Selection of Optimal Variants of Gō-Like Models of Proteins through Studies of Stretching

• Published in: Biophysical journal 2008-10, Vol.95 (7), p.3174-3191
• Main Authors: Sułkowska, Joanna I., Cieplak, Marek
• Format: Article
• Language: English
• Subjects: Analysis of Variance; Biomechanical Phenomena; Biophysical Theory and Modeling; Models, Molecular; Molecular biology; Protein Conformation; Protein Folding; Proteins; Proteins - chemistry; Proteins - metabolism; Reproducibility of Results; Temperature; Thermodynamics
• ISSN: 0006-3495; 1542-0086
• DOI: 10.1529/biophysj.107.127233

The Gō-like models of proteins are constructed based on the knowledge of the native conformation. However, there are many possible choices of a Hamiltonian for which the ground state coincides with the native state. Here, we propose to use experimental data on protein stretching to determine what choices are most adequate physically. This criterion is motivated by the fact that stretching processes usually start with the native structure, in the vicinity of which the Gō-like models should work the best. Our selection procedure is applied to 62 different versions of the Gō model and is based on 28 proteins. We consider different potentials, contact maps, local stiffness energies, and energy scales—uniform and nonuniform. In the latter case, the strength of the nonuniformity was governed either by specificity or by properties related to positioning of the side groups. Among them is the simplest variant: uniform couplings with no i, i + 2 contacts. This choice also leads to good folding properties in most cases. We elucidate relationship between the local stiffness described by a potential which involves local chirality and the one which involves dihedral and bond angles. The latter stiffness improves folding but there is little difference between them when it comes to stretching.