1
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Cai H, Zhang Z, Wang M, Zhong B, Li Q, Zhong Y, Wu Y, Ying T, Tang J. Pretrainable geometric graph neural network for antibody affinity maturation. Nat Commun 2024; 15:7785. [PMID: 39242604 DOI: 10.1038/s41467-024-51563-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 08/13/2024] [Indexed: 09/09/2024] Open
Abstract
Increasing the binding affinity of an antibody to its target antigen is a crucial task in antibody therapeutics development. This paper presents a pretrainable geometric graph neural network, GearBind, and explores its potential in in silico affinity maturation. Leveraging multi-relational graph construction, multi-level geometric message passing and contrastive pretraining on mass-scale, unlabeled protein structural data, GearBind outperforms previous state-of-the-art approaches on SKEMPI and an independent test set. A powerful ensemble model based on GearBind is then derived and used to successfully enhance the binding of two antibodies with distinct formats and target antigens. ELISA EC50 values of the designed antibody mutants are decreased by up to 17 fold, and KD values by up to 6.1 fold. These promising results underscore the utility of geometric deep learning and effective pretraining in macromolecule interaction modeling tasks.
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Affiliation(s)
- Huiyu Cai
- BioGeometry, Beijing, China
- Mila-Québec AI Institute, Montréal, QC, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, QC, Canada
| | - Zuobai Zhang
- Mila-Québec AI Institute, Montréal, QC, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, QC, Canada
| | - Mingkai Wang
- Shanghai Engineering Research Center for Synthetic Immunology, Fudan University, Shanghai, China
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Bozitao Zhong
- Mila-Québec AI Institute, Montréal, QC, Canada
- Department of Computer Science and Operations Research, Université de Montréal, Montréal, QC, Canada
| | - Quanxiao Li
- Shanghai Engineering Research Center for Synthetic Immunology, Fudan University, Shanghai, China
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yuxuan Zhong
- Shanghai Engineering Research Center for Synthetic Immunology, Fudan University, Shanghai, China
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Yanling Wu
- Shanghai Engineering Research Center for Synthetic Immunology, Fudan University, Shanghai, China.
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Tianlei Ying
- Shanghai Engineering Research Center for Synthetic Immunology, Fudan University, Shanghai, China.
- MOE/NHC/CAMS Key Laboratory of Medical Molecular Virology, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical Sciences, Fudan University, Shanghai, China.
| | - Jian Tang
- BioGeometry, Beijing, China.
- Mila-Québec AI Institute, Montréal, QC, Canada.
- Department of Decision Sciences, HEC Montréal, Montréal, QC, Canada.
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2
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Zhou Y, Myung Y, Rodrigues CM, Ascher D. DDMut-PPI: predicting effects of mutations on protein-protein interactions using graph-based deep learning. Nucleic Acids Res 2024; 52:W207-W214. [PMID: 38783112 PMCID: PMC11223791 DOI: 10.1093/nar/gkae412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/30/2024] [Accepted: 05/02/2024] [Indexed: 05/25/2024] Open
Abstract
Protein-protein interactions (PPIs) play a vital role in cellular functions and are essential for therapeutic development and understanding diseases. However, current predictive tools often struggle to balance efficiency and precision in predicting the effects of mutations on these complex interactions. To address this, we present DDMut-PPI, a deep learning model that efficiently and accurately predicts changes in PPI binding free energy upon single and multiple point mutations. Building on the robust Siamese network architecture with graph-based signatures from our prior work, DDMut, the DDMut-PPI model was enhanced with a graph convolutional network operated on the protein interaction interface. We used residue-specific embeddings from ProtT5 protein language model as node features, and a variety of molecular interactions as edge features. By integrating evolutionary context with spatial information, this framework enables DDMut-PPI to achieve a robust Pearson correlation of up to 0.75 (root mean squared error: 1.33 kcal/mol) in our evaluations, outperforming most existing methods. Importantly, the model demonstrated consistent performance across mutations that increase or decrease binding affinity. DDMut-PPI offers a significant advancement in the field and will serve as a valuable tool for researchers probing the complexities of protein interactions. DDMut-PPI is freely available as a web server and an application programming interface at https://biosig.lab.uq.edu.au/ddmut_ppi.
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Affiliation(s)
- Yunzhuo Zhou
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - YooChan Myung
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
| | - Carlos H M Rodrigues
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
| | - David B Ascher
- The Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Queensland 4072, Australia
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia
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3
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Wiseglass G, Rubinstein R. Following the Evolutionary Paths of Dscam1 Proteins toward Highly Specific Homophilic Interactions. Mol Biol Evol 2024; 41:msae141. [PMID: 38989909 PMCID: PMC11272049 DOI: 10.1093/molbev/msae141] [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: 03/20/2024] [Revised: 06/05/2024] [Accepted: 07/05/2024] [Indexed: 07/12/2024] Open
Abstract
Many adhesion proteins, evolutionarily related through gene duplication, exhibit distinct and precise interaction preferences and affinities crucial for cell patterning. Yet, the evolutionary paths by which these proteins acquire new specificities and prevent cross-interactions within their family members remain unknown. To bridge this gap, this study focuses on Drosophila Down syndrome cell adhesion molecule-1 (Dscam1) proteins, which are cell adhesion proteins that have undergone extensive gene duplication. Dscam1 evolved under strong selective pressure to achieve strict homophilic recognition, essential for neuronal self-avoidance and patterning. Through a combination of phylogenetic analyses, ancestral sequence reconstruction, and cell aggregation assays, we studied the evolutionary trajectory of Dscam1 exon 4 across various insect lineages. We demonstrated that recent Dscam1 duplications in the mosquito lineage bind with strict homophilic specificities without any cross-interactions. We found that ancestral and intermediate Dscam1 isoforms maintained their homophilic binding capabilities, with some intermediate isoforms also engaging in promiscuous interactions with other paralogs. Our results highlight the robust selective pressure for homophilic specificity integral to the Dscam1 function within the process of neuronal self-avoidance. Importantly, our study suggests that the path to achieving such selective specificity does not introduce disruptive mutations that prevent self-binding but includes evolutionary intermediates that demonstrate promiscuous heterophilic interactions. Overall, these results offer insights into evolutionary strategies that underlie adhesion protein interaction specificities.
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Affiliation(s)
- Gil Wiseglass
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Rotem Rubinstein
- School of Neurobiology, Biochemistry and Biophysics, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
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4
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Ozden B, Şamiloğlu E, Özsan A, Erguven M, Yükrük C, Koşaca M, Oktayoğlu M, Menteş M, Arslan N, Karakülah G, Barlas AB, Savaş B, Karaca E. Benchmarking the accuracy of structure-based binding affinity predictors on Spike-ACE2 deep mutational interaction set. Proteins 2024; 92:529-539. [PMID: 37991066 DOI: 10.1002/prot.26645] [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: 02/23/2023] [Revised: 10/25/2023] [Accepted: 11/13/2023] [Indexed: 11/23/2023]
Abstract
Since the start of COVID-19 pandemic, a huge effort has been devoted to understanding the Spike (SARS-CoV-2)-ACE2 recognition mechanism. To this end, two deep mutational scanning studies traced the impact of all possible mutations across receptor binding domain (RBD) of Spike and catalytic domain of human ACE2. By concentrating on the interface mutations of these experimental data, we benchmarked six commonly used structure-based binding affinity predictors (FoldX, EvoEF1, MutaBind2, SSIPe, HADDOCK, and UEP). These predictors were selected based on their user-friendliness, accessibility, and speed. As a result of our benchmarking efforts, we observed that none of the methods could generate a meaningful correlation with the experimental binding data. The best correlation is achieved by FoldX (R = -0.51). When we simplified the prediction problem to a binary classification, that is, whether a mutation is enriching or depleting the binding, we showed that the highest accuracy is achieved by FoldX with a 64% success rate. Surprisingly, on this set, simple energetic scoring functions performed significantly better than the ones using extra evolutionary-based terms, as in Mutabind and SSIPe. Furthermore, we demonstrated that recent AI approaches, mmCSM-PPI and TopNetTree, yielded comparable performances to the force field-based techniques. These observations suggest plenty of room to improve the binding affinity predictors in guessing the variant-induced binding profile changes of a host-pathogen system, such as Spike-ACE2. To aid such improvements we provide our benchmarking data at https://github.com/CSB-KaracaLab/RBD-ACE2-MutBench with the option to visualize our mutant models at https://rbd-ace2-mutbench.github.io/.
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Affiliation(s)
- Burcu Ozden
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Eda Şamiloğlu
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Atakan Özsan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mehmet Erguven
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Can Yükrük
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Mehdi Koşaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Melis Oktayoğlu
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Muratcan Menteş
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Nazmiye Arslan
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
| | - Gökhan Karakülah
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Ayşe Berçin Barlas
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Büşra Savaş
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
| | - Ezgi Karaca
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Izmir, Turkey
- Izmir International Biomedicine and Genome Institute, Dokuz Eylül University, Izmir, Turkey
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5
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Marsili L, Davis JL, Espay AJ, Gilthorpe J, Williams C, Kauffman MA, Porollo A. SOD1-Related Cerebellar Ataxia and Motor Neuron Disease: Cp Variant as Functional Modifier? CEREBELLUM (LONDON, ENGLAND) 2024; 23:205-209. [PMID: 36757662 DOI: 10.1007/s12311-023-01527-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 02/01/2023] [Indexed: 02/10/2023]
Abstract
We describe a novel superoxide dismutase (SOD1) mutation-associated clinical phenotype of cerebellar ataxia and motor neuron disease with a variant in the ceruloplasmin (Cp) gene, which may have possibly contributed to a multi-factorial phenotype, supported by genetic and protein structure analyses.
