predictive ability of SIGMA. We further explored combining SIGMA with other top-tier predictors to create SIGMA+, proving highly effective for variant pathogenicity prediction (AUC = 0.966). To facilitate the application of SIGMA, we pre-computed SIGMA scores for over 48 million possible missense variants across 3,454 disease-associated genes and developed an interactive online platform (https://www.sigma-pred.org/). Overall, by leveraging protein structure information, SIGMA offers an accurate structure-based approach to evaluating the pathogenicity of missense variants.
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Affiliation(s)
- Hengqiang Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Huakang Du
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Sen Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Zefu Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Yaqi Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Kexin Xu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Bowen Liu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Xi Cheng
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Wen Wen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Guozhuang Li
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Guilin Chen
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Zhengye Zhao
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China
| | - Guixing Qiu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Pengfei Liu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Baylor Genetics, Houston, TX 77021, USA
| | - Terry Jianguo Zhang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Zhihong Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China; Medical Research Center, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Medical Research Center of Orthopedics, Chinese Academy of Medical Sciences, Beijing 100730, China.
| | - Nan Wu
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China; Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Beijing 100730, China; Key Laboratory of Big Data for Spinal Deformities, Chinese Academy of Medical Sciences, Beijing 100730, China.
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Zhang MF, Xie WL, Chen C, Li CX, Xu JH. Computational redesign of taxane-10β-hydroxylase for de novo biosynthesis of a key paclitaxel intermediate. Appl Microbiol Biotechnol 2023; 107:7105-7117. [PMID: 37736790 DOI: 10.1007/s00253-023-12784-x] [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: 06/22/2023] [Revised: 08/27/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023]
Abstract
Paclitaxel (Taxol®) is the most popular anticancer diterpenoid predominantly present in Taxus. The core skeleton of paclitaxel is highly modified, but researches on the cytochrome P450s involved in post-modification process remain exceedingly limited. Herein, the taxane-10β-hydroxylase (T10βH) from Taxus cuspidata, which is the third post-modification enzyme that catalyzes the conversion of taxadiene-5α-yl-acetate (T5OAc) to taxadiene-5α-yl-acetoxy-10β-ol (T10OH), was investigated in Escherichia coli by combining computation-assisted protein engineering and metabolic engineering. The variant of T10βH, M3 (I75F/L226K/S345V), exhibited a remarkable 9.5-fold increase in protein expression, accompanied by respective 1.3-fold and 2.1-fold improvements in turnover frequency (TOF) and total turnover number (TTN). Upon integration into the engineered strain, the variant M3 resulted in a substantial enhancement in T10OH production from 0.97 to 2.23 mg/L. Ultimately, the titer of T10OH reached 3.89 mg/L by fed-batch culture in a 5-L bioreactor, representing the highest level reported so far for the microbial de novo synthesis of this key paclitaxel intermediate. This study can serve as a valuable reference for further investigation of other P450s associated with the artificial biosynthesis of paclitaxel and other terpenoids. KEY POINTS: • The T10βH from T. cuspidata was expressed and engineered in E. coli unprecedentedly. • The expression and activity of T10βH were improved through protein engineering. • De novo biosynthesis of T10OH was achieved in E. coli with a titer of 3.89 mg/L.
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Affiliation(s)
- Mei-Fang Zhang
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Wen-Liang Xie
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Cheng Chen
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Chun-Xiu Li
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Jian-He Xu
- State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
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Nishikino T, Hijikata A, Kojima S, Shirai T, Kainosho M, Homma M, Miyanoiri Y. Changes in the hydrophobic network of the FliG MC domain induce rotational switching of the flagellar motor. iScience 2023; 26:107320. [PMID: 37520711 PMCID: PMC10372836 DOI: 10.1016/j.isci.2023.107320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 04/18/2023] [Accepted: 07/04/2023] [Indexed: 08/01/2023] Open
Abstract
The FliG protein plays a pivotal role in switching the rotational direction of the flagellar motor between clockwise and counterclockwise. Although we previously showed that mutations in the Gly-Gly linker of FliG induce a defect in switching rotational direction, the detailed molecular mechanism was not elucidated. Here, we studied the structural changes in the FliG fragment containing the middle and C-terminal regions, named FliGMC, and the switch-defective FliGMC-G215A, using nuclear magnetic resonance (NMR) and molecular dynamics simulations. NMR analysis revealed multiple conformations of FliGMC, and the exchange process between these conformations was suppressed by the G215A residue substitution. Furthermore, changes in the intradomain orientation of FliG were induced by changes in hydrophobic interaction networks throughout FliG. Our finding applies to FliG in a ring complex in the flagellar basal body, and clarifies the switching mechanism of the flagellar motor.
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Affiliation(s)
- Tatsuro Nishikino
- Laboratory for Ultra-High Magnetic Field NMR Spectroscopy, Research Center for Next-Generation Protein Sciences, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Atsushi Hijikata
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Seiji Kojima
- Division of Biological Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Tsuyoshi Shirai
- Department of Bioscience, Nagahama Institute of Bio-Science and Technology, 1266 Tamura, Nagahama, Shiga 526-0829, Japan
| | - Masatsune Kainosho
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Graduate School of Science, Tokyo Metropolitan University, 1-1 Minami-ohsawa, Hachioji, Tokyo 192-0397, Japan
| | - Michio Homma
- Division of Biological Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
- Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yohei Miyanoiri
- Laboratory for Ultra-High Magnetic Field NMR Spectroscopy, Research Center for Next-Generation Protein Sciences, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
- Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
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Pastore A, Temussi PA. Unfolding under Pressure: An NMR Perspective. Chembiochem 2023; 24:e202300164. [PMID: 37154795 DOI: 10.1002/cbic.202300164] [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: 02/28/2023] [Revised: 05/06/2023] [Accepted: 05/08/2023] [Indexed: 05/10/2023]
Abstract
This review aims to analyse the role of solution nuclear magnetic resonance spectroscopy in pressure-induced in vitro studies of protein unfolding. Although this transition has been neglected for many years because of technical difficulties, it provides important information about the forces that keep protein structure together. We first analyse what pressure unfolding is, then provide a critical overview of how NMR spectroscopy has contributed to the field and evaluate the observables used in these studies. Finally, we discuss the commonalities and differences between pressure-, cold- and heat-induced unfolding. We conclude that, despite specific peculiarities, in both cold and pressure denaturation the important contribution of the state of hydration of nonpolar side chains is a major factor that determines the pressure dependence of the conformational stability of proteins.
