Toward the Accuracy and Speed of Protein Side-Chain Packing: A Systematic Study on Rotamer Libraries

Abstract

Protein rotamers refer to the conformational isomers taken by the side-chains of amino acids to accommodate specific structural folding environments. Since accurate modeling of atomic interactions is difficult, rotamer information collected from experimentally solved protein structures is often used to guide side-chain packing in protein folding and sequence design studies. Many rotamer libraries have been built in the literature but there is little quantitative guidance on which libraries should be chosen for different structural modeling studies. Here, we performed a comparative study of six widely used rotamer libraries and systematically examined their suitability for protein folding and sequence design in four aspects: (1) side-chain match accuracy, (2) side-chain conformation prediction, (3) de novo protein sequence design, and (4) computational time cost. We demonstrated that, compared to the backbone-dependent rotamer libraries (BBDRLs), the backbone-independent rotamer libraries (BBIRLs) generated conformations that more closely matched the native conformations due to the larger number of rotamers in the local rotamer search spaces. However, more practically, using an optimized physical energy function incorporated into a simulated annealing Monte Carlo searching scheme, we showed that utilization of the BBDRLs could result in higher accuracies in side-chain prediction and higher sequence recapitulation rates in protein design experiments. Detailed data analyses showed that the major advantage of BBDRLs lies in the energy term derived from the rotamer probabilities that are associated with the individual backbone torsion angle subspaces. This term is important for distinguishing between amino acid identities as well as the rotamer conformations of an amino acid. Meanwhile, the backbone torsion angle subspace-specific rotamer search drastically speeds up the searching time, despite the significantly larger number of total rotamers in the BBDRLs. These results should provide important guidance for the development and selection of rotamer libraries for practical protein design and structure prediction studies.

Figure 1.

Dihedral angle (χ_1–4) reproduction rates (a) and the minimal side-chain RMSD achievable (b) using rotamer libraries L1—L6 on 136 proteins.

Figure 2.

Native sequence recapitulation (a) on 136 proteins and the distribution of sequence identities (b) between the native and designed sequences obtained using rotamer libraries L1—L6.

Figure 3.

Average CPU time for side-chain prediction (a) and de novo sequence design (b) on 136 proteins.

Figure 4.

Native sequence recapitulation (a) on 136 proteins and the distribution of sequence identities (b) between the native and designed sequences obtained using rotamer libraries L1—L3 when the rotamer probability term (E_ROT) was disabled.

Figure 5.

Native sequence recapitulation (a) on 136 proteins and the average sequence identity (b) between the native and designed sequences achieved by adding native conformers to rotamer libraries L1—L6.