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Balaram's main area of research has been the investigation of the structure, conformation, and biological activity of designed and natural peptides. To do this, he has extensively used techniques such as Nuclear Magnetic Resonance spectroscopy, Infrared spectroscopy, and Circular Dichroism, along with X-ray crystallography. He has been a major contributor to the evaluation of factors influencing the folding and conformations of designed peptides, and has investigated structural elements playing a key role in the formation of secondary structural motifs such as helices, beta turns, and sheets. Along with Isabella Karle, a frequent collaborator, he has also pioneered the use of alpha-amino isobutyric acid.
This contained a variety of very unusual amino acid residues.  The sequence was shown to be: N-acetyl-L-pip-AIB-L-pip-AIB-AIB-L-leu-beta-ala-gly-AIB-AIB-L-pip-AIB-gly-L-leu-L-iva-AIB-X. PIP = pipecolic acid, AIB = alpha-amino-isobutyric acid, leu = leucine, iva = isovaline, gly = glycine. This is a potent inhibitor of the mitochodrial ATPase activity.