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Osterne VJ, Pinto-Junior VR, Oliveira MV, Nascimento KS, Van Damme EJ, Cavada BS. Computational insights into the circular permutation roles on ConA binding and structural stability. Curr Res Struct Biol 2024; 7:100140. [PMID: 38559841 PMCID: PMC10979261 DOI: 10.1016/j.crstbi.2024.100140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 04/04/2024] Open
Abstract
The mechanisms behind Concanavalin A (ConA) circular permutation have been under investigation since 1985. Although a vast amount of information is available about this lectin and its applications, the exact purpose of its processing remains unclear. To shed light on this, this study employed computer simulations to compare the unprocessed ProConA with the mature ConA. This approach aimed to reveal the importance of the post-translational modifications, especially how they affect the lectin stability and carbohydrate-binding properties. To achieve these goals, we conducted 200 ns molecular dynamics simulations and trajectory analyses on the monomeric forms of ProConA and ConA (both unbound and in complex with D-mannose and the GlcNAc2Man9 N-glycan), as well as on their oligomeric forms. Our findings reveal significant stability differences between ProConA and ConA at both the monomeric and tetrameric levels, with ProConA exhibiting consistently lower stability parameters compared to ConA. In terms of carbohydrate binding properties, however, both lectins showed remarkable similarities in their interaction profiles, contact numbers, and binding free energies with D-mannose and the high-mannose N-glycan. Overall, our results suggest that the processing of ProConA significantly enhances the stability of the mature lectin, especially in maintaining the tetrameric oligomer, without substantially affecting its carbohydrate-binding properties.
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Affiliation(s)
- Vinicius J.S. Osterne
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Vanir R. Pinto-Junior
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
- Department of Physics, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
| | - Messias V. Oliveira
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
| | - Kyria S. Nascimento
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
| | - Els J.M. Van Damme
- Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Benildo S. Cavada
- Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil
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Nascimento KS, Santiago MQ, Pinto-Junior VR, Osterne VJS, Martins FWV, Nascimento APM, Wolin IAV, Heinrich IA, Martins MGQ, Silva MTL, Lossio CF, Rocha CRC, Leal RB, Cavada BS. Structural analysis of Dioclea lasiocarpa lectin: A C6 cells apoptosis-inducing protein. Int J Biochem Cell Biol 2017; 92:79-89. [DOI: 10.1016/j.biocel.2017.09.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 09/15/2017] [Accepted: 09/18/2017] [Indexed: 12/16/2022]
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Pinto-Junior VR, Osterne VJS, Santiago MQ, Correia JLA, Pereira-Junior FN, Leal RB, Pereira MG, Chicas LS, Nagano CS, Rocha BAM, Silva-Filho JC, Ferreira WP, Rocha CRC, Nascimento KS, Assreuy AMS, Cavada BS. Structural studies of a vasorelaxant lectin from Dioclea reflexa Hook seeds: Crystal structure, molecular docking and dynamics. Int J Biol Macromol 2017; 98:12-23. [DOI: 10.1016/j.ijbiomac.2017.01.092] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/16/2017] [Accepted: 01/20/2017] [Indexed: 01/15/2023]
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Molecular modeling, docking and dynamics simulations of the Dioclea lasiophylla Mart. Ex Benth seed lectin: An edematogenic and hypernociceptive protein. Biochimie 2017; 135:126-136. [DOI: 10.1016/j.biochi.2017.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/09/2017] [Indexed: 12/18/2022]
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