1
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Wang B, Zhou X, Wang Y, Gao Y, Nakanishi H, Fujita M, Li Z. Enhancement of thermostability and expression level of Rasamsonia emersonii lipase in Pichia pastoris and its application in biodiesel production in a continuous flow reactor. Int J Biol Macromol 2024; 278:134481. [PMID: 39127275 DOI: 10.1016/j.ijbiomac.2024.134481] [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: 04/29/2024] [Revised: 07/27/2024] [Accepted: 08/02/2024] [Indexed: 08/12/2024]
Abstract
The acidic lipase from Rasamsonia emersonii named LIPR has great potential for biodiesel synthesis due to its strong methanol tolerance. Nonetheless, the limited thermostability of LIPR and low expression level in Escherichia coli remain major obstacles to its use in biodiesel synthesis. To enhance the thermostability, the mutant LIPR harboring mutations A126C-P238C for the formation of a new disulfide bond and amino acid substitution D214L was obtained through rational design. To our delight, the thermostability of LIPR mutant was greatly improved. Moreover, a comprehensive optimization strategy, such as employing the Mss signal peptide, co-expressing the molecular chaperone protein disulfide isomerase (PDI), knocking out the vacuolar sorting receptor gene VPS10-01, and overexpressing the dihydroxyacetone synthase gene DAS2, was adopted to obtain the combination-optimized mutant Pichia pastoris strain GS54. Furthermore, the biodiesel synthetic capability with the mutant GS54-LIPR was verified and the production yield was 52.2 % after 24 h in a shake flask. Subsequently, a continuous flow system was adopted to increase the biodiesel yield to 73.6 % within 3 h, demonstrating its efficacy in enhancing enzyme biocatalysis. The engineered GS54-LIPR mutant lipase is an efficient and reusable biocatalyst for the sustained production of biodiesel in a continuous flow reaction.
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Affiliation(s)
- Buqing Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Xiaoman Zhou
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yasen Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Yahui Gao
- School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Hideki Nakanishi
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Morihisa Fujita
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China; Institute for Glyco-Core Research, Gifu University, Gifu, Japan
| | - Zijie Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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2
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Diaz DJ, Gong C, Ouyang-Zhang J, Loy JM, Wells J, Yang D, Ellington AD, Dimakis AG, Klivans AR. Stability Oracle: a structure-based graph-transformer framework for identifying stabilizing mutations. Nat Commun 2024; 15:6170. [PMID: 39043654 PMCID: PMC11266546 DOI: 10.1038/s41467-024-49780-2] [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: 10/04/2023] [Accepted: 06/14/2024] [Indexed: 07/25/2024] Open
Abstract
Engineering stabilized proteins is a fundamental challenge in the development of industrial and pharmaceutical biotechnologies. We present Stability Oracle: a structure-based graph-transformer framework that achieves SOTA performance on accurately identifying thermodynamically stabilizing mutations. Our framework introduces several innovations to overcome well-known challenges in data scarcity and bias, generalization, and computation time, such as: Thermodynamic Permutations for data augmentation, structural amino acid embeddings to model a mutation with a single structure, a protein structure-specific attention-bias mechanism that makes transformers a viable alternative to graph neural networks. We provide training/test splits that mitigate data leakage and ensure proper model evaluation. Furthermore, to examine our data engineering contributions, we fine-tune ESM2 representations (Prostata-IFML) and achieve SOTA for sequence-based models. Notably, Stability Oracle outperforms Prostata-IFML even though it was pretrained on 2000X less proteins and has 548X less parameters. Our framework establishes a path for fine-tuning structure-based transformers to virtually any phenotype, a necessary task for accelerating the development of protein-based biotechnologies.
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Affiliation(s)
- Daniel J Diaz
- UT Austin, Department of Computer Science, Austin, TX, 78712, USA.
- Intelligent Proteins, LLC, Austin, TX, 78712, USA.
- UT Austin, Department of Chemistry, Austin, TX, 78712, USA.
| | - Chengyue Gong
- UT Austin, Department of Computer Science, Austin, TX, 78712, USA
| | | | - James M Loy
- Intelligent Proteins, LLC, Austin, TX, 78712, USA
- UT Austin, Department of Molecular Biosciences, Austin, TX, 78712, USA
| | - Jordan Wells
- UT Austin, McKetta Department of Chemical Engineering, Austin, TX, 78712, USA
| | - David Yang
- UT Austin, Department of Molecular Biosciences, Austin, TX, 78712, USA
| | | | - Alexandros G Dimakis
- UT Austin, Chandra Family Department of Electrical and Computer Engineering, Austin, TX, 78712, USA
| | - Adam R Klivans
- UT Austin, Department of Computer Science, Austin, TX, 78712, USA
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3
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Cuturello F, Celoria M, Ansuini A, Cazzaniga A. Enhancing predictions of protein stability changes induced by single mutations using MSA-based Language Models. Bioinformatics 2024; 40:btae447. [PMID: 39012369 PMCID: PMC11269464 DOI: 10.1093/bioinformatics/btae447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/19/2024] [Accepted: 07/10/2024] [Indexed: 07/17/2024] Open
Abstract
MOTIVATION Protein Language Models offer a new perspective for addressing challenges in structural biology, while relying solely on sequence information. Recent studies have investigated their effectiveness in forecasting shifts in thermodynamic stability caused by single amino acid mutations, a task known for its complexity due to the sparse availability of data, constrained by experimental limitations. To tackle this problem, we introduce two key novelties: leveraging a Protein Language Model that incorporates Multiple Sequence Alignments to capture evolutionary information, and using a recently released mega-scale dataset with rigorous data pre-processing to mitigate overfitting. RESULTS We ensure comprehensive comparisons by fine-tuning various pre-trained models, taking advantage of analyses such as ablation studies and baselines evaluation. Our methodology introduces a stringent policy to reduce the widespread issue of data leakage, rigorously removing sequences from the training set when they exhibit significant similarity with the test set. The MSA Transformer emerges as the most accurate among the models under investigation, given its capability to leverage co-evolution signals encoded in aligned homologous sequences. Moreover, the optimized MSA Transformer outperforms existing methods and exhibits enhanced generalization power, leading to a notable improvement in predicting changes in protein stability resulting from point mutations. AVAILABILITY AND IMPLEMENTATION Code and data at https://github.com/RitAreaSciencePark/PLM4Muts. SUPPLEMENTARY INFORMATION Supplementary Information is available at Bioinformatics online.
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Affiliation(s)
- Francesca Cuturello
- Research and Technology Institute, , AREA Science Park, Trieste 34149, Italy
| | - Marco Celoria
- Research and Technology Institute, , AREA Science Park, Trieste 34149, Italy
- HPC Department, , CINECA National Supercomputing Center, Bologna 40033, Italy
| | - Alessio Ansuini
- Research and Technology Institute, , AREA Science Park, Trieste 34149, Italy
| | - Alberto Cazzaniga
- Research and Technology Institute, , AREA Science Park, Trieste 34149, Italy
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4
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Chen Y, Lee K, Woo J, Kim DW, Keum C, Babbi G, Casadio R, Martelli PL, Savojardo C, Manfredi M, Shen Y, Sun Y, Katsonis P, Lichtarge O, Pejaver V, Seward DJ, Kamandula A, Bakolitsa C, Brenner SE, Radivojac P, O’Donnell-Luria A, Mooney SD, Jain S. Evaluating predictors of kinase activity of STK11 variants identified in primary human non-small cell lung cancers. RESEARCH SQUARE 2024:rs.3.rs-4587317. [PMID: 39011112 PMCID: PMC11247923 DOI: 10.21203/rs.3.rs-4587317/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
Critical evaluation of computational tools for predicting variant effects is important considering their increased use in disease diagnosis and driving molecular discoveries. In the sixth edition of the Critical Assessment of Genome Interpretation (CAGI) challenge, a dataset of 28 STK11 rare variants (27 missense, 1 single amino acid deletion), identified in primary non-small cell lung cancer biopsies, was experimentally assayed to characterize computational methods from four participating teams and five publicly available tools. Predictors demonstrated a high level of performance on key evaluation metrics, measuring correlation with the assay outputs and separating loss-of-function (LoF) variants from wildtype-like (WT-like) variants. The best participant model, 3Cnet, performed competitively with well-known tools. Unique to this challenge was that the functional data was generated with both biological and technical replicates, thus allowing the assessors to realistically establish maximum predictive performance based on experimental variability. Three out of the five publicly available tools and 3Cnet approached the performance of the assay replicates in separating LoF variants from WT-like variants. Surprisingly, REVEL, an often-used model, achieved a comparable correlation with the real-valued assay output as that seen for the experimental replicates. Performing variant interpretation by combining the new functional evidence with computational and population data evidence led to 16 new variants receiving a clinically actionable classification of likely pathogenic (LP) or likely benign (LB). Overall, the STK11 challenge highlights the utility of variant effect predictors in biomedical sciences and provides encouraging results for driving research in the field of computational genome interpretation.
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Affiliation(s)
- Yile Chen
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, 98105, WA, USA
| | - Kyoungyeul Lee
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Junwoo Woo
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Dong-wook Kim
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Changwon Keum
- 3billion, 3billion Biotechnology company, Seoul, South Korea
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Rita Casadio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Pier Luigi Martelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Matteo Manfredi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843, TX, USA
| | - Yuanfei Sun
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, 77843, TX, USA
| | - Panagiotis Katsonis
- Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Olivier Lichtarge
- Molecular and Human Genetics, Baylor College of Medicine, Houston, 77030, TX, USA
| | - Vikas Pejaver
- Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
| | - David J. Seward
- Department of Pathology, University of Vermont, Burlington, 5445, VT, USA
| | - Akash Kamandula
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
| | | | | | - Predrag Radivojac
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
| | - Anne O’Donnell-Luria
- Division of Genetics and Genomics, Boston Children’s Hospital, Harvard Medical School, Boston, 02115, MA, USA
- Broad Center for Mendelian Genomics, Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, 02142, MA, USA
| | - Sean D. Mooney
- Center for Information Technology, National Institutes of Health, Bethesda, 20892, MD, USA
| | - Shantanu Jain
- Khoury College of Computer Sciences, Northeastern University, Boston, 02115, MA, USA
- The Institute for Experiential AI, Northeastern University, Boston, 02115, MA, USA
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Narayanan KK, Weigle AT, Xu L, Mi X, Zhang C, Chen LQ, Procko E, Shukla D. Deep mutational scanning reveals sequence to function constraints for SWEET family transporters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.28.601307. [PMID: 39005363 PMCID: PMC11244857 DOI: 10.1101/2024.06.28.601307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Protein science is entering a transformative phase enabled by deep mutational scans that provide an unbiased view of the residue level interactions that mediate function. However, it has yet to be extensively used to characterize the mutational and evolutionary landscapes of plant proteins. Here, we apply the method to explore sequence-function relationships within the sugar transporter AtSWEET13. DMS results describe how mutational interrogation throughout different regions of the protein affects AtSWEET13 abundance and transport function. Our results identify novel transport-enhancing mutations that are validated using the FRET sensor assays. Extending DMS results to phylogenetic analyses reveal the role of transmembrane helix 4 (TM4) which makes the SWEET family transporters distinct from prokaryotic SemiSWEETs. We show that transmembrane helix 4 is intolerant to motif swapping with other clade-specific SWEET TM4 compositions, despite accommodating single point-mutations towards aromatic and charged polar amino acids. We further show that the transfer learning approaches based on physics and ML based In silico variant prediction tools have limited utility for engineering plant proteins as they were unable to reproduce our experimental results. We conclude that DMS can produce datasets which, when combined with the right predictive computational frameworks, can direct plant engineering efforts through derivative phenotype selection and evolutionary insights.
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Affiliation(s)
- Krishna K. Narayanan
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Austin T. Weigle
- Department of Chemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lingyun Xu
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Xuenan Mi
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Chen Zhang
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Li-Qing Chen
- Department of Plant Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Erik Procko
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
- Cyrus Biotechnology, Inc., Seattle, Washington 98121, United States
| | - Diwakar Shukla
- Department of Chemical & Biomolecular Engineering; Department of Plant Biology; Department of Bioengineering; Department of Chemistry, Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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6
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Chu SKS, Narang K, Siegel JB. Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset. PLoS Comput Biol 2024; 20:e1012248. [PMID: 39038042 PMCID: PMC11293664 DOI: 10.1371/journal.pcbi.1012248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 08/01/2024] [Accepted: 06/13/2024] [Indexed: 07/24/2024] Open
Abstract
Protein stability plays a crucial role in a variety of applications, such as food processing, therapeutics, and the identification of pathogenic mutations. Engineering campaigns commonly seek to improve protein stability, and there is a strong interest in streamlining these processes to enable rapid optimization of highly stabilized proteins with fewer iterations. In this work, we explore utilizing a mega-scale dataset to develop a protein language model optimized for stability prediction. ESMtherm is trained on the folding stability of 528k natural and de novo sequences derived from 461 protein domains and can accommodate deletions, insertions, and multiple-point mutations. We show that a protein language model can be fine-tuned to predict folding stability. ESMtherm performs reasonably on small protein domains and generalizes to sequences distal from the training set. Lastly, we discuss our model's limitations compared to other state-of-the-art methods in generalizing to larger protein scaffolds. Our results highlight the need for large-scale stability measurements on a diverse dataset that mirrors the distribution of sequence lengths commonly observed in nature.
