What is the shape of the distribution of protein conformations at equilibrium?

Abstract

According to the thermodynamic hypothesis, the native state of proteins is that in which the free energy of the system is at its lowest, so that at normal temperature and pressure, proteins evolve to that state. We selected four proteins representative of each of the four classes, and for each protein make four simulations, one starting from the native structure and the other three starting from the structure obtained by threading the sequence of one protein onto the native backbone fold of the other three proteins. Because of their large conformational distances with respect to the native structure, the three alternative initial structures cannot be considered as local minima within the native ensemble of the corresponding protein. As expected, the initial native states are preserved in the .5 μs simulations performed here and validate the simulations. On the other hand, when the initial state is not native, an analysis of the trajectories does not reveal any evolution towards the native state, during that time. These results indicate that the distribution of protein conformations is multipeak shaped, so that apart from the peak corresponding to the native state, there are other peaks associated with average structures that are very different from the native and that can last as long as the native state.

Keywords:

• protein folding
• thermodynamic hypothesis
• kinetic mechanism
• molecular dynamics

Acknowledgements

The first author acknowledges partial support from the European Regional Development Fund (ERDF) through the COMPETE – Operational Competitiveness Programme and from national funds through FCT – Foundation for Science and Technology, Portugal, under the project “PEst-C/MAR/LA0015/2011. The second author is thankful to the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) and to the Conselho Nacional de Desenvolvimento Cientfico e Tecnológico (CNPq) for financial support.