Secondary structure determines protein topology

Abstract

Using a test set of 13 small, compact proteins, we demonstrate that a remarkably simple protocol can capture native topology from secondary structure information alone, in the absence of long-range interactions. It has been a long-standing open question whether such information is sufficient to determine a protein's fold. Indeed, even the far simpler problem of reconstructing the three-dimensional structure of a protein from its exact backbone torsion angles has remained a difficult challenge owing to the small, but cumulative, deviations from ideality in backbone planarity, which, if ignored, cause large errors in structure. As a familiar example, a small change in an elbow angle causes a large displacement at the end of your arm; the longer the arm, the larger the displacement. Here, correct secondary structure assignments (alpha-helix, beta-strand, beta-turn, polyproline II, coil) were used to constrain polypeptide backbone chains devoid of side chains, and the most stable folded conformations were determined, using Monte Carlo simulation. Just three terms were used to assess stability: molecular compaction, steric exclusion, and hydrogen bonding. For nine of the 13 proteins, this protocol restricts the main chain to a surprisingly small number of energetically favorable topologies, with the native one prominent among them.

Figure 1.

(A) The protein G (1pgb) backbone simulated using only secondary structure constraints and steric exclusion. The native structure (left) and the five conformers with lowest RMSD to the native structure are shown; none of the five capture native topology. The overall population has a mean radius of gyration, <Rg>, resembling that of unfolded proteins. Monte Carlo simulations were performed as described in the text with steric exclusion as the sole criterion for acceptance. (B) Conformations of the protein G backbone simulated as in A plus a confinement score. The native structure (left) and the five conformers with lowest RMSD to the native structure (RMSD of 5.0 Å–5.5 Å) are shown. Although compact, the population still lacks native topology. The confinement score is described in Materials and Methods. (C) Conformations of the protein G backbone simulated as in B plus a hydrogen bond score. The native structure (left) and five conformers with lowest normalized RMSD to the native structure (RMSD of 1.9 Å–3.2 Å) are shown. Conformers having native topology are now abundant. The hydrogen bond score is described in Materials and Methods.

Figure 2.

Proteins with correct topology and low RMSD scores. In each case, the native structure is on the left, and the structure with lowest RMSD from the largest cluster is on the right, labeled with its RMSD.

Figure 3.

Proteins with similar topology but poor accuracy. In each case, the native structure is on the left, and the structure with lowest RMSD from the largest cluster is on the right, labeled with its RMSD. For the two helical proteins, hydrogen bonds alone are insufficient to select the correct helix orientation; long-range hydrophobic interactions are probably required. The two larger proteins have more complicated topologies and may also suffer from omission of long-range interactions.