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Affiliation(s)
- Annalisa Pastore
- European Synchrotron Radiation Facilities, 71 Ave des Martyrs, 38000, Grenoble, France
- The Wohl Institute, King's College London, 5 Cutcombe Rd, SE59RT, London, UK
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8
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Krempl C, Wurm JP, Beck Erlach M, Kremer W, Sprangers R. Insights into the Structure of Invisible Conformations of Large Methyl Group Labeled Molecular Machines from High Pressure NMR. J Mol Biol 2023; 435:167922. [PMID: 37330282 DOI: 10.1016/j.jmb.2022.167922] [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: 10/19/2022] [Revised: 12/08/2022] [Accepted: 12/11/2022] [Indexed: 06/19/2023]
Abstract
Most proteins are highly flexible and can adopt conformations that deviate from the energetically most favorable ground state. Structural information on these lowly populated, alternative conformations is often lacking, despite the functional importance of these states. Here, we study the pathway by which the Dcp1:Dcp2 mRNA decapping complex exchanges between an autoinhibited closed and an open conformation. We make use of methyl Carr-Purcell-Meiboom-Gill (CPMG) NMR relaxation dispersion (RD) experiments that report on the population of the sparsely populated open conformation as well as on the exchange rate between the two conformations. To obtain volumetric information on the open conformation as well as on the transition state structure we made use of RD measurements at elevated pressures. We found that the open Dcp1:Dcp2 conformation has a lower molecular volume than the closed conformation and that the transition state is close in volume to the closed state. In the presence of ATP the volume change upon opening of the complex increases and the volume of the transition state lies in-between the volumes of the closed and open state. These findings show that ATP has an effect on the volume changes that are associated with the opening-closing pathway of the complex. Our results highlight the strength of pressure dependent NMR methods to obtain insights into structural features of protein conformations that are not directly observable. As our work makes use of methyl groups as NMR probes we conclude that the applied methodology is also applicable to high molecular weight complexes.
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Affiliation(s)
- Christina Krempl
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Jan Philip Wurm
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Markus Beck Erlach
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Werner Kremer
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany
| | - Remco Sprangers
- Institute of Biophysics and Physical Biochemistry, Regensburg Center for Biochemistry, University of Regensburg, 93053 Regensburg, Germany.
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Zhang Z, Long M, Zheng N, Deng Y, Wang Q, Osire T, Xia X. Redesign of γ-glutamyl transpeptidase from Bacillus subtilis for high-level production of L-theanine by cavity topology engineering. Appl Microbiol Biotechnol 2023; 107:3551-3564. [PMID: 37099056 DOI: 10.1007/s00253-023-12544-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 04/12/2023] [Accepted: 04/16/2023] [Indexed: 04/27/2023]
Abstract
L-Theanine is a multifunctional nonprotein amino acid found naturally in tea leaves. It has been developed as a commercial product for a wide range of applications in the food, pharmaceutical, and healthcare industries. However, L-theanine production catalyzed by γ-glutamyl transpeptidase (GGT) is limited by the low catalytic efficiency and specificity of this class of enzymes. Here, we developed a strategy for cavity topology engineering (CTE) based on the cavity geometry of GGT from B. subtilis 168 (CGMCC 1.1390) to obtain an enzyme with high catalytic activity and applied it to the synthesis of L-theanine. Three potential mutation sites, M97, Y418, and V555, were identified using the internal cavity as a probe, and residues G, A, V, F, Y, and Q, which may affect the shape of the cavity, were obtained directly by computer statistical analysis without energy calculations. Finally, 35 mutants were obtained. The optimal mutant Y418F/M97Q showed a 4.8-fold improvement in catalytic activity and a 25.6-fold increase in catalytic efficiency. The recombinant enzyme Y418F/M97Q exhibited a high space-time productivity of 15.4 g L-1 h-1 by whole-cell synthesis in a 5 L bioreactor, which was one of the highest concentrations reported so far at 92.4 g L-1. Overall, this strategy is expected to enhance the enzymatic activity associated with the synthesis of L-theanine and its derivatives.Key points • Cavity topology engineering was used to modify the GGT for L-theanine biocatalysis. • The catalytic efficiency of GGT was increased by 25.6-fold. • Highest productivity of L-theanine reached 15.4 g L -1 h-1 (92.4 g L-1) in a 5 L bioreactor.
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Affiliation(s)
- Zehua Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Mengfei Long
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Nan Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Yu Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Qiong Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Tolbert Osire
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen, 518172, Guangdong, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, China.
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10
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Zhang Z, Long M, Zheng N, Lü X, Zhu C, Osire T, Xia X. Inside Out Computational Redesign of Cavities for Improving Thermostability and Catalytic Activity of Rhizomucor Miehei Lipase. Appl Environ Microbiol 2023; 89:e0217222. [PMID: 36912632 PMCID: PMC10057959 DOI: 10.1128/aem.02172-22] [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: 12/22/2022] [Accepted: 02/15/2023] [Indexed: 03/14/2023] Open
Abstract
Cavities are created by hydrophobic interactions between residue side chain atoms during the folding of enzymes. Redesigning cavities can improve the thermostability and catalytic activity of the enzyme; however, the synergistic effect of cavities remains unclear. In this study, Rhizomucor miehei lipase (RML) was used as a model to explore volume fluctuation and spatial distribution changes of the internal cavities, which could reveal the roles of internal cavities in the thermostability and catalytic activity. We present an inside out cavity engineering (CE) strategy based on computational techniques to explore how changes in the volumes and spatial distribution of cavities affect the thermostability and catalytic activity of the enzyme. We obtained 12 single-point mutants, among which the melting temperatures (Tm) of 8 mutants showed an increase of more than 2°C. Sixteen multipoint mutations were further designed by spatial distribution rearrangement of internal cavities. The Tm of the most stable triple variant, with mutations including T21V (a change of T to V at position 21), S27A, and T198L (T21V/S27A/T198L), was elevated by 11.0°C, together with a 28.7-fold increase in the half-life at 65°C and a specific activity increase of 9.9-fold (up to 5,828 U mg-1), one of the highest lipase activities reported. The possible mechanism of decreased volumes and spatial rearrangement of the internal cavities improved the stability of the enzyme, optimizing the outer substrate tunnel to improve the catalytic efficiency. Overall, the inside out computational redesign of cavities method could help to deeply understand the effect of cavities on enzymatic stability and activity, which would be beneficial for protein engineering efforts to optimize natural enzymes. IMPORTANCE In the present study, R. miehei lipase, which is widely used in various industries, provides an opportunity to explore the effects of internal cavities on the thermostability and catalytic activity of enzymes. Here, we execute high hydrostatic pressure molecular dynamics (HP-MD) simulations to screen the critical internal cavity and reshape the internal cavities through site-directed mutation. We show that as the global internal cavity volume decreases, cavity rearrangement can improve the stability of the protein while optimizing the substrate channel to improve the catalytic efficiency. Our results provide significant insights into understanding the mechanism of action of the internal cavity. Our strategy is expected to be applied to other enzymes to promote increases in thermostability and catalytic activity.
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Affiliation(s)
- Zehua Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Mengfei Long
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Nan Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiang Lü
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Cailin Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Tolbert Osire
- Faculty of Biology, Shenzhen MSU-BIT University, Guangdong, China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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11
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Zhang S, McCallum SA, Gillilan R, Wang J, Royer CA. High Pressure CPMG and CEST Reveal That Cavity Position Dictates Distinct Dynamic Disorder in the PP32 Repeat Protein. J Phys Chem B 2022; 126:10597-10607. [PMID: 36455152 PMCID: PMC10314987 DOI: 10.1021/acs.jpcb.2c05498] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Given the central role of conformational dynamics in protein function, it is essential to characterize the time scales and structures associated with these transitions. High pressure (HP) perturbation favors transitions to excited states because they typically occupy a smaller molar volume, thus facilitating characterization of conformational dynamics. Repeat proteins, with their straightforward architecture, provide good models for probing the sequence dependence of protein conformational dynamics. Investigations of chemical exchange by 15N CPMG relaxation dispersion analysis revealed that introduction of a cavity via substitution of isoleucine 7 by alanine in the N-terminal capping motif of the pp32 leucine-rich repeat protein leads to pressure-dependent conformational exchange detected on the 500 μs-2 ms CPMG time scale. Exchange amplitude decreased from the N- to C-terminus, revealing a gradient of conformational exchange across the protein. In contrast, introduction of a cavity in the central core of pp32 via the L60A mutation led to pressure-induced exchange on a slower (>2 ms) time scale detected by 15N-CEST analysis. Excited state 15N chemical shifts indicated that in the excited state detected by HP CEST, the N-terminal region is mostly unfolded, while the core retains native-like structure. These HP chemical exchange measurements reveal that cavity position dictates exchange on distinct time scales, highlighting the subtle, yet central role of sequence in determining protein conformational dynamics.
