801
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Kumar A, Chan J, Taguchi M, Kono H. Interplay among transacting factors around promoter in the initial phases of transcription. Curr Opin Struct Biol 2021; 71:7-15. [PMID: 34111671 DOI: 10.1016/j.sbi.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/20/2021] [Accepted: 04/27/2021] [Indexed: 10/21/2022]
Abstract
The initiation signals are raised around the promoter by one of the general transcription factors, triggering a sequence of events that lead to mRNA transcript formation from target genes. Both specific noncoding DNA regions and transacting, macromolecular assemblies are intricately involved and indispensable. The transition between the subsequent transcriptional stages is accompanied by stage-specific signals and structural changes in the macromolecular assemblies and facilitated by the recruitment/removal of other chromatin and transcription-associated elements. Here, we discuss the choreography of transacting factors around promoter in the establishment and effectuation of the initial phases of transcription such as NDR formation, +1 nucleosome positioning, promoter DNA opening, and RNAPII promoter escape from a structural viewpoint.
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Affiliation(s)
- Amarjeet Kumar
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Justin Chan
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Masahiko Taguchi
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto, 619-0215, Japan.
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802
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Raghav PK, Gangenahalli G. PU.1 Mimic Synthetic Peptides Selectively Bind with GATA-1 and Allow c-Jun PU.1 Binding to Enhance Myelopoiesis. Int J Nanomedicine 2021; 16:3833-3859. [PMID: 34113102 PMCID: PMC8187006 DOI: 10.2147/ijn.s303235] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Hematopoietic stem cells' commitment to myelopoiesis builds immunity to prevent infection. This process is controlled through transcription factor, especially Purine rich box 1 (PU.1) protein, which plays a central role in regulating myelopoiesis. The β3/β4 region of PU.1 accommodates a coactivator transcription factor, c-Jun, to activate myelopoiesis. However, an erythroid transcription factor, GATA-1, competes with c-Jun for the β3/β4 region, abolishing myelopoiesis and promoting erythropoiesis. This competitive regulation decides the hematopoietic stem cells' commitment towards either erythroid or myeloid lineage. METHODS Therefore, this study investigated the in vitro and in vivo effect of novel synthetic PU.1 β3/β4 mimic peptide analogs and peptide-loaded hydrophilic poly(D,L-lactide-co-glycolide) (PLGA) nanoparticles. RESULTS The designed peptides significantly increase the expression of corresponding myeloid markers, specifically CD33 in vitro. However, the in vivo delivery of peptide-loaded PLGA nanoparticles, which have sustained release effect of peptides, increases 10.8% of granulocytes as compared to control. CONCLUSION The observations showed that the fabricated nanoparticles protected the loaded peptides from the harsh intracellular environment for a longer duration without causing any toxicity. These findings highlight the possibility to use these peptides and peptide-loaded nanoparticles to increase hematopoietic stem cell commitment to myeloid cells in case of opportunistic infection.
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Affiliation(s)
- Pawan Kumar Raghav
- Division of Stem Cell and Gene Therapy Research, Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi, 110054, India
| | - Gurudutta Gangenahalli
- Division of Stem Cell and Gene Therapy Research, Institute of Nuclear Medicine and Allied Sciences (INMAS), Delhi, 110054, India
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803
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Burley SK, Berman HM. Open-access data: A cornerstone for artificial intelligence approaches to protein structure prediction. Structure 2021; 29:515-520. [PMID: 33984281 PMCID: PMC8178243 DOI: 10.1016/j.str.2021.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/08/2021] [Accepted: 04/23/2021] [Indexed: 12/28/2022]
Abstract
The Protein Data Bank (PDB) was established in 1971 to archive three-dimensional (3D) structures of biological macromolecules as a public good. Fifty years later, the PDB is providing millions of data consumers around the world with open access to more than 175,000 experimentally determined structures of proteins and nucleic acids (DNA, RNA) and their complexes with one another and small-molecule ligands. PDB data users are working, teaching, and learning in fundamental biology, biomedicine, bioengineering, biotechnology, and energy sciences. They also represent the fields of agriculture, chemistry, physics and materials science, mathematics, statistics, computer science, and zoology, and even the social sciences. The enormous wealth of 3D structure data stored in the PDB has underpinned significant advances in our understanding of protein architecture, culminating in recent breakthroughs in protein structure prediction accelerated by artificial intelligence approaches and deep or machine learning methods.
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Affiliation(s)
- Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Rutgers Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08903, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, CA 92093, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Helen M Berman
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA; The Bridge Institute, Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA.
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804
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Hu XL, Lu H, Hassan MM, Zhang J, Yuan G, Abraham PE, Shrestha HK, Villalobos Solis MI, Chen JG, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Cheng ZMM, Yang X. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. HORTICULTURE RESEARCH 2021; 8:130. [PMID: 34059650 PMCID: PMC8167165 DOI: 10.1038/s41438-021-00570-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 04/26/2021] [Indexed: 05/02/2023]
Abstract
Small secreted proteins (SSPs) are less than 250 amino acids in length and are actively transported out of cells through conventional protein secretion pathways or unconventional protein secretion pathways. In plants, SSPs have been found to play important roles in various processes, including plant growth and development, plant response to abiotic and biotic stresses, and beneficial plant-microbe interactions. Over the past 10 years, substantial progress has been made in the identification and functional characterization of SSPs in several plant species relevant to agriculture, bioenergy, and horticulture. Yet, there are potentially a lot of SSPs that have not been discovered in plant genomes, which is largely due to limitations of existing computational algorithms. Recent advances in genomics, transcriptomics, and proteomics research, as well as the development of new computational algorithms based on machine learning, provide unprecedented capabilities for genome-wide discovery of novel SSPs in plants. In this review, we summarize known SSPs and their functions in various plant species. Then we provide an update on the computational and experimental approaches that can be used to discover new SSPs. Finally, we discuss strategies for elucidating the biological functions of SSPs in plants.
