Native-like Protein Structures Research Articles

Identifying native-like protein structures using physics-based potentials.

As the field of structural genomics matures, new methods will be required that can accurately and rapidly distinguish reliable structure predictions from those that are more dubious. We present a method based on the CHARMM gas phase implicit hydrogen force field in conjunction with a generalized Born implicit solvation term that allows one to make such discrimination. We begin by analyzing pairs of threaded structures from the EMBL database, and find that it is possible to identify the misfolded structures with over 90% accuracy. Further, we find that misfolded states are generally favored by the solvation term due to the mispairing of favorable intramolecular ionic contacts. We also examine 29 sets of 29 misfolded globin sequences from Levitt's "Decoys 'R' Us" database generated using a sequence homology-based method. Again, we find that discrimination is possible with approximately 90% accuracy. Also, even in these less distorted structures, mispairing of ionic contacts results in a more favorable solvation energy for misfolded states. This is also found to be the case for collapsed, partially folded conformations of CspA and protein G taken from folding free energy calculations. We also find that the inclusion of the generalized Born solvation term, in postprocess energy evaluation, improves the correlation between structural similarity and energy in the globin database. This significantly improves the reliability of the hypothesis that more energetically favorable structures are also more similar to the native conformation. Additionally, we examine seven extensive collections of misfolded structures created by Park and Levitt using a four-state reduced model also contained in the "Decoys 'R' Us" database. Results from these large databases confirm those obtained in the EMBL and misfolded globin databases concerning predictive accuracy, the energetic advantage of misfolded proteins regarding the solvation component, and the improved correlation between energy and structural similarity due to implicit solvation. Z-scores computed for these databases are improved by including the generalized Born implicit solvation term, and are found to be comparable to trained and knowledge-based scoring functions. Finally, we briefly explore the dynamic behavior of a misfolded protein relative to properly folded conformations. We demonstrate that the misfolded conformation diverges quickly from its initial structure while the properly folded states remain stable. Proteins in this study are shown to be more stable than their misfolded counterparts and readily identified based on energetic as well as dynamic criteria. In summary, we demonstrate the utility of physics-based force fields in identifying native-like conformations in a variety of preconstructed structural databases. The details of this discrimination are shown to be dependent on the construction of the structural database.

Solution Structure of a Designed Four-α-Helix Bundle Maquette Scaffold

The solution structure of a de novo designed disulfide-bridged two-R-helix peptide that self-assembles to form a 2-fold symmetric four-R-helix bundle protein (R'-SS-R')2 has been solved by NMR spectroscopy. The 33-residue peptide, (R'-SH), that is the basic building block of the bundle has been recombinantly expressed. The three-dimensional structure of the asymmetric unit of the bundle has been determined using interproton distance restraints derived from the nuclear Overhauser effect (NOE), covalent torsion angle restraints derived from three bond scalar coupling constants, and longer range angular restraints derived from residual dipolar couplings. The covalent R'-SS-Runit forms a pair of parallel R-helices that use heptad a-, d-, e-, and g-side chains to form a hydrophobic core extending the length of the molecule. The distribution of polar and nonpolar side chains on the surface of R'-SS-Rstructure is asymmetric. The hydrophilic face is comprised of glutamate and lysine side chains, while the opposite face is comprised of leucine, isoleucine, phenylalanine, tryptophan, and neutral histidine side chains. Equilibrium sedimentation analysis, size-exclusion chromatography, pulsed field gradient translation diffusion measurements, and a rotational correlation time derived from 15 N NMR relaxation studies all indicate that the covalent R'-SS-Runit forms a noncovalent dimer, (R'-SS-R')2, in solution. The structure confirms many expected design features and illuminates an apparent dichotomy of structure where the helical interface of the disulfide bridged two- R-helix peptide appears nativelike while the adjacent, noncovalent interface shows non-nativelike behavior. Available evidence indicates the four R-helix bundle can adopt either an anti or syn topology. The structure is discussed with respect to the potential origins of conformational specificity and nativelike protein structure.

Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins.

We describe the development of a scoring function based on the decomposition P(structure/sequence) proportional to P(sequence/structure) *P(structure), which outperforms previous scoring functions in correctly identifying native-like protein structures in large ensembles of compact decoys. The first term captures sequence-dependent features of protein structures, such as the burial of hydrophobic residues in the core, the second term, universal sequence-independent features, such as the assembly of beta-strands into beta-sheets. The efficacies of a wide variety of sequence-dependent and sequence-independent features of protein structures for recognizing native-like structures were systematically evaluated using ensembles of approximately 30,000 compact conformations with fixed secondary structure for each of 17 small protein domains. The best results were obtained using a core scoring function with P(sequence/structure) parameterized similarly to our previous work (Simons et al., J Mol Biol 1997;268:209-225] and P(structure) focused on secondary structure packing preferences; while several additional features had some discriminatory power on their own, they did not provide any additional discriminatory power when combined with the core scoring function. Our results, on both the training set and the independent decoy set of Park and Levitt (J Mol Biol 1996;258:367-392), suggest that this scoring function should contribute to the prediction of tertiary structure from knowledge of sequence and secondary structure.