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Affiliation(s)
- Siwen Zhang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy NY USA 12180
| | - Scott A. McCallum
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy NY USA 12180
| | - Richard Gillilan
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY USA 14853
| | - Jinqiu Wang
- Graduate Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy NY USA 12180
| | - Catherine A. Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy NY USA 12180
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12
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de Oliveira GAP, Arruda HRS, de Andrade GC, Silva JL. Evolutionary Role of Water-Accessible Cavities in Src Homology 2 (SH2) Domains. J Phys Chem B 2022; 126:8689-8698. [PMID: 36281877 DOI: 10.1021/acs.jpcb.2c05409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Protein excited states are fundamental in the understanding of biological function, despite the fact they are hardly observed using traditional biophysical methodologies. Pressure perturbation coupled with nuclear magnetic resonance (NMR) spectroscopy is a powerful physicochemical tool to glance at these low-populated high-energy states on a residue-by-residue basis and underpin mechanistic insights into protein functionalities. Here we performed pressure titrations using NMR spectroscopy and relaxation dispersion experiments to identify the low-lying energetic states of the c-Abl SH2 domain. By showing that the SH2 excited state contains a hydrated hydrophobic cavity, fast-exchange motions, and highly conserved residues facing the water-accessible hole, we discuss the implications of water-protein interactions in SH2 modules achieving high-affinity binding and promiscuous phospho-Tyr peptide recognition.
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Affiliation(s)
- Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ21941-902, Brazil
| | - Hiam R S Arruda
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ21941-902, Brazil
| | - Guilherme C de Andrade
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ21941-902, Brazil
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ21941-902, Brazil
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13
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Loss of stability and unfolding cooperativity in hPGK1 upon gradual structural perturbation of its N-terminal domain hydrophobic core. Sci Rep 2022; 12:17200. [PMID: 36229482 PMCID: PMC9561527 DOI: 10.1038/s41598-022-22088-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/10/2022] [Indexed: 01/06/2023] Open
Abstract
Phosphoglycerate kinase has been a model for the stability, folding cooperativity and catalysis of a two-domain protein. The human isoform 1 (hPGK1) is associated with cancer development and rare genetic diseases that affect several of its features. To investigate how mutations affect hPGK1 folding landscape and interaction networks, we have introduced mutations at a buried site in the N-terminal domain (F25 mutants) that either created cavities (F25L, F25V, F25A), enhanced conformational entropy (F25G) or introduced structural strain (F25W) and evaluated their effects using biophysical experimental and theoretical methods. All F25 mutants folded well, but showed reduced unfolding cooperativity, kinetic stability and altered activation energetics according to the results from thermal and chemical denaturation analyses. These alterations correlated well with the structural perturbation caused by mutations in the N-terminal domain and the destabilization caused in the interdomain interface as revealed by H/D exchange under native conditions. Importantly, experimental and theoretical analyses showed that these effects are significant even when the perturbation is mild and local. Our approach will be useful to establish the molecular basis of hPGK1 genotype-phenotype correlations due to phosphorylation events and single amino acid substitutions associated with disease.
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14
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Opanasyuk O, Barth A, Peulen TO, Felekyan S, Kalinin S, Sanabria H, Seidel CA. Unraveling multi-state molecular dynamics in single-molecule FRET experiments. II. Quantitative analysis of multi-state kinetic networks. J Chem Phys 2022; 157:031501. [DOI: 10.1063/5.0095754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Single-molecule Förster Resonance Energy Transfer (smFRET) experiments are ideally suited to resolve the structural dynamics of biomolecules. A significant challenge to date is capturing and quantifying the exchange between multiple conformational states, mainly when these dynamics occur on the sub-millisecond timescale. Many methods for quantitative analysis are challenged if more than two states are involved, and the appropriate choice of the number of states in the kinetic network is difficult. An additional complication arises if dynamically active molecules coexist with pseudo-static molecules in similar conformational states with undistinguishable FRET efficiencies. To address these problems, we developed a quantitative integrative analysis framework that combines the information from FRET-lines that relate average fluorescence lifetimes and intensities in two-dimensional burst frequency histograms, fluorescence decays obtained by time-correlated single photon counting, photon distribution analysis of the intensities and fluorescence correlation spectroscopy. Individually, these methodologies provide ambiguous results for the characterization of dynamics in complex kinetic networks. However, the global analysis approach enables accurate determination of the number of states, their kinetic connectivity, the transition rate constants, and species fractions. To challenge the potential of smFRET experiments studying multi-state kinetic networks, we apply our integrative framework using a set of synthetic data for three-state systems with different kinetic connectivity and exchange rates. Our methodology paves the way towards an integrated analysis of multiparameter smFRET experiments that spans all dimensions of the experimental data. Finally, we propose a workflow for the analysis and show examples that demonstrate the usefulness of this toolkit for dynamic structural biology.
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Affiliation(s)
| | | | | | - Suren Felekyan
- PC-II, Heinrich Heine University Düsseldorf Department of Chemistry, Germany
| | - Stanislav Kalinin
- Institut für Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany
| | | | - Claus A.M. Seidel
- Institut fuer Physikalische Chemie, Heinrich-Heine-Universität Düsseldorf, Germany
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15
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Pacheco-Garcia JL, Loginov DS, Anoz-Carbonell E, Vankova P, Palomino-Morales R, Salido E, Man P, Medina M, Naganathan AN, Pey AL. Allosteric Communication in the Multifunctional and Redox NQO1 Protein Studied by Cavity-Making Mutations. Antioxidants (Basel) 2022; 11:antiox11061110. [PMID: 35740007 PMCID: PMC9219786 DOI: 10.3390/antiox11061110] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 02/01/2023] Open
Abstract
Allosterism is a common phenomenon in protein biochemistry that allows rapid regulation of protein stability; dynamics and function. However, the mechanisms by which allosterism occurs (by mutations or post-translational modifications (PTMs)) may be complex, particularly due to long-range propagation of the perturbation across protein structures. In this work, we have investigated allosteric communication in the multifunctional, cancer-related and antioxidant protein NQO1 by mutating several fully buried leucine residues (L7, L10 and L30) to smaller residues (V, A and G) at sites in the N-terminal domain. In almost all cases, mutated residues were not close to the FAD or the active site. Mutations L→G strongly compromised conformational stability and solubility, and L30A and L30V also notably decreased solubility. The mutation L10A, closer to the FAD binding site, severely decreased FAD binding affinity (≈20 fold vs. WT) through long-range and context-dependent effects. Using a combination of experimental and computational analyses, we show that most of the effects are found in the apo state of the protein, in contrast to other common polymorphisms and PTMs previously characterized in NQO1. The integrated study presented here is a first step towards a detailed structural–functional mapping of the mutational landscape of NQO1, a multifunctional and redox signaling protein of high biomedical relevance.