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Affiliation(s)
- Xiao-Li Hu
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jin Zhang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Paul E Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Him K Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Genome Science and Technology, University of Tennessee, Knoxville, TN, USA
| | | | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Gerald A Tuskan
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Zong-Ming Max Cheng
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China.
| | - Xiaohan Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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805
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Güngör T, Ozleyen A, Yılmaz YB, Siyah P, Ay M, Durdağı S, Tumer TB. New nimesulide derivatives with amide/sulfonamide moieties: Selective COX-2 inhibition and antitumor effects. Eur J Med Chem 2021; 221:113566. [PMID: 34077833 DOI: 10.1016/j.ejmech.2021.113566] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/15/2021] [Accepted: 05/18/2021] [Indexed: 12/16/2022]
Abstract
Seventeen new amide/sulfonamide containing nimesulide derivatives were synthesized and characterized by several spectroscopic techniques and primarily investigated for their inhibitory potential on COX enzymes and other pro-inflammatory factors. Experimental analyses showed that among seventeen compounds, N8 and N10 have remarkable potency and selectivity for the COX-2 enzyme over COX-1 at very low doses as compared to nimesulide. Moreover, both N8 and N10 selectively reduced the Lipopolysaccharide (LPS)-stimulated COX-2 mRNA expression level while the COX-1 level remained stable. Both PGE2 release and nitric oxide production in macrophage cells were significantly suppressed by the N8 and N10 treatment groups. In silico ADME/Tox, molecular docking and molecular dynamics (MD) simulations were also conducted. Additionally, all compounds were also screened in a panel of cancer cell lines for their antiproliferative properties by MTT and SRB assays. Compound N17 exhibited a considerable antiproliferative effect on the colon (IC50: 9.24 μM) and breast (IC50: 11.35 μM) cancer cell lines. N17 exposure for 48 h decreased expression of anti-apoptotic protein BCL-2 and increased the expression of apoptogenic BAX. Besides, the BAX/BCL-2 ratio was increased with visible ultrastructural changes and apoptotic bodies under scanning electron microscopy. In order to investigate the structural and dynamical properties of selected hits on the target structures, multiscale molecular modeling studies are also conducted. Our combined in silico and in vitro results suggest that N8 and N10 could be further developed as potential nonsteroidal anti-inflammatory drugs (NSAIDs), while cytotoxic N17 might be studied as a potential lead compound that could be developed as an anticancer agent.
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Affiliation(s)
- Tuğba Güngör
- Department of Chemistry, Faculty of Sciences and Arts, Natural Products and Drug Research Laboratory, Çanakkale Onsekiz Mart University, Çanakkale, 17020, Turkey.
| | - Adem Ozleyen
- Graduate Program of Biomolecular Sciences, School of Graduate Studies, Canakkale Onsekiz Mart University, 17020, Çanakkale, Turkey; School of Chemistry, University of Leicester, LE1 7RH, Leicester, United Kingdom
| | - Yakup Berkay Yılmaz
- Graduate Program of Biomolecular Sciences, School of Graduate Studies, Canakkale Onsekiz Mart University, 17020, Çanakkale, Turkey; Department of Molecular Biology and Genetics, Faculty of Arts and Science, Çanakkale Onsekiz Mart University, 17020, Çanakkale, Turkey
| | - Pinar Siyah
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34353, Istanbul, Turkey
| | - Mehmet Ay
- Department of Chemistry, Faculty of Sciences and Arts, Natural Products and Drug Research Laboratory, Çanakkale Onsekiz Mart University, Çanakkale, 17020, Turkey
| | - Serdar Durdağı
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahçeşehir University, 34353, Istanbul, Turkey
| | - Tugba Boyunegmez Tumer
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Çanakkale Onsekiz Mart University, 17020, Çanakkale, Turkey.
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806
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Liu B, Jiang F, Sun J, Wang F, Liu K. Biomacromolecule-based photo-thermal agents for tumor treatment. J Mater Chem B 2021; 9:7007-7022. [PMID: 34023868 DOI: 10.1039/d1tb00725d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cancer treatment has become one of the biggest challenges in modern medicine. Recently, many efforts have been devoted to treat tumors by surgical resection, radiotherapy, or chemotherapy. In comparison to these methods, photo-thermal therapy (PTT) with noninvasive, controllable, direct, and precise characteristics has received tremendous attention in eliminating tumor cells over the past decades. In particular, PTT based on biomacromolecule-based photo-thermal agents (PTAs) outperforms other systems with high photo-thermal efficiency, simple coating, and low immunogenicity. Considering the unique advantages of biomacromolecule-based PTAs in tumor treatment, it is necessary to summarize the recent progress in the field of biomacromolecule-based PTAs for tumor treatment. Herein, this minireview outlines recent progress in the fabrication and applications of biomacromolecule-based PTAs. Within this framework, various types of biomacromolecule-based PTAs are highlighted, including cell-based agents, protein-based agents, nucleotide-based agents, and polysaccharide-based PTAs. In each section, the functional design, photo-thermal effects, and potential clinical applications of each type of PTA are discussed. Finally, a brief perspective for the development of biomacromolecule-based PTAs is presented.
