Collapse and Folding of Block Copolymers


The protein folding problem involves an attempt to elucidate the tertiary structure of biologically active proteins from their amino acid sequence. One approach to this problem is to strip the protein of all its complexity and to build up knowledge of folding, starting from the very simplest systems. The aim of this approach is to bring to light some of the very general laws of polymer/protein folding. In our research we use a model polymer chain consisting of alternating sequences of hydrophilic and hydrophobic segments. At sufficiently low temperatures this chain undergoes a "collapse" transition, in which the hydrophobic regions micro phase separate from the hydrophilic ones. Our aim is to elucidate general dynamical laws governing this type of "collapse" using Brownian dynamics simulations. Even for a relatively simple system such as this, the computer time required to obtain good results is very large. Where previous studies were restricted to equilibrium conditions, the new APAC National Facility will allow us to examine the much more interesting and physically relevant problem of dynamics.


Principal Investigator

David Williams
Applied Mathematics
RSPhysSE
ANU

Project

x20

Facilities Used

SC

Co-Investigator

Ira Cooke
Applied Mathematics
RSPhysSE
ANU

RFCD Codes

240202, 249901


Significant Achievements, Anticipated Outcomes and Future Work

Our research looks at the collapse of copolymers where one monomer type is in a good solvent and the other is in a poor solvent. One of the key differences between such copolymer systems and those of homopolymers (one monomer type only) is the additional variability afforded by different backbone chain sequences. The influence of backbone chain sequence on polymer collapse is clearly of relevance to the important question of bio polymer folding but is presently not well understood. As a beginning to this type of work we have made a study of the effect of sequence "blockyness" on the collapse of polymers from random coil to compact globule. In this work, polymers were represented by simple bead and spring models, and the collapse process was studied using Langevin dynamics simulations over a range of temperatures. We found that "blockyness" has a strong influence on the thermodynamics and kinetics of collapse and also on the nature of the collapsed state.

Having completed an initial study of the effect of blockyness on collapse, our attention in the coming year will turn towards a more detailed study of the nature of collapsed states. Of particular interest is the formation of intra-chain micelles (see illustration), which show promise as drug delivery agents. Our aim will be to determine the mechanisms underlying their formation and stability, as well as the number that form along a given polymer chain.

Collapsed state of a polymer in aqueous solution with alternating hydrophilic (light) and hydrophobic (dark) monomers. Note the presence of micelle like structures.

 

Computational Techniques Used

The primary computational task in our work is the calculation of forces for Langevin dynamics simulations. We make use of standard algorithms for this type of work such as nesting lists and lookup tables.