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Affiliation(s)
- Juan Luis Pacheco-Garcia
- Departamento de Química Física, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
- Correspondence: (J.L.P.-G.); (A.L.P.); Tel.: +34-958243173 (A.L.P.)
| | - Dmitry S. Loginov
- Institute of Microbiology—BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, 252 50 Vestec, Czech Republic; (D.S.L.); (P.M.)
| | - Ernesto Anoz-Carbonell
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50009 Zaragoza, Spain; (E.A.-C.); (M.M.)
| | - Pavla Vankova
- Institute of Biotechnology—BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, 252 50 Vestec, Czech Republic;
- Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030/8, 128 43 Prague, Czech Republic
| | - Rogelio Palomino-Morales
- Departamento de Bioquímica y Biología Molecular I, Facultad de Ciencias y Centro de Investigaciones Biomédicas (CIBM), Universidad de Granada, 18016 Granada, Spain;
| | - Eduardo Salido
- Center for Rare Diseases (CIBERER), Hospital Universitario de Canarias, Universidad de la Laguna, 38320 Tenerife, Spain;
| | - Petr Man
- Institute of Microbiology—BioCeV, Academy of Sciences of the Czech Republic, Prumyslova 595, 252 50 Vestec, Czech Republic; (D.S.L.); (P.M.)
| | - Milagros Medina
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de Ciencias, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI) (GBsC-CSIC Joint Unit), Universidad de Zaragoza, 50009 Zaragoza, Spain; (E.A.-C.); (M.M.)
| | - Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras (IITM), Chennai 600036, India;
| | - Angel L. Pey
- Departamento de Química Física, Unidad de Excelencia en Química Aplicada a Biomedicina y Medioambiente e Instituto de Biotecnología, Universidad de Granada, Av. Fuentenueva s/n, 18071 Granada, Spain
- Correspondence: (J.L.P.-G.); (A.L.P.); Tel.: +34-958243173 (A.L.P.)
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16
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Gomari MM, Rostami N, Faradonbeh DR, Asemaneh HR, Esmailnia G, Arab S, Farsimadan M, Hosseini A, Dokholyan NV. Evaluation of pH change effects on the HSA folding and its drug binding characteristics, a computational biology investigation. Proteins 2022; 90:1908-1925. [DOI: 10.1002/prot.26386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 04/24/2022] [Accepted: 04/26/2022] [Indexed: 11/12/2022]
Affiliation(s)
- Mohammad Mahmoudi Gomari
- Student Research Committee, Iran University of Medical Sciences Tehran Iran
- Department of Medical Biotechnology, Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering Arak University Arak Iran
| | - Davood Rabiei Faradonbeh
- Department of Medical Biotechnology School of Advanced Technologies in Medicine, Tehran University of Medical Sciences Tehran Iran
| | - Hamid Reza Asemaneh
- Polymer Research Center, Department of Chemical Engineering Razi University Kermanshah Iran
| | - Giti Esmailnia
- Department of Medical Biotechnology, Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Shahriar Arab
- Department of Biophysics School of Biological Sciences, Tarbiat Modares University Tehran Iran
| | - Marziye Farsimadan
- Department of Biology, Faculty of Sciences University of Guilan Rasht Iran
| | - Arshad Hosseini
- Department of Medical Biotechnology, Faculty of Allied Medicine Iran University of Medical Sciences Tehran Iran
| | - Nikolay V. Dokholyan
- Department of Pharmacology, Department of Biochemistry & Molecular Biology Pennsylvania State University College of Medicine Hershey Pennsylvania USA
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17
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Biomolecules under Pressure: Phase Diagrams, Volume Changes, and High Pressure Spectroscopic Techniques. Int J Mol Sci 2022; 23:ijms23105761. [PMID: 35628571 PMCID: PMC9144967 DOI: 10.3390/ijms23105761] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/18/2022] [Accepted: 05/19/2022] [Indexed: 02/06/2023] Open
Abstract
Pressure is an equally important thermodynamical parameter as temperature. However, its importance is often overlooked in the biophysical and biochemical investigations of biomolecules and biological systems. This review focuses on the application of high pressure (>100 MPa = 1 kbar) in biology. Studies of high pressure can give insight into the volumetric aspects of various biological systems; this information cannot be obtained otherwise. High-pressure treatment is a potentially useful alternative method to heat-treatment in food science. Elevated pressure (up to 120 MPa) is present in the deep sea, which is a considerable part of the biosphere. From a basic scientific point of view, the application of the gamut of modern spectroscopic techniques provides information about the conformational changes of biomolecules, fluctuations, and flexibility. This paper reviews first the thermodynamic aspects of pressure science, the important parameters affecting the volume of a molecule. The technical aspects of high pressure production are briefly mentioned, and the most common high-pressure-compatible spectroscopic techniques are also discussed. The last part of this paper deals with the main biomolecules, lipids, proteins, and nucleic acids: how they are affected by pressure and what information can be gained about them using pressure. I I also briefly mention a few supramolecular structures such as viruses and bacteria. Finally, a subjective view of the most promising directions of high pressure bioscience is outlined.
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18
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Hueting DA, Vanga SR, Syrén PO. Thermoadaptation in an Ancestral Diterpene Cyclase by Altered Loop Stability. J Phys Chem B 2022; 126:3809-3821. [PMID: 35583961 PMCID: PMC9169049 DOI: 10.1021/acs.jpcb.1c10605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Thermostability is
the key to maintain the structural integrity
and catalytic activity of enzymes in industrial biotechnological processes,
such as terpene cyclase-mediated generation of medicines, chiral synthons,
and fine chemicals. However, affording a large increase in the thermostability
of enzymes through site-directed protein engineering techniques can
constitute a challenge. In this paper, we used ancestral sequence
reconstruction to create a hyperstable variant of the ent-copalyl diphosphate synthase PtmT2, a terpene cyclase involved in
the assembly of antibiotics. Molecular dynamics simulations on the
μs timescale were performed to shed light on possible molecular
mechanisms contributing to activity at an elevated temperature and
the large 40 °C increase in melting temperature observed for
an ancestral variant of PtmT2. In silico analysis
revealed key differences in the flexibility of a loop capping the
active site, between extant and ancestral proteins. For the modern
enzyme, the loop collapses into the active site at elevated temperatures,
thus preventing biocatalysis, whereas the loop remains in a productive
conformation both at ambient and high temperatures in the ancestral
variant. Restoring a Pro loop residue introduced in the ancestral
variant to the corresponding Gly observed in the extant protein led
to reduced catalytic activity at high temperatures, with only moderate
effects on the melting temperature, supporting the importance of the
flexibility of the capping loop in thermoadaptation. Conversely, the
inverse Gly to Pro loop mutation in the modern enzyme resulted in
a 3-fold increase in the catalytic rate. Despite an overall decrease
in maximal activity of ancestor compared to wild type, its increased
thermostability provides a robust backbone amenable for further enzyme
engineering. Our work cements the importance of loops in enzyme catalysis
and provides a molecular mechanism contributing to thermoadaptation
in an ancestral enzyme.
