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Planas-Iglesias J, Opaleny F, Ulbrich P, Stourac J, Sanusi Z, Pinto GP, Schenkmayerova A, Byska J, Damborsky J, Kozlikova B, Bednar D. LoopGrafter: a web tool for transplanting dynamical loops for protein engineering. Nucleic Acids Res 2022; 50:W465-W473. [PMID: 35438789 PMCID: PMC9252738 DOI: 10.1093/nar/gkac249] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/15/2022] [Accepted: 04/01/2022] [Indexed: 01/01/2023] Open
Abstract
The transplantation of loops between structurally related proteins is a compelling method to improve the activity, specificity and stability of enzymes. However, despite the interest of loop regions in protein engineering, the available methods of loop-based rational protein design are scarce. One particular difficulty related to loop engineering is the unique dynamism that enables them to exert allosteric control over the catalytic function of enzymes. Thus, when engaging in a transplantation effort, such dynamics in the context of protein structure need consideration. A second practical challenge is identifying successful excision points for the transplantation or grafting. Here, we present LoopGrafter (https://loschmidt.chemi.muni.cz/loopgrafter/), a web server that specifically guides in the loop grafting process between structurally related proteins. The server provides a step-by-step interactive procedure in which the user can successively identify loops in the two input proteins, calculate their geometries, assess their similarities and dynamics, and select a number of loops to be transplanted. All possible different chimeric proteins derived from any existing recombination point are calculated, and 3D models for each of them are constructed and energetically evaluated. The obtained results can be interactively visualized in a user-friendly graphical interface and downloaded for detailed structural analyses.
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Affiliation(s)
- Joan Planas-Iglesias
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
| | - Filip Opaleny
- Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
| | - Pavol Ulbrich
- Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
| | - Zainab Sanusi
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
| | - Andrea Schenkmayerova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
| | - Jan Byska
- Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
| | - Barbora Kozlikova
- Department of Visual Computing, Faculty of Informatics, Masaryk University, 602 00 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic.,International Clinical Research Center, St Anne's University Hospital Brno, 656 916 Brno, Czech Republic
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Barozet A, Chacón P, Cortés J. Current approaches to flexible loop modeling. Curr Res Struct Biol 2021; 3:187-191. [PMID: 34409304 PMCID: PMC8361254 DOI: 10.1016/j.crstbi.2021.07.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 06/30/2021] [Accepted: 07/25/2021] [Indexed: 01/14/2023] Open
Abstract
Loops are key components of protein structures, involved in many biological functions. Due to their conformational variability, the structural investigation of loops is a difficult topic, requiring a combination of experimental and computational methods. This paper provides a brief overview of current computational approaches to flexible loop modeling, and presents the main ingredients of the most standard protocols. Despite great progress in recent years, accurately modeling the conformational variability of long flexible loops remains a challenging problem. Future advances in this field will likely come from a tight coupling of experimental and computational techniques, which would enable a better understanding of the relationships between loop sequence, structural flexibility, and functional roles. In fine, accurate loop modeling will open the road to loop design problems of interest for applications in biomedicine and biotechnology.
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Affiliation(s)
- Amélie Barozet
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
| | - Pablo Chacón
- Department of Biological Physical Chemistry, Rocasolano Physical Chemistry Institute C.S.I.C., Madrid, Spain
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, Toulouse, France
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Moradi M, Hosseinkhani S, Arab SS, Khammari A. Effects of Linker Flexibility and Conformational Changes of IP3 Receptor on Split Luciferase Complementation Assay. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2423. [PMID: 34056016 PMCID: PMC8148647 DOI: 10.30498/ijb.2020.2423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background: IP3-induced Ca2+ release, mediated by IP3R, is one of the most momentous cellular signaling mechanisms that regulate in a wide variety of essential cellular functions. Involvement of disrupted IP3 signaling pathways in numerous pathophysiology conditions is implicated to find the best methods for its measurement. Hence, several different biosensors have developed to monitor temporal changes of IP3 by using the IP3-binding domain of IP3 receptors. Objectives: Based on a previous study, we developed and characterized a series of bioluminescent biosensors using the human type-II IP3 receptor ligand binding domain (residues 1–604), named LAIRE (luminescent analyzer for IP3 receptor element) to study the effect of flexible and rigid linkers on the luminescence intensity of split luciferase. The effect of a mutation in IP3 binding residues and suppressor domain in the IP3 binding domain on luciferase complementary assay is also investigated. Materials and Methods: In the present study, first IP3-binding domain (residues 1-604) of IP3-receptor type 2 (LAIRE) was fused between complementary non-functional fragments of firefly luciferase and then the rigid linker sequence (LLRAIEAQQHLL), selected by ProDA database, introduced between Nluc and ligand binding domain and compared with that of the flexible linker ((GGGGS)2) in LAIRE chimera. The IP3-insensitive mutant of the biosensor was constructed using the Stratagene QuikChange® procedure. In order to the analysis of the dynamical movements of selected structures in the large-scale, coarse-graining method of molecular dynamics simulation (1µs) was applied. Results: As expected, the flexible linker brings two inactive fragments of luciferase together relative to the rigid linker and leads to complementation of luciferase activity, which is detected using luciferin. However, this conformational flexibility in linker increases background to noise ratio and attenuates fold induction. Conclusions: It seems that the ligand binding properties of IP3 binding core make it more suitable for the design of biosensor than the ligand binding domain.
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Affiliation(s)
- Maryam Moradi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Anahita Khammari
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Sepehri S, Arab SS, Behmanesh M, H. Sajedi R. Directed Blocking of TGF-β Receptor I Binding Site Using Tailored Peptide Segments to Inhibit its Signaling Pathway. IRANIAN JOURNAL OF BIOTECHNOLOGY 2020; 18:e2561. [PMID: 32884960 PMCID: PMC7461711 DOI: 10.30498/ijb.2020.197161.2561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND TGF-β isoforms play crucial roles in diverse cellular processes. Therefore, targeting and inhibiting TGF-β signaling pathway provides a potential therapeutic opportunity. TGF-β isoforms bind and bring the receptors (TβRII and TβRI) together to form a signaling complex in an ordered manner. OBJECTIVES Herein, an antagonistic variant of TGF-β (AnTβ) has been designed and prepared to inhibit the formation of signaling complex and consequently its signaling pathway. This TGF-β homodimeric variant contains intact TβRII binding sites and blocked TβRI binding sites by substituting three peptide segments. So, AnTβ could only bind to TβRII, but prevent binding and recruitment of TβRI to form a signaling complex. MATERIALS AND METHODS A reliable model of AnTβ was built and refined using molecular dynamics (MD) simulation, followed by investigating the interactions of AnTβ with the receptors using in silico docking studies. After expression of disulfide-linked AnTβ in a SHuffle strain and purification of the protein using affinity chromatography, its biological activity was evaluated using Mink lung epithelial cells (Mvl Lu). RESULTS No meaningful significant changes in AnTβ structure were observed when compared with the native protein. Based on the docking analysis, AnTβ binds to TβRII similar to TGF-β and its binding to TβRI was diminished considerably which was consistent with our design purpose. Cell-based bioassay indicated that AnTβ could modulate TGF-β-induced cell growth inhibition. CONCLUSIONS Our analysis suggests that the antagonistic potency of AnTβ can be used as an anti-TGFβ signaling factor in the future perspectives.
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Affiliation(s)
- Sepideh Sepehri
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - S. Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mehrdad Behmanesh
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Reza H. Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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