Computational insights into the circular permutation roles on ConA binding and structural stability

Vinicius J S Osterne; Vanir R Pinto-Junior; Messias V Oliveira; Kyria S Nascimento; Els J M Van Damme; Benildo S Cavada

doi:10.1016/j.crstbi.2024.100140

Computational insights into the circular permutation roles on ConA binding and structural stability

Curr Res Struct Biol. 2024 Mar 23:7:100140. doi: 10.1016/j.crstbi.2024.100140. eCollection 2024.

Authors

Vinicius J S Osterne¹, Vanir R Pinto-Junior^{2

3}, Messias V Oliveira², Kyria S Nascimento², Els J M Van Damme¹, Benildo S Cavada²

Affiliations

¹ Laboratory of Biochemistry and Glycobiology, Department of Biotechnology, Ghent University, 9000, Ghent, Belgium.
² Laboratory of Biologically Active Molecules, Department of Biochemistry and Molecular Biology, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil.
³ Department of Physics, Federal University of Ceara, 60.440-970, Fortaleza, CE, Brazil.

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.

Keywords: Bioinformatics; Circular permutation; Concanavalin A; Lectin.