Rigorous analysis of free solution glycosaminoglycan dynamics using simple, new tools

Abstract

Heparin/heparan sulfates (H/HS) are ubiquitous biopolymers that interact with many proteins to induce a range of biological functions. Unfortunately, how these biopolymers recognize their preferred protein targets remain poorly understood. It is suggested that computational simulations offer attractive avenues but a number of challenges, e.g., difficulty of selecting a comprehensive force field, few simple tools to interpret data, among others, remain. This work addresses several such challenges so as to help ease the implementation and analysis of computational experiments. First, this work presents a rigorous comparison of two different recent force fields, CHARMM36 and GLYCAM06, for H/HS studies. Second, it introduces two new straightforward parameters, i.e., end-to-end distance and minimum volume enclosing ellipsoid, to understand the myriad conformational forms of oligosaccharides that evolve over time in water. Third, it presents an application to elucidate the number and nature of inter and intramolecular, nondirect bridging water molecules, which help stabilize unique forms of H/HS. The results show that nonspecialists can use either CHARMM36 or GLYCAM06 force fields because both gave comparable results, albeit with small differences. The comparative study shows that the HS hexasaccharide samples a range of conformations with nearly equivalent energies, which could be the reason for its recognition by different proteins. Finally, analysis of the nondirect water bridges across the dynamics trajectory shows their importance in stabilization of certain conformational forms, which may become important for protein recognition. Overall, the work aids nonspecialists employ computational studies for understanding the solution behavior of H/HS.

In-Depth Molecular Dynamics Study of All Possible Chondroitin Sulfate Disaccharides Reveals Key Insight into Structural Heterogeneity and Dynamism

“…Yet, it is important to ascertain that essentially the entire conformational space is sampled within the simulation timeframe. To ensure this, MD experiments on GAG oligosaccharides have been performed over a wide range (ns→µs) [ 22 , 23 , 36 , 37 , 41 ]. It is important to use an appropriate simulation time that ensures optimal sampling without extending the duration unnecessarily.…”

“…Intra-Molecular Hydrogen Bonds and Conformational Dynamism— The number and nature of intra-molecular hydrogen bonds (H-bonds) formed during MD simulations were analyzed using cpptraj. H-bonds were defined using 3.0 Å and 135° cut offs between appropriate donor and acceptor atoms, respectively, as described earlier [ 23 , 34 , 50 , 51 ]. Figure S9 shows the formation of H-bonds, if any, in conformations corresponding to the global minimum for all 16 disaccharides.…”

“…Inter-Molecular H-Bonds and Topological Preferences— Although sulfate groups dominate the interaction of GAGs with proteins, solvent molecules, i.e., H 2 O, play a key role in generating and maintaining local topologies for protein recognition [ 4 , 23 , 39 , 52 ]. In fact, nearly all crystal structures display GAG-bound water molecules [ 52 ].…”

“…One reason for this is that computational studies on CS in particular, and GAGs in general, are difficult. The large number of building blocks, e.g., 16 in the case of CS, which does not include DS building blocks, imposes significant challenges in terms of computational time and analysis [ 21 , 22 , 23 , 24 ]. In fact, no examples of computationally designed CS sequences that have reached a high level of clinical development are available in the literature.…”

The Influences of Sulphation, Salt Type, and Salt Concentration on the Structural Heterogeneity of Glycosaminoglycans

“…Other biophysical approaches for studying GAGs include X-ray crystallography, of GAGs alone [ 31 , 32 ] or in complex with proteins [ 33 , 34 , 35 , 36 , 37 , 38 ], as well as solution nuclear magnetic resonance (NMR) spectroscopy [ 39 , 40 ]. Compared to experimental techniques, MD simulations are an attractive and relatively inexpensive tool for exploring conformational transitions in GAGs at a microsecond time scale and with atomic resolution [ 41 , 42 , 43 , 44 ]. Simulations have been used extensively to study the conformational plasticity of different GAGs including hyaluronan [ 45 ], chondroitin sulphate [ 46 ], and heparan sulphate [ 47 ].…”