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Affiliation(s)
- Simon K. S. Chu
- Biophysics Graduate Program, University of California Davis, Davis, California, United States of America
| | - Kush Narang
- College of Biological Sciences, University of California Davis, Davis, California, United States of America
| | - Justin B. Siegel
- Genome Center, University of California Davis, Davis, California, United States of America
- Department of Chemistry, University of California Davis, Davis, California, United States of America
- Department of Biochemistry and Molecular Medicine, University of California Davis, Davis, California, United States of America
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Lin YJ, Menon AS, Hu Z, Brenner SE. Variant Impact Predictor database (VIPdb), version 2: Trends from 25 years of genetic variant impact predictors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600283. [PMID: 38979289 PMCID: PMC11230257 DOI: 10.1101/2024.06.25.600283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background Variant interpretation is essential for identifying patients' disease-causing genetic variants amongst the millions detected in their genomes. Hundreds of Variant Impact Predictors (VIPs), also known as Variant Effect Predictors (VEPs), have been developed for this purpose, with a variety of methodologies and goals. To facilitate the exploration of available VIP options, we have created the Variant Impact Predictor database (VIPdb). Results The Variant Impact Predictor database (VIPdb) version 2 presents a collection of VIPs developed over the past 25 years, summarizing their characteristics, ClinGen calibrated scores, CAGI assessment results, publication details, access information, and citation patterns. We previously summarized 217 VIPs and their features in VIPdb in 2019. Building upon this foundation, we identified and categorized an additional 186 VIPs, resulting in a total of 403 VIPs in VIPdb version 2. The majority of the VIPs have the capacity to predict the impacts of single nucleotide variants and nonsynonymous variants. More VIPs tailored to predict the impacts of insertions and deletions have been developed since the 2010s. In contrast, relatively few VIPs are dedicated to the prediction of splicing, structural, synonymous, and regulatory variants. The increasing rate of citations to VIPs reflects the ongoing growth in their use, and the evolving trends in citations reveal development in the field and individual methods. Conclusions VIPdb version 2 summarizes 403 VIPs and their features, potentially facilitating VIP exploration for various variant interpretation applications. Availability VIPdb version 2 is available at https://genomeinterpretation.org/vipdb.
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Affiliation(s)
- Yu-Jen Lin
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Computational Biology, University of California, Berkeley, California 94720, USA
| | - Arul S. Menon
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- College of Computing, Data Science, and Society, University of California, Berkeley, California 94720, USA
| | - Zhiqiang Hu
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
- Currently at: Illumina, Foster City, California 94404, USA
| | - Steven E. Brenner
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Center for Computational Biology, University of California, Berkeley, California 94720, USA
- College of Computing, Data Science, and Society, University of California, Berkeley, California 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
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Qiu Y, Huang T, Cai YD. Review of predicting protein stability changes upon variations. Proteomics 2024; 24:e2300371. [PMID: 38643379 DOI: 10.1002/pmic.202300371] [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: 01/30/2024] [Revised: 04/07/2024] [Accepted: 04/08/2024] [Indexed: 04/22/2024]
Abstract
Forecasting alterations in protein stability caused by variations holds immense importance. Improving the thermal stability of proteins is important for biomedical and industrial applications. This review discusses the latest methods for predicting the effects of mutations on protein stability, databases containing protein mutations and thermodynamic parameters, and experimental techniques for efficiently assessing protein stability in high-throughput settings. Various publicly available databases for protein stability prediction are introduced. Furthermore, state-of-the-art computational approaches for anticipating protein stability changes due to variants are reviewed. Each method's types of features, base algorithm, and prediction results are also detailed. Additionally, some experimental approaches for verifying the prediction results of computational methods are introduced. Finally, the review summarizes the progress and challenges of protein stability prediction and discusses potential models for future research directions.
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Affiliation(s)
- Yiling Qiu
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
- School of Mathematics and Statistics, Guangdong University of Technology, Guangzhou, China
| | - Tao Huang
- Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yu-Dong Cai
- School of Life Sciences, Shanghai University, Shanghai, China
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Song R, Zhang J, Zhu M, Lin L, Wei W, Wei D. Computer-aided rational design strategy based on protein surface charge to improve the thermal stability of a novel esterase from Geobacillus jurassicus. Biotechnol Lett 2024; 46:443-458. [PMID: 38523202 DOI: 10.1007/s10529-024-03473-4] [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: 10/08/2023] [Revised: 01/11/2024] [Accepted: 02/10/2024] [Indexed: 03/26/2024]
Abstract
OBJECTIVES Although Geobacillus are significant thermophilic bacteria source, there are no reports of thermostable esterase gene in Geobacillus jurassicus or rational design strategies to increase the thermal stability of esterases. RESULTS Gene gju768 showed a highest similarity of 15.20% to esterases from Geobacillus sp. with detail enzymatic properties. Using a combination of Gibbs Unfolding Free Energy (∆∆G) calculator and the distance from the mutation site to the catalytic site (DsCα-Cα) to screen suitable mutation sites with elimination of negative surface charge, the mutants (D24N, E221Q, and E253Q) displayed stable mutants with higher thermal stability than the wild-type (WT). Mutant E253Q exhibited the best thermal stability, with a half-life (T1/2) at 65 °C of 32.4 min, which was 1.8-fold of the WT (17.9 min). CONCLUSION Cloning of gene gju768 and rational design based on surface charge engineering contributed to the identification of thermostable esterase from Geobacillus sp. and the exploration of evolutionary strategies for thermal stability.
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Affiliation(s)
- Runfei Song
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China
| | - Jin Zhang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China
| | - Mengyu Zhu
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China
| | - Lin Lin
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
- Research Laboratory for Functional Nanomaterial, National Engineering Research Center for Nanotechnology, Shanghai, 200241, People's Republic of China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, 130 Meilong Road, 200237, Shanghai, People's Republic of China
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10
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Zhang J, Lin L, Wei W, Wei D. Identification, Characterization, and Computer-Aided Rational Design of a Novel Thermophilic Esterase from Geobacillus subterraneus, and Application in the Synthesis of Cinnamyl Acetate. Appl Biochem Biotechnol 2024; 196:3553-3575. [PMID: 37713064 DOI: 10.1007/s12010-023-04697-2] [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] [Accepted: 08/16/2023] [Indexed: 09/16/2023]
Abstract
Investigation of a novel thermophilic esterase gene from Geobacillus subterraneus DSMZ 13552 indicated a high amino acid sequence similarity of 25.9% to a reported esterase from Geobacillus sp. A strategy that integrated computer-aided rational design tools was developed to select mutation sites. Six mutants were selected from four criteria based on the simulated saturation mutation (including 19 amino acid residues) results. Of these, the mutants Q78Y and G119A were found to retain 87% and 27% activity after incubation at 70 °C for 20 min, compared with the 19% activity for the wild type. Subsequently, a double-point mutant (Q78Y/G119A) was obtained and identified with optimal temperature increase from 65 to 70 °C and a 41.51% decrease in Km. The obtained T1/2 values of 42.2 min (70 °C) and 16.9 min (75 °C) for Q78Y/G119A showed increases of 340% and 412% compared with that in the wild type. Q78Y/G119A was then employed as a biocatalyst to synthesize cinnamyl acetate, for which the conversion rate reached 99.40% with 0.3 M cinnamyl alcohol at 60 °C. The results validated the enhanced enzymatic properties of the mutant and indicated better prospects for industrial application as compared to that in the wild type. This study reported a method by which an enzyme could evolve to achieve enhanced thermostability, thereby increasing its potential for industrial applications, which could also be expanded to other esterases.
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Affiliation(s)
- Jin Zhang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
| | - Lin Lin
- School of Chemical and Environmental Engineering, Shanghai Institute of Technology, Shanghai, 201418, People's Republic of China
- Research Laboratory for Functional Nanomaterial, National Engineering Research Center for Nanotechnology, Shanghai, 200241, People's Republic of China
| | - Wei Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China.
| | - Dongzhi Wei
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, People's Republic of China
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11
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Du Z, Huang X, Li H, Zheng M, Hong T, Li Z, Du X, Jiang Z, Ni H, Li Q, Zhu Y. Improvement of thermostability by increasing rigidity in the finger regions and flexibility in the catalytic pocket area of Pseudoalteromonas porphyrae κ-carrageenase. World J Microbiol Biotechnol 2024; 40:216. [PMID: 38802708 DOI: 10.1007/s11274-024-04029-4] [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: 01/23/2024] [Accepted: 05/20/2024] [Indexed: 05/29/2024]
Abstract
Poor thermostability reduces the industrial application value of κ-carrageenase. In this study, the PoPMuSiC algorithm combined with site-directed mutagenesis was applied to improve the thermostability of the alkaline κ-carrageenase from Pseudoalteromonas porphyrae. The mutant E154A with improved thermal stability was successfully obtained using this strategy after screening seven rationally designed mutants. Compared with the wild-type κ-carrageenase (WT), E154A improved the activity by 29.4% and the residual activity by 51.6% after treatment at 50 °C for 30 min. The melting temperature (Tm) values determined by circular dichroism were 66.4 °C and 64.6 °C for E154A and WT, respectively. Molecular dynamics simulation analysis of κ-carrageenase showed that the flexibility decreased within the finger regions (including F1, F2, F3, F5 and F6) and the flexibility improved in the catalytic pocket area of the mutant E154A. The catalytic tunnel dynamic simulation analysis revealed that E154A led to enlarged catalytic tunnel volume and increased rigidity of the enzyme-substrate complex. The increasing rigidity within the finger regions and more flexible catalytic pocket of P. porphyrae κ-carrageenase might be a significant factor for improvement of the thermostability of the mutant κ-carrageenase E154A. The proposed rational design strategy could be applied to improve the enzyme kinetic stability of other industrial enzymes. Moreover, the hydrolysates of κ-carrageenan digested by the mutant E154A demonstrated increased scavenging activities against hydroxyl (OH) radicals and 2,2'-azinobis(3-ethylbenzothiazoline)-6-sulfonic acid (ABTS) radicals compared with the undigested κ-carrageenan.
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Affiliation(s)
- Zeping Du
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Xiaoyi Huang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Hebin Li
- Department of Pharmacy, Xiamen Medical College, Xiamen, 361008, China
| | - Mingjing Zheng
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Tao Hong
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Zhipeng Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Xiping Du
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Zedong Jiang
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Hui Ni
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Qingbiao Li
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China
| | - Yanbing Zhu
- College of Ocean Food and Biological Engineering, Jimei University, Xiamen, 361021, China.
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12
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Tabler CO, Wegman SJ, Alhusaini N, Lee NF, Tilton JC. Premature Activation of the HIV-1 Protease Is Influenced by Polymorphisms in the Hinge Region. Viruses 2024; 16:849. [PMID: 38932142 PMCID: PMC11209583 DOI: 10.3390/v16060849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/21/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
HIV-1 protease inhibitors are an essential component of antiretroviral therapy. However, drug resistance is a pervasive issue motivating a persistent search for novel therapies. Recent reports found that when protease activates within the host cell's cytosol, it facilitates the pyroptotic killing of infected cells. This has led to speculation that promoting protease activation, rather than inhibiting it, could help to eradicate infected cells and potentially cure HIV-1 infection. Here, we used a nanoscale flow cytometry-based assay to characterize protease resistance mutations and polymorphisms. We quantified protease activity, viral concentration, and premature protease activation and confirmed previous findings that major resistance mutations generally destabilize the protease structure. Intriguingly, we found evidence that common polymorphisms in the hinge domain of protease can influence its susceptibility to premature activation. This suggests that viral heterogeneity could pose a considerable challenge for therapeutic strategies aimed at inducing premature protease activation in the future.
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Affiliation(s)
| | | | | | | | - John C. Tilton
- Center for Proteomics and Bioinformatics, Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA; (C.O.T.); (N.A.)
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13
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Lin MC, Kuo WH, Chen SY, Hsu JY, Lu LY, Wang CC, Chen YJ, Tsai JS, Li HJ. Ago2/CAV1 interaction potentiates metastasis via controlling Ago2 localization and miRNA action. EMBO Rep 2024; 25:2441-2478. [PMID: 38649663 PMCID: PMC11094075 DOI: 10.1038/s44319-024-00132-7] [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: 11/07/2023] [Revised: 03/22/2024] [Accepted: 03/27/2024] [Indexed: 04/25/2024] Open
Abstract
Ago2 differentially regulates oncogenic and tumor-suppressive miRNAs in cancer cells. This discrepancy suggests a secondary event regulating Ago2/miRNA action in a context-dependent manner. We show here that a positive charge of Ago2 K212, that is preserved by SIR2-mediated Ago2 deacetylation in cancer cells, is responsible for the direct interaction between Ago2 and Caveolin-1 (CAV1). Through this interaction, CAV1 sequesters Ago2 on the plasma membranes and regulates miRNA-mediated translational repression in a compartment-dependent manner. Ago2/CAV1 interaction plays a role in miRNA-mediated mRNA suppression and in miRNA release via extracellular vesicles (EVs) from tumors into the circulation, which can be used as a biomarker of tumor progression. Increased Ago2/CAV1 interaction with tumor progression promotes aggressive cancer behaviors, including metastasis. Ago2/CAV1 interaction acts as a secondary event in miRNA-mediated suppression and increases the complexity of miRNA actions in cancer.
