1
|
Li X, Zhang F, Zheng L, Guo J. Advancing ecotoxicity assessment: Leveraging pre-trained model for bee toxicity and compound degradability prediction. JOURNAL OF HAZARDOUS MATERIALS 2024; 475:134828. [PMID: 38876015 DOI: 10.1016/j.jhazmat.2024.134828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/09/2024] [Accepted: 06/03/2024] [Indexed: 06/16/2024]
Abstract
The prediction of ecological toxicity plays an increasingly important role in modern society. However, the existing models often suffer from poor performance and limited predictive capabilities. In this study, we propose a novel approach for ecological toxicity assessment based on pre-trained models. By leveraging pre-training techniques and graph neural network models, we establish a highperformance predictive model. Furthermore, we incorporate a variational autoencoder to optimize the model, enabling simultaneous discrimination of toxicity to bees and molecular degradability. Additionally, despite the low similarity between the endogenous hormones in bees and the compounds in our dataset, our model confidently predicts that these hormones are non-toxic to bees, which further strengthens the credibility and accuracy of our model. We also discovered the negative correlation between the degradation and bee toxicity of compounds. In summary, this study presents an ecological toxicity assessment model with outstanding performance. The proposed model accurately predicts the toxicity of chemicals to bees and their degradability capabilities, offering valuable technical support to relevant fields.
Collapse
Affiliation(s)
- Xinkang Li
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao
| | - Feng Zhang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Liangzhen Zheng
- Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518000, China; Zelixir Biotech Company Ltd. Shanghai, China.
| | - Jingjing Guo
- Centre in Artificial Intelligence Driven Drug Discovery, Faculty of Applied Sciences, Macao Polytechnic University, 999078, Macao.
| |
Collapse
|
2
|
Moonitz SA, Do NT, Noriega R. Electrostatic modulation of multiple binding events between loquacious-PD and double-stranded RNA. Phys Chem Chem Phys 2024; 26:20739-20744. [PMID: 39049620 DOI: 10.1039/d4cp02151g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Electrostatics can alter the RNA-binding properties of proteins that display structure selectivity without sequence specificity. Loquacious-PD relies on this broad scope response to mediate the interaction of endonucleases with double stranded RNAs. Multimodal spectroscopic probes with in situ perturbations reveal an efficient and stable binding mechanism that disfavors high protein density complexes and is sensitive to local electrostatics.
Collapse
Affiliation(s)
- Sasha A Moonitz
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
| | - Nhat T Do
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
| | - Rodrigo Noriega
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA.
| |
Collapse
|
3
|
Ye X, Yang W, Yi S, Zhao Y, Varani G, Jankowsky E, Yang F. Two distinct binding modes provide the RNA-binding protein RbFox with extraordinary sequence specificity. Nat Commun 2023; 14:701. [PMID: 36759600 PMCID: PMC9911399 DOI: 10.1038/s41467-023-36394-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 01/30/2023] [Indexed: 02/11/2023] Open
Abstract
Specificity of RNA-binding proteins for target sequences varies considerably. Yet, it is not understood how certain few proteins achieve markedly higher sequence specificity than most others. Here we show that the RNA Recognition Motif of RbFox accomplishes extraordinary sequence specificity by employing functionally and structurally distinct binding modes. Affinity measurements of RbFox for all binding site variants reveal the existence of two distinct binding modes. The first exclusively accommodates cognate and closely related RNAs with high affinity. The second mode accommodates all other RNAs with reduced affinity by imposing large thermodynamic penalties on non-cognate sequences. NMR studies indicate marked structural differences between the two binding modes, including large conformational rearrangements distant from the RNA-binding site. Distinct binding modes by a single RNA-binding module explain extraordinary sequence selectivity and reveal an unknown layer of functional diversity, cross talk and regulation in RNA-protein interactions.