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Affiliation(s)
- Bin Liu
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun 130033, China and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Fuquan Jiang
- Department of Urology, China-Japan Union Hospital of Jilin University, Changchun 130033, China
| | - Jing Sun
- Institute of Organic Chemistry, University of Ulm, Albert-Einstein-Allee 11, 89081, Ulm, Germany
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China and Department of Chemistry, Tsinghua University, Beijing 100084, China
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807
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Han Y, Wang Z, Wei Z, Liu J, Li J. Machine learning builds full-QM precision protein force fields in seconds. Brief Bioinform 2021; 22:6279287. [PMID: 34017993 DOI: 10.1093/bib/bbab158] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/29/2021] [Accepted: 04/04/2021] [Indexed: 11/14/2022] Open
Abstract
Full-quantum mechanics (QM) calculations are extraordinarily precise but difficult to apply to large systems, such as biomolecules. Motivated by the massive demand for efficient calculations for large systems at the full-QM level and by the significant advances in machine learning, we have designed a neural network-based two-body molecular fractionation with conjugate caps (NN-TMFCC) approach to accelerate the energy and atomic force calculations of proteins. The results show very high precision for the proposed NN potential energy surface models of residue-based fragments, with energy root-mean-squared errors (RMSEs) less than 1.0 kcal/mol and force RMSEs less than 1.3 kcal/mol/Å for both training and testing sets. The proposed NN-TMFCC method calculates the energies and atomic forces of 15 representative proteins with full-QM precision in 10-100 s, which is thousands of times faster than the full-QM calculations. The computational complexity of the NN-TMFCC method is independent of the protein size and only depends on the number of residue species, which makes this method particularly suitable for rapid prediction of large systems with tens of thousands or even hundreds of thousands of times acceleration. This highly precise and efficient NN-TMFCC approach exhibits considerable potential for performing energy and force calculations, structure predictions and molecular dynamics simulations of proteins with full-QM precision.
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Affiliation(s)
| | | | - Zhiyun Wei
- Shanghai First Maternity and Infant Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jinyun Liu
- Key Laboratory of Functional Molecular Solids of Ministry of Education, Anhui Normal University, China
| | - Jinjin Li
- Key Laboratory for Thin Film and Microfabrication of Ministry of Education, Department of Micro/Nano Electronics, Shanghai Jiao Tong University, China
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808
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Visual pH Sensors: From a Chemical Perspective to New Bioengineered Materials. Molecules 2021; 26:molecules26102952. [PMID: 34065629 PMCID: PMC8156760 DOI: 10.3390/molecules26102952] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 05/11/2021] [Accepted: 05/14/2021] [Indexed: 02/05/2023] Open
Abstract
Many human activities and cellular functions depend upon precise pH values, and pH monitoring is considered a fundamental task. Colorimetric and fluorescence sensors for pH measurements are chemical and biochemical tools able to sense protons and produce a visible signal. These pH sensors are gaining widespread attention as non-destructive tools, visible to the human eye, that are capable of a real-time and in-situ response. Optical “visual” sensors are expanding researchers’ interests in many chemical contexts and are routinely used for biological, environmental, and medical applications. In this review we provide an overview of trending colorimetric, fluorescent, or dual-mode responsive visual pH sensors. These sensors include molecular synthetic organic sensors, metal organic frameworks (MOF), engineered sensing nanomaterials, and bioengineered sensors. We review different typological chemical entities of visual pH sensors, three-dimensional structures, and signaling mechanisms for pH sensing and applications; developed in the past five years. The progression of this review from simple organic molecules to biological macromolecules seeks to benefit beginners and scientists embarking on a project of pH sensing development, who needs background information and a quick update on advances in the field. Lessons learned from these tools will aid pH determination projects and provide new ways of thinking for cell bioimaging or other cutting-edge in vivo applications.
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809
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Wu Z, Wang Q, Yang H, Wang J, Li W, Liu G, Yang Y, Zhao Y, Tang Y. Discovery of Natural Products Targeting NQO1 via an Approach Combining Network-Based Inference and Identification of Privileged Substructures. J Chem Inf Model 2021; 61:2486-2498. [PMID: 33955748 DOI: 10.1021/acs.jcim.1c00260] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
NAD(P)H:quinone oxidoreductase 1 (NQO1) has been shown to be a potential therapeutic target for various human diseases, such as cancer and neurodegenerative disorders. Recent advances in computational methods, especially network-based methods, have made it possible to identify novel compounds for a target with high efficiency and low cost. In this study, we designed a workflow combining network-based methods and identification of privileged substructures to discover new compounds targeting NQO1 from a natural product library. According to the prediction results, we purchased 56 compounds for experimental validation. Without the assistance of privileged substructures, 31 compounds (31/56 = 55.4%) showed IC50 < 100 μM, and 11 compounds (11/56 = 19.6%) showed IC50 < 10 μM. With the assistance of privileged substructures, the two success rates were increased to 61.8 and 26.5%, respectively. Seven natural products further showed inhibitory activity on NQO1 at the cellular level, which may serve as lead compounds for further development. Moreover, network analysis revealed that osthole may exert anticancer effects against multiple cancer types by inhibiting not only carbonic anhydrases IX and XII but also NQO1. Our workflow and computational methods can be easily applied in other targets and become useful tools in drug discovery and development.
