Unraveling the structural and molecular properties of 34-residue levans with various branching degrees by replica exchange molecular dynamics simulations

Abstract

Levan has various potential applications in the pharmaceutical and food industries, such as cholesterol-lowering agents and prebiotics, due to its beneficial properties, which depend on its length and branching degree. A previous study also found that the branching degree of levan affected anti-tumor activities against SNU-1 and HepG2 tumor cell lines. Despite its promising potential, the properties of levans with different branching degrees are not well understood at the molecular level. In two models of the generalized Born implicit solvent (GBHCT and GBOBC1), we employed replica-exchange molecular dynamics simulations to explore conformational spaces of 34-residue levans (L34) with branching degrees of zero (LFO34B0), one (LFO34B1), three (LFO34B3) and five (LFO34B5), as well as to elucidate their structural and molecular properties. To ensure a fair comparison of the effects of branching degree on these properties, we focused on analyzing the properties of the central 21-residue of the main chains of all systems. Our results show that all major representative conformations tend to form helix-like structures with kinks, where two-kink helix-like structures have the highest population. As branching degree increases, the population of helix-like structures with zero or one kink tends to increase slightly. As the number of kinks in the structures with the same branching degree increases, the average values of the lengths and angles among centers of masses of three consecutive turns of residue i, i+3, and i+6 tended to decrease. Due to its highest occurring frequencies, the O6 (i)-H3O (i+1) hydrogen bond could be important for helix-like structure formation. Moreover, hydrogen bonds forming among the branching residue (br), branching position (bp) and other residues of L34B1, L34B3 and L34B5 were identified. The O1(bp)-H3O(br), O1(br)-H3O(br) and O5(br)-H1O(br) hydrogen bonds were found in the first-, second- and third-highest occurrence frequencies, respectively. Our study provides novel and important insights into conformational spaces and the structural and molecular properties of 34-residue levans with various branching degrees, which tend to form helix-like structures with kinks.

Fig 1

(a) Levan structure. (b) Simplified models of L_34B0, L_34B1, L_34B3 and L_34B5. LC₂₁ and the first, second and third frames of reference for angle_3tc21 measurement are also shown. (c) Example of angle_3tc21 measurement for structure of L_34B3, using the first frame of reference.

Fig 2. Relative free energy (kcal/mol) maps of L_34B0 (a), L_34B1 (b), L_34B3 (c) and L_34B5 (d) simulated in the GB_HCT model, as characterized by the number of kinks of the central 21 residue region of the main chain and LC₂₁.

Their major representative conformers and populations are also shown.

Fig 3. Relative free energy (kcal/mol) maps of L_34B0 (a), L_34B1 (b), L_34B3 (c) and L_34B5 (d) simulated in GB_OBC1 model as characterized by number of kinks in the central 21 residue of the main chain and LC₂₁.

Their major representative conformers and populations are also shown.

Fig 4

(a) Hydrogen bonds found in main chains. Middle; O6_(i)—H3O_(i+1) hydrogen bond. Right; O1_(i)—H3O_(i) hydrogen bond. Left; O5_(i)—H1O_(i) hydrogen bond. (b) Hydrogen bonds involved in branching residues. The two-kink helix-like structure of L_34B3 simulated in the GB_HCT model is shown as an example. Hydrogen bonds are represented as dashed lines. The levan chain and fructosyl units are represented as ribbons and filled yellow representations, respectively.

Fig 5. The occurrence frequencies of ω, ψ and ϕ between every two fructosyl residues of LFO_34B0, LFO_34B1, LFO_34B3 and LFO_34B5 simulated in the GB_HCT model.

Each dihedral angle is shown in different color.