Abstract
Ribitol (C5H12O5), an acyclic sugar alcohol, is present on mammalian α-dystroglycan as a component of O-mannose glycan. In this study, we examine the conformation and dynamics of ribitol by database analysis, experiments, and computational methods. Database analysis reveals that the anti-conformation (180°) is populated at the C3–C4 dihedral angle, while the gauche conformation (±60°) is seen at the C2–C3 dihedral angle. Such conformational asymmetry was born out in a solid-state 13C-NMR spectrum of crystalline ribitol, where C1 and C5 signals are unequal. On the other hand, solution 13C-NMR has identical chemical shifts for C1 and C5. NMR 3J coupling constants and OH exchange rates suggest that ribitol is an equilibrium of conformations, under the influence of hydrogen bonds and/or steric hinderance. Molecular dynamics (MD) simulations allowed us to discuss such a chemically symmetric molecule, pinpointing the presence of asymmetric conformations evidenced by the presence of correlations between C2–C3 and C3–C4 dihedral angles. These findings provide a basis for understanding the dynamic structure of ribitol and the function of ribitol-binding enzymes.
Highlights
Ribitol (C5H12O5) is an acyclic sugar alcohol and a component of teichoic acid found in Gram-positive bacteria [1] (Figure 1)
Laminin is known to interact with ribitol-containing O-mannose glycans, and the ribitol residues are likely acting as a hinge in bridging laminin and α-dystroglycan
Our present study aims to build on previous knowledge on the conformation of ribitol and to deepen our understanding of static and dynamic structures of ribitol through database analysis, experimental NMR analysis, and Molecular dynamics (MD) simulation
Summary
Ribitol (C5H12O5) is an acyclic sugar alcohol and a component of teichoic acid found in Gram-positive bacteria [1] (Figure 1). When the configurations of alternate carbons are the same (D and D or L and L), the Cn-O and Cn+2-O bonds align in parallel This arrangement causes steric hindrance such that the carbon chain changes its conformation to bent and non-planar. The crystal structure of ribitol adopts a bent conformation, avoiding the steric hindrance induced by a stretched planar zigzag structure. Thi−s71s76u7 ggests that −i1n17t46e7rmolecular in44t..e55raction with21w..39 ater mole[N1c5Au] les 149 may be inv9o4lved in the var8i3ous conformat1i5o6ns of ribitol It s4.e4ems that the2p.2hosphory[l1a6t]ion 131 of ribitol −d1o3e6s not signific−a1n43tly change th−e1r58ibitol conforma5.t0ion, although2.7it needs fu[1r6t]her. In4h.5igh-resolutio-n structures[o1f2]ribitol (PDB ID;−56I1AI and 4Q0S−)1,7h1ydrogen bon7d3ing with surro4u.6nding water -molecules is[o1b3s]erved (Figure 2−c6). In4h.5igh-resolutio-n structures[o1f2]ribitol (PDB ID;−56I1AI and 4Q0S−)1,7h1ydrogen bon7d3ing with surro4u.6nding water -molecules is[o1b3s]erved (Figure 2−c6)1 This sugg−e1st7s0that interm7o3lecular intera4c.t6ion with wat-er molecule[s1m4]ay be involved1i6n6the various c6o0nformations1o7f0ribitol. It seem4.s5that the pho1s.6phorylationNoAf ribitol dstouedsyn. oIn−t−1st67hi2g4ins ipfiacpaenrt,lywc−eh71ma67n7aginelythfeocruibsi−t1oo17n4l67croibniftoorl.mation44,..55although it
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