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Affiliation(s)
- Zengrui Wu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Qiaohui Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.,Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Hongbin Yang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiye Wang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yi Yang
- Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.,CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuzheng Zhao
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.,Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Center for Biomanufacturing Technology, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Yun Tang
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
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810
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Lynch ML, Snell EH, Bowman SEJ. Structural biology in the time of COVID-19: perspectives on methods and milestones. IUCRJ 2021; 8:335-341. [PMID: 33953920 PMCID: PMC8086156 DOI: 10.1107/s2052252521003948] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
The global COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has wreaked unprecedented havoc on global society, in terms of a huge loss of life and burden of morbidity, economic upheaval and social disruption. Yet the sheer magnitude and uniqueness of this event has also spawned a massive mobilization of effort in the scientific community to investigate the virus, to develop therapeutics and vaccines, and to understand the public health impacts. Structural biology has been at the center of these efforts, and so it is advantageous to take an opportunity to reflect on the status of structural science vis-à-vis its role in the fight against COVID-19, to register the unprecedented response and to contemplate the role of structural biology in addressing future outbreak threats. As the one-year anniversary of the World Health Organization declaration that COVID-19 is a pandemic has just passed, over 1000 structures of SARS-CoV-2 biomolecules have been deposited in the Worldwide Protein Data Bank (PDB). It is rare to obtain a snapshot of such intense effort in the structural biology arena and is of special interest as the 50th anniversary of the PDB is celebrated in 2021. It is additionally timely as it overlaps with a period that has been termed the 'resolution revolution' in cryoelectron microscopy (CryoEM). CryoEM has recently become capable of producing biomolecular structures at similar resolutions to those traditionally associated with macromolecular X-ray crystallo-graphy. Examining SARS-CoV-2 protein structures that have been deposited in the PDB since the virus was first identified allows a unique window into the power of structural biology and a snapshot of the advantages of the different techniques available, as well as insight into the complementarity of the structural methods.
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Affiliation(s)
- Miranda L. Lynch
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Edward H. Snell
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Department of Materials Design and Innovation, The State University of New York at Buffalo, Buffalo, NY 14203, USA
| | - Sarah E. J. Bowman
- Hauptman–Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, NY 14203, USA
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences at The State University of New York at Buffalo, Buffalo, NY 14023, USA
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811
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Kimber TB, Chen Y, Volkamer A. Deep Learning in Virtual Screening: Recent Applications and Developments. Int J Mol Sci 2021; 22:4435. [PMID: 33922714 PMCID: PMC8123040 DOI: 10.3390/ijms22094435] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 01/03/2023] Open
Abstract
Drug discovery is a cost and time-intensive process that is often assisted by computational methods, such as virtual screening, to speed up and guide the design of new compounds. For many years, machine learning methods have been successfully applied in the context of computer-aided drug discovery. Recently, thanks to the rise of novel technologies as well as the increasing amount of available chemical and bioactivity data, deep learning has gained a tremendous impact in rational active compound discovery. Herein, recent applications and developments of machine learning, with a focus on deep learning, in virtual screening for active compound design are reviewed. This includes introducing different compound and protein encodings, deep learning techniques as well as frequently used bioactivity and benchmark data sets for model training and testing. Finally, the present state-of-the-art, including the current challenges and emerging problems, are examined and discussed.
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Affiliation(s)
| | | | - Andrea Volkamer
- In Silico Toxicology and Structural Bioinformatics, Institute of Physiology, Charité-Universitätsmedizin Berlin, Charitéplatz 1, 10117 Berlin, Germany; (T.B.K.); (Y.C.)
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812
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PyPLIF HIPPOS-Assisted Prediction of Molecular Determinants of Ligand Binding to Receptors. Molecules 2021; 26:molecules26092452. [PMID: 33922338 PMCID: PMC8122758 DOI: 10.3390/molecules26092452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/03/2023] Open
Abstract
Identification of molecular determinants of receptor-ligand binding could significantly increase the quality of structure-based virtual screening protocols. In turn, drug design process, especially the fragment-based approaches, could benefit from the knowledge. Retrospective virtual screening campaigns by employing AutoDock Vina followed by protein-ligand interaction fingerprinting (PLIF) identification by using recently published PyPLIF HIPPOS were the main techniques used here. The ligands and decoys datasets from the enhanced version of the database of useful decoys (DUDE) targeting human G protein-coupled receptors (GPCRs) were employed in this research since the mutation data are available and could be used to retrospectively verify the prediction. The results show that the method presented in this article could pinpoint some retrospectively verified molecular determinants. The method is therefore suggested to be employed as a routine in drug design and discovery.
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813
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Yu B, Iwahara J. Experimental approaches for investigating ion atmospheres around nucleic acids and proteins. Comput Struct Biotechnol J 2021; 19:2279-2285. [PMID: 33995919 PMCID: PMC8102144 DOI: 10.1016/j.csbj.2021.04.033] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/14/2021] [Accepted: 04/14/2021] [Indexed: 01/26/2023] Open
Abstract
Ionic interactions are crucial to biological functions of DNA, RNA, and proteins. Experimental research on how ions behave around biological macromolecules has lagged behind corresponding theoretical and computational research. In the 21st century, quantitative experimental approaches for investigating ionic interactions of biomolecules have become available and greatly facilitated examinations of theoretical electrostatic models. These approaches utilize anomalous small-angle X-ray scattering, atomic emission spectroscopy, mass spectrometry, or nuclear magnetic resonance (NMR) spectroscopy. We provide an overview on the experimental methodologies that can quantify and characterize ions within the ion atmospheres around nucleic acids, proteins, and their complexes.
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Affiliation(s)
- Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
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814
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Shen L, Bai J, Wang J, Shen B. The fourth scientific discovery paradigm for precision medicine and healthcare: Challenges ahead. PRECISION CLINICAL MEDICINE 2021; 4:80-84. [PMID: 35694156 PMCID: PMC8982559 DOI: 10.1093/pcmedi/pbab007] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 04/13/2021] [Accepted: 04/13/2021] [Indexed: 02/05/2023] Open
Abstract
With the progression of modern information techniques, such as next generation sequencing (NGS), Internet of Everything (IoE) based smart sensors, and artificial intelligence algorithms, data-intensive research and applications are emerging as the fourth paradigm for scientific discovery. However, we face many challenges to practical application of this paradigm. In this article, 10 challenges to data-intensive discovery and applications in precision medicine and healthcare are summarized and the future perspectives on next generation medicine are discussed.