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Affiliation(s)
- Meng-Chieh Lin
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Wen-Hung Kuo
- Department of Surgery, National Taiwan University Hospital, Taipei, 100229, Taiwan
| | - Shih-Yin Chen
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, 35053, Taiwan
- Institute of Biotechnology, National Tsing Hua University, Hsinchu, 30013, Taiwan
| | - Jing-Ya Hsu
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Li-Yu Lu
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Chen-Chi Wang
- Department of Surgery, National Taiwan University Hospital, Taipei, 100229, Taiwan
| | - Yi-Ju Chen
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Jia-Shiuan Tsai
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, 35053, Taiwan
| | - Hua-Jung Li
- Institute of Cellular and System Medicine, National Health Research Institutes, Miaoli, 35053, Taiwan.
- Program in Tissue Engineering and Regenerative Medicine, National Chung Hsing University, Taichung City, 402, Taiwan.
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14
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Lyu Q, Lin Y, Pan Y, Guan X, Ji X, Peng M, Li Q, Wang Z, Zhang Z, Luo Z, Su P, Wang J. The polymorphism analysis for CD36 among platelet donors. Sci Rep 2024; 14:8534. [PMID: 38609394 PMCID: PMC11014998 DOI: 10.1038/s41598-024-58491-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
CD36 may defect on platelets and/or monocytes in healthy individuals, which was defined as CD36 deficiency. However, we did not know the correlation between the molecular and protein levels completely. Here, we aim to determine the polymorphisms of the CD36 gene, RNA level, and CD36 on platelets and in plasma. The individuals were sequenced by Sanger sequencing. Bioinformational analysis was used by the HotMuSiC, CUPSAT, SAAFEC-SEQ, and FoldX. RNA analysis and CD36 protein detection were performed by qPCR, flow cytometry, and ELISA. In this study, we found c.1228_1239delATTGTGCCTATT (allele frequency = 0.0072) with the highest frequency among our cohort, and one mutation (c.1329_1354dupGATAGAAATGATCTTACTCAGTGTTG) was not present in the dbSNP database. 5 mutations located in the extracellular domain sequencing region with confirmation in deficient individuals, of which c.284T>C, c.512A>G, c.572C>T, and c.869T>C were found to have a deleterious impact on CD36 protein stability. Furthermore, the MFI of CD36 expression on platelets in the mutation-carry, deleterious-effect, and deficiency group was significantly lower than the no-mutation group (P < 0.0500). In addition, sCD36 levels in type II individuals were significantly lower compared with positive controls (P = 0.0060). Nevertheless, we found the presence of sCD36 in a type I individual. RNA analysis showed CD36 RNA levels in platelets of type II individuals were significantly lower than the positive individuals (P = 0.0065). However, no significant difference was observed in monocytes (P = 0.7500). We identified the most prevalent mutation (c.1228_1239delATTGTGCCTATT) among Kunming donors. Besides, our results suggested RNA level alterations could potentially underlie type II deficiency. Furthermore, sCD36 may hold promise for assessing immune reaction risk in CD36-deficient individuals, but more studies should be conducted to validate this hypothesis.
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Affiliation(s)
- Qilu Lyu
- Clinical Transfusion Research Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
- Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, 610052, Sichuan, China
| | - Yuwei Lin
- Clinical Transfusion Research Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
- Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, 610052, Sichuan, China
- School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Yiming Pan
- Clinical Transfusion Research Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
- Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, 610052, Sichuan, China
| | - Xiaoyu Guan
- Department of Blood Transfusion, The Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, Sichuan, China
| | - Xin Ji
- Clinical Transfusion Research Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China
- Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, 610052, Sichuan, China
| | - Mozhen Peng
- Yunnan Kunming Blood Center, Kunming, 650000, Yunnan, China
| | - Qian Li
- Yunnan Kunming Blood Center, Kunming, 650000, Yunnan, China
| | - Zhijang Wang
- Yunnan Kunming Blood Center, Kunming, 650000, Yunnan, China
| | - Zhihui Zhang
- Yunnan Kunming Blood Center, Kunming, 650000, Yunnan, China
| | - Zhen Luo
- Yunnan Kunming Blood Center, Kunming, 650000, Yunnan, China.
| | - Pincan Su
- Department of Transfusion Medicine, Affiliated Hospital of Yunnan University, Kunming, 650000, Yunnan, China.
| | - Jue Wang
- Clinical Transfusion Research Center, Institute of Blood Transfusion, Chinese Academy of Medical Sciences and Peking Union Medical College, Chengdu, 610052, Sichuan, China.
- Key Laboratory of Transfusion Adverse Reactions, CAMS, Chengdu, 610052, Sichuan, China.
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15
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Wang Y, Liu W, Peng S, Chen Y, Chen F, Zhang A, Chen K. Enhancing thermostability of tryptophan hydroxylase via protein engineering and its application in 5-hydroxytryptophan production. Int J Biol Macromol 2024; 264:130609. [PMID: 38437933 DOI: 10.1016/j.ijbiomac.2024.130609] [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: 01/14/2024] [Revised: 03/01/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
5-Hydroxytryptophan (5-HTP), as the precursor of serotonin and melatonin in animals, can regulate mood, sleep, and behavior, which is widely used in pharmaceutical and health products industry. The enzymatic production of 5-hydroxytryptophan (5-HTP) from L-tryptophan (L-Trp) using tryptophan hydroxylase (TPH) show huge potential in application due to its advantages, such as mild reaction conditions, avoidance of protection/deprotection processes, excellent regioselectivity and considerable catalytic efficiency, compared with chemical synthesis and natural extraction. However, the low thermostability of TPH restricted its hydroxylation efficiency toward L-Trp. In this study, we aimed to improve the thermostability of TPH via semi-rational design guided by (folding free energy) ΔΔG fold calculation. After two rounds of evolution, two beneficial mutants M1 (S422V) and M30 (V275L/I412K) were obtained. Thermostability evaluation showed that M1 and M30 possessed 5.66-fold and 6.32-fold half-lives (t1/2) at 37 °C, and 4.2 °C and 6.0 °C higher melting temperature (Tm) than the WT, respectively. The mechanism behind thermostability improvement was elucidated with molecular dynamics simulation. Furthermore, biotransformation of 5-HTP from L-Trp was performed, M1 and M30 displayed 1.80-fold and 2.30-fold than that of WT, respectively. This work provides important insights into the thermostability enhancement of TPH and generate key mutants that could be robust candidates for practical production of 5-HTP.
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Affiliation(s)
- Yingying Wang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Wei Liu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Shiguo Peng
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Yan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Feifei Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China
| | - Alei Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
| | - Kequan Chen
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing 211816, PR China.
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16
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Shang W, Hu X, Lin X, Li S, Xiong S, Huang B, Wang X. Iterative In Silico Screening for Optimizing Stable Conformation of Anti-SARS-CoV-2 Nanobodies. Pharmaceuticals (Basel) 2024; 17:424. [PMID: 38675386 PMCID: PMC11054880 DOI: 10.3390/ph17040424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 03/20/2024] [Accepted: 03/23/2024] [Indexed: 04/28/2024] Open
Abstract
Nanobodies (Nbs or VHHs) are single-domain antibodies (sdAbs) derived from camelid heavy-chain antibodies. Nbs have special and unique characteristics, such as small size, good tissue penetration, and cost-effective production, making Nbs a good candidate for the diagnosis and treatment of viruses and other pathologies. Identifying effective Nbs against COVID-19 would help us control this dangerous virus or other unknown variants in the future. Herein, we introduce an in silico screening strategy for optimizing stable conformation of anti-SARS-CoV-2 Nbs. Firstly, various complexes containing nanobodies were downloaded from the RCSB database, which were identified from immunized llamas. The primary docking between Nbs and the SARS-CoV-2 spike protein receptor-binding domain was performed through the ClusPro program, with the manual screening leaving the reasonable conformation to the next step. Then, the binding distances of atoms between the antigen-antibody interfaces were measured through the NeighborSearch algorithm. Finally, filtered nanobodies were acquired according to HADDOCK scores through HADDOCK docking the COVID-19 spike protein with nanobodies under restrictions of calculated molecular distance between active residues and antigenic epitopes less than 4.5 Å. In this way, those nanobodies with more reasonable conformation and stronger neutralizing efficacy were acquired. To validate the efficacy ranking of the nanobodies we obtained, we calculated the binding affinities (∆G) and dissociation constants (Kd) of all screened nanobodies using the PRODIGY web tool and predicted the stability changes induced by all possible point mutations in nanobodies using the MAESTROWeb server. Furthermore, we examined the performance of the relationship between nanobodies' ranking and their number of mutation-sensitive sites (Spearman correlation > 0.68); the results revealed a robust correlation, indicating that the superior nanobodies identified through our screening process exhibited fewer mutation hotspots and higher stability. This correlation analysis demonstrates the validity of our screening criteria, underscoring the suitability of these nanobodies for future development and practical implementation. In conclusion, this three-step screening strategy iteratively in silico greatly improved the accuracy of screening desired nanobodies compared to using only ClusPro docking or default HADDOCK docking settings. It provides new ideas for the screening of novel antibodies and computer-aided screening methods.
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Affiliation(s)
| | | | | | | | | | - Bingding Huang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; (W.S.); (X.H.); (X.L.); (S.L.); (S.X.)
| | - Xin Wang
- College of Big Data and Internet, Shenzhen Technology University, Shenzhen 518118, China; (W.S.); (X.H.); (X.L.); (S.L.); (S.X.)
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17
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Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024; 30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [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: 01/04/2024] [Indexed: 02/24/2024]
Abstract
Directed evolution stands as a seminal technology for generating novel protein functionalities, a cornerstone in biocatalysis, metabolic engineering, and synthetic biology. Today, with the development of various mutagenesis methods and advanced analytical machines, the challenge of diversity generation and high-throughput screening platforms is largely solved, and one of the remaining challenges is: how to empower the potential of single beneficial substitutions with recombination to achieve the epistatic effect. This review overviews experimental and computer-assisted recombination methods in protein engineering campaigns. In addition, integrated and machine learning-guided strategies were highlighted to discuss how these recombination approaches contribute to generating the screening library with better diversity, coverage, and size. A decision tree was finally summarized to guide the further selection of proper recombination strategies in practice, which was beneficial for accelerating protein engineering.
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Affiliation(s)
- Xinyue Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Anni Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Xiujuan Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
| | - Haiyang Cui
- School of Life Sciences, Nanjing Normal University, No. 2 Xuelin Road, Nanjing, 210097, China
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18
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Vincenzi M, Mercurio FA, Autiero I, Leone M. Cancer-Related Mutations in the Sam Domains of EphA2 Receptor and Ship2 Lipid Phosphatase: A Computational Study. Molecules 2024; 29:1024. [PMID: 38474536 DOI: 10.3390/molecules29051024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 02/09/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
The lipid phosphatase Ship2 interacts with the EphA2 receptor by forming a heterotypic Sam (sterile alpha motif)-Sam complex. Ship2 works as a negative regulator of receptor endocytosis and consequent degradation, and anti-oncogenic effects in cancer cells should be induced by hindering its association with EphA2. Herein, a computational approach is presented to investigate the relationship between Ship2-Sam/EphA2-Sam interaction and cancer onset and further progression. A search was first conducted through the COSMIC (Catalogue of Somatic Mutations in Cancer) database to identify cancer-related missense mutations positioned inside or close to the EphA2-Sam and Ship2-Sam reciprocal binding interfaces. Next, potential differences in the chemical-physical properties of mutant and wild-type Sam domains were evaluated by bioinformatics tools based on analyses of primary sequences. Three-dimensional (3D) structural models of mutated EphA2-Sam and Ship2-Sam domains were built as well and deeply analysed with diverse computational instruments, including molecular dynamics, to classify potentially stabilizing and destabilizing mutations. In the end, the influence of mutations on the EphA2-Sam/Ship2-Sam interaction was studied through docking techniques. This in silico approach contributes to understanding, at the molecular level, the mutation/cancer relationship by predicting if amino acid substitutions could modulate EphA2 receptor endocytosis.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Ida Autiero
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy
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19
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Gallo E. Revolutionizing Synthetic Antibody Design: Harnessing Artificial Intelligence and Deep Sequencing Big Data for Unprecedented Advances. Mol Biotechnol 2024:10.1007/s12033-024-01064-2. [PMID: 38308755 DOI: 10.1007/s12033-024-01064-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/02/2024] [Indexed: 02/05/2024]
Abstract
Synthetic antibodies (Abs) represent a category of engineered proteins meticulously crafted to replicate the functions of their natural counterparts. Such Abs are generated in vitro, enabling advanced molecular alterations associated with antigen recognition, paratope site engineering, and biochemical refinements. In a parallel realm, deep sequencing has brought about a paradigm shift in molecular biology. It facilitates the prompt and cost-effective high-throughput sequencing of DNA and RNA molecules, enabling the comprehensive big data analysis of Ab transcriptomes, including specific regions of interest. Significantly, the integration of artificial intelligence (AI), based on machine- and deep- learning approaches, has fundamentally transformed our capacity to discern patterns hidden within deep sequencing big data, including distinctive Ab features and protein folding free energy landscapes. Ultimately, current AI advances can generate approximations of the most stable Ab structural configurations, enabling the prediction of de novo synthetic Abs. As a result, this manuscript comprehensively examines the latest and relevant literature concerning the intersection of deep sequencing big data and AI methodologies for the design and development of synthetic Abs. Together, these advancements have accelerated the exploration of antibody repertoires, contributing to the refinement of synthetic Ab engineering and optimizations, and facilitating advancements in the lead identification process.