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Affiliation(s)
- Luca Marsili
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, OH, Cincinnati, USA.
| | - Jennie L Davis
- Valley Neuroscience Institute, University of Washington-Valley Medical Center, Renton, WA, USA
| | - Alberto J Espay
- James J. and Joan A. Gardner Center for Parkinson's Disease and Movement Disorders, Department of Neurology, University of Cincinnati, OH, Cincinnati, USA
| | - Jonathan Gilthorpe
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Chloe Williams
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
| | - Marcelo A Kauffman
- Consultorio Y Laboratorio de Neurogenética, Centro Universitario de Neurología José María Ramos Mejía, Buenos Aires, Argentina
| | - Aleksey Porollo
- Center for Autoimmune Genomics and Etiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
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6
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Jarończyk M. Software for Predicting Binding Free Energy of Protein-Protein Complexes and Their Mutants. Methods Mol Biol 2024; 2780:139-147. [PMID: 38987468 DOI: 10.1007/978-1-0716-3985-6_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
Protein-protein binding affinity prediction is important for understanding complex biochemical pathways and to uncover protein interaction networks. Quantitative estimation of the binding affinity changes caused by mutations can provide critical information for protein function annotation and genetic disease diagnoses. The binding free energies of protein-protein complexes can be predicted using several computational tools. This chapter is a summary of software developed for the prediction of binding free energies for protein-protein complexes and their mutants.
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7
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Tsishyn M, Pucci F, Rooman M. Quantification of biases in predictions of protein-protein binding affinity changes upon mutations. Brief Bioinform 2023; 25:bbad491. [PMID: 38197311 PMCID: PMC10777193 DOI: 10.1093/bib/bbad491] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 10/02/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024] Open
Abstract
Understanding the impact of mutations on protein-protein binding affinity is a key objective for a wide range of biotechnological applications and for shedding light on disease-causing mutations, which are often located at protein-protein interfaces. Over the past decade, many computational methods using physics-based and/or machine learning approaches have been developed to predict how protein binding affinity changes upon mutations. They all claim to achieve astonishing accuracy on both training and test sets, with performances on standard benchmarks such as SKEMPI 2.0 that seem overly optimistic. Here we benchmarked eight well-known and well-used predictors and identified their biases and dataset dependencies, using not only SKEMPI 2.0 as a test set but also deep mutagenesis data on the severe acute respiratory syndrome coronavirus 2 spike protein in complex with the human angiotensin-converting enzyme 2. We showed that, even though most of the tested methods reach a significant degree of robustness and accuracy, they suffer from limited generalizability properties and struggle to predict unseen mutations. Interestingly, the generalizability problems are more severe for pure machine learning approaches, while physics-based methods are less affected by this issue. Moreover, undesirable prediction biases toward specific mutation properties, the most marked being toward destabilizing mutations, are also observed and should be carefully considered by method developers. We conclude from our analyses that there is room for improvement in the prediction models and suggest ways to check, assess and improve their generalizability and robustness.
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Affiliation(s)
- Matsvei Tsishyn
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
| | - Fabrizio Pucci
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
| | - Marianne Rooman
- Computational Biology and Bioinformatics, Université Libre de Bruxelles, Roosevelt Ave, 1050, Brussels, Belgium
- Interuniversity Institute of Bioinformatics in Brussels, Brussels, Belgium
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8
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Bouhaddou M, Reuschl AK, Polacco BJ, Thorne LG, Ummadi MR, Ye C, Rosales R, Pelin A, Batra J, Jang GM, Xu J, Moen JM, Richards AL, Zhou Y, Harjai B, Stevenson E, Rojc A, Ragazzini R, Whelan MVX, Furnon W, De Lorenzo G, Cowton V, Syed AM, Ciling A, Deutsch N, Pirak D, Dowgier G, Mesner D, Turner JL, McGovern BL, Rodriguez ML, Leiva-Rebollo R, Dunham AS, Zhong X, Eckhardt M, Fossati A, Liotta NF, Kehrer T, Cupic A, Rutkowska M, Mena I, Aslam S, Hoffert A, Foussard H, Olwal CO, Huang W, Zwaka T, Pham J, Lyons M, Donohue L, Griffin A, Nugent R, Holden K, Deans R, Aviles P, Lopez-Martin JA, Jimeno JM, Obernier K, Fabius JM, Soucheray M, Hüttenhain R, Jungreis I, Kellis M, Echeverria I, Verba K, Bonfanti P, Beltrao P, Sharan R, Doudna JA, Martinez-Sobrido L, Patel AH, Palmarini M, Miorin L, White K, Swaney DL, Garcia-Sastre A, Jolly C, Zuliani-Alvarez L, Towers GJ, Krogan NJ. SARS-CoV-2 variants evolve convergent strategies to remodel the host response. Cell 2023; 186:4597-4614.e26. [PMID: 37738970 PMCID: PMC10604369 DOI: 10.1016/j.cell.2023.08.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/22/2023] [Accepted: 08/22/2023] [Indexed: 09/24/2023]
Abstract
SARS-CoV-2 variants of concern (VOCs) emerged during the COVID-19 pandemic. Here, we used unbiased systems approaches to study the host-selective forces driving VOC evolution. We discovered that VOCs evolved convergent strategies to remodel the host by modulating viral RNA and protein levels, altering viral and host protein phosphorylation, and rewiring virus-host protein-protein interactions. Integrative computational analyses revealed that although Alpha, Beta, Gamma, and Delta ultimately converged to suppress interferon-stimulated genes (ISGs), Omicron BA.1 did not. ISG suppression correlated with the expression of viral innate immune antagonist proteins, including Orf6, N, and Orf9b, which we mapped to specific mutations. Later Omicron subvariants BA.4 and BA.5 more potently suppressed innate immunity than early subvariant BA.1, which correlated with Orf6 levels, although muted in BA.4 by a mutation that disrupts the Orf6-nuclear pore interaction. Our findings suggest that SARS-CoV-2 convergent evolution overcame human adaptive and innate immune barriers, laying the groundwork to tackle future pandemics.
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Affiliation(s)
- Mehdi Bouhaddou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Immunology, and Molecular Genetics (MIMG), University of California, Los Angeles, Los Angeles, CA, USA; Institute for Quantitative and Computational Biosciences (QCBio), University of California, Los Angeles, Los Angeles, CA, USA; Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ann-Kathrin Reuschl
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK
| | - Benjamin J Polacco
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Lucy G Thorne
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK
| | - Manisha R Ummadi
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Chengjin Ye
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Romel Rosales
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Adrian Pelin
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jyoti Batra
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Gwendolyn M Jang
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jiewei Xu
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jack M Moen
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Alicia L Richards
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Yuan Zhou
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Bhavya Harjai
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Erica Stevenson
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ajda Rojc
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Roberta Ragazzini
- Division of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Matthew V X Whelan
- Division of Infection and Immunity, University College London, London, UK
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Giuditta De Lorenzo
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Abdullah M Syed
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Alison Ciling
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Noa Deutsch
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Daniel Pirak
- School of Electrical Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Giulia Dowgier
- COVID Surveillance Unit, The Francis Crick Institute, London, UK
| | - Dejan Mesner
- Division of Infection and Immunity, University College London, London, UK
| | - Jane L Turner
- Division of Infection and Immunity, University College London, London, UK
| | - Briana L McGovern
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - M Luis Rodriguez
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rocio Leiva-Rebollo
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alistair S Dunham
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden, UK
| | - Xiaofang Zhong
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Manon Eckhardt
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Andrea Fossati
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Nicholas F Liotta
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA
| | - Thomas Kehrer
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Anastasija Cupic
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Magdalena Rutkowska
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Graduate School of Biomedical Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ignacio Mena
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Sadaf Aslam
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Alyssa Hoffert
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Helene Foussard
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Charles Ochieng' Olwal
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; West African Centre for Cell Biology of Infectious Pathogens (WACCBIP), University of Ghana, Accra, Ghana; Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
| | - Weiqing Huang
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Thomas Zwaka
- Huffington Center for Cell-based Research in Parkinson's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Cell, Developmental and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Black Family Stem Cell Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - John Pham
- Synthego Corporation, Redwood City, CA, USA
| | | | | | | | | | | | | | | | | | | | - Kirsten Obernier
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Jacqueline M Fabius
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Margaret Soucheray
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Ruth Hüttenhain
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Irwin Jungreis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Manolis Kellis
- MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ignacia Echeverria
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Kliment Verba
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Paola Bonfanti
- Division of Infection and Immunity, University College London, London, UK; Epithelial Stem Cell Biology and Regenerative Medicine Laboratory, The Francis Crick Institute, London, UK
| | - Pedro Beltrao
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK; Institute of Molecular Systems Biology, Department of Biology, ETH Zürich, Zurich, Switzerland
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Jennifer A Doudna
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, Berkeley, CA, USA; Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Luis Martinez-Sobrido
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Arvind H Patel
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Lisa Miorin
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kris White
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Danielle L Swaney
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
| | - Adolfo Garcia-Sastre
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, NY, USA; The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA; Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Clare Jolly
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK.
| | - Lorena Zuliani-Alvarez
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
| | - Greg J Towers
- QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Division of Infection and Immunity, University College London, London, UK.
| | - Nevan J Krogan
- Quantitative Biosciences Institute (QBI), University of California, San Francisco, San Francisco, CA, USA; QBI Coronavirus Research Group (QCRG), University of California, San Francisco, San Francisco, CA, USA; Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA; Gladstone Institute of Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA.
