Protein folding physical properties

One drawback to a molecular dynamics simulation is that the trajectory length calculated in a reasonable time is several orders of magnitude shorter than any chemical process and most physical processes, which occur in nanoseconds or longer. This allows yon to study properties that change w ithin shorter time periods (such as energy finctnations and atomic positions), but not long-term processes like protein folding. 

Many biological molecules, such as proteins, are large and have complex structures. Proteins are composed of a sequence of units, called amino acids, which are joined by a strong covalent bond known as a peptide bond. But proteins also fold up into a certain shape, which is vital to their function—a protein that loses its shape cannot fulfill its function as an enzyme or a transporter. The sequence of amino acids determines the shape 20 different amino acids are found in proteins, and each one has slightly different chemical and physical properties. For example, some amino acids are hydrophilic, readily interacting... 

The network of chemical bonds within molecules only partially determines the chemical and physical properties. Intermolecular interactions cause gases to deviate from the ideal gas law (as we will discuss in Chapter 7) or condense into liquids. Interactions between nonbonded atoms in the same molecule cause proteins to fold into specific configurations, which catalyze chemical reactions critical to life. 

In 1987 [8] and again in 1993 [9], it was pointed out that the hydrophobic liquid model could not be entirely adapted to protein folding, since it completely fails to explain the effects of pressure. Kauzmann points out that volume and enthalpy changes are equally fundamental properties of the unfolding process, and no model can be considered acceptable unless it accounts for the entire thermodynamic behaviour In his Reminiscences from a Life in Protein Physical Chemistry [10], Kauzmann further states ... 

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