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Affiliation(s)
- Eugenio Gallo
- Avance Biologicals, Department of Medicinal Chemistry, 950 Dupont Street, Toronto, ON, M6H 1Z2, Canada.
- RevivAb, Department of Protein Engineering, Av. Ipiranga, 6681, Partenon, Porto Alegre, RS, 90619-900, Brazil.
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20
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Galano‐Frutos JJ, Sancho J. Energy, water, and protein folding: A molecular dynamics-based quantitative inventory of molecular interactions and forces that make proteins stable. Protein Sci 2024; 33:e4905. [PMID: 38284492 PMCID: PMC10804899 DOI: 10.1002/pro.4905] [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: 06/21/2023] [Revised: 12/12/2023] [Accepted: 01/05/2024] [Indexed: 01/30/2024]
Abstract
Protein folding energetics can be determined experimentally on a case-by-case basis but it is not understood in sufficient detail to provide deep control in protein design. The fundamentals of protein stability have been outlined by calorimetry, protein engineering, and biophysical modeling, but these approaches still face great difficulty in elucidating the specific contributions of the intervening molecules and physical interactions. Recently, we have shown that the enthalpy and heat capacity changes associated to the protein folding reaction can be calculated within experimental error using molecular dynamics simulations of native protein structures and their corresponding unfolded ensembles. Analyzing in depth molecular dynamics simulations of four model proteins (CI2, barnase, SNase, and apoflavodoxin), we dissect here the energy contributions to ΔH (a key component of protein stability) made by the molecular players (polypeptide and solvent molecules) and physical interactions (electrostatic, van der Waals, and bonded) involved. Although the proteins analyzed differ in length, isoelectric point and fold class, their folding energetics is governed by the same quantitative pattern. Relative to the unfolded ensemble, the native conformations are enthalpically stabilized by comparable contributions from protein-protein and solvent-solvent interactions, and almost equally destabilized by interactions between protein and solvent molecules. The native protein surface seems to interact better with water than the unfolded one, but this is outweighed by the unfolded surface being larger. From the perspective of physical interactions, the native conformations are stabilized by van de Waals and Coulomb interactions and destabilized by conformational strain arising from bonded interactions. Also common to the four proteins, the sign of the heat capacity change is set by interactions between protein and solvent molecules or, from the alternative perspective, by Coulomb interactions.
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Affiliation(s)
- Juan José Galano‐Frutos
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
| | - Javier Sancho
- Biocomputation and Complex Systems Physics Institute (BIFI)‐Joint Unit GBsC‐CSICUniversity of ZaragozaZaragozaSpain
- Departamento de Bioquímica y Biología Molecular y Celular, Facultad de CienciasUniversity of ZaragozaZaragozaSpain
- Aragon Health Research Institute (IIS Aragón)ZaragozaSpain
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21
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Sivadas A, Rathore S, Sahana S, Jolly B, Bhoyar RC, Jain A, Sharma D, Imran M, Senthilvel V, Divakar MK, Mishra A, Sivasubbu S, Scaria V. The genomic landscape of CYP2D6 variation in the Indian population. Pharmacogenomics 2024; 25:147-160. [PMID: 38426301 DOI: 10.2217/pgs-2023-0233] [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] [Indexed: 03/02/2024] Open
Abstract
Aim: The CYP2D6 gene is highly polymorphic, causing large interindividual variability in the metabolism of several clinically important drugs. Materials & methods: The authors investigated the diversity and distribution of CYP2D6 alleles in Indians using whole genome sequences (N = 1518). Functional consequences were assessed using pathogenicity scores and molecular dynamics simulations. Results: The analysis revealed population-specific CYP2D6 alleles (*86, *7, *111, *112, *113, *99) and remarkable differences in variant and phenotype frequencies with global populations. The authors observed that one in three Indians could benefit from a dose alteration for psychiatric drugs with accurate CYP2D6 phenotyping. Molecular dynamics simulations revealed large conformational fluctuations, confirming the predicted reduced function of *86 and *113 alleles. Conclusion: The findings emphasize the utility of comprehensive CYP2D6 profiling for aiding precision public health.
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Affiliation(s)
- Ambily Sivadas
- Division of Nutrition, St. John's Research Institute, St. John's National Academy of Health Sciences, Bangalore, Karnataka, 560034, India
| | - Surabhi Rathore
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - S Sahana
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Bani Jolly
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Rahul C Bhoyar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Abhinav Jain
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Disha Sharma
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Mohamed Imran
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Vigneshwar Senthilvel
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Mohit Kumar Divakar
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Anushree Mishra
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Sridhar Sivasubbu
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
- Vishwanath Cancer Care Foundation, B 702, 7th Floor, Neelkanth Business Park Kirol Village, Vidya Vihar, West Mumbai, 400086, India
| | - Vinod Scaria
- CSIR Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
- Vishwanath Cancer Care Foundation, B 702, 7th Floor, Neelkanth Business Park Kirol Village, Vidya Vihar, West Mumbai, 400086, India
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22
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Rodrigues CHM, Portelli S, Ascher DB. Exploring the effects of missense mutations on protein thermodynamics through structure-based approaches: findings from the CAGI6 challenges. Hum Genet 2024:10.1007/s00439-023-02623-4. [PMID: 38227011 DOI: 10.1007/s00439-023-02623-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/18/2023] [Indexed: 01/17/2024]
Abstract
Missense mutations are known contributors to diverse genetic disorders, due to their subtle, single amino acid changes imparted on the resultant protein. Because of this, understanding the impact of these mutations on protein stability and function is crucial for unravelling disease mechanisms and developing targeted therapies. The Critical Assessment of Genome Interpretation (CAGI) provides a valuable platform for benchmarking state-of-the-art computational methods in predicting the impact of disease-related mutations on protein thermodynamics. Here we report the performance of our comprehensive platform of structure-based computational approaches to evaluate mutations impacting protein structure and function on 3 challenges from CAGI6: Calmodulin, MAPK1 and MAPK3. Our stability predictors have achieved correlations of up to 0.74 and AUCs of 1 when predicting changes in ΔΔG for MAPK1 and MAPK3, respectively, and AUC of up to 0.75 in the Calmodulin challenge. Overall, our study highlights the importance of structure-based approaches in understanding the effects of missense mutations on protein thermodynamics. The results obtained from the CAGI6 challenges contribute to the ongoing efforts to enhance our understanding of disease mechanisms and facilitate the development of personalised medicine approaches.
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Affiliation(s)
- Carlos H M Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - Stephanie Portelli
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, VIC, 3004, Australia.
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, QLD, 4072, Australia.
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23
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Liu B, Jiang Y, Yang Y, Chen JX. OmeDDG: Improved Protein Mutation Stability Prediction Based on Predicted 3D Structures. J Phys Chem B 2024; 128:67-76. [PMID: 38130113 DOI: 10.1021/acs.jpcb.3c05601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Determining changes in the protein's thermal stability following mutations is critical in protein engineering and understanding pathogenic missense mutations. Despite the development of various computational methods to predict the effects of single-point mutations, their accuracy remains limited. In this study, we propose a new computational method, OmeDDG, that more accurately predicts mutation-induced Gibbs free energy changes in protein folding (ΔΔG). OmeDDG takes the sequences of wild-type and mutant proteins as input, utilizes OmegaFold to obtain the 3D structure, employs a convolutional neural network to extract structural features, and combines them with protein mutation features and pretraining features to predict the stability of single-point mutations in proteins. We performed a comprehensive comparison between OmeDDG and other available prediction methods on four blind test datasets, confirming that OmeDDG can effectively enhance protein mutation prediction performance. Notably, on the antisymmetric dataset Ssym, OmeDDG achieves the best performance, demonstrating favorable antisymmetry with PCC = 0.79 and RMSE = 0.96 for forward mutations and PCC = 0.77 and RMSE = 0.97 for reverse mutant types.
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Affiliation(s)
- Baoying Liu
- School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
| | - Yongquan Jiang
- School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
- Artificial Intelligence Research Institute, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
| | - Yan Yang
- School of Computing and Artificial Intelligence, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
- Artificial Intelligence Research Institute, Southwest Jiaotong University, Chengdu 611756, Sichuan, China
| | - Jim X Chen
- Department of Computer Science, George Mason University, Fairfax, Virginia 22030-4444, United States
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24
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Wang T, Jin X, Lu X, Min X, Ge S, Li S. Empirical validation of ProteinMPNN's efficiency in enhancing protein fitness. Front Genet 2024; 14:1347667. [PMID: 38274106 PMCID: PMC10808456 DOI: 10.3389/fgene.2023.1347667] [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: 12/01/2023] [Accepted: 12/20/2023] [Indexed: 01/27/2024] Open
Abstract
Introduction: Protein engineering, which aims to improve the properties and functions of proteins, holds great research significance and application value. However, current models that predict the effects of amino acid substitutions often perform poorly when evaluated for precision. Recent research has shown that ProteinMPNN, a large-scale pre-training sequence design model based on protein structure, performs exceptionally well. It is capable of designing mutants with structures similar to the original protein. When applied to the field of protein engineering, the diverse designs for mutation positions generated by this model can be viewed as a more precise mutation range. Methods: We collected three biological experimental datasets and compared the design results of ProteinMPNN for wild-type proteins with the experimental datasets to verify the ability of ProteinMPNN in improving protein fitness. Results: The validation on biological experimental datasets shows that ProteinMPNN has the ability to design mutation types with higher fitness in single and multi-point mutations. We have verified the high accuracy of ProteinMPNN in protein engineering tasks from both positive and negative perspectives. Discussion: Our research indicates that using large-scale pre trained models to design protein mutants provides a new approach for protein engineering, providing strong support for guiding biological experiments and applications in biotechnology.
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Affiliation(s)
- Tianshu Wang
- School of Informatics, Institute of Artificial Intelligence, Xiamen University, Xiamen, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, China
| | - Xiaocheng Jin
- State Key Laboratory of Vaccines for Infectious Diseases, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, China
- School of Public Health, Xiamen University, Xiamen, China
| | - Xiaoli Lu
- Information and Networking Center, Xiamen University, Xiamen, China
| | - Xiaoping Min
- School of Informatics, Institute of Artificial Intelligence, Xiamen University, Xiamen, China
- State Key Laboratory of Vaccines for Infectious Diseases, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, China
| | - Shengxiang Ge
- State Key Laboratory of Vaccines for Infectious Diseases, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, China
- School of Public Health, Xiamen University, Xiamen, China
| | - Shaowei Li
- State Key Laboratory of Vaccines for Infectious Diseases, Xiamen University, Xiamen, China
- National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Xiamen University, Xiamen, China
- State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, Xiamen University, Xiamen, China
- School of Public Health, Xiamen University, Xiamen, China
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25
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Ariaeenejad S, Gharechahi J, Foroozandeh Shahraki M, Fallah Atanaki F, Han JL, Ding XZ, Hildebrand F, Bahram M, Kavousi K, Hosseini Salekdeh G. Precision enzyme discovery through targeted mining of metagenomic data. NATURAL PRODUCTS AND BIOPROSPECTING 2024; 14:7. [PMID: 38200389 PMCID: PMC10781932 DOI: 10.1007/s13659-023-00426-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]
Abstract
Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.