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9
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Shirvanizadeh N, Vihinen M. VariBench, new variation benchmark categories and data sets. FRONTIERS IN BIOINFORMATICS 2023; 3:1248732. [PMID: 37795169 PMCID: PMC10546188 DOI: 10.3389/fbinf.2023.1248732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/08/2023] [Indexed: 10/06/2023] Open
Affiliation(s)
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, Lund, Sweden
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10
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Mumphrey MB, Hosseini N, Parolia A, Geng J, Zou W, Raghavan M, Chinnaiyan A, Cieslik M. Distinct mutational processes shape selection of MHC class I and class II mutations across primary and metastatic tumors. Cell Rep 2023; 42:112965. [PMID: 37597185 DOI: 10.1016/j.celrep.2023.112965] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/15/2023] [Accepted: 07/26/2023] [Indexed: 08/21/2023] Open
Abstract
Disruption of antigen presentation via loss of major histocompatibility complex (MHC) expression is a strategy whereby cancer cells escape immune surveillance and develop resistance to immunotherapy. Here, we develop the personalized genomics algorithm Hapster and accurately call somatic mutations within the MHC genes of 10,001 primary and 2,199 metastatic tumors, creating a catalog of 1,663 non-synonymous mutations that provide key insights into MHC mutagenesis. We find that MHC class I genes are among the most frequently mutated genes in both primary and metastatic tumors, while MHC class II mutations are more restricted. Recurrent deleterious mutations are found within haplotype- and cancer-type-specific hotspots associated with distinct mutational processes. Functional classification of MHC residues reveals significant positive selection for mutations disruptive to the B2M, peptide, and T cell binding interfaces, as well as to MHC chaperones.
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Affiliation(s)
- Michael B Mumphrey
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Noshad Hosseini
- Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Abhijit Parolia
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jie Geng
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Weiping Zou
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA; Center of Excellence for Cancer Immunology and Immunotherapy, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Malini Raghavan
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Arul Chinnaiyan
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Ann Arbor, MI 48109, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI 48109, USA
| | - Marcin Cieslik
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA; Department of Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI 48109, USA; University of Michigan Rogel Cancer Center, Ann Arbor, MI 48109, USA.
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11
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Chen Z, Wang X, Chen X, Huang J, Wang C, Wang J, Wang Z. Accelerating therapeutic protein design with computational approaches toward the clinical stage. Comput Struct Biotechnol J 2023; 21:2909-2926. [PMID: 38213894 PMCID: PMC10781723 DOI: 10.1016/j.csbj.2023.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/11/2023] [Accepted: 04/27/2023] [Indexed: 01/13/2024] Open
Abstract
Therapeutic protein, represented by antibodies, is of increasing interest in human medicine. However, clinical translation of therapeutic protein is still largely hindered by different aspects of developability, including affinity and selectivity, stability and aggregation prevention, solubility and viscosity reduction, and deimmunization. Conventional optimization of the developability with widely used methods, like display technologies and library screening approaches, is a time and cost-intensive endeavor, and the efficiency in finding suitable solutions is still not enough to meet clinical needs. In recent years, the accelerated advancement of computational methodologies has ushered in a transformative era in the field of therapeutic protein design. Owing to their remarkable capabilities in feature extraction and modeling, the integration of cutting-edge computational strategies with conventional techniques presents a promising avenue to accelerate the progression of therapeutic protein design and optimization toward clinical implementation. Here, we compared the differences between therapeutic protein and small molecules in developability and provided an overview of the computational approaches applicable to the design or optimization of therapeutic protein in several developability issues.
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Affiliation(s)
- Zhidong Chen
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Xinpei Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Xu Chen
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Juyang Huang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Chenglin Wang
- Shenzhen Qiyu Biotechnology Co., Ltd, Shenzhen 518107, China
| | - Junqing Wang
- School of Pharmaceutical Sciences, Shenzhen Campus of Sun Yat-sen University, Shenzhen 518107, China
| | - Zhe Wang
- Department of Pathology, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen 518033, China
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12
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Braunstein EM, Imada E, Pasca S, Wang S, Chen H, Alba C, Hupalo DN, Wilkerson M, Dalgard CL, Ghannam J, Liu Y, Marchionni L, Moliterno A, Hourigan CS, Gondek LP. Recurrent germline variant in ATM associated with familial myeloproliferative neoplasms. Leukemia 2023; 37:627-635. [PMID: 36543879 DOI: 10.1038/s41375-022-01797-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022]
Abstract
Genetic predisposition (familial risk) in the myeloproliferative neoplasms (MPNs) is more common than the risk observed in most other cancers, including breast, prostate, and colon. Up to 10% of MPNs are considered to be familial. Recent genome-wide association studies have identified genomic loci associated with an MPN diagnosis. However, the identification of variants with functional contributions to the development of MPN remains limited. In this study, we have included 630 MPN patients and whole genome sequencing was performed in 64 individuals with familial MPN to uncover recurrent germline predisposition variants. Both targeted and unbiased filtering of single nucleotide variants (SNVs) was performed, with a comparison to 218 individuals with MPN unselected for familial status. This approach identified an ATM L2307F SNV occurring in nearly 8% of individuals with familial MPN. Structural protein modeling of this variant suggested stabilization of inactive ATM dimer, and alteration of the endogenous ATM locus in a human myeloid cell line resulted in decreased phosphorylation of the downstream tumor suppressor CHEK2. These results implicate ATM, and the DNA-damage response pathway, in predisposition to MPN.
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Affiliation(s)
- Evan M Braunstein
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.,Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Eddie Imada
- Division of Computational and Systems Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Sergiu Pasca
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Shiyu Wang
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
| | - Hang Chen
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA.,Committee on Genetics, Genomics and Systems Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Camille Alba
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA.,The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Dan N Hupalo
- Henry Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Matthew Wilkerson
- Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Clifton L Dalgard
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.,Department of Anatomy Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Jack Ghannam
- Laboratory of Myeloid Malignancies, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yujia Liu
- Department of Biochemistry and Molecular Biology, Biological Sciences Division, University of Chicago, Chicago, IL, USA
| | - Luigi Marchionni
- Division of Computational and Systems Pathology, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alison Moliterno
- Division of Hematology, Department of Medicine, Johns Hopkins Hospital, Baltimore, MD, USA
| | - Christopher S Hourigan
- Laboratory of Myeloid Malignancies, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Lukasz P Gondek
- Division of Hematological Malignancies, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA.
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13
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Rajkovic A, Kanchugal S, Abdurakhmanov E, Howard R, Wärmländer S, Erwin J, Barrera Saldaña HA, Gräslund A, Danielson H, Flores SC. Amino acid substitutions in human growth hormone affect secondary structure and receptor binding. PLoS One 2023; 18:e0282741. [PMID: 36952491 PMCID: PMC10035860 DOI: 10.1371/journal.pone.0282741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 02/22/2023] [Indexed: 03/25/2023] Open
Abstract
The interaction between human Growth Hormone (hGH) and hGH Receptor (hGHR) has basic relevance to cancer and growth disorders, and hGH is the scaffold for Pegvisomant, an anti-acromegaly therapeutic. For the latter reason, hGH has been extensively engineered by early workers to improve binding and other properties. We are particularly interested in E174 which belongs to the hGH zinc-binding triad; the substitution E174A is known to significantly increase binding, but to now no explanation has been offered. We generated this and several computationally-selected single-residue substitutions at the hGHR-binding site of hGH. We find that, while many successfully slow down dissociation of the hGH-hGHR complex once bound, they also slow down the association of hGH to hGHR. The E174A substitution induces a change in the Circular Dichroism spectrum that suggests the appearance of coiled-coiling. Here we show that E174A increases affinity of hGH against hGHR because the off-rate is slowed down more than the on-rate. For E174Y (and certain mutations at other sites) the slowdown in on-rate was greater than that of the off-rate, leading to decreased affinity. The results point to a link between structure, zinc binding, and hGHR-binding affinity in hGH.
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Affiliation(s)
- Andrei Rajkovic
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Sandesh Kanchugal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | | | - Rebecca Howard
- Department of Biochemistry and Biophysics, Stockholm University, Frescati, Sweden
| | - Sebastian Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, Frescati, Sweden
| | - Joseph Erwin
- Department of Biochemistry and Biophysics, Stockholm University, Frescati, Sweden
| | | | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, Frescati, Sweden
| | | | - Samuel Coulbourn Flores
- Department of Biochemistry and Biophysics, Stockholm University, Frescati, Sweden
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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14
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Romero-Molina S, Ruiz-Blanco YB, Mieres-Perez J, Harms M, Münch J, Ehrmann M, Sanchez-Garcia E. PPI-Affinity: A Web Tool for the Prediction and Optimization of Protein-Peptide and Protein-Protein Binding Affinity. J Proteome Res 2022; 21:1829-1841. [PMID: 35654412 PMCID: PMC9361347 DOI: 10.1021/acs.jproteome.2c00020] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Virtual screening
of protein–protein and protein–peptide
interactions is a challenging task that directly impacts the processes
of hit identification and hit-to-lead optimization in drug design
projects involving peptide-based pharmaceuticals. Although several
screening tools designed to predict the binding affinity of protein–protein
complexes have been proposed, methods specifically developed to predict
protein–peptide binding affinity are comparatively scarce.
Frequently, predictors trained to score the affinity of small molecules
are used for peptides indistinctively, despite the larger complexity
and heterogeneity of interactions rendered by peptide binders. To
address this issue, we introduce PPI-Affinity, a tool that leverages
support vector machine (SVM) predictors of binding affinity to screen
datasets of protein–protein and protein–peptide complexes,
as well as to generate and rank mutants of a given structure. The
performance of the SVM models was assessed on four benchmark datasets,
which include protein–protein and protein–peptide binding
affinity data. In addition, we evaluated our model on a set of mutants
of EPI-X4, an endogenous peptide inhibitor of the chemokine receptor
CXCR4, and on complexes of the serine proteases HTRA1 and HTRA3 with
peptides. PPI-Affinity is freely accessible at https://protdcal.zmb.uni-due.de/PPIAffinity.