Collapse
Affiliation(s)
- Xuan Ye
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Wen Yang
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Greater Bay Biomedical InnoCenter, Shenzhen Bay Laboratory, Shenzhen, 518055, China
| | - Soon Yi
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Yanan Zhao
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080, China
| | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, WA, USA.
| | - Eckhard Jankowsky
- Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
- Moderna Therapeutics, 200 Technology Square, Cambridge, MA, USA.
| | - Fan Yang
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, 150080, China.
| |
Collapse
|
4
|
Duss O, Stepanyuk GA, Puglisi JD, Williamson JR. Transient Protein-RNA Interactions Guide Nascent Ribosomal RNA Folding. Cell 2019; 179:1357-1369.e16. [PMID: 31761533 DOI: 10.1016/j.cell.2019.10.035] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/18/2019] [Accepted: 10/28/2019] [Indexed: 11/28/2022]
Abstract
Ribosome assembly is an efficient but complex and heterogeneous process during which ribosomal proteins assemble on the nascent rRNA during transcription. Understanding how the interplay between nascent RNA folding and protein binding determines the fate of transcripts remains a major challenge. Here, using single-molecule fluorescence microscopy, we follow assembly of the entire 3' domain of the bacterial small ribosomal subunit in real time. We find that co-transcriptional rRNA folding is complicated by the formation of long-range RNA interactions and that r-proteins self-chaperone the rRNA folding process prior to stable incorporation into a ribonucleoprotein (RNP) complex. Assembly is initiated by transient rather than stable protein binding, and the protein-RNA binding dynamics gradually decrease during assembly. This work questions the paradigm of strictly sequential and cooperative ribosome assembly and suggests that transient binding of RNA binding proteins to cellular RNAs could provide a general mechanism to shape nascent RNA folding during RNP assembly.
Collapse
Affiliation(s)
- Olivier Duss
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Galina A Stepanyuk
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Joseph D Puglisi
- Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
| | - James R Williamson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
| |
Collapse
|
5
|
Lau MWL, Ferré-D'Amaré AR. Many Activities, One Structure: Functional Plasticity of Ribozyme Folds. Molecules 2016; 21:molecules21111570. [PMID: 27869745 PMCID: PMC6273943 DOI: 10.3390/molecules21111570] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/12/2016] [Accepted: 11/14/2016] [Indexed: 01/01/2023] Open
Abstract
Catalytic RNAs, or ribozymes, are involved in a number of essential biological processes, such as replication of RNA genomes and mobile genetic elements, RNA splicing, translation, and RNA degradation. The function of ribozymes requires the formation of active sites decorated with RNA functional groups within defined three-dimensional (3D) structures. The genotype (sequence) of RNAs ultimately determines what 3D structures they adopt (as a function of their environmental conditions). These 3D structures, in turn, give rise to biochemical activity, which can further elaborate them by catalytic rearrangements or association with other molecules. The fitness landscape of a non-periodic linear polymer, such as RNA, relates its primary structure to a phenotype. Two major challenges in the analysis of ribozymes is to map all possible genotypes to their corresponding catalytic activity (that is, to determine their fitness landscape experimentally), and to understand whether their genotypes and three-dimensional structures can support multiple different catalytic functions. Recently, the combined results of experiments that employ in vitro evolution methods, high-throughput sequencing and crystallographic structure determination have hinted at answers to these two questions: while the fitness landscape of ribozymes is rugged, meaning that their catalytic activity cannot be optimized by a smooth trajectory in sequence space, once an RNA achieves a stable three-dimensional fold, it can be endowed with distinctly different biochemical activities through small changes in genotype. This functional plasticity of highly structured RNAs may be particularly advantageous for the adaptation of organisms to drastic changes in selective pressure, or for the development of new biotechnological tools.
Collapse
Affiliation(s)
- Matthew W L Lau
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.
| | - Adrian R Ferré-D'Amaré
- National Heart, Lung and Blood Institute, 50 South Drive, MSC 8012, Bethesda, MD 20892-8012, USA.
| |
Collapse
|