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Affiliation(s)
- Shohreh Ariaeenejad
- Department of Systems and Synthetic Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Javad Gharechahi
- Human Genetics Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Mehdi Foroozandeh Shahraki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Fereshteh Fallah Atanaki
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Jian-Lin Han
- Livestock Genetics Program, International Livestock Research, Institute (ILRI), Nairobi, 00100, Kenya
- CAAS-ILRI Joint Laboratory On Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100193, China
| | - Xue-Zhi Ding
- Key Laboratory of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, 730050, China
| | - Falk Hildebrand
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich, Norfolk, UK
- Digital Biology, Earlham Institute, Norwich, Norfolk, UK
| | - Mohammad Bahram
- Department of Ecology, Swedish University of Agricultural Sciences, Ulls Väg 16, 756 51, Uppsala, Sweden
- Department of Botany, Institute of Ecology and Earth Sciences, University of Tartu, 40 Lai St, Tartu, Estonia
| | - Kaveh Kavousi
- Laboratory of Complex Biological Systems and Bioinformatics (CBB), Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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26
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Ghaedizadeh S, Zeinali M, Dabirmanesh B, Rasekh B, Khajeh K, Banaei-Moghaddam AM. Rational design engineering of a more thermostable Sulfurihydrogenibium yellowstonense carbonic anhydrase for potential application in carbon dioxide capture technologies. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140962. [PMID: 37716447 DOI: 10.1016/j.bbapap.2023.140962] [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: 06/19/2023] [Revised: 08/18/2023] [Accepted: 09/06/2023] [Indexed: 09/18/2023]
Abstract
Implementing hyperthermostable carbonic anhydrases into CO2 capture and storage technologies in order to increase the rate of CO2 absorption from the industrial flue gases is of great importance from technical and economical points of view. The present study employed a combination of in silico tools to further improve thermostability of a known thermostable carbonic anhydrase from Sulfurihydrogenibium yellowstonense. Experimental results showed that our rationally engineered K100G mutant not only retained the overall structure and catalytic efficiency but also showed a 3 °C increase in the melting temperature and a two-fold improvement in the enzyme half-life at 85 °C. Based on the molecular dynamics simulation results, rearrangement of salt bridges and hydrogen interactions network causes a reduction in local flexibility of the K100G variant. In conclusion, our study demonstrated that thermostability can be improved through imposing local structural rigidity by engineering a single-point mutation on the surface of the enzyme.
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Affiliation(s)
- Shima Ghaedizadeh
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Majid Zeinali
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry (RIPI), Tehran, Iran.
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Behnam Rasekh
- Microbiology and Biotechnology Research Group, Research Institute of Petroleum Industry (RIPI), Tehran, Iran
| | - Khosrow Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ali Mohammad Banaei-Moghaddam
- Laboratory of Genomics and Epigenomics (LGE), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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27
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Zheng F, Liu Y, Yang Y, Wen Y, Li M. Assessing computational tools for predicting protein stability changes upon missense mutations using a new dataset. Protein Sci 2024; 33:e4861. [PMID: 38084013 PMCID: PMC10751734 DOI: 10.1002/pro.4861] [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: 09/28/2023] [Revised: 11/14/2023] [Accepted: 12/06/2023] [Indexed: 12/28/2023]
Abstract
Insight into how mutations affect protein stability is crucial for protein engineering, understanding genetic diseases, and exploring protein evolution. Numerous computational methods have been developed to predict the impact of amino acid substitutions on protein stability. Nevertheless, comparing these methods poses challenges due to variations in their training data. Moreover, it is observed that they tend to perform better at predicting destabilizing mutations than stabilizing ones. Here, we meticulously compiled a new dataset from three recently published databases: ThermoMutDB, FireProtDB, and ProThermDB. This dataset, which does not overlap with the well-established S2648 dataset, consists of 4038 single-point mutations, including over 1000 stabilizing mutations. We assessed these mutations using 27 computational methods, including the latest ones utilizing mega-scale stability datasets and transfer learning. We excluded entries with overlap or similarity to training datasets to ensure fairness. Pearson correlation coefficients for the tested tools ranged from 0.20 to 0.53 on unseen data, and none of the methods could accurately predict stabilizing mutations, even those performing well in anti-symmetric property analysis. While most methods present consistent trends for predicting destabilizing mutations across various properties such as solvent exposure and secondary conformation, stabilizing mutations do not exhibit a clear pattern. Our study also suggests that solely addressing training dataset bias may not significantly enhance accuracy of predicting stabilizing mutations. These findings emphasize the importance of developing precise predictive methods for stabilizing mutations.
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Affiliation(s)
- Feifan Zheng
- MOE Key Laboratory of Geriatric Diseases and ImmunologySchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow UniversitySuzhouChina
| | - Yang Liu
- MOE Key Laboratory of Geriatric Diseases and ImmunologySchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow UniversitySuzhouChina
| | - Yan Yang
- MOE Key Laboratory of Geriatric Diseases and ImmunologySchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow UniversitySuzhouChina
| | - Yuhao Wen
- MOE Key Laboratory of Geriatric Diseases and ImmunologySchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow UniversitySuzhouChina
| | - Minghui Li
- MOE Key Laboratory of Geriatric Diseases and ImmunologySchool of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow UniversitySuzhouChina
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28
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Rout M, Mishra S, Panda S, Dehury B, Pati S. Lipid and cholesterols modulate the dynamics of SARS-CoV-2 viral ion channel ORF3a and its pathogenic variants. Int J Biol Macromol 2024; 254:127986. [PMID: 37944718 DOI: 10.1016/j.ijbiomac.2023.127986] [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: 08/24/2023] [Revised: 11/06/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023]
Abstract
SARS-CoV-2 accessory protein, ORF3a is a putative ion channel which immensely contributes to viral pathogenicity by modulating host immune responses and virus-host interactions. Relatively high expression of ORF3a in diseased individuals and implication with inflammasome activation, apoptosis and autophagy inhibition, ratifies as an effective target for developing vaccines and therapeutics. Herein, we present the elusive dynamics of ORF3a-dimeric state using all-atoms molecular dynamics (MD) simulations at μ-seconds scale in a heterogeneous lipid-mimetic system in multiple replicates. Additionally, we also explore the effect of non-synonymous pathogenic mutations on ORF3a ion channel activity and viral pathogenicity in different SARS-CoV-2 variants using various structure-based protein stability (ΔΔG) tools and computational saturation mutagenesis. Our study ascertains the role of phosphatidylcholines and cholesterol in modulating the structure of ORF3a, which perturbs the size and flexibility of the polar cavity that allows permeation of large cations. Discrete trend in ion channel pore radius and area per lipid arises the premise that presence of lipids might also affect the overall conformation of ORF3a. MD structural-ensembles, in some replicates rationalize the crucial role of TM2 in maintaining the native structure of ORF3a. We also infer that loss of structural stability primarily grounds for pathogenicity in more than half of the pathogenic variants of ORF3a. Overall, the effect of mutation on alteration of ion permeability of ORF3a, proposed in this study brings mechanistic insights into variant consequences on viral membrane proteins of SARS-CoV-2, which can be utilized for the development of novel therapeutics to treat COVID-19 and other coronavirus diseases.
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Affiliation(s)
- Madhusmita Rout
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Sarbani Mishra
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Sunita Panda
- Mycology Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India.
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Chandrasekharpur, Bhubaneswar 751023, Odisha, India.
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29
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Rollo C, Pancotti C, Birolo G, Rossi I, Sanavia T, Fariselli P. Influence of Model Structures on Predictors of Protein Stability Changes from Single-Point Mutations. Genes (Basel) 2023; 14:2228. [PMID: 38137050 PMCID: PMC10742815 DOI: 10.3390/genes14122228] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Missense variation in genomes can affect protein structure stability and, in turn, the cell physiology behavior. Predicting the impact of those variations is relevant, and the best-performing computational tools exploit the protein structure information. However, most of the current protein sequence variants are unresolved, and comparative or ab initio tools can provide a structure. Here, we evaluate the impact of model structures, compared to experimental structures, on the predictors of protein stability changes upon single-point mutations, where no significant changes are expected between the original and the mutated structures. We show that there are substantial differences among the computational tools. Methods that rely on coarse-grained representation are less sensitive to the underlying protein structures. In contrast, tools that exploit more detailed molecular representations are sensible to structures generated from comparative modeling, even on single-residue substitutions.
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Affiliation(s)
- Cesare Rollo
- Department of Medical Sciences, University Torino, 10126 Torino, Italy (G.B.); (I.R.); (T.S.); (P.F.)
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30
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Dunsche L, Ivanisenko N, Riemann S, Schindler S, Beissert S, Angeli C, Kreis S, Tavassoli M, Lavrik I, Kulms D. A cytosolic mutp53(E285K) variant confers chemoresistance of malignant melanoma. Cell Death Dis 2023; 14:831. [PMID: 38097548 PMCID: PMC10721616 DOI: 10.1038/s41419-023-06360-4] [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: 07/19/2023] [Revised: 11/29/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
Malignant melanoma (MM) is known to be intrinsically chemoresistant, even though only ~20% of MM carry mutations of the tumor suppressor p53. Despite improvement of systemic therapy the mortality rate of patients suffering from metastatic MM is still ~70%, highlighting the need for alternative treatment options or for the re-establishment of conventional therapeutic approaches, including chemotherapy. Screening the p53 mutation status in a cohort of 19 patient-derived melanoma samples, we identified one rarely described missense mutation of p53 leading to E285K amino acid exchange (mutp53(E285K)). Employing structural and computational analysis we revealed a major role of E285 residue in maintaining stable conformation of wild-type p53 (wtp53). E285K mutation was predicted to cause interruption of a salt-bridge network affecting the conformation of the C-terminal helix of the DNA-binding domain (DBD) thereby preventing DNA interaction. In this context, a cluster of frequently mutated amino acid residues in cancer was identified to putatively lead to similar structural effects as E285K substitution (E285 cluster). Functional analysis, including knockdown of endogenous p53 and reconstitution with diverse p53 missense mutants confirmed mutp53(E285K) to have lost transcriptional activity, to be localized in the cytosol of cancer cells, by both means conferring chemoresistance. Re-sensitization to cisplatin-induced cell death was achieved using clinically approved compounds aiming to restore p53 wild-type function (PRIMA1-Met), or inhibition of AKT-driven MAPK survival pathways (afuresertib), in both cases being partially due to ferroptosis induction. Consequently, active ferroptosis induction using the GPX4 inhibitor RSL3 proved superior in tumorselectively fighting MM cells. Due to high prevalence of the E285-cluster mutations in MM as well as in a variety of other tumor types, we conclude this cluster to serve an important function in tumor development and therapy and suggest new implications for ferroptosis induction in therapeutic applications fighting MM in particular and cancer in general.
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Affiliation(s)
- Luise Dunsche
- Experimental Dermatology, Department of Dermatology, TU-Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases, TU-Dresden, 01307, Dresden, Germany
| | - Nikita Ivanisenko
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, 39106, Magdeburg, Germany
| | - Shamala Riemann
- Experimental Dermatology, Department of Dermatology, TU-Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases, TU-Dresden, 01307, Dresden, Germany
| | - Sebastian Schindler
- Experimental Dermatology, Department of Dermatology, TU-Dresden, 01307, Dresden, Germany
- National Center for Tumor Diseases, TU-Dresden, 01307, Dresden, Germany
| | - Stefan Beissert
- Experimental Dermatology, Department of Dermatology, TU-Dresden, 01307, Dresden, Germany
| | - Cristian Angeli
- Department of Life Science and Medicine, University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Stephanie Kreis
- Department of Life Science and Medicine, University of Luxembourg, Belvaux, 4367, Luxembourg
| | - Mahvash Tavassoli
- Molecular Oncology, Guy's Hospital, Kings College London, London, SE1 1UL, UK
| | - Inna Lavrik
- Translational Inflammation Research, Medical Faculty, Center of Dynamic Systems, Otto von Guericke University, 39106, Magdeburg, Germany
| | - Dagmar Kulms
- Experimental Dermatology, Department of Dermatology, TU-Dresden, 01307, Dresden, Germany.
- National Center for Tumor Diseases, TU-Dresden, 01307, Dresden, Germany.
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31
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Weissenow K, Rost B. Rendering protein mutation movies with MutAmore. BMC Bioinformatics 2023; 24:469. [PMID: 38087198 PMCID: PMC10714560 DOI: 10.1186/s12859-023-05610-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/08/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND The success of AlphaFold2 in reliable protein three-dimensional (3D) structure prediction, assists the move of structural biology toward studies of protein dynamics and mutational impact on structure and function. This transition needs tools that qualitatively assess alternative 3D conformations. RESULTS We introduce MutAmore, a bioinformatics tool that renders individual images of protein 3D structures for, e.g., sequence mutations into a visually intuitive movie format. MutAmore streamlines a pipeline casting single amino-acid variations (SAVs) into a dynamic 3D mutation movie providing a qualitative perspective on the mutational landscape of a protein. By default, the tool first generates all possible variants of the sequence reachable through SAVs (L*19 for proteins with L residues). Next, it predicts the structural conformation for all L*19 variants using state-of-the-art models. Finally, it visualizes the mutation matrix and produces a color-coded 3D animation. Alternatively, users can input other types of variants, e.g., from experimental structures. CONCLUSION MutAmore samples alternative protein configurations to study the dynamical space accessible from SAVs in the post-AlphaFold2 era of structural biology. As the field shifts towards the exploration of alternative conformations of proteins, MutAmore aids in the understanding of the structural impact of mutations by providing a flexible pipeline for the generation of protein mutation movies using current and future structure prediction models.