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Affiliation(s)
- David A Hueting
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Sudarsana R Vanga
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
| | - Per-Olof Syrén
- School of Engineering Sciences in Chemistry, Biotechnology and Health, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm 114 28, Sweden.,School of Engineering Sciences in Chemistry, Biotechnology and Health, Department of Fibre and Polymer Technology, KTH Royal Institute of Technology, Stockholm 114 28, Sweden
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19
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Dubois C, Lahfa M, Pissarra J, de Guillen K, Barthe P, Kroj T, Roumestand C, Padilla A. Combining High-Pressure NMR and Geometrical Sampling to Obtain a Full Topological Description of Protein Folding Landscapes: Application to the Folding of Two MAX Effectors from Magnaporthe oryzae. Int J Mol Sci 2022; 23:ijms23105461. [PMID: 35628267 PMCID: PMC9141691 DOI: 10.3390/ijms23105461] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/10/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022] Open
Abstract
Despite advances in experimental and computational methods, the mechanisms by which an unstructured polypeptide chain regains its unique three-dimensional structure remains one of the main puzzling questions in biology. Single-molecule techniques, ultra-fast perturbation and detection approaches and improvement in all-atom and coarse-grained simulation methods have greatly deepened our understanding of protein folding and the effects of environmental factors on folding landscape. However, a major challenge remains the detailed characterization of the protein folding landscape. Here, we used high hydrostatic pressure 2D NMR spectroscopy to obtain high-resolution experimental structural information in a site-specific manner across the polypeptide sequence and along the folding reaction coordinate. We used this residue-specific information to constrain Cyana3 calculations, in order to obtain a topological description of the entire folding landscape. This approach was used to describe the conformers populating the folding landscape of two small globular proteins, AVR-Pia and AVR-Pib, that belong to the structurally conserved but sequence-unrelated MAX effectors superfamily. Comparing the two folding landscapes, we found that, in spite of their divergent sequences, the folding pathway of these two proteins involves a similar, inescapable, folding intermediate, even if, statistically, the routes used are different.
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Affiliation(s)
- Cécile Dubois
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34000 Montpellier, France
| | - Mounia Lahfa
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34000 Montpellier, France
| | - Joana Pissarra
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34000 Montpellier, France
| | - Karine de Guillen
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34000 Montpellier, France
| | - Philippe Barthe
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34000 Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, University of Montpellier, INRAE, CIRAD, Institut Agro, IRD, 34000 Montpellier, France
| | - Christian Roumestand
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34000 Montpellier, France
| | - André Padilla
- Centre de Biologie Structurale, University of Montpellier, INSERM U1054, CNRS UMR 5048, 34000 Montpellier, France
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20
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Wakamoto T, Yamamoto J, Senzaki S, Koide R, Kitazawa S, Kitahara R. Amplification of the Specific Conformational Fluctuation of Proteins by Site-Specific Mutagenesis and Hydrostatic Pressure. J Phys Chem B 2022; 126:1868-1875. [PMID: 35213155 DOI: 10.1021/acs.jpcb.1c10082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Conformational fluctuation, namely, protein interconversion between different conformations, is crucial to protein function. Outer surface protein A (OspA), comprising N- and C-terminal globular domains linked by a central β-sheet, is expressed on the surface of Borrelia burgdorferi, the causative agent of Lyme disease, and recognizes the TROSPA receptor in the tick gut. Solution nuclear magnetic resonance studies have shown that the central β-sheet and C-terminal domain containing TROSPA recognition sites are less stable than the N-terminal domain, revealing an intermediate conformation between the basic folded and completely unfolded proteins. We previously suggested that exposure of receptor-binding sites following denaturation of the C-terminal domain is advantageous for OspA binding to the receptor. Here, we observed amplification of a specific protein fluctuation by pressure perturbation and site-specific mutagenesis. The salt-bridge-destabilized mutant E160D and the cavity-enlarged mutant I243A favored the intermediate. The proportion of the intermediate accounted for almost 100% in E160D at 250 MPa. Strategies using a suitably chosen point mutation with high pressure are generally applicable for amplification of specific conformational fluctuation and potentially improve our understanding of the intermediate conformations of proteins. Knowledge of various conformations, including OspA intermediates, may be useful for designing a vaccine for Lyme disease.
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Affiliation(s)
- Takuro Wakamoto
- Graduate School of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Junya Yamamoto
- Graduate School of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Sho Senzaki
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Reina Koide
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Soichiro Kitazawa
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Ryo Kitahara
- Graduate School of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan.,College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
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21
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Prangé T, Carpentier P, Dhaussy AC, van der Linden P, Girard E, Colloc'h N. Comparative study of the effects of high hydrostatic pressure per se and high argon pressure on urate oxidase ligand stabilization. Acta Crystallogr D Struct Biol 2022; 78:162-173. [DOI: 10.1107/s2059798321012134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/15/2021] [Indexed: 11/11/2022] Open
Abstract
The stability of the tetrameric enzyme urate oxidase in complex with excess of 8-azaxanthine was investigated either under high hydrostatic pressure per se or under a high pressure of argon. The active site is located at the interface of two subunits, and the catalytic activity is directly related to the integrity of the tetramer. This study demonstrates that applying pressure to a protein–ligand complex drives the thermodynamic equilibrium towards ligand saturation of the complex, revealing a new binding site. A transient dimeric intermediate that occurs during the pressure-induced dissociation process was characterized under argon pressure and excited substates of the enzyme that occur during the catalytic cycle can be trapped by pressure. Comparison of the different structures under pressure infers an allosteric role of the internal hydrophobic cavity in which argon is bound, since this cavity provides the necessary flexibility for the active site to function.
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22
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Kitahara R, Yamazaki R, Ide F, Li S, Shiramasa Y, Sasahara N, Yoshizawa T. Pressure-Jump Kinetics of Liquid-Liquid Phase Separation: Comparison of Two Different Condensed Phases of the RNA-Binding Protein, Fused in Sarcoma. J Am Chem Soc 2021; 143:19697-19702. [PMID: 34787417 DOI: 10.1021/jacs.1c07571] [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
The RNA-binding protein fused in sarcoma (FUS) undergoes liquid-liquid phase separation (LLPS) both in vivo and in vitro. Self-assembled liquid droplets of FUS transform into reversible hydrogels and into more irreversible and toxic aggregates. Although LLPS can be a precursor of irreversible aggregates, a generic method to study kinetics of the formation of LLPS has not been developed. Here, we demonstrated the pressure-jump kinetics of phase transition between the 1-phase state and FUS-LLPS states observed at low pressure (<2 kbar, LP-LLPS) and high pressure (>2 kbar, HP-LLPS) using high-pressure UV/vis spectroscopy. Absorbance (turbidity) changes were reproduced repeatedly using pressure cycles. The Johnson-Mehl-Avrami-Kolmogorov theory was used to understand droplet formation occurring via nucleation and growth. The Avrami exponent n, representing the dimensionality of growing droplets, and the reaction rate constant k were calculated. The HP-LLPS formation rate was ∼2-fold slower than that of LP-LLPS. The Avrami exponent obtained for both LLPS states could be explained by diffusion-limited growth. Nucleation and growth rates decreased during LP-LLPS formation (n = 0.51), and the nucleation rate decreased with a constant growth rate in HP-LLPS formation (n = 1.4). The HP-LLPS vanishing rate was ∼20-fold slower than that of LP-LLPS. This difference in vanishing rates indicates a stronger intermolecular interaction in HP-LLPS than in LP-LLPS, which might promote transformation into irreversible aggregates in the droplets. Further, direct transition from HP-LLPS to LP-LLPS was observed. This indicates that interconversion between LP-LLPS and HP-LLPS occurs in equilibrium. Formation of reversible liquid droplets, followed by phase transition into another liquid phase, could thus be part of the physiological maturation process of FUS-LLPS.
