Efficient Construction of Atomic-Resolution Models of Non-Sulfated Chondroitin Glycosaminoglycan Using Molecular Dynamics Data

Abstract

Glycosaminoglycans (GAGs) are linear, structurally diverse, conformationally complex carbohydrate polymers that may contain up to 200 monosaccharides. These characteristics present a challenge for studying GAG conformational thermodynamics at atomic resolution using existing experimental methods. Molecular dynamics (MD) simulations can overcome this challenge but are only feasible for short GAG polymers. To address this problem, we developed an algorithm that applies all conformational parameters contributing to GAG backbone flexibility (i.e., bond lengths, bond angles, and dihedral angles) from unbiased all-atom explicit-solvent MD simulations of short GAG polymers to rapidly construct models of GAGs of arbitrary length. The algorithm was used to generate non-sulfated chondroitin 10- and 20-mer ensembles which were compared to MD-generated ensembles for internal validation. End-to-end distance distributions in constructed and MD-generated ensembles have minimal differences, suggesting that our algorithm produces conformational ensembles that mimic the backbone flexibility seen in simulation. Non-sulfated chondroitin 100- and 200-mer ensembles were constructed within a day, demonstrating the efficiency of the algorithm and reduction in time and computational cost compared to simulation.

Constructing 3-Dimensional Atomic-Resolution Models of Nonsulfated Glycosaminoglycans with Arbitrary Lengths Using Conformations from Molecular Dynamics

“…System construction, energy minimization, and heating followed the same protocol we described previously [ 33 ]. Briefly, all polymers were constructed with an explicit solvent using the CHARMM software [ 83 , 84 , 85 ] v. c41b2 with the CHARMM36 (C36) biomolecular force field for carbohydrates [ 57 , 61 , 62 , 63 ].…”

“…Production simulations were performed using a similar protocol as previously described [ 33 ] but with a longer timescale and lower frequency for saving snapshots. Briefly, using the CHARMM software, each of four replicates (per GAG system) was equilibrated.…”

“…The MD-generated conformational datasets described above made up the database used for the algorithm we developed to generate GAG polymer conformational ensembles of user-specified length and with a user-specified number of conformations (previously described) [ 33 ]. Essentially, our algorithm (1) incorporates all bond, bond angle, and dihedral angle conformational parameters from MD simulation of GAG 20-mers, (2) treats monosaccharide rings and glycosidic linkages independently, (3) performs a restrained energy minimization on each constructed conformation to relieve steric overlap while maintaining polymer conformation, and (4) applies a bond potential energy cutoff to exclude conformations that remain nonphysical after minimization.…”

“…Structural complexities arise from nontemplate-based synthesis [ 26 ] and variable sulfation [ 27 ], which means a single GAG type can have variable lengths and sulfation patterns, making it polydisperse and heterogeneous. Conformational complexities result from glycosidic linkage flexibility [ 28 , 29 , 30 , 31 , 32 , 33 ] and ring puckering [ 33 ]. There are several experimental techniques for studying GAGs, including liquid chromatography-mass spectrometry (LC-MS) [ 34 , 35 , 36 ], X-ray crystallography [ 37 , 38 , 39 , 40 , 41 , 42 ], and nuclear magnetic resonance (NMR) [ 43 , 44 , 45 , 46 ], but no single technique is able to account for all of these complexities.…”

“…As an alternative approach to obtaining atomic-resolution, three-dimensional, conformational ensembles of long GAG biopolymers, we developed an algorithm that uses glycosidic linkage and monosaccharide ring conformations from unbiased all-atom explicit-solvent MD simulations [ 57 , 61 , 62 , 63 ] of GAG 20-mers (i.e., 20 monosaccharide units) to rapidly generate GAG polymer conformational ensembles of user-specified length and with a user-specified number of conformations [ 33 ]. In our previous work, we examined nonsulfated chondroitin GAGs.…”