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Liu Y, Du N, Qian B, Zou C, Yu Z, Xu F, Wang L, Qin S, You F, Tan X. Characteristics of Shisa Family Genes in Zebrafish. Int J Mol Sci 2023; 24:14062. [PMID: 37762365 PMCID: PMC10531659 DOI: 10.3390/ijms241814062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/03/2023] [Accepted: 08/12/2023] [Indexed: 09/29/2023] Open
Abstract
Shisa represents a type of single-transmembrane adaptor protein containing an N-terminal cysteine-rich domain and a proline-rich C-terminal region. Nine shisa subfamily genes have been proposed in most vertebrates; however, some might be species-specific. The number of shisa genes present in zebrafish remains unclear. This study aimed to investigate the evolutionary relationships among shisa family genes in zebrafish (TU strain) using phylogenetic and syntenic analyses. The function of shisa-2 was preliminarily examined via CRISPR/Cas13d-mediated knockdown. Following identification in zebrafish, 10 shisa family genes, namely shisa-1, 2, 3, 4, 5, 6, 7, 8, 9a, and 9b, were classified into three main clades and six subclades. Their encoding proteins contained a cysteine-rich N-terminal domain and a proline-rich C-terminal region containing different motifs. A specific syntenic block containing atp8a2 and shisa-2 was observed to be conserved across all species. Furthermore, all these genes were expressed during embryogenesis. Shisa-2 was expressed in the presomitic mesoderm, somites, and so on. Shisa-2 was identified as a regulator of the expression of the somite formation marker mesp-ab. Overall, our study provides new insights into the evolution of shisa family genes and the control of shisa-2 over the convergent extension cells of somitic precursors in zebrafish.
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Affiliation(s)
- Yansong Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Y.L.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China (F.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Na Du
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China (F.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Beibei Qian
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China (F.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Congcong Zou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China (F.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Zhouxin Yu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; (Y.L.)
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China (F.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Fei Xu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China (F.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Lijuan Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China (F.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Sishi Qin
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China (F.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
- University of Chinese Academy of Sciences, Beijing 10049, China
| | - Feng You
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China (F.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Xungang Tan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao 266071, China (F.Y.)
- Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
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Ahalawat N, Sahil M, Mondal J. Resolving Protein Conformational Plasticity and Substrate Binding via Machine Learning. J Chem Theory Comput 2023; 19:2644-2657. [PMID: 37068044 DOI: 10.1021/acs.jctc.2c00932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
A long-standing target in elucidating the biomolecular recognition process is the identification of binding-competent conformations of the receptor protein. However, protein conformational plasticity and the stochastic nature of the recognition processes often preclude the assignment of a specific protein conformation to an individual ligand-bound pose. Here, we demonstrate that a computational framework coined as RF-TICA-MD, which integrates an ensemble decision-tree-based Random Forest (RF) machine learning (ML) technique with an unsupervised dimension reduction approach time-structured independent component analysis (TICA), provides an efficient and unambiguous solution toward resolving protein conformational plasticity and the substrate binding process. In particular, we consider multimicrosecond-long molecular dynamics (MD) simulation trajectories of a ligand recognition process in solvent-inaccessible cavities of archetypal proteins T4 lysozyme and cytochrome P450cam. We show that in a scenario in which clear correspondence between protein conformation and binding-competent macrostates could not be obtained via an unsupervised dimension reduction approach, an a priori decision-tree-based supervised classification of the simulated recognition trajectories via RF would help characterize key amino acid residue pairs of the protein that are deemed sensitive for ligand binding. A subsequent unsupervised dimensional reduction of the selected residue pairs via TICA would then delineate a conformational landscape of protein which is able to demarcate ligand-bound poses from unbound ones. The proposed RF-TICA-MD approach is shown to be data agnostic and found to be robust when using other ML-based classification methods such as XGBoost. As a promising spinoff of the protocol, the framework is found to be capable of identifying distal protein locations which would be allosterically important for ligand binding and would characterize their roles in recognition pathways. A Python implementation of a proposed ML workflow is available in GitHub https://github.com/navjeet0211/rf-tica-md.
