The thermodynamics and statistical mechanics of protein folding

The physics of self-organization and complexity is manifested on a variety of biological scales, from large ecosystems to the molecular level. Protein molecules exhibit characteristics of complex systems in terms of their structure, dynamics, and function. Proteins have the extraordinary ability to fold to a specific functional three-dimensional shape, starting from a random coil, in a biologically relevant time. How they accomplish this is one of the secrets of life. In this work, theoretical research into understanding this remarkable behavior is discussed. Thermodynamic and statistical mechanical tools are used in order to investigate the protein folding dynamics and stability. Theoretical analyses of the results from computer simulation of the dynamics of a four-helix bundle show that the excluded volume entropic effects are very important in protein dynamics and crucial for protein stability. The dramatic effects of changing the size of sidechains imply that a strategic placement of amino acid residues with a particular size may be an important consideration in protein engineering. Another investigation deals with modeling protein structural transitions as a phase transition. Using finite size scaling theory, the nature of unfolding transition of a four-helix bundle protein was investigated and critical exponents for the transition were calculated for various hydrophobic strengths in the core. It is found that the order of the transition changes from first to higher order as the strength of the hydrophobic interaction in the core region is significantly increased. Finally, a detailed kinetic and thermodynamic analysis was carried out in a model two-helix bundle. The connection between the structural free-energy landscape and folding kinetics was quantified. I show how simple protein engineering, by changing the hydropathy of a small number of amino acids, can enhance protein folding by significantly changing the free energy landscape so that kinetic traps are removed. The results have general applicability in protein engineering as well as understanding the underlying physical mechanisms of protein folding. ^

Fibrations and contact structures

We prove that a closed 3-dimensional manifold is a torus bundle over the circle if and only if it carries a closed nonsingular 1-form which is linearly deformable into contact forms.

Rank and k-nullity of contact manifolds

We prove that the dimension of the 1-nullity distribution N(1) on a closed Sasakian manifold M of rankl is at least equal to 2l−1 provided that M has an isolated closed characteristic. The result is then used to provide some examples of k-contact manifolds which are not Sasakian. On a closed, 2n+1-dimensional Sasakian manifold of positive bisectional curvature, we show that either the dimension of N(1) is less than or equal to n+1 or N(1) is the entire tangent bundle TM. In the latter case, the Sasakian manifold Mis isometric to a quotient of the Euclidean sphere under a finite group of isometries. We also point out some interactions between k-nullity, Weinstein conjecture, and minimal unit vector fields.