How the polypeptide chain of a protein adopts its unique and biologically active three-dimensional structure is one of the most fundamental question in biology. To learn about the mechanism of protein folding, it is important to characterize the physical properties of intermediates in this reaction and to identify specific interactions that fold or unfold proteins. Specifically we propose heteronuclear NMR experiments to study the detailed mechanism of the acid-induced unfolding of apomyoglobin that proceeds from a """"""""native"""""""" state N at pH 6 through partially unfolded intermediates I to the unfolded state U at pH 2. Protonation of histidine H24 and H119 has been suggested to trigger the N to I transition by breaking a specific hydrogen bond between H24 and H119 side chains. 1H-15N HMBC experiments will be used to follow the protonation and tautomeric state of all histidine residues at various pH values. Aspartic acid residues that may be responsible for the I to U transition will be identified by modified 1H-13C CT-HCACO experiments at various pH values using apomyoglobin specifically labeled with 13C aspartic acid. Recent 1H NMR experiments suggested the existence of an intermediate in the unfolding reaction of ribonuclease A. Further characterization of this unfolding intermediates would provide valuable information about the transition state of the reaction and therefore about the mechanism of unfolding. We propose to use 19F NMR in a real-time NMR unfolding experiment to test whether this intermediate has the properties of a dry molten globule, namely, freely rotating side chains in an unhydrated protein interior.
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