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Affiliation(s)
- Konstantin Weissenow
- Department of Informatics, Bioinformatics and Computational Biology i12, TUM (Technical University of Munich), Boltzmannstr. 3, 85748, Garching, Munich, Germany.
- TUM Graduate School, Center of Doctoral Studies in Informatics and Its Applications (CeDoSIA), Boltzmannstr. 11, 85748, Garching, Germany.
| | - Burkhard Rost
- Department of Informatics, Bioinformatics and Computational Biology i12, TUM (Technical University of Munich), Boltzmannstr. 3, 85748, Garching, Munich, Germany
- Institute for Advanced Study (TUM-IAS), Lichtenbergstr. 2a, 85748, Garching, Munich, Germany
- TUM School of Life Sciences Weihenstephan (WZW), Alte Akademie 8, Freising, Germany
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Murthy TPK, Shukla R, Durga Prasad N, Swetha P, Shreyas S, Singh TR, Pattabiraman R, Nair SS, Mathew BB, Kumar KM. Comprehensive analysis of non-synonymous missense SNPs of human galactose mutarotase (GALM) gene: an integrated computational approach. J Biomol Struct Dyn 2023; 41:11178-11192. [PMID: 36591702 DOI: 10.1080/07391102.2022.2160813] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/15/2022] [Indexed: 01/03/2023]
Abstract
Missense Non-synonymous single nucleotide polymorphisms (nsSNPs) of Galactose Mutarotase (GALM) are associated with the Novel type of Galactosemia (Galactosemia type 4) together with symptoms such as high blood galactose levels and eye cataracts. The objective of the present study was to identify deleterious nsSNPs of GALM recorded on the dbSNP database through comprehensive insilico analysis. Among the 319 missense nsSNPs reported, various insilco tools predicted R78S, R82G, A163E, P210S, Y281C, E307G and F339C as the most deleterious mutations. Structural analysis, PTM analysis and molecular dynamics simulations (MDS) were carried out to understand the effect of these mutations on the structural and physicochemical properties of the GALM protein. The residues R82G and E307G were found to be part of the binding site that resulted in decreased surface accessibility. Replacing the charged wild-type residue with a neutral mutant type affected its substrate binding. All 7 mutations were found to increase the rigidity of the protein structure, which is unfavorable during ligand binding. The mutation F339E made the protein structure more rigid than all the other mutations. Y281 is a phosphorylated site, and therefore, less significant structural changes were observed when compared to other mutations; however, it may have significant differences in the usual functioning of the protein. In summary, the structural and functional analysis of missense SNPs of GALM is important to reduce the number of potential mutations to be evaluated in vitro to understand the association with some genetic diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- T P Krishna Murthy
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Rohit Shukla
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - N Durga Prasad
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Praveen Swetha
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - S Shreyas
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Tiratha Raj Singh
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | - Ramya Pattabiraman
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Shishira S Nair
- Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India
| | - Blessy B Mathew
- Department of Biotechnology, Dayananda Sagar College of Engineering, Bengaluru, Karnataka, Inida
| | - K M Kumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, Puducherry, India
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Wang S, Tang H, Shan P, Wu Z, Zuo L. ProS-GNN: Predicting effects of mutations on protein stability using graph neural networks. Comput Biol Chem 2023; 107:107952. [PMID: 37643501 DOI: 10.1016/j.compbiolchem.2023.107952] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Predicting protein stability change upon variation through a computational approach is a valuable tool to unveil the mechanisms of mutation-induced drug failure and develop immunotherapy strategies. Some previous machine learning-based techniques exhibit anti-symmetric bias toward destabilizing situations, whereas others struggle with generalization to unseen examples. To address these issues, we propose a gated graph neural network-based approach to predict changes in protein stability upon mutation. The model uses message passing to encode the links between the molecular structure and property after eliminating the non-mutant structure and creating input feature vectors. While doing so, it also incorporates the coordinates of the raw atoms to provide spatial insights into the chemical systems. We test the model on the Ssym, Myoglobin, Broom, and p53 datasets to demonstrate the generalization performance. Compared to existing approaches, our proposed method achieves improved linearity with symmetry in less time. The code for this study is available at: https://github.com/HongzhouTang/Pros-GNN.
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Affiliation(s)
- Shuyu Wang
- Department of Control Engineering, Northeastern University, Qinhuangdao Campus, Qinhuangdao 066001, China.
| | - Hongzhou Tang
- Department of Control Engineering, Northeastern University, Qinhuangdao Campus, Qinhuangdao 066001, China
| | - Peng Shan
- Department of Control Engineering, Northeastern University, Qinhuangdao Campus, Qinhuangdao 066001, China
| | - Zhaoxia Wu
- Department of Control Engineering, Northeastern University, Qinhuangdao Campus, Qinhuangdao 066001, China
| | - Lei Zuo
- Department of Marine Engineering, University of Michigan, Ann Arbor 48109, USA
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Kurniawan J, Ishida T. Comparing Supervised Learning and Rigorous Approach for Predicting Protein Stability upon Point Mutations in Difficult Targets. J Chem Inf Model 2023; 63:6778-6788. [PMID: 37897811 DOI: 10.1021/acs.jcim.3c00750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
Abstract
Accurate prediction of protein stability upon a point mutation has important applications in drug discovery and personalized medicine. It remains a challenging issue in computational biology. Existing computational prediction methods, which range from mechanistic to supervised learning approaches, have experienced limited progress over the last few decades. This stagnation is largely due to their heavy reliance on both the quantity and quality of the training data. This is evident in recent state-of-the-art methods that continue to yield substantial errors on two challenging blind test sets: frataxin and p53, with average root-mean-square errors exceeding 3 and 1.5 kcal/mol, respectively, which is still above the theoretical 1 kcal/mol prediction barrier. Rigorous approaches, on the other hand, offer greater potential for accuracy without relying on training data but are computationally demanding and require both wild-type and mutant structure information. Although they showed high accuracy for conserving mutations, their performance is still limited for charge-changing mutation cases. This might be due to the lack of an available mutant structure, often represented by a simplified capped peptide. The recent advances in protein structure prediction methods now make it possible to obtain structures comparable to experimental ones, including complete mutant structure information. In this work, we compare the performance of supervised learning-based methods and rigorous approaches for predicting protein stability on point mutations in difficult targets: frataxin and p53. The rigorous alchemical method significantly surpasses state-of-the-art techniques in terms of both the root-mean-squared error and Pearson correlation coefficient in these two challenging blind test sets. Additionally, we propose an improved alchemical method that employs the pmx double-system/single-box approach to accurately predict the folding free energy change upon both conserving and charge-changing mutations. The enhanced protocol can accurately predict both types of mutations, thereby outperforming existing state-of-the-art methods in overall performance.
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Affiliation(s)
- Jason Kurniawan
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Takashi Ishida
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, Tokyo 152-8550, Japan
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Sapozhnikov Y, Patel JS, Ytreberg FM, Miller CR. Statistical modeling to quantify the uncertainty of FoldX-predicted protein folding and binding stability. BMC Bioinformatics 2023; 24:426. [PMID: 37953256 PMCID: PMC10642056 DOI: 10.1186/s12859-023-05537-0] [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: 05/08/2023] [Accepted: 10/17/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Computational methods of predicting protein stability changes upon missense mutations are invaluable tools in high-throughput studies involving a large number of protein variants. However, they are limited by a wide variation in accuracy and difficulty of assessing prediction uncertainty. Using a popular computational tool, FoldX, we develop a statistical framework that quantifies the uncertainty of predicted changes in protein stability. RESULTS We show that multiple linear regression models can be used to quantify the uncertainty associated with FoldX prediction for individual mutations. Comparing the performance among models with varying degrees of complexity, we find that the model precision improves significantly when we utilize molecular dynamics simulation as part of the FoldX workflow. Based on the model that incorporates information from molecular dynamics, biochemical properties, as well as FoldX energy terms, we can generally expect upper bounds on the uncertainty of folding stability predictions of ± 2.9 kcal/mol and ± 3.5 kcal/mol for binding stability predictions. The uncertainty for individual mutations varies; our model estimates it using FoldX energy terms, biochemical properties of the mutated residue, as well as the variability among snapshots from molecular dynamics simulation. CONCLUSIONS Using a linear regression framework, we construct models to predict the uncertainty associated with FoldX prediction of stability changes upon mutation. This technique is straightforward and can be extended to other computational methods as well.
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Affiliation(s)
- Yesol Sapozhnikov
- Program in Bioinformatics and Computational Biology, University of Idaho, Moscow, ID, 83844, USA
| | - Jagdish Suresh Patel
- Department of Chemical and Biological Engineering, University of Idaho, Moscow, ID, 83844, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83844, USA
| | - F Marty Ytreberg
- Department of Physics, University of Idaho, Moscow, ID, 83844, USA
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83844, USA
| | - Craig R Miller
- Department of Biological Sciences, University of Idaho, Moscow, ID, 83844, USA.
- Institute for Modeling Collaboration and Innovation, University of Idaho, Moscow, ID, 83844, USA.
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36
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Swain PS, Panda S, Pati S, Dehury B. Computational saturation mutagenesis to explore the effect of pathogenic mutations on extra-cellular domains of TREM2 associated with Alzheimer's and Nasu-Hakola disease. J Mol Model 2023; 29:360. [PMID: 37924367 DOI: 10.1007/s00894-023-05770-7] [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: 07/25/2023] [Accepted: 10/25/2023] [Indexed: 11/06/2023]
Abstract
CONTEXT The specialised family of triggering receptors expressed on myeloid cells (TREMs) plays a pivotal role in causing neurodegenerative disorders and activating microglial anti-inflammatory responses. Nasu-Hakola disease (NHD), a rare autosomal recessive disorder, has been associated with mutations in TREM2, which is also responsible for raising the risk of Alzheimer's disease (AD). Herein, we have made an endeavour to differentiate the confirmed pathogenic variants in TREM2 extra-cellular domain (ECD) linked with NHD and AD using mutation-induced fold stability change (∆∆G), with the computation of 12distinct structure-based methods through saturation mutagenesis. Correlation analysis between relative solvent accessibility (RSA) and ∆∆G expresses the discrete distributive behaviour of mutants associated with TREM2 in AD (R2 = 0.061) and NHD (R2 = 0.601). Our findings put an emphasis on W50 and V126 as major players in maintaining V-like domain in TREM2. Interestingly, we discern that both of them interact with a common residue Y108, which is dissolved upon mutation. This Y108 could have structural or functional role for TREM2 which can be an ideal candidate for further study. Furthermore, the residual interaction network highlights the importance of R47 and R62 in maintaining the CDR loops that are crucial for ligand binding. Future studies using biophysical characterisation of ligand interactions in TREM2-ECD would be helpful for the development of novel therapeutics for AD and NHD. METHODS ConSurf algorithm and ENDscript were used to determine the position and conservation of each residue in the wild-type ECD of TREM2. The mutation-induced fold stability change (∆∆G) of confirmed pathogenic mutants associated with NHD and AD was estimated using 12 state-of-the-art structure-based protein stability tools. Furthermore, we also computed the effect of random mutation on these sites using computational saturation mutagenesis. Linear regression analysis was performed using mutants ∆∆G and RSA through GraphPad software. In addition, a comprehensive non-bonded residual interaction network (RIN) of wild type and its mutants of TREM2-ECD was enumerated using RING3.0.
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Affiliation(s)
- Preety Sthutika Swain
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Sunita Panda
- Mycology Laboratory, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India
| | - Sanghamitra Pati
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
| | - Budheswar Dehury
- Bioinformatics Division, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, 751023, Odisha, India.
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37
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Umerenkov D, Nikolaev F, Shashkova TI, Strashnov PV, Sindeeva M, Shevtsov A, Ivanisenko NV, Kardymon OL. PROSTATA: a framework for protein stability assessment using transformers. Bioinformatics 2023; 39:btad671. [PMID: 37935419 PMCID: PMC10651431 DOI: 10.1093/bioinformatics/btad671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/25/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023] Open
Abstract
MOTIVATION Accurate prediction of change in protein stability due to point mutations is an attractive goal that remains unachieved. Despite the high interest in this area, little consideration has been given to the transformer architecture, which is dominant in many fields of machine learning. RESULTS In this work, we introduce PROSTATA, a predictive model built in a knowledge-transfer fashion on a new curated dataset. PROSTATA demonstrates advantage over existing solutions based on neural networks. We show that the large improvement margin is due to both the architecture of the model and the quality of the new training dataset. This work opens up opportunities to develop new lightweight and accurate models for protein stability assessment. AVAILABILITY AND IMPLEMENTATION PROSTATA is available at https://github.com/AIRI-Institute/PROSTATA and https://prostata.airi.net.