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Affiliation(s)
- Navjeet Ahalawat
- Department of Bioinformatics and Computational Biology, College of Biotechnology, CCS Haryana Agricultural University, Hisar 125 004, Haryana, India
| | - Mohammad Sahil
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500046, India
| | - Jagannath Mondal
- Center for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad 500046, India
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Sukumaran SK, Palayyan SR. Sweet Taste Signaling: The Core Pathways and Regulatory Mechanisms. Int J Mol Sci 2022; 23:8225. [PMID: 35897802 DOI: 10.3390/ijms23158225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/23/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Sweet taste, a proxy for sugar-derived calories, is an important driver of food intake, and animals have evolved robust molecular and cellular machinery for sweet taste signaling. The overconsumption of sugar-derived calories is a major driver of obesity and other metabolic diseases. A fine-grained appreciation of the dynamic regulation of sweet taste signaling mechanisms will be required for designing novel noncaloric sweeteners with better hedonic and metabolic profiles and improved consumer acceptance. Sweet taste receptor cells express at least two signaling pathways, one mediated by a heterodimeric G-protein coupled receptor encoded by taste 1 receptor members 2 and 3 (TAS1R2 + TAS1R3) genes and another by glucose transporters and the ATP-gated potassium (KATP) channel. Despite these important discoveries, we do not fully understand the mechanisms regulating sweet taste signaling. We will introduce the core components of the above sweet taste signaling pathways and the rationale for having multiple pathways for detecting sweet tastants. We will then highlight the roles of key regulators of the sweet taste signaling pathways, including downstream signal transduction pathway components expressed in sweet taste receptor cells and hormones and other signaling molecules such as leptin and endocannabinoids.
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Cobos ES, Sánchez IE, Chemes LB, Martinez JC, Murciano-Calles J. A Thermodynamic Analysis of the Binding Specificity between Four Human PDZ Domains and Eight Host, Viral and Designed Ligands. Biomolecules 2021; 11:biom11081071. [PMID: 34439737 PMCID: PMC8393326 DOI: 10.3390/biom11081071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/14/2021] [Accepted: 07/16/2021] [Indexed: 02/01/2023] Open
Abstract
PDZ domains are binding modules mostly involved in cell signaling and cell–cell junctions. These domains are able to recognize a wide variety of natural targets and, among the PDZ partners, viruses have been discovered to interact with their host via a PDZ domain. With such an array of relevant and diverse interactions, PDZ binding specificity has been thoroughly studied and a traditional classification has grouped PDZ domains in three major specificity classes. In this work, we have selected four human PDZ domains covering the three canonical specificity-class binding mode and a set of their corresponding binders, including host/natural, viral and designed PDZ motifs. Through calorimetric techniques, we have covered the entire cross interactions between the selected PDZ domains and partners. The results indicate a rather basic specificity in each PDZ domain, with two of the domains that bind their cognate and some non-cognate ligands and the two other domains that basically bind their cognate partners. On the other hand, the host partners mostly bind their corresponding PDZ domain and, interestingly, the viral ligands are able to bind most of the studied PDZ domains, even those not previously described. Some viruses may have evolved to use of the ability of the PDZ fold to bind multiple targets, with resulting affinities for the virus–host interactions that are, in some cases, higher than for host–host interactions.
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Affiliation(s)
- Eva S. Cobos
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
| | - Ignacio E. Sánchez
- Laboratorio de Fisiología de Proteínas, Facultad de Ciencias Exactas y Naturales, Consejo Nacional de Investigaciones Científicas y Técnicas, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), Universidad de Buenos Aires, 1428 Buenos Aires, Argentina;
| | - Lucía B. Chemes
- Instituto de Investigaciones Biotecnológicas (IIBiO-CONICET), Universidad Nacional de San Martín, 1650 Buenos Aires, Argentina;
| | - Jose C. Martinez
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
| | - Javier Murciano-Calles
- Departamento Química Física, Unidad de Excelencia de Química Aplicada a Biomedicina y Medioambiente, Facultad de Ciencias, e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain; (E.S.C.); (J.C.M.)