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Affiliation(s)
- Li Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jinwei Bai
- Library of West-China Hospital, Sichuan University, Chengdu 610041, China
| | - Jiao Wang
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Bairong Shen
- Institutes for Systems Genetics, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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815
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Oh SJ. Computational evaluation of interactions between olfactory receptor OR2W1 and its ligands. Genomics Inform 2021; 19:e9. [PMID: 33840173 PMCID: PMC8042298 DOI: 10.5808/gi.21026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 11/20/2022] Open
Abstract
Mammalian olfactory receptors are a family of G protein‒coupled receptors (GPCRs) that occupy a large part of the genome. In human genes, olfactory receptors account for more than 40% of all GPCRs. Several types of GPCR structures have been identified, but there is no single olfactory receptor whose structure has been determined experimentally to date. The aim of this study was to model the interactions between an olfactory receptor and its ligands at the molecular level to provide hints on the binding modes between the OR2W1 olfactory receptor and its agonists and inverse agonists. The results demonstrated the modes of ligand binding in a three-dimensional model of OR2W1 and showed a statistically significant difference in binding affinity to the olfactory receptor between agonists and inverse agonists.
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Affiliation(s)
- S June Oh
- Department of Pharmacology, Inje University College of Medicine, Busan 47392, Korea
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816
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Ho TYH, Shao A, Lu Z, Savilahti H, Menolascina F, Wang L, Dalchau N, Wang B. A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction. Nat Commun 2021; 12:2200. [PMID: 33850130 PMCID: PMC8044194 DOI: 10.1038/s41467-021-22404-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/12/2021] [Indexed: 12/31/2022] Open
Abstract
Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augment a mini-Mu transposon-based screening approach and devise the intein-assisted bisection mapping (IBM) method. IBM robustly reveals clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further show that the use of inteins expands functional sequence space for splitting a protein. We also demonstrate the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins, and that basal activities of highly active proteins can be mitigated by splitting them. Our work offers a generalizable and systematic route towards creating split protein-intein fusions for synthetic biology.
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Affiliation(s)
- Trevor Y H Ho
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Hangzhou Innovation Centre, Zhejiang University, Hangzhou, China.,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Alexander Shao
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Microsoft Research, Cambridge, UK
| | - Zeyu Lu
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Filippo Menolascina
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, UK
| | - Lei Wang
- School of Engineering, Westlake University, Hangzhou, China
| | | | - Baojun Wang
- Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh, Edinburgh, UK. .,Hangzhou Innovation Centre, Zhejiang University, Hangzhou, China. .,College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China. .,ZJU-UoE Joint Research Centre for Engineering Biology, Zhejiang University, Haining, China.
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817
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Network Pharmacology and Molecular Docking Suggest the Mechanism for Biological Activity of Rosmarinic Acid. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2021; 2021:5190808. [PMID: 33936238 PMCID: PMC8055417 DOI: 10.1155/2021/5190808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 02/24/2021] [Accepted: 03/30/2021] [Indexed: 12/31/2022]
Abstract
Rosmarinic acid (RosA) is a natural phenolic acid compound, which is mainly extracted from Labiatae and Arnebia. At present, there is no systematic analysis of its mechanism. Therefore, we used the method of network pharmacology to analyze the mechanism of RosA. In our study, PubChem database was used to search for the chemical formula and the Chemical Abstracts Service (CAS) number of RosA. Then, the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform (TCMSP) was used to evaluate the pharmacodynamics of RosA, and the Comparative Toxicogenomics Database (CTD) was used to identify the potential target genes of RosA. In addition, the Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of target genes were carried out by using the web-based gene set analysis toolkit (WebGestalt). At the same time, we uploaded the targets to the STRING database to obtain the protein interaction network. Then, we carried out a molecular docking about targets and RosA. Finally, we used Cytoscape to establish a visual protein-protein interaction network and drug-target-pathway network and analyze these networks. Our data showed that RosA has good biological activity and drug utilization. There are 55 target genes that have been identified. Then, the bioinformatics analysis and network analysis found that these target genes are closely related to inflammatory response, tumor occurrence and development, and other biological processes. These results demonstrated that RosA can act on a variety of proteins and pathways to form a systematic pharmacological network, which has good value in drug development and utilization.
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818
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Schoeder C, Schmitz S, Adolf-Bryfogle J, Sevy AM, Finn JA, Sauer MF, Bozhanova NG, Mueller BK, Sangha AK, Bonet J, Sheehan JH, Kuenze G, Marlow B, Smith ST, Woods H, Bender BJ, Martina CE, del Alamo D, Kodali P, Gulsevin A, Schief WR, Correia BE, Crowe JE, Meiler J, Moretti R. Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design. Biochemistry 2021; 60:825-846. [PMID: 33705117 PMCID: PMC7992133 DOI: 10.1021/acs.biochem.0c00912] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/02/2021] [Indexed: 01/16/2023]
Abstract
Structure-based antibody and antigen design has advanced greatly in recent years, due not only to the increasing availability of experimentally determined structures but also to improved computational methods for both prediction and design. Constant improvements in performance within the Rosetta software suite for biomolecular modeling have given rise to a greater breadth of structure prediction, including docking and design application cases for antibody and antigen modeling. Here, we present an overview of current protocols for antibody and antigen modeling using Rosetta and exemplify those by detailed tutorials originally developed for a Rosetta workshop at Vanderbilt University. These tutorials cover antibody structure prediction, docking, and design and antigen design strategies, including the addition of glycans in Rosetta. We expect that these materials will allow novice users to apply Rosetta in their own projects for modeling antibodies and antigens.
