Computational simulations assessment of mutations impact on streptokinase (SK) from a group G streptococci with enhanced activity – insights into the functional roles of structural dynamics flexibility of SK and stabilization of SK–μplasmin catalytic complex

Abstract

Streptokinase (SK), a plasminogen activator (PA) that converts inactive plasminogen (Pg) to plasmin (Pm), is a protein secreted by groups A, C, and G streptococci (GAS, GCS, and GGS, respectively), with high sequence divergence and functional heterogeneity. While roles of some residual changes in altered SK functionality are shown, the underlying structural mechanisms are less known. Herein, using computational approaches, we analyzed the conformational basis for the increased activity of SK from a GGS (SKG132) isolate with four natural residual substitutions (Ile33Phe, Arg45Gln, Asn228Lys, Phe287Ile) compared to the standard GCS (SKC). Using the crystal structure of SK.Pm catalytic complex as main template SKC.μPm catalytic complex was modeled through homology modeling process and validated by several online validation servers. Subsequently, SKG132.μPm structure was constructed by altering the corresponding residual substitutions. Results of three independent MD simulations showed increased RMSF values for SKG132.μPm, indicating the enhanced structural flexibility compared to SKC.μPm, specially in 170 and 250 loops and three regions: R1 (149–161), R2 (182–215) and R3 (224–229). In parallel, the average number of Hydrogen bonds in 170 loop, R2 and R3 (especially for Asn228Lys) of SKG132 compared to that of the SKC was decreased. Accordingly, residue interaction networks (RINs) analyses indicated that Asn228Lys might induce more level of structural flexibility by generation of free Lys256, while Phe287Ile and Ile33Phe enhanced the stabilization of the SKG132.μPm catalytic complex. These results denoted the potential role of the optimal dynamic state and stabilized catalytic complex for increased PA potencies of SK as a thrombolytic drug.

Keywords:

• activity
• molecular dynamics simulation
• plasminogen
• residue interaction network
• streptokinase

Abbreviations:

• Cα: C-alpha
• RMSD: Root mean square deviation
• RMSF: Root mean square fluctuation
• Hbonds: Hydrogen bonds
• RINs: Residue interaction networks
• RING: Residue interaction network generator
• VDW: van der Waals
• MD simulation: Molecular dynamics simulation
• Pg: Plasminogen
• Pm: Plasmin
• μPm: microplasmin
• SK: Streptokinase
• PAs: Plasminogen activators
• tPAs: Tissue type-PAs
• K: kringle
• R: Region
• PDB: Protein Data Bank

Acknowledgments

This study was financially supported by Pasteur Institute of Iran in partial fulfillment of the PhD thesis of Mrs. Faegheh Kazemi in medical biotechnology program.