- Correspondence:
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Bousova K, Bednarova L, Zouharova M, Vetyskova V, Postulkova K, Hofbauerová K, Petrvalska O, Vanek O, Tripsianes K, Vondrasek J. The order of PDZ3 and TrpCage in fusion chimeras determines their properties-a biophysical characterization. Protein Sci 2021; 30:1653-1666. [PMID: 33969912 DOI: 10.1002/pro.4107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 11/09/2022]
Abstract
Most of the structural proteins known today are composed of domains that carry their own functions while keeping their structural properties. It is supposed that such domains, when taken out of the context of the whole protein, can retain their original structure and function to a certain extent. Information on the specific functional and structural characteristics of individual domains in a new context of artificial fusion proteins may help to reveal the rules of internal and external domain communication. Moreover, this could also help explain the mechanism of such communication and address how the mutual allosteric effect plays a role in a such multi-domain protein system. The simple model system of the two-domain fusion protein investigated in this work consisted of a well-folded PDZ3 domain and an artificially designed small protein domain called Tryptophan Cage (TrpCage). Two fusion proteins with swapped domain order were designed to study their structural and functional features as well as their biophysical properties. The proteins composed of PDZ3 and TrpCage, both identical in amino acid sequence but different in composition (PDZ3-TrpCage, TrpCage-PDZ3), were studied using circualr dichroism (CD) spectrometry, analytical ultracentrifugation, and molecular dynamic simulations. The biophysical analysis uncovered different structural and denaturation properties of both studied proteins, revealing their different unfolding pathways and dynamics.
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Affiliation(s)
- Kristyna Bousova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Lucie Bednarova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
| | - Monika Zouharova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic.,Second Faculty of Medicine, Charles University, Prague 5, Czech Republic
| | - Veronika Vetyskova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic.,Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague 6, Czech Republic
| | - Klara Postulkova
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic.,Second Faculty of Medicine, Charles University, Prague 5, Czech Republic
| | - Kateřina Hofbauerová
- Faculty of Mathematics and Physics, Charles University, Prague 2, Czech Republic.,Institute of Microbiology of the Czech Academy of Sciences, Prague 4, Czech Republic
| | - Olivia Petrvalska
- Department of Structural Biology of Signalling Proteins, Division BIOCEV, Institute of Physiology, Vestec, Czech Republic
| | - Ondrej Vanek
- Department of Biochemistry, Faculty of Science, Charles University, Prague 2, Czech Republic
| | | | - Jiri Vondrasek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 6, Czech Republic
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Fusco G, Gianni S. Function, Regulation, and Dysfunction of Intrinsically Disordered Proteins. Life (Basel) 2021; 11:life11020140. [PMID: 33673214 PMCID: PMC7917908 DOI: 10.3390/life11020140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 02/07/2021] [Indexed: 12/16/2022] Open
Abstract
The discovery that a considerable fraction of the eukaryotic proteins lacks a well-defined three-dimensional structure in their native state has revolutionised our general understanding of proteins [...].
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Affiliation(s)
- Giuliana Fusco
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
- Correspondence: (G.F.); (S.G.)
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli,” Sapienza Università di Roma, 00185 Rome, Italy
- Correspondence: (G.F.); (S.G.)
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Dudola D, Hinsenkamp A, Gáspári Z. Ensemble-Based Analysis of the Dynamic Allostery in the PSD-95 PDZ3 Domain in Relation to the General Variability of PDZ Structures. Int J Mol Sci 2020; 21:ijms21218348. [PMID: 33172212 PMCID: PMC7672539 DOI: 10.3390/ijms21218348] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/28/2020] [Accepted: 10/30/2020] [Indexed: 11/16/2022] Open
Abstract
PDZ domains are abundant interaction hubs found in a number of different proteins and they exhibit characteristic differences in their structure and ligand specificity. Their internal dynamics have been proposed to contribute to their biological activity via changes in conformational entropy upon ligand binding and allosteric modulation. Here we investigate dynamic structural ensembles of PDZ3 of the postsynaptic protein PSD-95, calculated based on previously published backbone and side-chain S2 order parameters. We show that there are distinct but interdependent structural rearrangements in PDZ3 upon ligand binding and the presence of the intramolecular allosteric modulator helix α3. We have also compared these rearrangements in PDZ1-2 of PSD-95 and the conformational diversity of an extended set of PDZ domains available in the PDB database. We conclude that although the opening-closing rearrangement, occurring upon ligand binding, is likely a general feature for all PDZ domains, the conformer redistribution upon ligand binding along this mode is domain-dependent. Our findings suggest that the structural and functional diversity of PDZ domains is accompanied by a diversity of internal motional modes and their interdependence.
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Affiliation(s)
- Dániel Dudola
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083 Budapest, Hungary; (D.D.); (A.H.)
| | - Anett Hinsenkamp
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083 Budapest, Hungary; (D.D.); (A.H.)
- 3in-PPCU Research Group, 2500 Esztergom, Hungary
| | - Zoltán Gáspári
- Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Práter u. 50/A, 1083 Budapest, Hungary; (D.D.); (A.H.)
- Correspondence:
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