This seemingly paradoxical statement can be understood as follows. All potential hydrogen bond donors and acceptors in a protein will form hydrogen bonds whether in the native or denatured state. For a graphical representation of the contributions of D H and -T D S to the D G of protein folding, click here . D H predominates, but in some cases D S predominates. In proteins that contain them, disulfide bonds help to stabilize the native state, because the correct formation of disulfide bonds can only occur when the the two SH groups are positioned correctly.
Prolines often serve to delineate the amino terminal end of a helix.
Recently, the reverse change has been observed. The amino acid sequence of a protein contains all the information required for the protein to fold into the correct, biologically active, three-dimensional structure. The process most likely begins with the formation of secondary structural elements, which serve as nucleation foci around which the native structure of the protein can fold. It is likely that a -helices are the most important nucleation foci because they are formed from amino acids which are next to each other in the linear sequence, whereas b sheets are often formed by the interaction of strands that are far apart in the linear sequence. Ultimately these secondary structural domains will come together to form a structure with extensive secondary structure in a nearly native overall fold, but without the precisely oriented side chains of the final tertiary structure - the molten globule state.