How Cooperatively Folding Are Homopolymer Molecular Knots?

Journal Article · Thu Sep 22 00:00:00 EDT 2022 · Macromolecules

DOI:https://doi.org/10.1021/acs.macromol.2c00881· OSTI ID:1899348

Walker, Christopher C. ^[1]; Fobe, Theodore L. ^[2]; Shirts, Michael R. ^[2]

---

1. Univ. of Colorado, Boulder, CO (United States); University of Colorado Boulder
2. Univ. of Colorado, Boulder, CO (United States)

Detailed thermodynamic analysis of complex systems with multiple stable configurational states allows for insight into the cooperativity of each individual transition. In this work, we derive a heat capacity decomposition comprising contributions from each individual configurational state, which together sum to a baseline heat capacity, and contributions from each state-to-state transition. We apply this analysis framework to a series of replica exchange molecular dynamics simulations of linear and 1-1 coarse-grained homo-oligomer models, which fold into stable, configurationally well-defined molecular knots, in order to better understand the parameters leading to stable and cooperative folding of these knots. We find that a stiff harmonic backbone bending angle potential is key to achieving knots with specific 3D structures. Tuning the backbone equilibrium angle in small increments yields a variety of knot topologies. Populations of different knotted states as a function of temperature can also be manipulated by tuning the backbone torsion stiffness or by adding side-chain beads. We find that sharp total heat capacity peaks for the homo-oligomer knots are largely due to a coil-to-globule transition rather than a cooperative knotting step. Furthermore, in some cases, the cooperativity of globule-to-knot and coil-to-globule transitions is comparable, suggesting that highly cooperative folding to knotted structures can be achieved by refining the model parameters or adding sequence specificity.

• Research Organization: Univ. of Colorado, Boulder, CO (United States)
• Sponsoring Organization: National Science Foundation (NSF); USDOE Office of Science (SC), Basic Energy Sciences (BES)
• Grant/Contract Number: SC0018651
• OSTI ID: 1899348
• Journal Information: Macromolecules, Journal Name: Macromolecules Journal Issue: 19 Vol. 55; ISSN 0024-9297
• Publisher: American Chemical Society
• Country of Publication: United States
• Language: English

Related Subjects

36 MATERIALS SCIENCE
chemical structure
foldamers
heat capacity
knots
mathematical methods
phase transitions
stiffness
thermodynamics