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Affiliation(s)
- Sandra Romero-Molina
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Yasser B Ruiz-Blanco
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Joel Mieres-Perez
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Mirja Harms
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany.,Core Facility Functional Peptidomics, Ulm University Medical Center, Ulm 89081, Germany
| | - Michael Ehrmann
- Faculty of Biology, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
| | - Elsa Sanchez-Garcia
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Essen 45141, Germany
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15
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Xiong D, Lee D, Li L, Zhao Q, Yu H. Implications of disease-related mutations at protein-protein interfaces. Curr Opin Struct Biol 2022; 72:219-225. [PMID: 34959033 PMCID: PMC8863207 DOI: 10.1016/j.sbi.2021.11.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 11/01/2021] [Accepted: 11/18/2021] [Indexed: 02/03/2023]
Abstract
Protein-protein interfaces have been attracting great attention owing to their critical roles in protein-protein interactions and the fact that human disease-related mutations are generally enriched in them. Recently, substantial research progress has been made in this field, which has significantly promoted the understanding and treatment of various human diseases. For example, many studies have discovered the properties of disease-related mutations. Besides, as more large-scale experimental data become available, various computational approaches have been proposed to advance our understanding of disease mutations from the data. Here, we overview recent advances in characteristics of disease-related mutations at protein-protein interfaces, mutation effects on protein interactions, and investigation of mutations on specific diseases.
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Affiliation(s)
- Dapeng Xiong
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Dongjin Lee
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Le Li
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Qiuye Zhao
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
| | - Haiyuan Yu
- Department of Computational Biology, Cornell University, Ithaca, NY 14853, USA,Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY 14853, USA
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16
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Lim H, Jeon HN, Lim S, Jang Y, Kim T, Cho H, Pan JG, No KT. Evaluation of protein descriptors in computer-aided rational protein engineering tasks and its application in property prediction in SARS-CoV-2 spike glycoprotein. Comput Struct Biotechnol J 2022; 20:788-798. [PMID: 35222841 PMCID: PMC8841378 DOI: 10.1016/j.csbj.2022.01.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/18/2022] [Accepted: 01/27/2022] [Indexed: 11/13/2022] Open
Abstract
The importance of protein engineering in the research and development of biopharmaceuticals and biomaterials has increased. Machine learning in computer-aided protein engineering can markedly reduce the experimental effort in identifying optimal sequences that satisfy the desired properties from a large number of possible protein sequences. To develop general protein descriptors for computer-aided protein engineering tasks, we devised new protein descriptors, one sequence-based descriptor (PCgrades), and three structure-based descriptors (PCspairs, 3D-SPIEs_5.4 Å, and 3D-SPIEs_8Å). While the PCgrades and PCspairs include general and statistical information in physicochemical properties in single and pairwise amino acids respectively, the 3D-SPIEs include specific and quantum–mechanical information with parameterized quantum mechanical calculations (FMO2-DFTB3/D/PCM). To evaluate the protein descriptors, we made prediction models with the new descriptors and previously developed descriptors for diverse protein datasets including protein expression and binding affinity change in SARS-CoV-2 spike glycoprotein. As a result, the newly devised descriptors showed a good performance in diverse datasets, in which the PCspairs showed the best performance (R2=0.783 for protein expression and R2=0.711 for binding affinity). As a result, the newly devised descriptors showed a good performance in diverse datasets, in which the PCspairs showed the best performance. Similar approaches with those descriptors would be promising and useful if the prediction models are trained with sufficient quantitative experimental data from high-throughput assays for industrial enzymes or protein drugs.
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17
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Saha I, Ghosh N, Sharma N, Nandi S. Hotspot Mutations in SARS-CoV-2. Front Genet 2021; 12:753440. [PMID: 34912372 PMCID: PMC8667557 DOI: 10.3389/fgene.2021.753440] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/07/2021] [Indexed: 12/23/2022] Open
Abstract
Since its emergence in Wuhan, China, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has spread very rapidly around the world, resulting in a global pandemic. Though the vaccination process has started, the number of COVID-affected patients is still quite large. Hence, an analysis of hotspot mutations of the different evolving virus strains needs to be carried out. In this regard, multiple sequence alignment of 71,038 SARS-CoV-2 genomes of 98 countries over the period from January 2020 to June 2021 is performed using MAFFT followed by phylogenetic analysis in order to visualize the virus evolution. These steps resulted in the identification of hotspot mutations as deletions and substitutions in the coding regions based on entropy greater than or equal to 0.3, leading to a total of 45 unique hotspot mutations. Moreover, 10,286 Indian sequences are considered from 71,038 global SARS-CoV-2 sequences as a demonstrative example that gives 52 unique hotspot mutations. Furthermore, the evolution of the hotspot mutations along with the mutations in variants of concern is visualized, and their characteristics are discussed as well. Also, for all the non-synonymous substitutions (missense mutations), the functional consequences of amino acid changes in the respective protein structures are calculated using PolyPhen-2 and I-Mutant 2.0. In addition to this, SSIPe is used to report the binding affinity between the receptor-binding domain of Spike protein and human ACE2 protein by considering L452R, T478K, E484Q, and N501Y hotspot mutations in that region.
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Affiliation(s)
- Indrajit Saha
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, India
| | - Nimisha Ghosh
- Department of Computer Science and Information Technology, Institute of Technical Education and Research, Siksha 'O' Anusandhan (Deemed to be University), Bhubaneswar, India
| | - Nikhil Sharma
- Department of Electronics and Communication Engineering, Jaypee Institute of Information Technology, Noida, India
| | - Suman Nandi
- Department of Computer Science and Engineering, National Institute of Technical Teachers' Training and Research, Kolkata, India
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18
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Mishra S, Kumar S, Choudhuri KSR, Longkumer I, Koyyada P, Kharsyiemiong ET. Structural exploration with AlphaFold2-generated STAT3α structure reveals selective elements in STAT3α-GRIM-19 interactions involved in negative regulation. Sci Rep 2021; 11:23145. [PMID: 34848745 PMCID: PMC8633360 DOI: 10.1038/s41598-021-01436-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/28/2021] [Indexed: 11/18/2022] Open
Abstract
STAT3, an important transcription factor constitutively activated in cancers, is bound specifically by GRIM-19 and this interaction inhibits STAT3-dependent gene expression. GRIM-19 is therefore, considered as an inhibitor of STAT3 and may be an effective anti-cancer therapeutic target. While STAT3 exists in a dimeric form in the cytoplasm and nucleus, it is mostly present in a monomeric form in the mitochondria. Although GRIM-19-binding domains of STAT3 have been identified in independent experiments, yet the identified domains are not the same, and hence, discrepancies exist. Human STAT3-GRIM-19 complex has not been crystallised yet. Dictated by fundamental biophysical principles, the binding region, interactions and effects of hotspot mutations can provide us a clue to the negative regulatory mechanisms of GRIM-19. Prompted by the very nature of STAT3 being a challenging molecule, and to understand the structural basis of binding and interactions in STAT3α-GRIM-19 complex, we performed homology modelling and ab-initio modelling with evolutionary information using I-TASSER and avant-garde AlphaFold2, respectively, to generate monomeric, and subsequently, dimeric STAT3α structures. The dimeric form of STAT3α structure was observed to potentially exist in an anti-parallel orientation of monomers. We demonstrate that during the interactions with both unphosphorylated and phosphorylated STAT3α, the NTD of GRIM-19 binds most strongly to the NTD of STAT3α, in direct contrast to the earlier works. Key arginine residues at positions 57, 58 and 68 of GRIM-19 are mainly involved in the hydrogen-bonded interactions. An intriguing feature of these arginine residues is that these display a consistent interaction pattern across unphosphorylated and phosphorylated monomers as well as unphosphorylated dimers in STAT3α-GRIM-19 complexes. MD studies verified the stability of these complexes. Analysing the binding affinity and stability through free energy changes upon mutation, we found GRIM-19 mutations Y33P and Q61L and among GRIM-19 arginines, R68P and R57M, to be one of the top-most major and minor disruptors of binding, respectively. The proportionate increase in average change in binding affinity upon mutation was inclined more towards GRIM-19 mutants, leading to the surmise that GRIM-19 may play a greater role in the complex formation. These studies propound a novel structural perspective of STAT3α-GRIM-19 binding and inhibitory mechanisms in both the monomeric and dimeric forms of STAT3α as compared to that observed from the earlier experiments, these experimental observations being inconsistent among each other.
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Affiliation(s)
- Seema Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India.
| | - Santosh Kumar
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | | | - Imliyangla Longkumer
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Praveena Koyyada
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
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Havranek B, Chan KK, Wu A, Procko E, Islam SM. Computationally Designed ACE2 Decoy Receptor Binds SARS-CoV-2 Spike (S) Protein with Tight Nanomolar Affinity. J Chem Inf Model 2021; 61:4656-4669. [PMID: 34427448 PMCID: PMC8409145 DOI: 10.1021/acs.jcim.1c00783] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Indexed: 12/25/2022]
Abstract
Even with the availability of vaccines, therapeutic options for COVID-19 still remain highly desirable, especially in hospitalized patients with moderate or severe disease. Soluble ACE2 (sACE2) is a promising therapeutic candidate that neutralizes SARS CoV-2 infection by acting as a decoy. Using computational mutagenesis, we designed a number of sACE2 derivatives carrying three to four mutations. The top-predicted sACE2 decoy based on the in silico mutagenesis scan was subjected to molecular dynamics and free-energy calculations for further validation. After illuminating the mechanism of increased binding for our designed sACE2 derivative, the design was verified experimentally by flow cytometry and BLI-binding experiments. The computationally designed sACE2 decoy (ACE2-FFWF) bound the receptor-binding domain of SARS-CoV-2 tightly with low nanomolar affinity and ninefold affinity enhancement over the wild type. Furthermore, cell surface expression was slightly greater than wild-type ACE2, suggesting that the design is well-folded and stable. Having an arsenal of high-affinity sACE2 derivatives will help to buffer against the emergence of SARS CoV-2 variants. Here, we show that computational methods have become sufficiently accurate for the design of therapeutics for current and future viral pandemics.
