Structure of the native protein

One way to describe the unfolding process is the two-state model shown in Figure 4. It is an equilibrium, a single-transition step between the folded native (N) and the disordered, unfolded or denatured (D) species (36-38). An intermediate step, the formation of possible intermediates (I), can be present between the transformation from N to D. The intermediate state (I) has often been described as the molten globule, for example, for growth hormone (39). It is a stable compact, partly denatured species, which retains some ordered secondary structure but not the tertiary structure of the native protein (35,36,40,41). The aggregate (A) formed may occur from irreversible changes to the unfolded species (18,42-44). 

For a globular protein, considerably more information is needed. It is necessary to determine the way in which the helical and pleated-sheet sections fold back on each other, in addition to the positions of the side-chain atoms and any prosthetic groups. The interactions between the side chains play an important role in the folding of proteins. The folding pattern frequently brings residues that are separated in the amino acid sequence into proximity in the tertiary structure of the native protein. 

The structure of the native protein can be important in influencing the rate, extent, and effects of denaturation. Proline-rich peptides and proteins capable of a secondary helical structure appear to favor partially folded structures under denaturing conditions these are simultaneously present with random-coil denatured molecules (32). The presence of these two slowly interconverting conformers then leads to increased reversed-phase band broadening as above. Structural factors which disfavor protein denaturation can also operate to reduce band width. For the HIC separation of various apolipoproteins (96), it was found that more hydrophobic proteins gave narrower bands. This was attributed to a more structure conformer in the retained state for the more hydrophobic protein. That is, a single (native ) conformer exists during the separation of more hydrophobic proteins in this system, but some denaturation of less hydrophobic proteins occurs. 

First, a high resolution structure of the protein-ligand complex is required, since starting with less certain information (e.g., the structure of the native protein or a homology model of the protein based on the structures of similar proteins) is risky—reliance on inaccurate coordinates of active site residues quickly results in unrealistic binding free energies. 

It is unlikely that there is a one-to-one 3-D code. The fact that there are many different sequences resulting in the formation of the same 3-D structure means that if such a code exists, it must be very redundant. Also, the structure of the native protein is not unique. Proteins always experience structural fluctuations therefore, a given sequence of amino acids does not determine a unique set of coordinates for the folded form of the protein. 

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