advances-in-protein-chemistry

transport in the redox system of certain bacteria. Thermodynamic solidity has been focused in the research of this enzyme. Opposition to
the thermal unfolding is remarkable and irreversible unfolding appears at temperatures more than 70ºC. This unusual thermal resistance
is due to a number of different features like presence of disulphide bridges, hydrophobic effect, intra-molecular hydrogen bonds and
stabilization by Cu 2+ binding. The denaturing and/or unfolding depends upon two effects; a reversible endothermic mechanism which
involves the destruction of three-dimensional structure of azurin and an irreversible exothermic process which involves the aggregation
of polypeptide chain network [9].
Figure 5: 3d Structure of Azurin. (Rendered by Chimera, ver. 1.8)
Figure 6: Path Representing The Denaturation Of Proteins.
Pother and Potherse: A Thermodynamic Approach
Researchers have proposed that a protein is not a global thermodynamic system but a complicated one consisting of many subsystems.
Scrutinizing the thermodynamic aspects of proteins, two basic concepts of protein dynamics have been introduced by the investigators,
there were the pother and the potherse. The pother is considered the basic units of thermal motion of atoms while the potherse, in
contrast, is considered as a thermal system comprising many different pothers [10]. Thermodynamic conventional ideas contain particle
based concept in the axiomatic theory. On the other hand, the current approach carries pother as the elementary concept of the thermal
motion. Different types of thermal motions could be observed in protein including vibrational and rotational in nature due to the side
chains of the amino acids [11].
The pother is rotation around the C-N or C-C bond of peptide plain because these are responsible for the overall protein conformational
changes. The potherse which contain many subunits/subsystems considered to be thermodynamically stable when the pothers are stable
with respect to their thermal motions. As a result, a protein is not a global thermodynamic system but a complex of many subsystems.
Moreover, the relationship between pother and potherse could be considered as protein thermodynamic structure. In addition to the 3-D
structure, a protein can recognize its thermodynamic structure under different conditions [12,13].
The three-dimensional structure of protein molecules holds the inner thermal motion of amino acids and vice versa. Thermal
motions of individual particles influence the overall native form of protein structure. Therefore, the potherse has features of both protein
dynamics and stability of protein structure.
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