He received his second Ph.D. degree at Duke University where he was a Fulbright Scholar from 1964 to 1968. He worked in the laboratory of Charles Tanford, Department of Biochemistry in the protein folding area focussing his career on the folding thermodynamics and 
kinetics, properties of the native and the unfolded proteins. His early collaborative work in uncovering residual native protein structure, following treatment with heat, acid (low pH) experimentally in a number of model proteins in his lab was published in 1967. He actually performed equilibrium unfolding studies on ribonuclease protein in guanidine hydrochloride, the findings of which were acceptable for the aforementioned Ph.D. degree in biochemistry by Duke University (1968).
Salahuddin returned to AMU Aligarh and joined the Department of Biochemistry, Faculty of Medicine, J.N. Medical College in 1968 as a reader. Salahuddin was present at the foundation ceremony of the new IBU Building on 15 January 1986. The event was inaugurated by Abdus Salam. He performed a critical role toward the establishment of the Interdisciplinary Biotechnology Institute for Modern Biological and Biotechnological Education at Aligarh along with the AMU administration in 1984.