The present work reports the pH-induced conformational changes of pepsin in solution at room temperature. The conformational change makes the protein surface active. The protein was found. to be present in the partially denatured state at pH 8 as well as at pH 2. The fluorescence probe and circular dichroism (CD) spectra suggested that the most stable state of pepsin exists at pH 5. The binding affinities of pepsin in its native and denatured states for a D,L-carnitine-based cationic surfactant (3-hexadecylcarbamoyl-2-hydroxypropyl) trimethylammonium chloride (Cm-CAR) were examined at very low concentrations of the surfactant. The thermodynamics of the binding processes were investigated by use of isothermal titration calorimetry. The results were compared with those of (3-hexadecylcarbamoylpropyl)trimethylammonium chloride (C-16-PTAC), which is structurally similar to C-16-CAR, but without the secondary OH functionality near the headgroup. None of the surfactants were observed to undergo binding with pepsin at pH 2, in which it exists in the acid-denatured state. However, both of the surfactants were found to spontaneously bind to the most stable state at pH 5, the partially denatured state at pH 8, and the alkaline denatured state at pH 11. Despite the difference in the headgroup structure, both of the surfactants bind to the same warfarin binding site. Interestingly, the driving force for binding of C-16-CAR was found to be different from that of C-16-PTC at pH >= 5. The steric interaction of the headgroup in Cm-CAR was observed to have a significant effect on the binding process.