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Affiliation(s)
| | | | | | - Pavel V Strashnov
- Bioinformatics Group, AIRI, Moscow 121170, Russia
- Department of Computer Design and Technology, Bauman Moscow State Technical University, Moscow 105005, Russia
| | | | - Andrey Shevtsov
- Bioinformatics Group, AIRI, Moscow 121170, Russia
- Regulatory Transcriptomics and Epigenomics Group, Institute of Bioengineering, Research Center of Biotechnology RAS, Moscow 117036, Russia
| | - Nikita V Ivanisenko
- Bioinformatics Group, AIRI, Moscow 121170, Russia
- Laboratory of Computational Proteomics, Institute of Cytology and Genetics SB RAS, Novosibirsk 630090, Russia
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38
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Li J, Kang G, Wang J, Yuan H, Wu Y, Meng S, Wang P, Zhang M, Wang Y, Feng Y, Huang H, de Marco A. Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization. Int J Biol Macromol 2023; 247:125733. [PMID: 37423452 DOI: 10.1016/j.ijbiomac.2023.125733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 07/06/2023] [Indexed: 07/11/2023]
Abstract
Routinely screened antibody fragments usually require further in vitro maturation to achieve the desired biophysical properties. Blind in vitro strategies can produce improved ligands by introducing random mutations into the original sequences and selecting the resulting clones under more and more stringent conditions. Rational approaches exploit an alternative perspective that aims first at identifying the specific residues potentially involved in the control of biophysical mechanisms, such as affinity or stability, and then to evaluate what mutations could improve those characteristics. The understanding of the antigen-antibody interactions is instrumental to develop this process the reliability of which, consequently, strongly depends on the quality and completeness of the structural information. Recently, methods based on deep learning approaches critically improved the speed and accuracy of model building and are promising tools for accelerating the docking step. Here, we review the features of the available bioinformatic instruments and analyze the reports illustrating the result obtained with their application to optimize antibody fragments, and nanobodies in particular. Finally, the emerging trends and open questions are summarized.
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Affiliation(s)
- Jiaqi Li
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Guangbo Kang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Jiewen Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Haibin Yuan
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
| | - Yili Wu
- Zhejiang Provincial Clinical Research Center for Mental Disorders, School of Mental Health and the Affiliated Kangning Hospital, Institute of Aging, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Wenzhou Medical University, Oujiang Laboratory, Wenzhou, Zhejiang 325035, China
| | - Shuxian Meng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - Ping Wang
- New Technology R&D Department, Tianjin Modern Innovative TCM Technology Company Limited, Tianjin 300392, China
| | - Miao Zhang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; China Resources Biopharmaceutical Company Limited, Beijing 100029, China
| | - Yuli Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Tianjin Pharmaceutical Da Ren Tang Group Corporation Limited, Traditional Chinese Pharmacy Research Institute, Tianjin Key Laboratory of Quality Control in Chinese Medicine, Tianjin 300457, China; State Key Laboratory of Drug Delivery Technology and Pharmacokinetics, Tianjin Institute of Pharmaceutical Research, Tianjin 300193, China
| | - Yuanhang Feng
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China
| | - He Huang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, China; Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China.
| | - Ario de Marco
- Laboratory for Environmental and Life Sciences, University of Nova Gorica, Nova Gorica, Slovenia.
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Peka M, Balatsky V, Saienko A, Tsereniuk O. Bioinformatic analysis of the effect of SNPs in the pig TERT gene on the structural and functional characteristics of the enzyme to develop new genetic markers of productivity traits. BMC Genomics 2023; 24:487. [PMID: 37626279 PMCID: PMC10463782 DOI: 10.1186/s12864-023-09592-y] [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: 05/18/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Telomerase reverse transcriptase (TERT) plays a crucial role in synthesizing telomeric repeats that safeguard chromosomes from damage and fusion, thereby maintaining genome stability. Mutations in the TERT gene can lead to a deviation in gene expression, impaired enzyme activity, and, as a result, abnormal telomere shortening. Genetic markers of productivity traits in livestock can be developed based on the TERT gene polymorphism for use in marker-associated selection (MAS). In this study, a bioinformatic-based approach is proposed to evaluate the effect of missense single-nucleotide polymorphisms (SNPs) in the pig TERT gene on enzyme function and structure, with the prospect of developing genetic markers. RESULTS A comparative analysis of the coding and amino acid sequences of the pig TERT was performed with corresponding sequences of other species. The distribution of polymorphisms in the pig TERT gene, with respect to the enzyme's structural-functional domains, was established. A three-dimensional model of the pig TERT structure was obtained through homological modeling. The potential impact of each of the 23 missense SNPs in the pig TERT gene on telomerase function and stability was assessed using predictive bioinformatic tools utilizing data on the amino acid sequence and structure of pig TERT. CONCLUSIONS According to bioinformatic analysis of 23 missense SNPs of the pig TERT gene, a predictive effect of rs789641834 (TEN domain), rs706045634 (TEN domain), rs325294961 (TRBD domain) and rs705602819 (RTD domain) on the structural and functional parameters of the enzyme was established. These SNPs hold the potential to serve as genetic markers of productivity traits. Therefore, the possibility of their application in MAS should be further evaluated in associative analysis studies.
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Affiliation(s)
- Mykyta Peka
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013 Ukraine
- V. N. Karazin Kharkiv National University, 4 Svobody Sq, Kharkiv, 61022 Ukraine
| | - Viktor Balatsky
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013 Ukraine
- V. N. Karazin Kharkiv National University, 4 Svobody Sq, Kharkiv, 61022 Ukraine
| | - Artem Saienko
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013 Ukraine
| | - Oleksandr Tsereniuk
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013 Ukraine
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Bauer J, Rajagopal N, Gupta P, Gupta P, Nixon AE, Kumar S. How can we discover developable antibody-based biotherapeutics? Front Mol Biosci 2023; 10:1221626. [PMID: 37609373 PMCID: PMC10441133 DOI: 10.3389/fmolb.2023.1221626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/10/2023] [Indexed: 08/24/2023] Open
Abstract
Antibody-based biotherapeutics have emerged as a successful class of pharmaceuticals despite significant challenges and risks to their discovery and development. This review discusses the most frequently encountered hurdles in the research and development (R&D) of antibody-based biotherapeutics and proposes a conceptual framework called biopharmaceutical informatics. Our vision advocates for the syncretic use of computation and experimentation at every stage of biologic drug discovery, considering developability (manufacturability, safety, efficacy, and pharmacology) of potential drug candidates from the earliest stages of the drug discovery phase. The computational advances in recent years allow for more precise formulation of disease concepts, rapid identification, and validation of targets suitable for therapeutic intervention and discovery of potential biotherapeutics that can agonize or antagonize them. Furthermore, computational methods for de novo and epitope-specific antibody design are increasingly being developed, opening novel computationally driven opportunities for biologic drug discovery. Here, we review the opportunities and limitations of emerging computational approaches for optimizing antigens to generate robust immune responses, in silico generation of antibody sequences, discovery of potential antibody binders through virtual screening, assessment of hits, identification of lead drug candidates and their affinity maturation, and optimization for developability. The adoption of biopharmaceutical informatics across all aspects of drug discovery and development cycles should help bring affordable and effective biotherapeutics to patients more quickly.
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Affiliation(s)
- Joschka Bauer
- Early Stage Pharmaceutical Development Biologicals, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach/Riss, Germany
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
| | - Nandhini Rajagopal
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Priyanka Gupta
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Pankaj Gupta
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Andrew E. Nixon
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Sandeep Kumar
- In Silico Team, Boehringer Ingelheim, Hannover, Germany
- Biotherapeutics Discovery, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
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41
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Cheng W, Nian B. Computer-Aided Lipase Engineering for Improving Their Stability and Activity in the Food Industry: State of the Art. Molecules 2023; 28:5848. [PMID: 37570817 PMCID: PMC10421223 DOI: 10.3390/molecules28155848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
As some of the most widely used biocatalysts, lipases have exhibited extreme advantages in many processes, such as esterification, amidation, and transesterification reactions, which causes them to be widely used in food industrial production. However, natural lipases have drawbacks in terms of organic solvent resistance, thermostability, selectivity, etc., which limits some of their applications in the field of foods. In this systematic review, the application of lipases in various food processes was summarized. Moreover, the general structure of lipases is discussed in-depth, and the engineering strategies that can be used in lipase engineering are also summarized. The protocols of some classical methods are compared and discussed, which can provide some information about how to choose methods of lipase engineering. Thermostability engineering and solvent tolerance engineering are highlighted in this review, and the basic principles for improving thermostability and solvent tolerance are summarized. In the future, comput er-aided technology should be more emphasized in the investigation of the mechanisms of reactions catalyzed by lipases and guide the engineering of lipases. The engineering of lipase tunnels to improve the diffusion of substrates is also a promising prospect for further enhanced lipase activity and selectivity.
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Affiliation(s)
| | - Binbin Nian
- State Key Laboratory of Materials-Oriented Chemical Engineering, School of Pharmaceutical Sciences, Nanjing Tech University, Nanjing 210009, China;
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Zhang XE, Liu C, Dai J, Yuan Y, Gao C, Feng Y, Wu B, Wei P, You C, Wang X, Si T. Enabling technology and core theory of synthetic biology. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1742-1785. [PMID: 36753021 PMCID: PMC9907219 DOI: 10.1007/s11427-022-2214-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 02/09/2023]
Abstract
Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.
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Affiliation(s)
- Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chenli Liu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Junbiao Dai
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ping Wei
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Tong Si
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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Pandey P, Panday SK, Rimal P, Ancona N, Alexov E. Predicting the Effect of Single Mutations on Protein Stability and Binding with Respect to Types of Mutations. Int J Mol Sci 2023; 24:12073. [PMID: 37569449 PMCID: PMC10418460 DOI: 10.3390/ijms241512073] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 07/24/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
The development of methods and algorithms to predict the effect of mutations on protein stability, protein-protein interaction, and protein-DNA/RNA binding is necessitated by the needs of protein engineering and for understanding the molecular mechanism of disease-causing variants. The vast majority of the leading methods require a database of experimentally measured folding and binding free energy changes for training. These databases are collections of experimental data taken from scientific investigations typically aimed at probing the role of particular residues on the above-mentioned thermodynamic characteristics, i.e., the mutations are not introduced at random and do not necessarily represent mutations originating from single nucleotide variants (SNV). Thus, the reported performance of the leading algorithms assessed on these databases or other limited cases may not be applicable for predicting the effect of SNVs seen in the human population. Indeed, we demonstrate that the SNVs and non-SNVs are not equally presented in the corresponding databases, and the distribution of the free energy changes is not the same. It is shown that the Pearson correlation coefficients (PCCs) of folding and binding free energy changes obtained in cases involving SNVs are smaller than for non-SNVs, indicating that caution should be used in applying them to reveal the effect of human SNVs. Furthermore, it is demonstrated that some methods are sensitive to the chemical nature of the mutations, resulting in PCCs that differ by a factor of four across chemically different mutations. All methods are found to underestimate the energy changes by roughly a factor of 2.
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Affiliation(s)
- Preeti Pandey
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (P.P.); (S.K.P.); (P.R.)
| | - Shailesh Kumar Panday
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (P.P.); (S.K.P.); (P.R.)
| | - Prawin Rimal
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (P.P.); (S.K.P.); (P.R.)
| | - Nicolas Ancona
- Department of Biological Sciences, Clemson University, Clemson, SC 29634, USA;
| | - Emil Alexov
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, USA; (P.P.); (S.K.P.); (P.R.)
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Licata L, Via A, Turina P, Babbi G, Benevenuta S, Carta C, Casadio R, Cicconardi A, Facchiano A, Fariselli P, Giordano D, Isidori F, Marabotti A, Martelli PL, Pascarella S, Pinelli M, Pippucci T, Russo R, Savojardo C, Scafuri B, Valeriani L, Capriotti E. Resources and tools for rare disease variant interpretation. Front Mol Biosci 2023; 10:1169109. [PMID: 37234922 PMCID: PMC10206239 DOI: 10.3389/fmolb.2023.1169109] [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: 02/18/2023] [Accepted: 04/25/2023] [Indexed: 05/28/2023] Open
Abstract
Collectively, rare genetic disorders affect a substantial portion of the world's population. In most cases, those affected face difficulties in receiving a clinical diagnosis and genetic characterization. The understanding of the molecular mechanisms of these diseases and the development of therapeutic treatments for patients are also challenging. However, the application of recent advancements in genome sequencing/analysis technologies and computer-aided tools for predicting phenotype-genotype associations can bring significant benefits to this field. In this review, we highlight the most relevant online resources and computational tools for genome interpretation that can enhance the diagnosis, clinical management, and development of treatments for rare disorders. Our focus is on resources for interpreting single nucleotide variants. Additionally, we present use cases for interpreting genetic variants in clinical settings and review the limitations of these results and prediction tools. Finally, we have compiled a curated set of core resources and tools for analyzing rare disease genomes. Such resources and tools can be utilized to develop standardized protocols that will enhance the accuracy and effectiveness of rare disease diagnosis.
