Monte Carlo simulation of protein folding with orientation-dependent monomer-monomer interactions

Translocation of a proteinlike chain through a finite channel

We use the pruned-enriched-Rosenbluth method and the modified orientation-dependent monomer-monomer interaction model to study the translocation of a proteinlike chain through a finite channel. The mean-square radius of gyration per bond <S2>/N and shape factor <delta*> of proteinlike chains with different secondary structures transporting through a finite channel with different channel radii R=1, 2, 3, 4, and 20 are investigated in the translocation. The average Helmholtz free energy per bond A/N and the mechanical force f are also presented. A/N remains unchanged when X(0)<0 and X(0)>1, and decreases monotonously when 0.5<X(0)<0.1. Here X(0)=X/N identical with 2X/L,X is the position of the first monomer, N is chain length, and L is channel length. No free energy barrier is found in our calculation. f is negative and has a plateaulike behavior. The plateau becomes narrow and the value of f increases as R increases. The total energy per bond <U>/N is also calculated in the process of translocation. An energy barrier is shown. The proteinlike chains must cross this energy barrier when they escape from the channel. The position of the maximum of <U>/N depends on the secondary structures and the channel radius. We also discuss the average contact energy per bond <U>c/N, the average alpha-helical energy per bond <U>h/N, and the average beta-sheet energy per bond <U>b/N.

Adsorption of charged albumin subdomains on a graphite surface

We report some new molecular dynamics simulation results about the adsorption on a hydrophobic graphite surface of two albumin subdomains, each formed by three different alpha-helices, considering the correctly charged side groups at pH = 7 instead of the neutral ones as done in our previous exploratory paper (Raffaini and Ganazzoli, Langmuir 2003;19:3403-3412). We find that the presence of charges affects somewhat the initial adsorption stage on the electrostatically neutral surface, but not the final one. Thus, we recover the result that a monolayer of aminoacids is eventually formed, with a rough parallelism of distant strands to optimize both the intramolecular and the surface interactions. This feature is consistent with the adsorption on the hydrophobic surface being driven by dispersion forces only, and with the "soft" nature of albumin. Additional optimizations of the final monolayer carried out at pH = 3 and 11 do not modify appreciably this picture, suggesting that adsorption on graphite is basically independent of pH. The enhanced hydration of the final adsorption state due to the (delocalized) charges of the side groups is also discussed in comparison with similar results of the neutralized subdomains.

Protein adsorption on the hydrophilic surface of a glassy polymer: a computer simulation study

Using atomistic computer simulations, we study the adsorption of different globular protein fragments with different secondary structures on the surface of a hydrophilic glassy polymer, poly(vinyl alcohol), or PVA, and compare the results with our earlier calculations on hydrophobic graphite. The simulations were mainly carried out with implicit solvent in an effective dielectric medium by energy minimizations and molecular dynamics at room temperature. We find that on the hydrophilic PVA surface the fragments basically retain their globular shape with an incomplete denaturation, at variance with our earlier results for the same fragments on graphite. Correspondingly, the interaction energy between the fragments and the surface is significantly smaller than on graphite, both because less residues are in contact with the surface, and because they interact more weakly. Moreover, very few hydrogen bonds are formed between the adsorbate and the PVA surface, since both the protein fragments and the polymer chains separately optimize these interactions. Additional molecular dynamics simulations in explicit solvent were also performed to study the hydration of the adsorbed fragments and to estimate the possible solvation effects.

Molecular dynamics simulation of the adsorption of a fibronectin module on a graphite surface

We report atomistic simulations of the adsorption of a fibronectin type I module on a hydrophobic graphite surface. This module comprises only beta-sheets, unlike the albumin fragments previously investigated by us which contained only alpha-helices (Raffaini, G.; Ganazzoli, F. Langmuir 2003, 19, 3403-3412). As done in the latter case, most simulations are carried out in an effective dielectric medium by energy minimizations and molecular dynamics (MD). Further optimizations and MD runs in the explicit presence of water are also performed to assess the stability of the geometries found and to describe the solvation of the adsorbed fibronectin module. The initial adsorption is accompanied by local rearrangements of the strands in contact with the surface, but the overall molecular structure is largely preserved. Much larger rearrangements take place at longer times as found through the MD runs, with the molecule spreading as much as possible so as to maximize the surface coverage, hence the interaction energy, despite a significant strain energy. Energetic aspects of adsorption together with the concomitant size change are discussed in comparison with our previous results for two albumin fragments.

Protein refolding versus aggregation: computer simulations on an intermediate-resolution protein model

Computer simulations are performed on a system of eight model peptide chains to study how the competition between protein refolding and aggregation affects the optimal conditions for refolding of four-helix bundles. The discontinuous molecular dynamics algorithm is utilized along with an intermediate-resolution protein model that we developed for this work. Physically, the model is much more detailed than any model used to date for simulations of protein aggregation. Each model residue consists of a detailed, three-bead backbone and a simplified, single-bead side-chain. Excluded volume, hydrogen bond, and hydrophobic interactions are modeled with discontinuous (i.e. hard-sphere and square-well) potentials. Simulations efficiently sample conformational space, and complete folding trajectories from random initial configurations to two four-helix bundles are possible within two days on a single processor workstation. Folding of the bundles follows two main pathways, one through a trimeric intermediate and the other through an intermediate with two dimers. The proportion of trajectories that follow each route is significantly different for the eight-peptide system in this work than in a previously studied four-peptide system, which yields one four-helix bundle, suggesting, as our previous simulations have, that protein folding properties are strongly influenced by the presence of other proteins. Folding of the bundles is optimal within a fixed temperature range, with the high-temperature boundary a function of the complexity of the protein (or oligomer) to be folded and the low-temperature boundary a function of the complexity of the protein's environment. Above the optimal temperature range for folding, the model chains tend to unfold; below the optimal range, the model chains tend to aggregate. As has been seen previously, aggregates have substantial levels of native secondary structure, suggesting that aggregates are composed largely of partially folded intermediates, not denatured chains.

Folding of bundles of alpha-helices in solution, membranes, and adsorbed overlayers

We propose a coarse-grained lattice model for Monte Carlo simulations of folding of proteins consisting of several alpha-helices. A chain representing a protein is considered to contain A and B monomers forming relatively stiff A subchains, mimicking helices, and flexible B links between these subchains, respectively. Using this model, we simulate (1) folding of four-helix proteins in solution; (2) folding of membrane proteins containing one, two, or four helices; and (3) refolding of four-helix proteins adsorbed at the liquid-solid interface. For these cases, we show typical scenarios of protein folding and refolding and study the dependence of the folding time on the chain length. Combining the latter results with those already available in the literature, we discuss the relative rates of folding of proteins belonging to different classes.