Statistically Based Reduced Representation of Amino Acid Side Chains

Design of a rotamer library for coarse-grained models in protein-folding simulations

Rotamer libraries usually contain geometric information to trace an amino acid side chain, atom by atom, onto a protein backbone. These libraries have been widely used in protein design, structure refinement and prediction, homology modeling, and X-ray and NMR structure validation. However, they usually present too much information and are not always fully compatible with the coarse-grained models of the protein geometry that are frequently used to tackle the protein-folding problem through molecular simulation. In this work, we introduce a new backbone-dependent rotamer library for side chains compatible with low-resolution models in polypeptide chains. We have dispensed with an atomic description of proteins, representing each amino acid side chain by its geometric center (or centroid). The resulting rotamers have been estimated from a statistical analysis of a large structural database consisting of high-resolution X-ray protein structures. As additional information, each rotamer includes the frequency with which it has been found during the statistical analysis. More importantly, the library has been designed with a careful control to ensure that the vast majority of side chains in protein structures (at least 95% of residues) are properly represented. We have tested our library using an independent set of proteins, and our results support a good correlation between the reconstructed centroids from our rotamer library and those in the experimental structures. This new library can serve to improve the definition of side chain centroids in coarse-grained models, avoiding at the same time an excessive additional complexity in a geometric model for the polypeptide chain.

Minimal ensembles of side chain conformers for modeling protein-protein interactions

The goal of this article is to reduce the complexity of the side chain search within docking problems. We apply six methods of generating side chain conformers to unbound protein structures and determine their ability of obtaining the bound conformation in small ensembles of conformers. Methods are evaluated in terms of the positions of side chain end groups. Results for 68 protein complexes yield two important observations. First, the end-group positions change less than 1 Å on association for over 60% of interface side chains. Thus, the unbound protein structure carries substantial information about the side chains in the bound state, and the inclusion of the unbound conformation into the ensemble of conformers is very beneficial. Second, considering each surface side chain separately in its protein environment, small ensembles of low-energy states include the bound conformation for a large fraction of side chains. In particular, the ensemble consisting of the unbound conformation and the two highest probability predicted conformers includes the bound conformer with an accuracy of 1 Å for 78% of interface side chains. As more than 60% of the interface side chains have only one conformer and many others only a few, these ensembles of low-energy states substantially reduce the complexity of side chain search in docking problems. This approach was already used for finding pockets in protein-protein interfaces that can bind small molecules to potentially disrupt protein-protein interactions. Side-chain search with the reduced search space will also be incorporated into protein docking algorithms.

Molecular assessment of the elastic properties of collagen-like homotrimer sequences

Knowledge of the mechanical behavior of collagen molecules is critical for understanding the mechanical properties of collagen fibrils that constitute the main architectural building block of a number of connective tissues. In this study, the elastic properties of four different type I collagen 30-residue long molecular sequences, were studied by performing stretching simulations using the molecular mechanics approach. The energy-molecular length relationship was achieved by means of the geometry optimization procedure for collagen molecule strains up to 10%. The energy was interpolated by a second order function, and the second order of the derivative with respect to the mean length corresponded to the molecule stiffness. According to the hypothesis of linear elastic behavior, except for one sequence, the elastic modulus was around 2.40 GPa. These values are larger than fibril values, and they confirm the hypothesis that tendon mechanical properties are deeply related to tendon hierarchical structure. A possible explanation of the lowest values obtained for one sequence (1.33-1.53 GPa) is provided and discussed.