Amylose contributes to starch crystallinity, but the stability of packed amylose double helices in water at elevated temperature remains insufficiently characterized. Here, we used molecular dynamics simulations to test whether chain length affects the short-timescale stability of A-type amylose oligomers in water. Six systems differing in chain length (6, 12, or 24 glucose units per chain) and oligomer size (isolated double strand or dodecamer of six double strands) were simulated, and five independent 1-μs production runs were analyzed for each simulated condition. Oligomers with six glucose units showed structural collapse accompanied by increased water penetration. By contrast, dodecamers with 12 or 24 glucose units largely retained packed double-helical organization over the simulated timescale, although fraying was observed at their ends. These results indicate that chain length and lateral packing strongly affect the early structural response of amylose-like crystalline segments in hot water. The present simulations do not establish the ultimate fate of longer oligomers at longer timescales, but they identify a relative stability difference that is relevant to molecular interpretations of hydration-driven disordering in starch.
The structural feasibility of chain folding within an accepted cellulose-II structure is investigated in this study. We incorporate 3-residue and 5-residue folded glucosyl turns into a cellulose-II fibril crystal model to assess if the dominant structure can be retained. Ten candidate turn models were generated by meta...
Ling-Han Kong, S. J. Eichhorn, Richard A. Bryce· Biomacromolecules· 0 citations
Macromolecular coil-to-helix transitions simultaneously modify local geometry and persistence length, driving complex changes in overall chain size. Here, we apply the wormlike (persistent) chain model to both coil and helical fragments to examine how the degree of helicity, θ, and average helical fragment length, kh,...
Karthik C Sinha, Alexey A. Gavrilov, Artem M. Rumyantsev· Journal of Chemical Physics· 1 citation
This work presents a minimal coarse-grained molecular dynamics model for the coil-helix transition in polymers. We demonstrate that the addition of a Morse potential to a freely jointed chain with volume and bond potentials is sufficient to reproduce the essential thermodynamic features of the transition. From the simu...
Karthik C Sinha, Alexey A. Gavrilov, Artem M. Rumyantsev· Journal of Chemical Physics· 1 citation
Rec recombinant collagen mimetic peptides containing extended native sequences from the α1(I) and α2(I) chains of human type I collagen provide a plausible explanation for the longstanding paradox that extended collagen triple helices exhibit persistent sequence-dependent thermodynamic heterogeneity despite a two-state...
Sophie Youngji Xu, Sam Wong, Sally Tan et al.· bioRxiv· 0 citations
The dissolution of wax esters (WEs) in liquid oils plays a central role in the bulk solution thermodynamic characteristics, yet the molecular origins of their solubility remain poorly understood. In the current study, the fluid organization of WEs in medium-chain triacylglycerol (TAG) was explored using molecular dynam...
Daniel Golodnizky, H. Brykczynski, Carlos E. S. Bernardes et al.· The Physics of Fluids· 0 citations
Helical segments in polymer chains are often transient, finite, and dynamically evolving, yet their origin and stability remain incompletely understood. Here, we develop a minimal coarse-grained statistical-mechanical theory that explains how such "living helices" emerge in fluctuating polymer systems. Using a three-st...
Biman Bagchi· Journal of Chemical Physics· 0 citations
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