Topology of internally constrained polymer chains.

Area of Science:

• Complex systems biology
• Computational biophysics
• Polymer physics

Background:

• Linear chains, such as proteins and chromosomes, exhibit diverse topologies crucial for their function and potential toxicity.
• Understanding the control mechanisms governing transitions between these topological states is a significant challenge in various biological systems.

Purpose of the Study:

• To investigate how interactions with a binding partner influence the topological dynamics of a linear chain.
• To determine if external contacts can modulate the formation and stability of specific chain topologies.

Main Methods:

• Utilized Monte Carlo and Molecular Dynamics simulations to model a linear chain with intra-chain contacts.
• Analyzed the effect of two-point contacts with a binding partner on topological transitions.
• Computed 'folding-time landscapes' to map folding times across different topological states.

Main Results:

• Two point contacts with a binding partner are sufficient to either accelerate or decelerate the formation of specific topologies.
• These contacts deform the computed folding-time landscapes, altering the probability of occupying different topological states.
• Demonstrated external control over chain topology formation and dynamics.

Conclusions:

• External interactions, like those with binding partners, provide a mechanism to regulate the topological dynamics of linear chains.
• This control allows for directed formation of specific or more complex topologies.
• Findings have implications for understanding molecular chaperones, genome architecture, and evolutionary processes.