Structure and Function of Semaphorin-5A–Glycosaminoglycan Interactions

A genome-wide study also reported an association between Sema5A genetic variants and autism spectrum disorder [Weiss et al. (2009) Nature 461, [802][803][804][805][806][807][808].Its structure consists of an extracellular Sema domain, a plexin-semaphorin-integrin domain, seven thrombospondin type 1 repeat (TSR) sequences, a transmembrane region, and a cytoplasmic domain [Adams et al. (1996) Mech.Dev.57, 33-45].TSRs are a hallmark of Sema5A and they interact with heparan sulfate (HS) or chondroitin sulfate (CS) on proteoglycans [Kantor et al. (2004) Neuron 44, 961-975].Of note, HSs are required for Sema5A to exert its promotive effects on neurite outgrowth, while CS causes Sema5A to function as an inhibitory factor on neurite outgrowth.In other words, glycosaminoglycans (GAGs) mediate the functional switch of Sema-5A.In this report, we discuss a paper [Nagy et al. (2024) Nat.Commun.15, 2723] that provides insights into the details of the Sema5A-GAG interaction and its role in the regulation of projection elongation.The authors first determined the structure in Sema5A required for the Sema5A-GAG interaction.A previous study showed that TSR1-4 of Sema5A binds to GAG.They tested the binding of full-length TSR1-7, TSR2, and TSR3-4 to HS.The results showed that TSR1-7 and TSR3-4 bound to HS.However, TSR2 did not interact with HS.The crystal structures of TSR3-4 were examined using X-ray crystallography.They determined four Sema5ATSR3-4 crystal structures: the apo state and complexes with nitrate, sulfate, and the heparin disaccharide mimetic sucrose octasulfate.The authors consider that the four structures are essentially identical, but predict that conformational variation provides flexibility in the structure of the extracellular domain of Sema5A.The subsequent analyses focused on the structure of the nitrate moiety.Further analysis of TSR3 and TSR4 revealed a significant contribution of disulfide bonds in the TSR3 domain to the dimerization of Sema5A.The structure of TSR4 is unique, as there is no structural homolog of TSR4 in the Protein Data Bank.TSR4 assembles positively charged amino acid residues (K505, T732, K734, R747, and R749) to create a positively charged region.Subsequently, docking simulation of TSR3-4-NO3 with heparin tetrasaccharide was performed using a rigid-body docking analysis.Although the binding energy was not very high, it was predicted that 10 heparin tetrasaccharides would coil around the positively charged region.To confirm whether the formation of a positively