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Affiliation(s)
- Clara
T. Schoeder
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Samuel Schmitz
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Jared Adolf-Bryfogle
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Alexander M. Sevy
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
- Vanderbilt
Vaccine Center, Vanderbilt University Medical
Center, Nashville, Tennessee 37232-0417, United States
| | - Jessica A. Finn
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Vanderbilt
Vaccine Center, Vanderbilt University Medical
Center, Nashville, Tennessee 37232-0417, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Marion F. Sauer
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
- Vanderbilt
Vaccine Center, Vanderbilt University Medical
Center, Nashville, Tennessee 37232-0417, United States
| | - Nina G. Bozhanova
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Benjamin K. Mueller
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Amandeep K. Sangha
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Jaume Bonet
- Institute
of Bioengineering, École Polytechnique
Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Jonathan H. Sheehan
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Georg Kuenze
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Institute
for Drug Discovery, University Leipzig Medical
School, 04103 Leipzig, Germany
| | - Brennica Marlow
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
| | - Shannon T. Smith
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
| | - Hope Woods
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
| | - Brian J. Bender
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Department
of Pharmacology, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Cristina E. Martina
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Diego del Alamo
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Chemical
and Physical Biology Program, Vanderbilt
University, Nashville, Tennessee 37232-0301, United States
| | - Pranav Kodali
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - Alican Gulsevin
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
| | - William R. Schief
- Department
of Immunology and Microbiology, The Scripps
Research Institute, La Jolla, California 92037, United States
- IAVI
Neutralizing Antibody Center, The Scripps
Research Institute, La Jolla, California 92037, United States
| | - Bruno E. Correia
- Institute
of Bioengineering, École Polytechnique
Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - James E. Crowe
- Vanderbilt
Vaccine Center, Vanderbilt University Medical
Center, Nashville, Tennessee 37232-0417, United States
- Department
of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Department
of Pediatrics, Vanderbilt University Medical
Center, Nashville, Tennessee 37232, United States
| | - Jens Meiler
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
- Institute
for Drug Discovery, University Leipzig Medical
School, 04103 Leipzig, Germany
| | - Rocco Moretti
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37212, United States
- Center
for Structural Biology, Vanderbilt University, Nashville, Tennessee 37240-7917, United States
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819
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Gong W, Guerler A, Zhang C, Warner E, Li C, Zhang Y. Integrating Multimeric Threading With High-throughput Experiments for Structural Interactome of Escherichia coli. J Mol Biol 2021; 433:166944. [PMID: 33741411 DOI: 10.1016/j.jmb.2021.166944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 03/06/2021] [Accepted: 03/09/2021] [Indexed: 10/21/2022]
Abstract
Genome-wide protein-protein interaction (PPI) determination remains a significant unsolved problem in structural biology. The difficulty is twofold since high-throughput experiments (HTEs) have often a relatively high false-positive rate in assigning PPIs, and PPI quaternary structures are more difficult to solve than tertiary structures using traditional structural biology techniques. We proposed a uniform pipeline, Threpp, to address both problems. Starting from a pair of monomer sequences, Threpp first threads both sequences through a complex structure library, where the alignment score is combined with HTE data using a naïve Bayesian classifier model to predict the likelihood of two chains to interact with each other. Next, quaternary complex structures of the identified PPIs are constructed by reassembling monomeric alignments with dimeric threading frameworks through interface-specific structural alignments. The pipeline was applied to the Escherichia coli genome and created 35,125 confident PPIs which is 4.5-fold higher than HTE alone. Graphic analyses of the PPI networks show a scale-free cluster size distribution, consistent with previous studies, which was found critical to the robustness of genome evolution and the centrality of functionally important proteins that are essential to E. coli survival. Furthermore, complex structure models were constructed for all predicted E. coli PPIs based on the quaternary threading alignments, where 6771 of them were found to have a high confidence score that corresponds to the correct fold of the complexes with a TM-score >0.5, and 39 showed a close consistency with the later released experimental structures with an average TM-score = 0.73. These results demonstrated the significant usefulness of threading-based homologous modeling in both genome-wide PPI network detection and complex structural construction.
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Affiliation(s)
- Weikang Gong
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Aysam Guerler
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Elisa Warner
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chunhua Li
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China.
| | - Yang Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA; Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, 48109, USA.
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820
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Goodsell DS, Dutta S, Voigt M, Zardecki C. Molecular storytelling for online structural biology outreach and education. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:020401. [PMID: 33728361 PMCID: PMC7936881 DOI: 10.1063/4.0000077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 01/25/2021] [Indexed: 06/12/2023]
Abstract
Knowledge about the structure and function of biomolecules continues to grow exponentially, enabling us to "see" structural snapshots of biomolecular interactions and functional assemblies. At PDB-101, the educational portal of the RCSB Protein Data Bank, we have taken a storytelling approach to make this body of knowledge accessible and comprehensible to a wide community of students, educators, and the general public. For over 20 years, the Molecule of the Month series has utilized a traditional illustrated storytelling approach that is regularly adapted for classroom instruction. Similar visual and interactive storytelling approaches are used to present topical subjects at PDB-101 and full curricular materials and case studies for building a detailed narrative around topics of particular interest. This emphasis on storytelling led to the Video Challenge for High School students, now in its 8th year. In this Article, we will present some of the lessons we have learned for teaching and communicating structural biology using the PDB archive of biomolecular structures.
