Study On The Relationship Between Shared And Spesific Dynamics And Functions Of Secretory Phospholipase A₂ Family Members

Secretory phospholipase A₂（sPLA₂）family plays an important role in regulating the cell lipid metabolism and signaling transmission,involved in various acute and chronic inflammatory reactions.It is of great biological significance to study the mechanisms of structural dynamics for the shared and specific functions among sPLA₂family members.Here,we explore the issue through extensive analyses using a series of sequence-,structure-,and dynamics-based methods on the 130 sPLA₂family members.（1）First,the structural differences among the 130 sPLA₂family members were analyzed by the principal component analysis（PCA）method.And interestingly it is found that in the first two principle directions of difference,the members of similar functions（with high sequence identity）cluster together.The accurate clustering of different function groups of sPLA₂family members indicates that the structural similarities elucidated by PCA can be well traced back to their sequence similarities.Additionally,with 130 sPLA₂family members considered approximately as an equilibrium structure ensemble,the principle motional components obtained by PCA method suggests that the enzyme has an open-close motion,which helps widen the substrate binding channel,benefits for the binding between the enzyme with lipid,and furtherly facilitates the catalytic reaction of the enzyme.（2）Anisotropic network model（ANM）method was used to analyze the functional coupling motions of residues in sPLA₂family members.The obtained residue fluctuation cross-correlations indicate again the enzyme has an open-close motion.Additionally,it is observed that the core helical region（helix3 and helix4）bearing the catalytic role are dynamically strongly coupled,which is of a critical role in ensuring the stable exertion of the enzyme’s catalytic function.（3）Performing Gaussian network model（GNM）and sequence analyses,we found that the residues critical for enzyme catalysis and structure stabilization,such as catalytic residues and cysteine residues involved in disulfide bond formation,are highly conserved and undergo minimal movements,which is evolutionarily essential as their perturbation would impact the functions;while the four residue regions involved in the association with the calcium ion/membrane,are lowly conserved and of high mobility and large variations in low-to-intermediate frequency modes,which reflects the specificity of members.（4）The analyses from perturbation response scanning（PRS）to evaluate the responses of the whole structure to an external perturbation（simulating the binding of an allosteric agent）reveal that the above four member-specific regions（involved in the association with the calcium ion/membrane）have a high sensitivity to an external perturbation,suggesting their different roles in allosteric modulation,while those minimal sensitive residues are the shared characteristics across family members,which play an important role in maintaining structural stability.This study is helpful for understanding how sequences,structures and dynamics of sPLA₂family members evolve to ensure their common and specific functions,and can provide a guide for accurate design of proteins with finely tuned activities.