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Affiliation(s)
- Ryo Kitahara
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Ryota Yamazaki
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Fumika Ide
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Shujie Li
- Graduate School of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Yutaro Shiramasa
- College of Pharmaceutical Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Naoya Sasahara
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
| | - Takuya Yoshizawa
- College of Life Sciences, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
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23
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Murk K, Ornaghi M, Schiweck J. Profilin Isoforms in Health and Disease - All the Same but Different. Front Cell Dev Biol 2021; 9:681122. [PMID: 34458253 PMCID: PMC8387879 DOI: 10.3389/fcell.2021.681122] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/12/2021] [Indexed: 12/11/2022] Open
Abstract
Profilins are small actin binding proteins, which are structurally conserved throughout evolution. They are probably best known to promote and direct actin polymerization. However, they also participate in numerous cell biological processes beyond the roles typically ascribed to the actin cytoskeleton. Moreover, most complex organisms express several profilin isoforms. Their cellular functions are far from being understood, whereas a growing number of publications indicate that profilin isoforms are involved in the pathogenesis of various diseases. In this review, we will provide an overview of the profilin family and "typical" profilin properties including the control of actin dynamics. We will then discuss the profilin isoforms of higher animals in detail. In terms of cellular functions, we will focus on the role of Profilin 1 (PFN1) and Profilin 2a (PFN2a), which are co-expressed in the central nervous system. Finally, we will discuss recent findings that link PFN1 and PFN2a to neurological diseases, such as amyotrophic lateral sclerosis (ALS), Fragile X syndrome (FXS), Huntington's disease and spinal muscular atrophy (SMA).
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Affiliation(s)
- Kai Murk
- Institute of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Marta Ornaghi
- Institute of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Juliane Schiweck
- Institute of Biochemistry, Charité Universitätsmedizin Berlin, Berlin, Germany
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24
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Dass R, Corlianò E, Mulder FAA. The contribution of electrostatics to hydrogen exchange in the unfolded protein state. Biophys J 2021; 120:4107-4114. [PMID: 34370996 PMCID: PMC8510857 DOI: 10.1016/j.bpj.2021.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 06/20/2021] [Accepted: 08/03/2021] [Indexed: 12/03/2022] Open
Abstract
Although electrostatics have long been recognized to play an important role in hydrogen exchange (HX) with solvent, the quantitative assessment of its magnitude in the unfolded state has hitherto been lacking. This limits the utility of HX as a quantitative method to study protein stability, folding, and dynamics. Using the intrinsically disordered human protein α-synuclein as a proxy for the unfolded state, we show that a hybrid mean-field approach can effectively compute the electrostatic potential at all backbone amide positions along the chain. From the electrochemical potential, a fourfold reduction in hydroxide concentration near the protein backbone is predicted for the C-terminal domain, a prognosis that is in direct agreement with experimentally derived protection factors from NMR spectroscopy. Thus, impeded HX for the C-terminal region of α-synuclein is not the result of intramolecular hydrogen bonding and/or structure formation.
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Affiliation(s)
- Rupashree Dass
- Department of Chemistry and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Enrico Corlianò
- Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Frans A A Mulder
- Department of Chemistry and Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark.
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25
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Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR. BIOLOGY 2021; 10:biology10070656. [PMID: 34356511 PMCID: PMC8301334 DOI: 10.3390/biology10070656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022]
Abstract
Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CαHα groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CαHα, and CH3 groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CαHα when compared to amide groups.
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26
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Li M, Sun W, Tyurin VA, DeLucia M, Ahn J, Kagan VE, van der Wel PCA. Activation of Cytochrome C Peroxidase Function Through Coordinated Foldon Loop Dynamics upon Interaction with Anionic Lipids. J Mol Biol 2021; 433:167057. [PMID: 34033821 DOI: 10.1016/j.jmb.2021.167057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 02/06/2023]
Abstract
Cardiolipin (CL) is a mitochondrial anionic lipid that plays important roles in the regulation and signaling of mitochondrial apoptosis. CL peroxidation catalyzed by the assembly of CL-cytochrome c (cyt c) complexes at the inner mitochondrial membrane is a critical checkpoint. The structural changes in the protein, associated with peroxidase activation by CL and different anionic lipids, are not known at a molecular level. To better understand these peripheral protein-lipid interactions, we compare how phosphatidylglycerol (PG) and CL lipids trigger cyt c peroxidase activation, and correlate functional differences to structural and motional changes in membrane-associated cyt c. Structural and motional studies of the bound protein are enabled by magic angle spinning solid state NMR spectroscopy, while lipid peroxidase activity is assayed by mass spectrometry. PG binding results in a surface-bound state that preserves a nativelike fold, which nonetheless allows for significant peroxidase activity, though at a lower level than binding its native substrate CL. Lipid-specific differences in peroxidase activation are found to correlate to corresponding differences in lipid-induced protein mobility, affecting specific protein segments. The dynamics of omega loops C and D are upregulated by CL binding, in a way that is remarkably controlled by the protein:lipid stoichiometry. In contrast to complete chemical denaturation, membrane-induced protein destabilization reflects a destabilization of select cyt c foldons, while the energetically most stable helices are preserved. Our studies illuminate the interplay of protein and lipid dynamics in the creation of lipid peroxidase-active proteolipid complexes implicated in early stages of mitochondrial apoptosis.
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Affiliation(s)
- Mingyue Li
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Wanyang Sun
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Vladimir A Tyurin
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Maria DeLucia
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jinwoo Ahn
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Valerian E Kagan
- Department of Environmental and Occupational Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Institute for Regenerative Medicine, IM Sechenov, Moscow State Medical University, Moscow 119146, Russian Federation
| | - Patrick C A van der Wel
- Department of Structural Biology, University of Pittsburgh, Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Groningen, the Netherlands.
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27
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Fuji R, Umezawa K, Mizuguchi M, Ihara M. Protein Engineering of the Soluble Metal-dependent Formate Dehydrogenase from Escherichia coli. ANAL SCI 2021; 37:733-739. [PMID: 33455969 DOI: 10.2116/analsci.20scp15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Formate is the most targeted C1 building block and electron carrier in the post-petroleum era. Formate dehydrogenase (FDH), which catalyzes the production or degradation of formate, has acquired considerable attention. Among FDHs, a metal-dependent FDH that carries a complex active center, molybdenum-pterin cofactor, can directly transfer electrons from formate to other redox proteins without generating NAD(P)H. Previously, we reported an expression system for membrane-bound metal-dependent FDH from E. coli (encoded by the fdoG-fdoH-fdoI operon) and succeeded in its conversion to a soluble protein. However, this protein exhibited a too low stability to be purified and analyzed biochemically. In this study, we tried to improve the stability of heterologously expressed FDH through rational and irrational approaches. As a result, a mutant with the highest specific activity was obtained through a rational approach. This study not only yielded a promising FDH enzyme with enhanced activity and stability for industrial applications, but also offered relevant insights for the handling of recombinant large proteins.
