Geometry, thermodynamics, and protein |
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Authors: | Yi Fang Junmei Jing |
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Institution: | Centre for Bioinformation Science, Mathematical Sciences Institute, Australian National University, Canberra, ACT 0200, Australia |
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Abstract: | We derive a new continuous free energy formula for protein folding. We obtain the formula first by adding hydrophobic effect to a classical free energy formula for cavities in water. We then obtain the same formula by geometrically pursuing the structure that fits best the well-known global geometric features of native structures of globular proteins: 1. high density; 2. small surface area; 3. hydrophobic core; 4. forming domains for long polypeptide chains. Conformations of a protein are presented as an all atom CPK model where each atom is a ball B(xi,ri). All conformations satisfy generally defined steric conditions. For each conformation P of a globular protein, there is a closed thermodynamic system ΩP⊃P bounded by the molecular surface MP. Both methods derive the same free energy aV(P)+bA(P)+cW(P), where a,b,c>0, V(P), A(P), and W(P) are volume of ΩP, area of MP, and area of the hydrophobic surface WP⊂MP, which quantifies hydrophobic effect.Minimizing W(P) is sufficient to produce statistically significant native like secondary structures and hydrogen bonds in the proteins we simulated. |
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Keywords: | Hydrophobic effect Hydrophobic core Hydrophobic area Volume Area Hydrogen bond Constrained minimization Free energy Globular protein |
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