In silico unravelling of the Lactococcus lactis signal recognition particle and signal recognition particle receptor protein interfacial interaction

Abstract

The signal recognition particle (SRP) protein targeting pathway is highly conserved across all kingdoms of life. In bacteria, gene conservation and experimental data show that the Lactococcus lactis has the simplest version of protein secretion system compared to Escherichia coli and Bacillus subtilis which have more complex systems. L. lactis only possess the SRP pathway, where the specific interaction of its signal recognition particle protein (Ffh) and its SRP receptor protein (FtsY) is known to be essential for the efficiency and fidelity of its protein targeting. On this basis, modeling and characterization study of Ffh-FtsY will allow structural analysis and identification of crucial region and amino acids that are critical in Ffh-FtsY interaction during protein targeting. This work is the first attempt to model the L. lactis Ffh-FtsY complex using the blind docking approach. Modelled Ffh-FtsY showed that the complex interface was predominantly stabilized by hydrophobic interactions and hydrogen bonding with putative binding interfaces mostly confined at the motifs II (5’ TFRAGAIDQL 3’) and III (5’ DTAGR 3’) in each G domain of Ffh and FtsY. Three amino acids of Ffh-NG (Y141, L196 and I198) interact with four amino acids of FtsY-NG (V113, F141, L196 and A236) to form four hydrophobic interactions. 11 amino acids of Ffh-NG (D139, Y141, R142, A144, K168, G194, E197, I198, D199, E205 and Q232) interact with 12 amino acids of FtsY-NG (N111, R142, A143, G144, A165, D168, R195, Q197, N201, E205, N235 and Q239) to form 17 hydrogen bonds. Several highly conserved amino acids in motif II, amino acids D139, R142 and A144 of Ffh-NG and D139, R142 and A143 of FtsY-NG were expected to play important roles in initiating or regulating guanosine triphosphate hydrolysis. Mutations were introduced to the insertion binding domain (IBD) loop R142 of the putative GTP binding site. Mutations R142A and R142E of FtsY-NG significantly disrupted the predicted hydrogen bond that was required for GTP binding. L. lactis subsp. cremoris MG1363 Ffh and FtsY were successfully cloned, expressed and purified by three-step column chromatography. However, ineffective mass spectrometry analysis data of Ffh-FtsY NG has inhibited computational results validation. This structural information will allow for the rational design of L. lactis Ffh-FtsY association in the future.