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Affiliation(s)
- Rintaro Fuji
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University
| | - Koji Umezawa
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University.,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University
| | - Manami Mizuguchi
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University
| | - Masaki Ihara
- Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University.,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University
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28
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Lu Y, Biswas I, Villoutreix BO, Rezaie AR. Role of Gly197 in the structure and function of protein C. Biochim Biophys Acta Gen Subj 2021; 1865:129892. [PMID: 33722640 DOI: 10.1016/j.bbagen.2021.129892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/27/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
We previously demonstrated that heterozygous Gly197 to Arg mutation in PROC is associated with venous thrombosis due to the mutation abrogating both zymogenic and enzymatic activities of protein C and activated protein C (APC). In this study, we investigated the role of Gly197 on the structure and function of protein C by replacing it with Ala, Lys and Glu in separate constructs. Characterization of protein C mutants indicated their activation by thrombin is improved ~5-20-fold with the order of PC-G197K > PC-G197E > PC-G197A > PC-WT. Interestingly, the cofactor function of thrombomodulin (TM) in promoting the activation of zymogens by thrombin followed the reverse order of PC-WT > PC-G197A > PC-G197E > PC-G197K. The thrombin-generation inhibitory profiles of zymogens in a tissue factor-mediated thrombin generation assay using protein C-deficient plasma with or without supplementation with TM followed the same order of zymogen activation in the purified system. Evaluation of anticoagulant activities of APC derivatives by prothrombinase and aPTT assays revealed a normal activity for APC-G197A but dramatically impaired activity for the other two mutants. In the endothelial cell permeability assay, APC-G197A exhibited normal antiinflammatory activity, but the other two mutants were nearly inactive. These results suggest that Gly197 plays a key role in TM cofactor-dependent protein C activation by thrombin. It facilitates the recognition of protein C by thrombin in the presence of TM but impedes it in the absence of the cofactor. In APC, a small residue at this position is required for the proper folding/reactivity of the active-site pocket of the protease, a hypothesis supported by structural modeling.
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Affiliation(s)
- Yeling Lu
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, United States of America; Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Indranil Biswas
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, United States of America
| | - Bruno O Villoutreix
- INSERM 1141, NeuroDiderot, Université de Paris, Hôpital Robert-Debré, F-75019 Paris, France
| | - Alireza R Rezaie
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, United States of America; Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America.
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29
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Yang D, Reyes-De-Corcuera JI. Increased activity of alcohol oxidase at high hydrostatic pressure. Enzyme Microb Technol 2021; 145:109751. [PMID: 33750541 DOI: 10.1016/j.enzmictec.2021.109751] [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: 09/22/2020] [Revised: 12/18/2020] [Accepted: 01/20/2021] [Indexed: 10/22/2022]
Abstract
Alcohol oxidase (AOx) from P. pastoris has potential applications in the production of carbonyl compounds and for the detection and quantification of alcohols. However, AOx's poor stability and low activity have hindered its practical application. There are two fractions of AOx in P. pastoris with different thermal stability. High hydrostatic pressure (HHP) increased the activity of the labile (L) + resistant (R) combined fractions but not of the R fraction alone. The activity of the L + R fractions increased 2.4-fold at 160 MPa and 30 °C compared to the activity at 0.1 MPa. At higher temperatures, the increase in activity with pressure was greater due to the combined stabilization and activation effects. The reaction rate of the R fraction at 50 °C was 17.9 ± 3.6 or 17.7 ± 0.8 μM min-1 at 80 or 160 MPa, respectively, and was not significantly different from the activity of the L + R fractions under the same conditions (18.4 ± 2.7 μM min-1). The activation energy of the R fraction was not significantly different between 80 MPa (41.5 ± 10.5 kJ mol-1) and 160 MPa (43.8 ± 7.8 kJ mol-1). The combined increase in the stability of the R fraction at HHP enables the use of the enzyme at 50 °C with little loss of activity and an increased catalytic rate.
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Affiliation(s)
- Daoyuan Yang
- Department of Food Science and Technology, University of Georgia, Athens, GA 30602, USA
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30
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Sprangers R. High-pressure NMR measurements provide insights into the different structural states that proteins can adopt. Biophys J 2021; 120:749-751. [PMID: 33561391 DOI: 10.1016/j.bpj.2021.01.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 10/22/2022] Open
Affiliation(s)
- Remco Sprangers
- Department of Biophysics I, Regensburg Center for Biochemistry, University of Regensburg, Regensburg, Germany.
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31
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Chwastyk M, Panek EA, Malinowski J, Jaskólski M, Cieplak M. Properties of Cavities in Biological Structures-A Survey of the Protein Data Bank. Front Mol Biosci 2020; 7:591381. [PMID: 33240933 PMCID: PMC7677499 DOI: 10.3389/fmolb.2020.591381] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 10/06/2020] [Indexed: 11/13/2022] Open
Abstract
We performed a PDB-wide survey of proteins to assess their cavity content, using the SPACEBALL algorithm to calculate the cavity volumes. In addition, we determined the hydropathy character of the cavities. We demonstrate that the cavities of most proteins are hydrophilic, but smaller proteins tend to have cavities with hydrophobic walls. We propose criteria for distinguishing between cavities and pockets, and single out proteins with the largest cavities.
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Affiliation(s)
- Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Ewa A Panek
- Department of Biometry, Warsaw University of Life Sciences, Warsaw, Poland
| | - Jan Malinowski
- Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Mariusz Jaskólski
- Center for Biocrystallographic Research, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland.,Department of Crystallography, Faculty of Chemistry, Adam Mickiewicz University, Poznań, Poland
| | - Marek Cieplak
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
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32
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Pacheco-García JL, Cano-Muñoz M, Sánchez-Ramos I, Salido E, Pey AL. Naturally-Occurring Rare Mutations Cause Mild to Catastrophic Effects in the Multifunctional and Cancer-Associated NQO1 Protein. J Pers Med 2020; 10:E207. [PMID: 33153185 PMCID: PMC7711955 DOI: 10.3390/jpm10040207] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/27/2020] [Accepted: 11/02/2020] [Indexed: 12/13/2022] Open
Abstract
The functional and pathological implications of the enormous genetic diversity of the human genome are mostly unknown, primarily due to our unability to predict pathogenicity in a high-throughput manner. In this work, we characterized the phenotypic consequences of eight naturally-occurring missense variants on the multifunctional and disease-associated NQO1 protein using biophysical and structural analyses on several protein traits. Mutations found in both exome-sequencing initiatives and in cancer cell lines cause mild to catastrophic effects on NQO1 stability and function. Importantly, some mutations perturb functional features located structurally far from the mutated site. These effects are well rationalized by considering the nature of the mutation, its location in protein structure and the local stability of its environment. Using a set of 22 experimentally characterized mutations in NQO1, we generated experimental scores for pathogenicity that correlate reasonably well with bioinformatic scores derived from a set of commonly used algorithms, although the latter fail to semiquantitatively predict the phenotypic alterations caused by a significant fraction of mutations individually. These results provide insight into the propagation of mutational effects on multifunctional proteins, the implementation of in silico approaches for establishing genotype-phenotype correlations and the molecular determinants underlying loss-of-function in genetic diseases.