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Affiliation(s)
| | | | - Maria Voigt
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
| | - Christine Zardecki
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Rutgers, the State University of New Jersey, Piscataway, New Jersey 08854, USA
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821
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Halip L, Avram S, Neanu C. The B-factor index for the binding site (BFIbs) to prioritize crystal protein structures for docking. Struct Chem 2021. [DOI: 10.1007/s11224-021-01751-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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822
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Stuparević I, Novačić A, Rahmouni AR, Fernandez A, Lamb N, Primig M. Regulation of the conserved 3'-5' exoribonuclease EXOSC10/Rrp6 during cell division, development and cancer. Biol Rev Camb Philos Soc 2021; 96:1092-1113. [PMID: 33599082 DOI: 10.1111/brv.12693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 01/31/2023]
Abstract
The conserved 3'-5' exoribonuclease EXOSC10/Rrp6 processes and degrades RNA, regulates gene expression and participates in DNA double-strand break repair and control of telomere maintenance via degradation of the telomerase RNA component. EXOSC10/Rrp6 is part of the multimeric nuclear RNA exosome and interacts with numerous proteins. Previous clinical, genetic, biochemical and genomic studies revealed the protein's essential functions in cell division and differentiation, its RNA substrates and its relevance to autoimmune disorders and oncology. However, little is known about the regulatory mechanisms that control the transcription, translation and stability of EXOSC10/Rrp6 during cell growth, development and disease and how these mechanisms evolved from yeast to human. Herein, we provide an overview of the RNA- and protein expression profiles of EXOSC10/Rrp6 during cell division, development and nutritional stress, and we summarize interaction networks and post-translational modifications across species. Additionally, we discuss how known and predicted protein interactions and post-translational modifications influence the stability of EXOSC10/Rrp6. Finally, we explore the idea that different EXOSC10/Rrp6 alleles, which potentially alter cellular protein levels or affect protein function, might influence human development and disease progression. In this review we interpret information from the literature together with genomic data from knowledgebases to inspire future work on the regulation of this essential protein's stability in normal and malignant cells.
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Affiliation(s)
- Igor Stuparević
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, 10000, Croatia
| | - Ana Novačić
- Laboratory of Biochemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, 10000, Croatia
| | - A Rachid Rahmouni
- Centre de Biophysique Moléculaire, UPR4301 du CNRS, Orléans, 45071, France
| | - Anne Fernandez
- Institut de Génétique Humaine, UMR 9002 CNRS, Montpellier, France
| | - Ned Lamb
- Institut de Génétique Humaine, UMR 9002 CNRS, Montpellier, France
| | - Michael Primig
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, 35000, France
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823
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Rigden DJ, Fernández XM. The 2021 Nucleic Acids Research database issue and the online molecular biology database collection. Nucleic Acids Res 2021; 49:D1-D9. [PMID: 33396976 PMCID: PMC7778882 DOI: 10.1093/nar/gkaa1216] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 2021 Nucleic Acids Research database Issue contains 189 papers spanning a wide range of biological fields and investigation. It includes 89 papers reporting on new databases and 90 covering recent changes to resources previously published in the Issue. A further ten are updates on databases most recently published elsewhere. Seven new databases focus on COVID-19 and SARS-CoV-2 and many others offer resources for studying the virus. Major returning nucleic acid databases include NONCODE, Rfam and RNAcentral. Protein family and domain databases include COG, Pfam, SMART and Panther. Protein structures are covered by RCSB PDB and dispersed proteins by PED and MobiDB. In metabolism and signalling, STRING, KEGG and WikiPathways are featured, along with returning KLIFS and new DKK and KinaseMD, all focused on kinases. IMG/M and IMG/VR update in the microbial and viral genome resources section, while human and model organism genomics resources include Flybase, Ensembl and UCSC Genome Browser. Cancer studies are covered by updates from canSAR and PINA, as well as newcomers CNCdatabase and Oncovar for cancer drivers. Plant comparative genomics is catered for by updates from Gramene and GreenPhylDB. The entire Database Issue is freely available online on the Nucleic Acids Research website (https://academic.oup.com/nar). The NAR online Molecular Biology Database Collection has been substantially updated, revisiting nearly 1000 entries, adding 90 new resources and eliminating 86 obsolete databases, bringing the current total to 1641 databases. It is available at https://www.oxfordjournals.org/nar/database/c/.