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Affiliation(s)
- Brandon Havranek
- Department of Chemistry, University of
Illinois at Chicago, Chicago, Illinois 60607, United
States
| | - Kui K. Chan
- Orthogonal Biologics Inc.,
Urbana, Illinois 61801, United States
| | - Austin Wu
- Department of Computer Science,
Northwestern University, Evanston, Illinois 60208,
United States
| | - Erik Procko
- Department of Biochemistry and Cancer Center at
Illinois, University of Illinois, Urbana, Illinois 61801,
United States
| | - Shahidul M. Islam
- Department of Chemistry, University of
Illinois at Chicago, Chicago, Illinois 60607, United
States
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20
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Bhattacharjee MJ, Lin JJ, Chang CY, Chiou YT, Li TN, Tai CW, Shiu TF, Chen CA, Chou CY, Chakraborty P, Tseng YY, Wang LHC, Li WH. Identifying Primate ACE2 Variants That Confer Resistance to SARS-CoV-2. Mol Biol Evol 2021; 38:2715-2731. [PMID: 33674876 PMCID: PMC7989403 DOI: 10.1093/molbev/msab060] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
SARS-CoV-2 infects humans through the binding of viral S-protein (spike protein) to human angiotensin I converting enzyme 2 (ACE2). The structure of the ACE2-S-protein complex has been deciphered and we focused on the 27 ACE2 residues that bind to S-protein. From human sequence databases, we identified nine ACE2 variants at ACE2-S-protein binding sites. We used both experimental assays and protein structure analysis to evaluate the effect of each variant on the binding affinity of ACE2 to S-protein. We found one variant causing complete binding disruption, two and three variants, respectively, strongly and mildly reducing the binding affinity, and two variants strongly enhancing the binding affinity. We then collected the ACE2 gene sequences from 57 nonhuman primates. Among the 6 apes and 20 Old World monkeys (OWMs) studied, we found no new variants. In contrast, all 11 New World monkeys (NWMs) studied share four variants each causing a strong reduction in binding affinity, the Philippine tarsier also possesses three such variants, and 18 of the 19 prosimian species studied share one variant causing a strong reduction in binding affinity. Moreover, one OWM and three prosimian variants increased binding affinity by >50%. Based on these findings, we proposed that the common ancestor of primates was strongly resistant to and that of NWMs was completely resistant to SARS-CoV-2 and so is the Philippine tarsier, whereas apes and OWMs, like most humans, are susceptible. This study increases our understanding of the differences in susceptibility to SARS-CoV-2 infection among primates.
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Affiliation(s)
| | - Jinn-Jy Lin
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Chih-Yao Chang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yu-Ting Chiou
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Tian-Neng Li
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Chia-Wei Tai
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tz-Fan Shiu
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
| | - Chi-An Chen
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Chia-Yi Chou
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA
| | | | - Yan Yuan Tseng
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI, USA
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
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21
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Abbasi WA, Abbas SA, Andleeb S. PANDA: Predicting the change in proteins binding affinity upon mutations by finding a signal in primary structures. J Bioinform Comput Biol 2021; 19:2150015. [PMID: 34126874 DOI: 10.1142/s0219720021500153] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Accurately determining a change in protein binding affinity upon mutations is important to find novel therapeutics and to assist mutagenesis studies. Determination of change in binding affinity upon mutations requires sophisticated, expensive, and time-consuming wet-lab experiments that can be supported with computational methods. Most of the available computational prediction techniques depend upon protein structures that bound their applicability to only protein complexes with recognized 3D structures. In this work, we explore the sequence-based prediction of change in protein binding affinity upon mutation and question the effectiveness of [Formula: see text]-fold cross-validation (CV) across mutations adopted in previous studies to assess the generalization ability of such predictors with no known mutation during training. We have used protein sequence information instead of protein structures along with machine learning techniques to accurately predict the change in protein binding affinity upon mutation. Our proposed sequence-based novel change in protein binding affinity predictor called PANDA performs comparably to the existing methods gauged through an appropriate CV scheme and an external independent test dataset. On an external test dataset, our proposed method gives a maximum Pearson correlation coefficient of 0.52 in comparison to the state-of-the-art existing protein structure-based method called MutaBind which gives a maximum Pearson correlation coefficient of 0.59. Our proposed protein sequence-based method, to predict a change in binding affinity upon mutations, has wide applicability and comparable performance in comparison to existing protein structure-based methods. We made PANDA easily accessible through a cloud-based webserver and python code available at https://sites.google.com/view/wajidarshad/software and https://github.com/wajidarshad/panda, respectively.
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Affiliation(s)
- Wajid Arshad Abbasi
- Computational Biology and Data Analysis Lab., Department of Computer Sciences & Information Technology, King Abdullah Campus, University of Azad Jammu & Kashmir, Muzaffarabad, AJ&K 13100, Pakistan
| | - Syed Ali Abbas
- Computational Biology and Data Analysis Lab., Department of Computer Sciences & Information Technology, King Abdullah Campus, University of Azad Jammu & Kashmir, Muzaffarabad, AJ&K 13100, Pakistan
| | - Saiqa Andleeb
- Biotechnology Lab., Department of Zoology, King Abdullah Campus, University of Azad Jammu & Kashmir, Muzaffarabad, AJ&K 13100, Pakistan
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22
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Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CC, Lim WK, Lee JGH, Tan P, Umapathy G, Raveendran M, Alan Harris R, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Le MD, Manu S, Rabarivola CJ, Zaramody A, Andriaholinirina N, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KK, Rogers J, Marques‐Bonet T, Navarro A, Juan D, Arora PS, Higham JP. Variation in predicted COVID-19 risk among lemurs and lorises. Am J Primatol 2021; 83:e23255. [PMID: 33792947 PMCID: PMC8250314 DOI: 10.1002/ajp.23255] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 03/03/2021] [Accepted: 03/04/2021] [Indexed: 12/17/2022]
Abstract
The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 2 million fatalities since it first emerged in late 2019. As we write, infection rates are at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary target of SARS-CoV-2 is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predict that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results while finding additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.
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Affiliation(s)
- Amanda D. Melin
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
- Department of Medical GeneticsUniversity of CalgaryAlbertaCanada
- Alberta Children's Hospital Research InstituteUniversity of CalgaryAlbertaCanada
| | - Joseph D. Orkin
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Mareike C. Janiak
- School of Science, Engineering & EnvironmentUniversity of SalfordSalfordUK
| | - Alejandro Valenzuela
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Lukas Kuderna
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Frank Marrone
- Department of ChemistryNew York UniversityNew YorkUSA
| | - Hasinala Ramangason
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
| | - Julie E. Horvath
- Genomics & Microbiology Research LaboratoryNorth Carolina Museum of Natural SciencesRaleighNorth CarolinaUSA
- Department of Biological and Biomedical SciencesNorth Carolina Central UniversityDurhamNorth CarolinaUSA
- Department of Evolutionary AnthropologyDuke UniversityDurhamNorth CarolinaUSA
- Department of Biological SciencesNorth Carolina State UniversityRaleighNorth CarolinaUSA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate CenterLeibniz Institute for Primate ResearchGöettingenGermany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland and School of GeosciencesUniversity of EdinburghEdinburghUK
| | - Chiea Chuen Khor
- Genome Institute of SingaporeAgency for Science, Technology and ResearchSingapore
- Singapore Eye Research InstituteSingapore National Eye CentreSingapore
| | - Weng Khong Lim
- SingHealth Duke‐NUS Institute of Precision MedicineSingapore Health ServicesSingapore
- SingHealth Duke‐NUS Genomic Medicine CentreSingapore Health ServicesSingapore
- Cancer and Stem Cell Biology ProgramDuke‐NUS Medical SchoolSingapore
| | - Jessica G. H. Lee
- Department of Conservation, Research and Veterinary ServicesWildlife Reserves SingaporeSingapore
| | - Patrick Tan
- Genome Institute of SingaporeAgency for Science, Technology and ResearchSingapore
- SingHealth Duke‐NUS Institute of Precision MedicineSingapore Health ServicesSingapore
- Cancer and Stem Cell Biology ProgramDuke‐NUS Medical SchoolSingapore
| | - Govindhaswamy Umapathy
- CSIR‐Laboratory for the Conservation of Endangered SpeciesCentre for Cellular and Molecular BiologyHyderabadIndia
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Ivo Gut
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Marta Gut
- Universitat Pompeu Fabra (UPF)BarcelonaSpain
| | - Esther Lizano
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | - Tilo Nadler
- Cuc Phuong CommuneNho Quan DistrictNinh Binh ProvinceVietnam
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate CenterLeibniz Institute for Primate ResearchGoettingenGermany
- Leibniz Science Campus Primate CognitionGoettingenGermany
- Department of Primate CognitionGeorg‐August‐University, GoettingenGermany
| | - Minh D. Le
- Department of Environmental Ecology, University of Science and Central Institute for Natural Resources and Environmental StudiesVietnam National UniversityHanoiVietnam
| | - Sivakumara Manu
- CSIR‐Laboratory for the Conservation of Endangered SpeciesCentre for Cellular and Molecular BiologyHyderabadIndia
| | - Clément J. Rabarivola
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Alphonse Zaramody
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Nicole Andriaholinirina
- Life Sciences and Environment, Technology and Environment of MahajangaUniversity of MahajangaMahajangaMadagascar
| | - Steig E. Johnson
- Department of Anthropology and ArchaeologyUniversity of CalgaryAlbertaCanada
| | - Erich D. Jarvis
- The Vertebrate Genomes LabThe Rockefeller UniversityNew YorkNew YorkUSA
- Laboratory of Neurogenetics of LanguageThe Rockefeller UniversityNew YorkUnited States
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Olivier Fedrigo
- The Vertebrate Genomes LabThe Rockefeller UniversityNew YorkNew YorkUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