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Affiliation(s)
- Juan Luis Pacheco-García
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Mario Cano-Muñoz
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Isabel Sánchez-Ramos
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain; (J.L.P.-G.); (M.C.-M.); (I.S.-R.)
| | - Eduardo Salido
- Centre for Biomedical Research on Rare Diseases (CIBERER), Hospital Universitario de Canarias, 38320 Tenerife, Spain;
| | - Angel L. Pey
- Departamento de Química Física y Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente (UEQ), Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain
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33
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Becerra‐Flores M, Cardozo T. SARS-CoV-2 viral spike G614 mutation exhibits higher case fatality rate. Int J Clin Pract 2020; 74:e13525. [PMID: 32374903 PMCID: PMC7267315 DOI: 10.1111/ijcp.13525] [Citation(s) in RCA: 202] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 04/30/2020] [Accepted: 05/02/2020] [Indexed: 12/13/2022] Open
Abstract
AIM The COVID-19 pandemic is caused by infection with the SARS-CoV-2 virus. The major mutation detected to date in the SARS-CoV-2 viral envelope spike protein, which is responsible for virus attachment to the host and is also the main target for host antibodies, is a mutation of an aspartate (D) at position 614 found frequently in Chinese strains to a glycine (G). We sought to infer health impact of this mutation. RESULT Increased case fatality rate correlated strongly with the proportion of viruses bearing G614 on a country by country basis. The amino acid at position 614 occurs at an internal protein interface of the viral spike, and the presence of G at this position was calculated to destabilise a specific conformation of the viral spike, within which the key host receptor binding site is more accessible. CONCLUSION These results imply that G614 is a more pathogenic strain of SARS-CoV-2, which may influence vaccine design. The prevalence of this form of the virus should also be included in epidemiologic models predicting the COVID-19 health burden and fatality over time in specific regions. Physicians should be aware of this characteristic of the virus to anticipate the clinical course of infection.
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Affiliation(s)
- Manuel Becerra‐Flores
- Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
| | - Timothy Cardozo
- Department of Biochemistry and Molecular PharmacologyNYU Langone HealthNew YorkNYUSA
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34
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Mesophilic Pyrophosphatase Function at High Temperature: A Molecular Dynamics Simulation Study. Biophys J 2020; 119:142-150. [PMID: 32533942 DOI: 10.1016/j.bpj.2020.05.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 05/06/2020] [Accepted: 05/15/2020] [Indexed: 02/06/2023] Open
Abstract
The mesophilic inorganic pyrophosphatase from Escherichia coli (EcPPase) retains function at 353 K, the physiological temperature of hyperthermophilic Thermococcus thioreducens, whereas the homolog protein (TtPPase) from this hyperthermophilic organism cannot function at room temperature. To explain this asymmetric behavior, we examined structural and dynamical properties of the two proteins using molecular dynamics simulations. The global flexibility of TtPPase is significantly higher than its mesophilic homolog at all tested temperature/pressure conditions. However, at 353 K, EcPPase reduces its solvent-exposed surface area and increases subunit compaction while maintaining flexibility in its catalytic pocket. In contrast, TtPPase lacks this adaptability and has increased rigidity and reduced protein/water interactions in its catalytic pocket at room temperature, providing a plausible explanation for its inactivity near room temperature.
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Lu Y, Villoutreix BO, Biswas I, Ding Q, Wang X, Rezaie AR. Thr90Ser Mutation in Antithrombin is Associated with Recurrent Thrombosis in a Heterozygous Carrier. Thromb Haemost 2020; 120:1045-1055. [PMID: 32422680 DOI: 10.1055/s-0040-1710590] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Antithrombin (AT) is a serine protease inhibitor that regulates the activity of coagulation proteases of both intrinsic and extrinsic pathways. We identified an AT-deficient patient with a heterozygous Thr90Ser (T90S) mutation who experiences recurrent venous thrombosis. To understand the molecular basis of the clotting defect, we expressed AT-T90S in mammalian cells, purified it to homogeneity, and characterized its properties in established kinetics, binding, and coagulation assays. The possible effect of mutation on the AT structure was also evaluated by molecular modeling. Results demonstrate the inhibitory activity of AT-T90S toward thrombin and factor Xa has been impaired three- to fivefold in both the absence and presence of heparin. The affinity of heparin for AT-T90S has been decreased by four- to fivefold. Kinetic analysis revealed the stoichiometry of AT-T90S inhibition of both thrombin and factor Xa has been elevated by three- to fourfold in both the absence and presence of heparin, suggesting that the reactivity of coagulation proteases with AT-T90S has been elevated in the substrate pathway. The anticoagulant activity of AT-T90S has been significantly impaired as analyzed in the AT-deficient plasma supplemented with AT-T90S. The anti-inflammatory effect of AT-T90S was also decreased. Structural analysis predicts the shorter side-chain of Ser in AT-T90S has a destabilizing effect on the structure of AT and/or the AT-protease complex, possibly increasing the size of an internal cavity and altering a hydrogen-bonding network that modulates conformations of the allosterically linked heparin-binding site and reactive center loop of the serpin. This mutational effect increases the reactivity of AT-T90S with coagulation proteases in the substrate pathway.
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Affiliation(s)
- Yeling Lu
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States
| | - Bruno O Villoutreix
- Drugs and Molecules for Living Systems, Inserm, Institut Pasteur de Lille, University of Lille, Lille, France
| | - Indranil Biswas
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States
| | - Qiulan Ding
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuefeng Wang
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Alireza R Rezaie
- Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Oklahoma City, Oklahoma, United States.,Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States
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Resolving dynamics and function of transient states in single enzyme molecules. Nat Commun 2020; 11:1231. [PMID: 32144241 PMCID: PMC7060211 DOI: 10.1038/s41467-020-14886-w] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 02/08/2020] [Indexed: 11/23/2022] Open
Abstract
We use a hybrid fluorescence spectroscopic toolkit to monitor T4 Lysozyme (T4L) in action by unraveling the kinetic and dynamic interplay of the conformational states. In particular, by combining single-molecule and ensemble multiparameter fluorescence detection, EPR spectroscopy, mutagenesis, and FRET-positioning and screening, and other biochemical and biophysical tools, we characterize three short-lived conformational states over the ns-ms timescale. The use of 33 FRET-derived distance sets, to screen available T4L structures, reveal that T4L in solution mainly adopts the known open and closed states in exchange at 4 µs. A newly found minor state, undisclosed by, at present, more than 500 crystal structures of T4L and sampled at 230 µs, may be actively involved in the product release step in catalysis. The presented fluorescence spectroscopic toolkit will likely accelerate the development of dynamic structural biology by identifying transient conformational states that are highly abundant in biology and critical in enzymatic reactions. T4 Lysozyme (T4L) is a model protein whose structure is extensively studied. Here the authors combine single-molecule and ensemble FRET measurements, FRET-positioning and screening and EPR spectroscopy to study the structural dynamics of T4L and describe its conformational landscape during the catalytic cycle by an extended Michaelis–Menten mechanism and identify an excited conformational state of the enzyme.
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