Secondary globular structure of copolymers containing amphiphilic and hydrophilic units: Computer simulation analysis (original) (raw)

Globular structures of a helix-coil copolymer: Self-consistent treatment

The Journal of Chemical Physics, 2007

A self-consistent field theory was developed in the grand-canonical ensemble formulation to study transitions in a helix-coil multiblock globule. Helical and coil parts are treated as stiff rods and self-avoiding walks of variable lengths correspondingly. The resulting field-theory takes, in addition to the conventional Zimm-Bragg parameters, also three-dimensional interaction terms into account. The appropriate differential equations which determine the self-consistent fields were solved numerically with finite element method. Three different phase states are found: open chain, amorphous globule and nematic liquid-crystalline (LC) globule. The LC-globule formation is driven by the interplay between the hydrophobic helical segments attraction and the anisotropic globule surface energy of an entropic nature. The full phase diagram of the helix-coil copolymer was calculated and thoroughly discussed. The suggested theory shows a clear interplay between secondary and tertiary structures in globular homopolypeptides.

HA (Hydrophobic/Amphiphilic) Copolymer Model: Coil−Globule Transition versus Aggregation

Macromolecules, 2004

For simulating hydrophobic-amphiphilic (HA) copolymers, we have developed a "side-chain" HA model in which hydrophilic (P) interaction sites are attached to hydrophobic (H) main chain, thereby forming amphiphilic (A) monomer units, each with dualistic (hydrophobic/hydrophilic) properties. Using this coarse-grained model, we performed molecular dynamics simulations of the hydrophobically driven self-assembly in a selective solvent, for both single-chain and multichain systems. The focus is on the regime in which H and P interaction sites are strongly segregated. Single-chain simulations are performed for copolymers with the same HA composition but with different distribution of H and A monomer units along the hydrophobic backbone, including regular copolymers comprising H and A units in alternating sequence, (HA) x, regular multiblock copolymers (HLAL)x composed of H and A blocks of equal lengths L ) 3, and quasi-random proteinlike copolymers having quenched primary structure. In a solvent selectively poor for H sites, the proteinlike polyamphiphiles can readily adopt spherical-shaped compact conformations with the hydrophobic chain sections clustered at the globular core and the hydrophilic groups forming the envelope of this core and buffering it from solvent. Because of the fact that these globules are sizeand shape-persistent objects, they maintain their morphological integrity even in rather concentrated solutions where no large-scale aggregation is observed. Moreover, we find that the population of aggregates generally decreases with worsening solvent quality. The compact conformations of long regular copolymers tend to be strongly elongated in one direction.

Stability of dense hydrophobic-polar copolymer globules: Regular, random and designed sequences

The European Physical Journal E - Soft Matter, 2003

Stability of dense globular structures formed by amphiphilic copolymers consisting of hydrophobic (insoluble) units and a small fraction of single polar (soluble) monomer units is considered in the meanfield approximation for different types of unit distributions along the chain. Polar (P) units are located in a relatively thin surface layer due to their strong repulsion from hydrophobic (H) monomer units. We compared globules formed by different copolymer sequences with the same gross numbers of P-and H-units: regular HP-sequences (P-units separated by equal H-blocks), random copolymers (uncorrelated positions of P-units, i.e. Flory distribution of H-block lengths), proteinlike (PL) sequences (designed sequences involving both long H-blocks dominating by total mass, and short blocks dominating by number). We showed that PL-globules are more stable (lower free energy) and are characterized by a higher temperature of the coil-to-globule transition when compared with the other sequences mentioned above. We also considered HP-H-copolymers consisting of one long and many short hydrophobic blocks; we showed that it is these sequences that yield the dense globules corresponding to the lowest free energy.

Conformational properties of rigid-chain amphiphilic macromolecules: The phase diagram

Polymer Science Series A, 2008

The coil-globule transition in rigid-chain amphiphilic macromolecules was studied by means of computer simulation, and the phase diagrams for such molecules in the solvent quality-persistence length coordinates were constructed. It was shown that the type of phase diagram depends to a substantial extent on the degree of polymerization of a macromolecule. Relatively short amphiphilic macromolecules in the poor-solvent region always form a spherical globule, with the transition to this globule involving one or two intermediate conformations. These are the disk globule if the Kuhn segment is relatively large and the string of spherical micelles or the disk globule in the case of relative flexible chains. The phase diagram of a long rodlike amphiphilic chain turned out to be even more complex. Namely, three characteristic regions were distinguished in the region of a poor solvent, depending on the chain rigidity: the region of a cylindrical globule without certain order in the main chain, the region of the cylindrical globule with blobs having the collagen ordering of the chain, and the region of coexistence of collagen-like and toroidal globules. In the intermediate transitional region, not only conformations of strings of spherical micelle beads but also the necklace conformations in which the polymer chain in each bead has collagen ordering can occur in this case.

Protein-like copolymers: computer simulation

Physica A: Statistical Mechanics and its Applications, 1998

The notion of protein-like AB copolymers is introduced. Such copolymers can be generated with the help of the "instant image" of a dense homopolymer globule by assigning that the monomeric units closer to the globular surface are of A type, while the core is formed by the B type units. After that the primary structure of the chain is ÿxed, and one introduces di erent interaction potentials for A and B units. In doing so, we have in mind mainly aqueous systems and analogy with globular proteins, therefore A units are regarded as hydrophilic, and B units as hydrophobic. By means of Monte Carlo simulation using the bond uctuation model we study the coil-globule transition for a protein-like copolymer upon the increase of attraction of hydrophobic B units, and compare the results with those for random AB copolymers. From the analysis of the primary structure of protein-like copolymers one can see that the "degree of blockiness" of the protein-like sequence is higher than for random copolymers, therefore the copolymers with the "random-block" primary structure are generated for comparison as well (the average length of A and B sequences being the same as for protein-like copolymers). It is shown that the coil-globule transition in protein-like copolymers occurs at higher temperatures, is more abrupt and has faster kinetics than for random copolymers with the same A=B composition and for random-block copolymers with the same A=B composition and "degree of blockiness". The globules of protein-like copolymers exhibit a dense micelle-like core of hydrophobic B units stabilized by the long dangling loops of hydrophilic A units. Apparently, a protein-like copolymer "inherits" some of the properties of the "parent globule" which is re ected in the special long-range correlations in primary structure.

Thermodynamics of the coil to frozen globule transition in heteropolymers

1997

Recent analytic theories and computer simulations of heteropolymers have centered on the freezing transition of globular heteropolymers. We present a simple analytic theory to describe the coil to globule collapse in heteropolymers and compare this to the computer simulation of the exhaustive enumeration of all 18-mer cubic lattice polymer conformations. We find that the collapse transition from coil to frozen globule can either be first or second order.