- Kunming Natural History Museum of Zoology, Kunming Institute of ZoologyChinese Academy of SciencesKunmingChina
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
- China National GenebankBGI‐ShenzhenShenzhenChina
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingChina
| | | | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexasUSA
| | - Tomas Marques‐Bonet
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
- Institut Català de Paleontologia Miquel CrusafontUniversitat Autònoma de BarcelonaBarcelonaSpain
| | - Arcadi Navarro
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
- Catalan Institution of Research and Advanced Studies (ICREA)BarcelonaSpain
- CNAG‐CRG, Centre for Genomic Regulation (CRG)Barcelona Institute of Science and Technology (BIST)BarcelonaSpain
| | - David Juan
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia EvolutivaUniversitat Pompeu Fabra‐CSICBarcelonaSpain
| | | | - James P. Higham
- Department of AnthropologyNew York UniversityNew YorkNew YorkUSA
- New York Consortium in Evolutionary PrimatologyNew YorkNew YorkUSA
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23
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Chang J, Zhang C, Cheng H, Tan YW. Rational Design of Adenylate Kinase Thermostability through Coevolution and Sequence Divergence Analysis. Int J Mol Sci 2021; 22:2768. [PMID: 33803409 PMCID: PMC7967156 DOI: 10.3390/ijms22052768] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 01/09/2023] Open
Abstract
Protein engineering is actively pursued in industrial and laboratory settings for high thermostability. Among the many protein engineering methods, rational design by bioinformatics provides theoretical guidance without time-consuming experimental screenings. However, most rational design methods either rely on protein tertiary structure information or have limited accuracies. We proposed a primary-sequence-based algorithm for increasing the heat resistance of a protein while maintaining its functions. Using adenylate kinase (ADK) family as a model system, this method identified a series of amino acid sites closely related to thermostability. Single- and double-point mutants constructed based on this method increase the thermal denaturation temperature of the mesophilic Escherichia coli (E. coli) ADK by 5.5 and 8.3 °C, respectively, while preserving most of the catalytic function at ambient temperatures. Additionally, the constructed mutants have improved enzymatic activity at higher temperature.
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Affiliation(s)
- Jian Chang
- State Key Laboratory of Surface Physics, Multiscale Research Institute of Complex Systems, Department of Physics, Fudan University, Shanghai 200433, China; (J.C.); (H.C.)
| | - Chengxin Zhang
- School of Life Science, Fudan University, Shanghai 200433, China;
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huaqiang Cheng
- State Key Laboratory of Surface Physics, Multiscale Research Institute of Complex Systems, Department of Physics, Fudan University, Shanghai 200433, China; (J.C.); (H.C.)
| | - Yan-Wen Tan
- State Key Laboratory of Surface Physics, Multiscale Research Institute of Complex Systems, Department of Physics, Fudan University, Shanghai 200433, China; (J.C.); (H.C.)
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Melin AD, Orkin JD, Janiak MC, Valenzuela A, Kuderna L, Marrone F, Ramangason H, Horvath JE, Roos C, Kitchener AC, Khor CC, Lim WK, Lee JGH, Tan P, Umapathy G, Raveendran M, Harris RA, Gut I, Gut M, Lizano E, Nadler T, Zinner D, Johnson SE, Jarvis ED, Fedrigo O, Wu D, Zhang G, Farh KKH, Rogers J, Marques-Bonet T, Navarro A, Juan D, Arora PS, Higham JP. Variation in predicted COVID-19 risk among lemurs and lorises. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.02.03.429540. [PMID: 33564767 PMCID: PMC7872355 DOI: 10.1101/2021.02.03.429540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The novel coronavirus SARS-CoV-2, which in humans leads to the disease COVID-19, has caused global disruption and more than 1.5 million fatalities since it first emerged in late 2019. As we write, infection rates are currently at their highest point globally and are rising extremely rapidly in some areas due to more infectious variants. The primary viral target is the cellular receptor angiotensin-converting enzyme-2 (ACE2). Recent sequence analyses of the ACE2 gene predicts that many nonhuman primates are also likely to be highly susceptible to infection. However, the anticipated risk is not equal across the Order. Furthermore, some taxonomic groups show high ACE2 amino acid conservation, while others exhibit high variability at this locus. As an example of the latter, analyses of strepsirrhine primate ACE2 sequences to date indicate large variation among lemurs and lorises compared to other primate clades despite low sampling effort. Here, we report ACE2 gene and protein sequences for 71 individual strepsirrhines, spanning 51 species and 19 genera. Our study reinforces previous results and finds additional variability in other strepsirrhine species, and suggests several clades of lemurs have high potential susceptibility to SARS-CoV-2 infection. Troublingly, some species, including the rare and Endangered aye-aye (Daubentonia madagascariensis), as well as those in the genera Avahi and Propithecus, may be at high risk. Given that lemurs are endemic to Madagascar and among the primates at highest risk of extinction globally, further understanding of the potential threat of COVID-19 to their health should be a conservation priority. All feasible actions should be taken to limit their exposure to SARS-CoV-2.
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Affiliation(s)
- Amanda D. Melin
- Department of Anthropology and Archaeology, University of Calgary, Canada
- Department of Medical Genetics, University of Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
| | - Joseph D. Orkin
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Mareike C. Janiak
- School of Science, Engineering & Environment, University of Salford, United Kingdom
| | - Alejandro Valenzuela
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Lukas Kuderna
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Frank Marrone
- Department of Chemistry, New York University, United States
| | | | - Julie E. Horvath
- Genomics & Microbiology Research Laboratory, North Carolina Museum of Natural Sciences, Raleigh, NC, USA
- Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC, USA
- Department of Evolutionary Anthropology, Duke University, Durham, NC, USA
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Christian Roos
- Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Göettingen, Germany
| | - Andrew C. Kitchener
- Department of Natural Sciences, National Museums Scotland and School of Geosciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- Singapore Eye Research Institute, Singapore National Eye Centre, Singapore
| | - Weng Khong Lim
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
- SingHealth Duke-NUS Genomic Medicine Centre, Singapore Health Services, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Jessica G. H. Lee
- Department of Conservation, Research and Veterinary Services, Wildlife Reserves Singapore, Singapore
| | - Patrick Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore
- SingHealth Duke-NUS Institute of Precision Medicine, Singapore Health Services, Singapore
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
| | - Govindhaswamy Umapathy
- CSIR-Laboratory for the Conservation of Endangered Species, Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Muthuswamy Raveendran
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - R. Alan Harris
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Ivo Gut
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Marta Gut
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Esther Lizano
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | - Tilo Nadler
- Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam
| | - Dietmar Zinner
- Cognitive Ethology Laboratory, German Primate Center, Leibniz Institute for Primate Research, Goettingen, Germany
- Leibniz Science Campus Primate Cognition, Goettingen, Germany
- Department of Primate Cognition, Georg-August-University, Goettingen, Germany
| | - Steig E. Johnson
- Department of Anthropology and Archaeology, University of Calgary, Canada
| | - Erich D. Jarvis
- The Vertebrate Genomes Lab, The Rockefeller University, New York, United States
- Laboratory of Neurogenetics of Language, The Rockefeller University, New York, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Olivier Fedrigo
- The Vertebrate Genomes Lab, The Rockefeller University, New York, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland, United States
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guojie Zhang
- Villum Center for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, Denmark
- China National Genebank, BGI-Shenzhen, Shenzhen, 518083, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | | | - Jeffrey Rogers
- Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States
| | - Tomas Marques-Bonet
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Arcadi Navarro
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - David Juan
- Experimental and Health Sciences Department (DCEXS), Institut de Biologia Evolutiva, Universitat Pompeu Fabra-CSIC, Barcelona, Spain
| | | | - James P. Higham
- Department of Anthropology, New York University, United States
- New York Consortium in Evolutionary Primatology, New York, United States
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25
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Liu Y, He H, Xiao ZX, Ji A, Ye J, Sun Q, Cao Y. A systematic analysis of miRNA markers and classification algorithms for forensic body fluid identification. Brief Bioinform 2020; 22:6032627. [PMID: 33313714 DOI: 10.1093/bib/bbaa324] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/19/2020] [Accepted: 10/20/2020] [Indexed: 12/17/2022] Open
Abstract
Identifying the types of body fluids left at the crime scene can be essential to reconstructing the crime scene and inferring criminal behavior. MicroRNA (miRNA) molecule extracted from the trace of body fluids is one of the most promising biomarkers for the identification due to its high expression, extreme stability and tissue specificity. However, the detection of miRNA markers is not the answer to a yes-no question but the probability of an assumption. Therefore, it is a crucial task to develop complicated methods combining multi-miRNAs as well as computational algorithms to achieve the goal. In this study, we systematically analyzed the expression of 10 most probable body fluid-specific miRNA markers (miR-451a, miR-205-5p, miR-203a-3p, miR-214-3p, miR-144-3p, miR-144-5p, miR-654-5p, miR-888-5p, miR-891a-5p and miR-124-3p) in 605 body fluids-related samples, including peripheral blood, menstrual blood, saliva, semen and vaginal secretion. We introduced the kernel density estimation (KDE) method and six well-established methods to classify the body fluids in order to find the most optimal combinations of miRNA markers as well as the corresponding classifying method. The results show that the combination of miR-451a, miR-891a-5p, miR-144-5p and miR-203a-3p together with KDE can achieve the most accurate and robust performance according to the cross-validation, independent tests and random perturbation tests. This systematic analysis suggests a reference scheme for the identification of body fluids in an accurate and stable manner.
