Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection.

The energy landscape used by nature over evolutionary timescales to select protein sequences is essentially the same as the one that folds these sequences into functioning proteins, sometimes in microseconds. We show that genomic data, physical coarse-grained free energy functions, and family-specific information theoretic models can be combined to give consistent estimates of energy landscape ...

Information content of coevolutionary game landscapes

Coevolutionary game dynamics is the result of players that may change their strategies and their network of interaction. For such games, and based on interpreting strategies as configurations, strategy– to–payoff maps can be defined for every interaction network, which opens up to derive game landscapes. This paper presents an analysis of these game landscapes by their information content. By t...

Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding.

The energy landscape approach has played a fundamental role in advancing our understanding of protein folding. Here, we quantify protein folding energy landscapes by exploring the underlying density of states. We identify three quantities essential for characterizing landscape topography: the stabilizing energy gap between the native and nonnative ensembles δE, the energetic roughness ΔE, and t...

Kinetics and Thermodynamics of Membrane Protein Folding

Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in k...

Thermodynamics of Protein Folding and Stability