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Affiliation(s)
- Luana Licata
- Department of Biology, University of Rome Tor Vergata, Roma, Italy
| | - Allegra Via
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”, Roma, Italy
| | - Paola Turina
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giulia Babbi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | | | - Claudio Carta
- National Centre for Rare Diseases, Istituto Superiore di Sanità, Roma, Italy
| | - Rita Casadio
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Andrea Cicconardi
- Department of Physics, University of Genova, Genova, Italy
- Italiano di Tecnologia—IIT, Genova, Italy
| | - Angelo Facchiano
- National Research Council, Institute of Food Science, Avellino, Italy
| | - Piero Fariselli
- Department of Medical Sciences, University of Torino, Torino, Italy
| | - Deborah Giordano
- National Research Council, Institute of Food Science, Avellino, Italy
| | - Federica Isidori
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Anna Marabotti
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
| | - Pier Luigi Martelli
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Stefano Pascarella
- Department of Biochemical Sciences “A. Rossi Fanelli”, University of Rome “La Sapienza”, Roma, Italy
| | - Michele Pinelli
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
| | - Tommaso Pippucci
- Medical Genetics Unit, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Roberta Russo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Napoli, Italy
- CEINGE Biotecnologie Avanzate Franco Salvatore, Napoli, Italy
| | - Castrense Savojardo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Bernardina Scafuri
- Department of Chemistry and Biology “A. Zambelli”, University of Salerno, Fisciano, SA, Italy
| | | | - Emidio Capriotti
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
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David A, Sternberg MJE. Protein structure-based evaluation of missense variants: Resources, challenges and future directions. Curr Opin Struct Biol 2023; 80:102600. [PMID: 37126977 DOI: 10.1016/j.sbi.2023.102600] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 03/30/2023] [Accepted: 03/31/2023] [Indexed: 05/03/2023]
Abstract
We provide an overview of the methods that can be used for protein structure-based evaluation of missense variants. The algorithms can be broadly divided into those that calculate the difference in free energy (ΔΔG) between the wild type and variant structures and those that use structural features to predict the damaging effect of a variant without providing a ΔΔG. A wide range of machine learning approaches have been employed to develop those algorithms. We also discuss challenges and opportunities for variant interpretation in view of the recent breakthrough in three-dimensional structural modelling using deep learning.
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Affiliation(s)
- Alessia David
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - Michael J E Sternberg
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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46
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Hong T, Long L, Sang Y, Jiang Z, Ni H, Zheng M, Li L, Li Q, Zhu Y. Simultaneous enhancement of thermostability and catalytic activity of κ-carrageenase from Pseudoalteromonas tetraodonis by rational design. Enzyme Microb Technol 2023; 167:110241. [PMID: 37060759 DOI: 10.1016/j.enzmictec.2023.110241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 04/09/2023] [Accepted: 04/10/2023] [Indexed: 04/17/2023]
Abstract
κ-Carrageenase provides an attractive enzymatic approach to preparation of κ-carrageenan oligosaccharides. Pseudoalteromonas tetraodonis κ-carrageenase is active at the alkaline conditions but displays low thermostability. To further improve its enzymatic performance, two mutants of Q42V and I51H exhibiting both improved thermostability and enzyme activity were screened by the PoPMuSiC algorithm. Compared with the wild-type κ-carrageenase (WT), Q42V and I51H increased the enzyme activity by 20.9% and 25.4%, respectively. After treatment at 50 ℃ for 40 min, Q42V and I51H enhanced the residual activity by 31.1% and 25.9%, respectively. The Tm values of Q42V, I51H, and WT determined by differential scanning calorimetry were 58.2 ℃, 54.8 ℃, and 51.2 ℃, respectively. Compared with untreated and HCl-treated κ-carrageenans, Q42V-treated κ-carrageenan exhibited higher pancreatic lipase inhibitory activity. Molecular docking analysis indicated that the additional pi-sigma force and hydrophobic interaction in the enzyme-substrate complex could account for the increased catalytic activity of Q42V and I51H, respectively. Molecular dynamics analysis indicated that the improved thermostability of mutants Q42V and I51H could be attributed to the less structural deviation and the flexible changes of enzyme conformation at high temperature. This study provides new insight into κ-carrageenase performance improvement and identifies good candidates for their industrial applications.
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Affiliation(s)
- Tao Hong
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Liufei Long
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Yuyan Sang
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China
| | - Zedong Jiang
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Hui Ni
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Mingjing Zheng
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Lijun Li
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Qingbiao Li
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China
| | - Yanbing Zhu
- College of Food and Biological Engineering, Jimei University, Xiamen 361021, China; Fujian Provincial Key Laboratory of Food Microbiology and Enzyme Engineering, Xiamen 361021, China; Research Center of Food Biotechnology of Xiamen City, Xiamen 361021, China.
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47
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Fengmin L, Heng Z, Xiangjun Z, Xiaobo W, Huiyan L, Haitian F. Site-directed mutagenesis improves the practical application of L-glutamic acid decarboxylase in Escherichia coli. Eng Life Sci 2023; 23:e2200064. [PMID: 37025190 PMCID: PMC10071571 DOI: 10.1002/elsc.202200064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 01/11/2023] [Accepted: 02/26/2023] [Indexed: 04/08/2023] Open
Abstract
γ-Aminobutyric acid (GABA) is a kind of non-proteinogenic amino acid which is highly soluble in water and widely used in the food and pharmaceutical industries. Enzymatic conversion is an efficient method to produce GABA, whereby glutamic acid decarboxylase (GAD) is the key enzyme that catalyzes the process. The activity of wild-type GAD is usually limited by temperature, pH or biotin concentration, and hence directional modification is applied to improve its catalytic properties and practical application. GABA was produced using whole cell transformation of the recombinant strains Escherichia coli BL21(DE3)-Gad B, E. coli BL21(DE3)-Gad B-T62S and E. coli BL21(DE3)-Gad B-Q309A. The corresponding GABA concentrations in the fermentation broth were 219.09, 238.42, and 276.66 g/L, and the transformation rates were 78.02%, 85.04%, and 98.58%, respectively. The results showed that Gad B-T62S and Gad B-Q309A are two effective mutation sites. These findings may contribute to ideas for constructing potent recombinant strains for GABA production. Practical Application : Enzymatic properties of the GAD from Escherichia coli and GAD site-specific mutants were examined by analyzing their conserved sequences, substrate contacts, contact between GAD amino acid residues and mutation energy (ΔΔG) of the GAD mutants. The enzyme activity and stability of Gad B-T62S and Gad B-Q309A mutants were improved compared to Gad B. The kinetic parameters Km and Vmax of Gad B, Gad B-T62S, and Gad B-Q309A mutants were 11.3 ± 2.1 mM and 32.1 ± 2.4 U/mg, 7.3 ± 2.5 mM and 76.1 ± 3.1 U/mg, and 7.2 ± 3.8 mM and 87.3 ± 1.1 U/mg, respectively. GABA was produced using whole cell transformation of the recombinant strains E. coli BL21(DE3)-Gad B, E. coli BL21(DE3)-Gad B-T62S, and E. coli BL21(DE3)-Gad B-Q309A. The corresponding GABA concentrations in the fermentation broth were 219.09, 238.42, and 276.66 g/L, and the transformation rates were 78.02%, 85.04%, and 98.58%, respectively.
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Affiliation(s)
- Liu Fengmin
- School of Food and WineNingxia Key Laboratory for Food Microbial‐Applications Technology and Safety ControlNingxia UniversityYinchuanChina
| | - Zhang Heng
- School of Food and WineNingxia Key Laboratory for Food Microbial‐Applications Technology and Safety ControlNingxia UniversityYinchuanChina
| | - Zhang Xiangjun
- School of Food and WineNingxia Key Laboratory for Food Microbial‐Applications Technology and Safety ControlNingxia UniversityYinchuanChina
| | - Wei Xiaobo
- School of Food and WineNingxia Key Laboratory for Food Microbial‐Applications Technology and Safety ControlNingxia UniversityYinchuanChina
| | - Liu Huiyan
- School of Food and WineNingxia Key Laboratory for Food Microbial‐Applications Technology and Safety ControlNingxia UniversityYinchuanChina
| | - Fang Haitian
- School of Food and WineNingxia Key Laboratory for Food Microbial‐Applications Technology and Safety ControlNingxia UniversityYinchuanChina
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48
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Nezhad NG, Rahman RNZRA, Normi YM, Oslan SN, Shariff FM, Leow TC. Recent advances in simultaneous thermostability-activity improvement of industrial enzymes through structure modification. Int J Biol Macromol 2023; 232:123440. [PMID: 36708895 DOI: 10.1016/j.ijbiomac.2023.123440] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 01/27/2023]
Abstract
Engineered thermostable microbial enzymes are widely employed to catalyze chemical reactions in numerous industrial sectors. Although high thermostability is a prerequisite of industrial applications, enzyme activity is usually sacrificed during thermostability improvement. Therefore, it is vital to select the common and compatible strategies between thermostability and activity improvement to reduce mutants̕ libraries and screening time. Three functional protein engineering approaches, including directed evolution, rational design, and semi-rational design, are employed to manipulate protein structure on a genetic basis. From a structural standpoint, integrative strategies such as increasing substrate affinity; introducing electrostatic interaction; removing steric hindrance; increasing flexibility of the active site; N- and C-terminal engineering; and increasing intramolecular and intermolecular hydrophobic interactions are well-known to improve simultaneous activity and thermostability. The current review aims to analyze relevant strategies to improve thermostability and activity simultaneously to circumvent the thermostability and activity trade-off of industrial enzymes.
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Affiliation(s)
- Nima Ghahremani Nezhad
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Siti Nurbaya Oslan
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Enzyme and Microbial Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia.
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49
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Kan Y, Paung Y, Kim Y, Seeliger MA, Miller WT. Biochemical Studies of Systemic Lupus Erythematosus-Associated Mutations in Nonreceptor Tyrosine Kinases Ack1 and Brk. Biochemistry 2023; 62:1124-1137. [PMID: 36854171 PMCID: PMC10052838 DOI: 10.1021/acs.biochem.2c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Tyrosine kinases (TKs) play essential roles in signaling processes that regulate cell survival, migration, and proliferation. Dysregulation of tyrosine kinases underlies many disorders, including cancer, cardiovascular and developmental diseases, as well as pathologies of the immune system. Ack1 and Brk are nonreceptor tyrosine kinases (NRTKs) best known for their roles in cancer. Here, we have biochemically characterized novel Ack1 and Brk mutations identified in patients with systemic lupus erythematosus (SLE). These mutations are the first SLE-linked polymorphisms found among NRTKs. We show that two of the mutants are catalytically inactive, while the other three have reduced activity. To understand the structural changes associated with the loss-of-function phenotype, we solved the crystal structure of one of the Ack1 kinase mutants, K161Q. Furthermore, two of the mutated residues (Ack1 A156 and K161) critical for catalytic activity are highly conserved among other TKs, and their substitution in other members of the kinase family could have implications in cancer. In contrast to canonical gain-of-function mutations in TKs observed in many cancers, we report loss-of-function mutations in Ack1 and Brk, highlighting the complexity of TK involvement in human diseases.
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Affiliation(s)
- Yagmur Kan
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States
| | - YiTing Paung
- Department of Pharmacology, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States
| | - Yunyoung Kim
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States
| | - Markus A Seeliger
- Department of Pharmacology, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States
| | - W Todd Miller
- Department of Physiology and Biophysics, School of Medicine, Stony Brook University, Stony Brook, New York 11794-8661, United States
- Department of Veterans Affairs Medical Center, Northport, New York 11768, United States
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50
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Gu J, Xu Y, Nie Y. Role of distal sites in enzyme engineering. Biotechnol Adv 2023; 63:108094. [PMID: 36621725 DOI: 10.1016/j.biotechadv.2023.108094] [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: 08/02/2022] [Revised: 11/15/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023]
Abstract
The limitations associated with natural enzyme catalysis have triggered the rise of the field of protein engineering. Traditional rational design was based on the analysis of protein structural information and catalytic mechanisms to identify key active sites or ligand binding sites to reshape the substrate pocket. The role and significance of functional sites in the active center have been studied extensively. With a deeper understanding of the structure-catalysis relationship map, the entire protein molecule can be filled with residues that play a substantial role in its structure and function. However, the catalytic mechanism underlying distal mutations remains unclear. The aim of this review was to highlight the criticality of the distal site in enzyme engineering based on the following three aspects: What can distal mutations exert on function from mutability landscape? How do distal sites influence enzyme function? How to predict and design distal mutations? This review provides insights into the catalytic mechanism of enzymes from the global interaction network, knowledge from sequence-structure-dynamics-function relationships, and strategies for distal mutation-based protein engineering.
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Affiliation(s)
- Jie Gu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China
| | - Yan Xu
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China; State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Yao Nie
- Lab of Brewing Microbiology and Applied Enzymology, School of Biotechnology and Key laboratory of Industrial Biotechnology of Ministry of Education, Jiangnan University, Wuxi 214122, China; Suqian Industrial Technology Research Institute of Jiangnan University, Suqian 223814, China.
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