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Affiliation(s)
- Yang Liu
- College of Life Sciences, Sichuan University, China
| | - Hongxia He
- National Engineering Laboratory for Crime Scene Evidence Investigation and Examination, Institute of Forensic Science
| | - Zhi-Xiong Xiao
- College of Life Sciences, Sichuan University, Director of the Center of Growth, Metabolism and Aging
| | - Anquan Ji
- MPS's Key Laboratory of Forensic Genetics, National Engineering Laboratory for Crime Scene Evidence Investigation and Examination
| | - Jian Ye
- People's Public Security University of China
| | - Qifan Sun
- Institute of Biophysics, Chinese Academy of Sciences
| | - Yang Cao
- Institute of Biophysics, Chinese Academy of Sciences
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26
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Grimm M, Liu Y, Yang X, Bu C, Xiao Z, Cao Y. LigMate: A Multifeature Integration Algorithm for Ligand-Similarity-Based Virtual Screening. J Chem Inf Model 2020; 60:6044-6053. [DOI: 10.1021/acs.jcim.9b01210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maximilian Grimm
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yang Liu
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xiaocong Yang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Chunya Bu
- College of Biological Science and Engineering, Beijing University of Agriculture, Beijing 102206, China
| | - Zhixiong Xiao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yang Cao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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27
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Melin AD, Janiak MC, Marrone F, Arora PS, Higham JP. Comparative ACE2 variation and primate COVID-19 risk. Commun Biol 2020; 3:641. [PMID: 33110195 PMCID: PMC7591510 DOI: 10.1038/s42003-020-01370-w] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/08/2020] [Indexed: 12/11/2022] Open
Abstract
The emergence of SARS-CoV-2 has caused over a million human deaths and massive global disruption. The viral infection may also represent a threat to our closest living relatives, nonhuman primates. The contact surface of the host cell receptor, ACE2, displays amino acid residues that are critical for virus recognition, and variations at these critical residues modulate infection susceptibility. Infection studies have shown that some primate species develop COVID-19-like symptoms; however, the susceptibility of most primates is unknown. Here, we show that all apes and African and Asian monkeys (catarrhines), exhibit the same set of twelve key amino acid residues as human ACE2. Monkeys in the Americas, and some tarsiers, lemurs and lorisoids, differ at critical contact residues, and protein modeling predicts that these differences should greatly reduce SARS-CoV-2 binding affinity. Other lemurs are predicted to be closer to catarrhines in their susceptibility. Our study suggests that apes and African and Asian monkeys, and some lemurs, are likely to be highly susceptible to SARS-CoV-2. Urgent actions have been undertaken to limit the exposure of great apes to humans, and similar efforts may be necessary for many other primate species. Amanda Melin et al. compare variation in 29 primate species at 12 amino acid residue sites coded by the ACE2 gene and show that apes and African and Asian monkeys exhibit the same set of twelve key amino acid residues as human ACE2. These results suggest that these primates are likely to be susceptible to SARS-CoV-2, whereas ACE2 gene sequences and protein-protein interaction models suggest reduced susceptibility for platyrrhines, tarsiers, lorisoids, and some lemurs.
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Affiliation(s)
- Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada. .,Department of Medical Genetics, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada. .,Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Dr, NW, Calgary, AB, T2N 4N1, Canada.
| | - Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB, T2N 1N4, Canada.,Alberta Children's Hospital Research Institute, University of Calgary, 3330 Hospital Dr, NW, Calgary, AB, T2N 4N1, Canada
| | - Frank Marrone
- Department of Chemistry, New York University, 100 Washington Square East, 10th Floor, New York, NY, 10003, USA
| | - Paramjit S Arora
- Department of Chemistry, New York University, 100 Washington Square East, 10th Floor, New York, NY, 10003, USA
| | - James P Higham
- Department of Anthropology, New York University, 25 Waverly Place, New York, NY, 10003, USA. .,New York Consortium in Evolutionary Primatology, New York, NY, USA.
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28
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Meseguer A, Dominguez L, Bota PM, Aguirre‐Plans J, Bonet J, Fernandez‐Fuentes N, Oliva B. Using collections of structural models to predict changes of binding affinity caused by mutations in protein-protein interactions. Protein Sci 2020; 29:2112-2130. [PMID: 32797645 PMCID: PMC7513729 DOI: 10.1002/pro.3930] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/24/2022]
Abstract
Protein-protein interactions (PPIs) in all the molecular aspects that take place both inside and outside cells. However, determining experimentally the structure and affinity of PPIs is expensive and time consuming. Therefore, the development of computational tools, as a complement to experimental methods, is fundamental. Here, we present a computational suite: MODPIN, to model and predict the changes of binding affinity of PPIs. In this approach we use homology modeling to derive the structures of PPIs and score them using state-of-the-art scoring functions. We explore the conformational space of PPIs by generating not a single structural model but a collection of structural models with different conformations based on several templates. We apply the approach to predict the changes in free energy upon mutations and splicing variants of large datasets of PPIs to statistically quantify the quality and accuracy of the predictions. As an example, we use MODPIN to study the effect of mutations in the interaction between colicin endonuclease 9 and colicin endonuclease 2 immune protein from Escherichia coli. Finally, we have compared our results with other state-of-art methods.
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Affiliation(s)
- Alberto Meseguer
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health ScienceUniversitat Pompeu FabraBarcelonaCataloniaSpain
| | - Lluis Dominguez
- Integrative Biomedical Informatics Group (GRIB‐IMIM). Department of Experimental and Life SciencesUniversitat Pompeu FabraBarcelonaCataloniaSpain
| | - Patricia M. Bota
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health ScienceUniversitat Pompeu FabraBarcelonaCataloniaSpain
- Department of BiosciencesUniversitat de Vic‐Universitat Central de CatalunyaVicCataloniaSpain
| | - Joaquim Aguirre‐Plans
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health ScienceUniversitat Pompeu FabraBarcelonaCataloniaSpain
| | - Jaume Bonet
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health ScienceUniversitat Pompeu FabraBarcelonaCataloniaSpain
| | - Narcis Fernandez‐Fuentes
- Department of BiosciencesUniversitat de Vic‐Universitat Central de CatalunyaVicCataloniaSpain
- Institute of Biological, Environmental and Rural SciencesAberystwyth UniversityAberystwythUK
| | - Baldo Oliva
- Structural Bioinformatics Group, Research Programme on Biomedical Informatics, Department of Experimental and Health ScienceUniversitat Pompeu FabraBarcelonaCataloniaSpain
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29
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Characterization of the adipogenic protein E4orf1 from adenovirus 36 through an in silico approach. J Mol Model 2020; 26:285. [PMID: 32978703 DOI: 10.1007/s00894-020-04531-0] [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: 08/24/2019] [Accepted: 09/03/2020] [Indexed: 10/23/2022]
Abstract
Adenovirus 36 (Ad-36) is related to human obesity due to its adipogenic activity mediated by the early 4 open reading frame 1 (E4orf1) protein. Mechanisms underlying the adipogenic effect of E4orf1 are not completely understood; however, the proliferation and differentiation of fat cells are increased through the activation of the phosphatidyl inositol 3 kinase pathway by binding proteins containing PDZ domain. This study characterized E4orf1 tridimensional structure and analyzed its interactions with PDZ domain-containing proteins in order to provide new information about the behavior of this viral protein and its targets, which could provide an interesting druggable target for obesity-related cardiometabolic alterations. In silico strategies such as homology modeling, docking, and molecular dynamics (MD) were used to study the interaction of E4orf1 with five PDZ domains of disk large homolog 1 (PDZ-1 and PDZ-2), membrane-associated guanylate kinase 1 (PDZ-3), and multi-PDZ domain protein 1 (PDZ-7 and PDZ-10). Mutagenesis analysis of selected residues was performed to evaluate their effects on the stabilization of E4orf1:PDZ complexes. MD simulations showed that the E4orf1:PDZ10 complex was more stable than the others ones. The highly hydrophobic residues at the C-terminal region (114-125) of the E4orf1 are essential in the initial phase stabilization of the complexes. Moreover, the residues 80-85 in the core region contribute to longer stabilization of the E4orf1:PDZ10 complex, a result that was confirmed by in silico mutagenesis. In conclusion, E4orf1 forms a stable complex with PDZ10 domain, and the residues 80-85 are of particular importance. The characterization of E4orf1 interactions with PDZ domains provides an initial approach to discover druggable targets for Ad-36-induced obesity.