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Affiliation(s)
- Daniel J Rigden
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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824
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Li F, Shi Y, Yang X, Luo Z, Zhang G, Yu K, Li F, Chen L, Zhao Y, Xie Y, Wu Y, Yang J, Zhou X, Liu S. Anhydroicaritin Inhibits EMT in Breast Cancer by Enhancing GPX1 Expression: A Research Based on Sequencing Technologies and Bioinformatics Analysis. Front Cell Dev Biol 2021; 9:764481. [PMID: 35178395 PMCID: PMC8844201 DOI: 10.3389/fcell.2021.764481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 12/10/2021] [Indexed: 12/22/2022] Open
Abstract
Background: Breast cancer (BC) is the leading cause of cancer-related deaths among women worldwide. The application of advanced technology has promoted accurate diagnosis and treatment of cancer. Anhydroicaritin (AHI) is a flavonoid with therapeutic potential in BC treatment. The current study aimed to determine AHI's mechanism in BC treatment via RNA sequencing, comprehensive bioinformatics analysis, and experimental verification. Methods: Network pharmacology and MTT (3-(4,5)-dimethylthiazolyl-3,5- diphenyltetrazolium bromide) experiments were conducted to first confirm AHI's anti-BC effect. RNA sequencing was performed to identify the genes affected by AHI. Differential expression analysis, survival analysis, gene set enrichment analysis, and immune infiltration analysis were performed via bioinformatics analysis. Western blot analysis, reverse transcription-polymerase chain reaction (RT-PCR) experiment, molecular docking, and drug affinity responsive target stability (DARTS) experiments were also performed to confirm AHI's direct effect on glutathione peroxidase 1 (GPX1) expression. Confocal immunofluorescence analysis was conducted to verify AHI's effect on the occurrence and development of epithelial-mesenchymal transition (EMT). Finally, BC nude mouse xenografts were established, and AHI's molecular mechanism on BC was explored. Results: Network pharmacology results demonstrated that AHI's therapeutic targets on BC were related to the proliferation, invasion, and metastasis of BC cells. AHI significantly inhibited the proliferation of 4T1 and MDA-MB-231 BC cells in the MTT experiments. RNA sequencing results showed that AHI upregulated the GPX1 expression in the 4T1 and MDA-MB-231 BC cells. Next, bioinformatics analysis revealed that GPX1 is less expressed in BC than in normal breast tissues. Patients with high GPX1 expression levels tended to have prolonged overall survival and disease-free survival than patients with low GPX1 expression levels in BC. Western blot and RT-PCR experiments revealed that AHI increased the protein and mRNA levels of GPX1. Molecular docking and DARTS experiments confirmed the direct binding combination between AHI and GPX1. After the evaluation of the EMT scores of 1,078 patients with BC, we found a potential anti-BC role of GPX1 possibly via suppression of the malignant EMT. The confocal immunofluorescence analysis showed that AHI increased E-cadherin expression levels and reduced vimentin expression levels in BC cells. Animal experiments showed that AHI significantly inhibited tumor growth. AHI also inhibited EMT by enhancing GPX1 and caspase3 cleavage, hence inhibiting EMT markers (i.e., N-cadherin and vimentin) and Ki-67. Conclusion: GPX1 plays a critical role in BC, which may be a biomarker for the prognosis. In addition, AHI suppressed EMT by increasing GPX1 expression, which may serve as a potential therapy for BC treatment.
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Affiliation(s)
- Feifei Li
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Youyang Shi
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Xiaojuan Yang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Zhanyang Luo
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Guangtao Zhang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Kui Yu
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Feng Li
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Lixin Chen
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Youkang Zhao
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ying Xie
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Yuanyuan Wu
- Department of Gastroenterology, Naval Medical Center of PLA, Naval Military Medical University, Shanghai, China
- *Correspondence: Yuanyuan Wu, ; Jianfeng Yang, ; Xiqiu Zhou, ; Sheng Liu,
| | - Jianfeng Yang
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Yuanyuan Wu, ; Jianfeng Yang, ; Xiqiu Zhou, ; Sheng Liu,
| | - Xiqiu Zhou
- Department of Surgery, Pudong Branch of Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Yuanyuan Wu, ; Jianfeng Yang, ; Xiqiu Zhou, ; Sheng Liu,
| | - Sheng Liu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai, China
- *Correspondence: Yuanyuan Wu, ; Jianfeng Yang, ; Xiqiu Zhou, ; Sheng Liu,
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825
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Burley SK. Impact of structural biologists and the Protein Data Bank on small-molecule drug discovery and development. J Biol Chem 2021; 296:100559. [PMID: 33744282 PMCID: PMC8059052 DOI: 10.1016/j.jbc.2021.100559] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/02/2021] [Accepted: 03/16/2021] [Indexed: 12/12/2022] Open
Abstract
The Protein Data Bank (PDB) is an international core data resource central to fundamental biology, biomedicine, bioenergy, and biotechnology/bioengineering. Now celebrating its 50th anniversary, the PDB houses >175,000 experimentally determined atomic structures of proteins, nucleic acids, and their complexes with one another and small molecules and drugs. The importance of three-dimensional (3D) biostructure information for research and education obtains from the intimate link between molecular form and function evident throughout biology. Among the most prolific consumers of PDB data are biomedical researchers, who rely on the open access resource as the authoritative source of well-validated, expertly curated biostructures. This review recounts how the PDB grew from just seven protein structures to contain more than 49,000 structures of human proteins that have proven critical for understanding their roles in human health and disease. It then describes how these structures are used in academe and industry to validate drug targets, assess target druggability, characterize how tool compounds and other small-molecules bind to drug targets, guide medicinal chemistry optimization of binding affinity and selectivity, and overcome challenges during preclinical drug development. Three case studies drawn from oncology exemplify how structural biologists and open access to PDB structures impacted recent regulatory approvals of antineoplastic drugs.
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Affiliation(s)
- Stephen K Burley
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA; Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, New Brunswick, New Jersey, USA; Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, USA; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA.
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826
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Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alvarado LHA, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie-Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, de la Campa MOA, Paredes I, Wheeler B, Rupert A, Sam A, See K, Zapata SS, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first six months of the COVID-19 pandemic. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 33299989 DOI: 10.1101/2020.12.01.406637] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Three-dimensional structures of SARS-CoV-2 and other coronaviral proteins archived in the Protein Data Bank were used to analyze viral proteome evolution during the first six months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48,000 viral proteome sequences showed how each one of the 29 viral study proteins have undergone amino acid changes. Structural models computed for every unique sequence variant revealed that most substitutions map to protein surfaces and boundary layers with a minority affecting hydrophobic cores. Conservative changes were observed more frequently in cores versus boundary layers/surfaces. Active sites and protein-protein interfaces showed modest numbers of substitutions. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for six drug discovery targets and four structural proteins comprising the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and functional interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
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