A coarse-grained model for the formation of α helix with a noninteger period on simple cubic lattices

Effect of polymer rigidity on the phase behaviour of polymer adsorption on to planar surface

We study the process of a semiflexible polymer chain adsorption on to planar surface by the dynamic Monte Carlo (DMC) method, based on the 3D off-lattice model. Both the strength of attractive monomer-surface interaction (ε_a) and bending energy (b) have pronounced effect on the adsorption and shape of semiflexible polymer chain. The semiflexible polymer can just fully adsorb on to the surface at certain ε_a, which is defined as critical ε_a The essential features of the semiflexible polymer adsorption on to surface are that (i) the critical ε_a increases with increase in b; (ii) the shape of the fully adsorbed semiflexible polymer chain is film-like toroid, and the toroid becomes more and more perfect with increase in b In addition, the size of toroid and the number of turns of toroid can be controlled by the b and ε_a.

Wrapping/unwrapping transition of double-stranded DNA in DNA-nanosphere complexes induced by multivalent anions

Wrapping and unwrapping behaviors of double-stranded DNA around a positively charged nanosphere in solution are studied by using the coarse-grained molecular dynamics (CGMD) simulation method. When monovalent, divalent and trivalent anions are added to the DNA-nanosphere complex solution, double-stranded DNA binds with a nanosphere owing to strong electrostatic attraction. However, when tetravalent anions are added to the DNA-nanosphere complex solution, local charge inversion is observed for a high anion concentration of tetravalent anions and the double-stranded DNA can be unwrapped from the nanosphere because of the local charge inversion near the nanosphere. Moreover, the helical structure of DNA is damaged when double-stranded DNA wraps around the nanosphere and the helical structure can be rebuilt when the double-stranded DNA unwraps from the nanosphere. This study can help us understand how to control the release of DNA in DNA-nanosphere complexes.

Construction of an intermediate-resolution lattice model and re-examination of the helix-coil transition: a dynamic Monte Carlo simulation

In protein modeling, spatial resolution and computational efficiency are always incompatible. As a compromise, an intermediate-resolution lattice model has been constructed in the present work. Each residue is decomposed into four basic units, i.e. the α-carbon group, the carboxyl group, the imino group, and the side-chain group, and each basic coarse-grained unit is represented by a minimum cubic box with eight lattice sites. The spacing of the lattice is about 0.56 Å, holding the highest spatial resolution for the present lattice protein models. As the first report of this new model, the helix-coil transition of a polyalanine chain was examined via dynamic Monte Carlo simulation. The period of formed α-helix was about 3.68 residues, close to that of a natural α-helix. The resultant backbone motion was found to be in the realistic regions of the conformational space in the Ramachandran plot. Helix propagation constant and nucleation constant were further determined through the dynamic hydrogen bonding process and torsional angle variation, and the results were used to make comparison between classical Zimm-Bragg theory and Lifson-Roig theory based on the Qian-Schellman relationship. The simulation results confirmed that our lattice model can reproduce the helix-coil transition of polypeptide and construct a moderately fine α-helix conformation without significantly weakening the priority in efficiency for a lattice model.

The phase behavior of polyethylene ring chains

The equilibrium properties of an isolated polyethylene ring chain are studied by using molecular dynamics (MD) simulations. The results of an 80-bond linear chain are also presented, which are in agreement with previous studies of square-well chains and Lennard-Jones (LJ) homopolymers. Mainly, we focus on the collapse of polyethylene ring chains. At high temperatures, a fully oblate structure is observed for the ring chains with different chain lengths. For such an oblate structure, a shape factor of delta(*)=0.25 and a rodlike scaling relation between the radius of gyration and chain lengths could be deduced easily in theory, and the same results are obtained by our MD simulations. Such an oblate structure can be obtained by Monte Carlo simulation only for sufficient stiff ring chains. When the temperature decreases, an internal energy barrier is observed. This induces a strong peak in the heat capacity, denoting a gas-liquid-like transition. This energy barrier comes mainly from the local monomer-monomer interactions, i.e., the bond-stretching, the bond-bending, and the torsion potentials. A low temperature peak is also observed in the same heat capacity curve, representing a liquid-solid-like transition. These numerical simulation results support a two-stage collapse of polyethylene ring chains; however, the nature should be different from the square-well and LJ ring chains.

The effect of sequence on the conformational stability of a model heteropolymer in explicit water

We investigate the properties of a two-dimensional lattice heteropolymer model for a protein in which water is explicitly represented. The model protein distinguishes between hydrophobic and polar monomers through the effect of the hydrophobic monomers on the entropy and enthalpy of the hydrogen bonding of solvation shell water molecules. As experimentally observed, model heteropolymer sequences fold into stable native states characterized by a hydrophobic core to avoid unfavorable interactions with the solvent. These native states undergo cold, pressure, and thermal denaturation into distinct configurations for each type of unfolding transition. However, the heteropolymer sequence is an important element, since not all sequences will fold into stable native states at positive pressures. Simulation of a large collection of sequences indicates that these fall into two general groups, those exhibiting highly stable native structures and those that do not. Statistical analysis of important patterns in sequences shows a strong tendency for observing long blocks of hydrophobic or polar monomers in the most stable sequences. Statistical analysis also shows that alternation of hydrophobic and polar monomers appears infrequently among the most stable sequences. These observations are not absolute design rules and, in practice, these are not sufficient to rationally design very stable heteropolymers. We also study the effect of mutations on improving the stability of the model proteins, and demonstrate that it is possible to obtain a very stable heteropolymer from directed evolution of an initially unstable heteropolymer.