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30
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Huang Q, Wang K, Li H, Yi S, Zhao X. Enhancing cellulosic ethanol production through coevolution of multiple enzymatic characteristics of β-glucosidase from Penicillium oxalicum 16. Appl Microbiol Biotechnol 2020; 104:8299-8308. [PMID: 32857198 DOI: 10.1007/s00253-020-10858-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/04/2020] [Accepted: 08/23/2020] [Indexed: 01/04/2023]
Abstract
In previous studies, we isolated a novel β-glucosidase from Penicillium oxalicum 16 (16BGL), which is useful for producing cellulosic ethanol. However, 16BGL has a relatively low enzyme activity and product tolerance; besides, a huge gap exists between the optimum temperature of 16BGL (70 °C) and the fermentation temperature for producing cellulosic ethanol (40 °C). Here, we present a directed evolution-based study, which combines one-round error-prone PCR with three rounds of high-throughput screening, for coevolving multiple enzymatic characteristics of 16BGL. We identified an improved variant Y-1-B1 with a triple mutant (G414S/D421V/T441S). Y-1-B1 had an optimum temperature of 50 °C, much closer to the fermentation temperature. The catalytic efficiency of Y-1-B1 for hydrolyzing pNPG was 1355 mM-1 s-1 at 50 °C and pH 5, significantly higher than that of 16BGL (807 mM-1 s-1). Y-1-B1 also achieved a slightly reduced strength of product inhibition of 1.1 at a glucose concentration of 20 mM, compared with the ratio of 1.3 for 16BGL. A maximum titer of 6.9 g/L for ethanol production was achieved in the reaction with Y-1-B1, which was 22% higher than that achieved with 16BGL. Structure modeling revealed that the mutations are distant from the active-site pocket. Therefore, we performed molecular dynamics (MD) simulations to understand why these mutations can improve catalytic efficiency. MD simulation revealed that the nucleophilic residue Asp261 had a much closer contact with the glucosidic center of pNPG in the simulation with Y-1-B1 than that with 16BGL, suggesting that the mutant is more favorable for catalysis. KEY POINTS: • Multiple enzymatic properties of Penicillium oxalicum 16 BGL were coevolved. • A catalytically efficient triple mutant G414S/D421V/T441S was reported. • Molecular dynamics simulation supported the enhanced catalytic activity.
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Affiliation(s)
- Qiuxia Huang
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Kexin Wang
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Hanxin Li
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Shi Yi
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China
| | - Xihua Zhao
- College of Life Science, Jiangxi Normal University, Nanchang, 330022, China.
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31
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Melin AD, Janiak MC, Marrone F, Arora PS, Higham JP. Comparative ACE2 variation and primate COVID-19 risk. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.09.034967. [PMID: 32511330 PMCID: PMC7239060 DOI: 10.1101/2020.04.09.034967] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The emergence of the novel coronavirus SARS-CoV-2, which in humans is highly infectious and leads to the potentially fatal disease COVID-19, has caused hundreds of thousands of deaths and huge global disruption. The viral infection may also represent an existential threat to our closest living relatives, the nonhuman primates, many of which are endangered and often reduced to small populations. The virus engages the host cell receptor, angiotensin-converting enzyme-2 (ACE2), through the receptor binding domain (RBD) on the spike protein. The contact surface of ACE2 displays amino acid residues that are critical for virus recognition, and variations at these critical residues are likely to modulate infection susceptibility across species. While infection studies are emerging and have shown that some primates, such as rhesus macaques and vervet monkeys, develop COVID-19-like symptoms when exposed to the virus, the susceptibility of many other nonhuman primates is unknown. Here, we show that all apes, including chimpanzees, bonobos, gorillas, and orangutans, and all African and Asian monkeys (catarrhines), exhibit the same set of twelve key amino acid residues as human ACE2. Monkeys in the Americas, and some tarsiers, lemurs and lorisoids, differ at significant contact residues, and protein modeling predicts that these differences should greatly reduce the binding affinity of the ACE2 for the virus, hence moderating their susceptibility for infection. Other lemurs are predicted to be closer to catarrhines in their susceptibility. Our study suggests that apes and African and Asian monkeys, as well as some lemurs are all likely to be highly susceptible to SARS-CoV-2, representing a critical threat to their survival. Urgent actions have been undertaken to limit the exposure of Great Apes to humans, and similar efforts may be necessary for many other primate species.
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Affiliation(s)
- Amanda D Melin
- Department of Anthropology and Archaeology, University of Calgary, CA
- Department of Medical Genetics, University of Calgary, CA
- Alberta Children's Hospital Research Institute, University of Calgary, CA
| | - Mareike C Janiak
- Department of Anthropology and Archaeology, University of Calgary, CA
- Alberta Children's Hospital Research Institute, University of Calgary, CA
| | | | | | - James P Higham
- Department of Anthropology, New York University, US
- New York Consortium in Evolutionary Primatology, New York, US
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32
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Schmitt CA, Bergey CM, Jasinska AJ, Ramensky V, Burt F, Svardal H, Jorgensen MJ, Freimer NB, Grobler JP, Turner TR. ACE2 and TMPRSS2 variation in savanna monkeys (Chlorocebus spp.): Potential risk for zoonotic/anthroponotic transmission of SARS-CoV-2 and a potential model for functional studies. PLoS One 2020; 15:e0235106. [PMID: 32574196 PMCID: PMC7310727 DOI: 10.1371/journal.pone.0235106] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 06/08/2020] [Indexed: 01/04/2023] Open
Abstract
The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has devastated health infrastructure around the world. Both ACE2 (an entry receptor) and TMPRSS2 (used by the virus for spike protein priming) are key proteins to SARS-CoV-2 cell entry, enabling progression to COVID-19 in humans. Comparative genomic research into critical ACE2 binding sites, associated with the spike receptor binding domain, has suggested that African and Asian primates may also be susceptible to disease from SARS-CoV-2 infection. Savanna monkeys (Chlorocebus spp.) are a widespread non-human primate with well-established potential as a bi-directional zoonotic/anthroponotic agent due to high levels of human interaction throughout their range in sub-Saharan Africa and the Caribbean. To characterize potential functional variation in savanna monkey ACE2 and TMPRSS2, we inspected recently published genomic data from 245 savanna monkeys, including 163 wild monkeys from Africa and the Caribbean and 82 captive monkeys from the Vervet Research Colony (VRC). We found several missense variants. One missense variant in ACE2 (X:14,077,550; Asp30Gly), common in Ch. sabaeus, causes a change in amino acid residue that has been inferred to reduce binding efficiency of SARS-CoV-2, suggesting potentially reduced susceptibility. The remaining populations appear as susceptible as humans, based on these criteria for receptor usage. All missense variants observed in wild Ch. sabaeus populations are also present in the VRC, along with two splice acceptor variants (at X:14,065,076) not observed in the wild sample that are potentially disruptive to ACE2 function. The presence of these variants in the VRC suggests a promising model for SARS-CoV-2 infection and vaccine and therapy development. In keeping with a One Health approach, characterizing actual susceptibility and potential for bi-directional zoonotic/anthroponotic transfer in savanna monkey populations may be an important consideration for controlling COVID-19 epidemics in communities with frequent human/non-human primate interactions that, in many cases, may have limited health infrastructure.
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Affiliation(s)
- Christopher A. Schmitt
- Department of Anthropology, Boston University, Boston, Massachusetts, United States of America
| | - Christina M. Bergey
- Department of Genetics, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Anna J. Jasinska
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior,University of California—Los Angeles, Los Angeles, California, United States of America
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
- Eye on Primates, Los Angeles, California, United States of America
| | - Vasily Ramensky
- Federal State Institution “National Medical Research Center for Therapy and Preventive Medicine” of the Ministry of Healthcare of the Russian Federation, Moscow, Russia
| | - Felicity Burt
- Division of Medical Virology, National Health Laboratory Service, Bloemfontein, Free State, South Africa
- Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, Free State, South Africa
| | - Hannes Svardal
- Department of Biology, University of Antwerp, Antwerp, Belgium
- Naturalis Biodiversity Center, Leiden, The Netherlands
| | - Matthew J. Jorgensen
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Nelson B. Freimer
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior,University of California—Los Angeles, Los Angeles, California, United States of America
| | - J. Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, Free State, South Africa
| | - Trudy R. Turner
- Department of Genetics, University of the Free State, Bloemfontein, Free State, South Africa
- Department of Anthropology, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin, United States of America
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Huang X, Pearce R, Zhang Y. De novo design of protein peptides to block association of the SARS-CoV-2 spike protein with human ACE2. Aging (Albany NY) 2020; 12:11263-11276. [PMID: 32544884 PMCID: PMC7343451 DOI: 10.18632/aging.103416] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Accepted: 05/25/2020] [Indexed: 12/15/2022]
Abstract
The outbreak of COVID-19 has now become a global pandemic that has severely impacted lives and economic stability. There is, however, no effective antiviral drug that can be used to treat COVID-19 to date. Built on the fact that SARS-CoV-2 initiates its entry into human cells by the receptor binding domain (RBD) of its spike protein binding to the angiotensin-converting enzyme 2 (hACE2), we extended a recently developed approach, EvoDesign, to design multiple peptide sequences that can competitively bind to the SARS-CoV-2 RBD to inhibit the virus from entering human cells. The protocol starts with the construction of a hybrid peptidic scaffold by linking two fragments grafted from the interface of the hACE2 protein (a.a. 22-44 and 351-357) with a linker glycine, which is followed by the redesign and refinement simulations of the peptide sequence to optimize its binding affinity to the interface of the SARS-CoV-2 RBD. The binding experiment analyses showed that the designed peptides exhibited a significantly stronger binding potency to hACE2 than the wild-type hACE2 receptor (with -53.35 vs. -46.46 EvoEF2 energy unit scores for the top designed and wild-type peptides, respectively). This study demonstrates a new avenue to utilize computationally designed peptide motifs to treat the COVID-19 disease by blocking the critical spike-RBD and hACE2 interactions.
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Affiliation(s)
- Xiaoqiang Huang
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI 48109, USA
| | - Robin Pearce
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI 48109, USA
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, Ann Arbor, MI 48109, USA.,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
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