Chaperone proteins and their cochaperones are perhaps one of the most intriguing systems for investigation. Ubiquitous in nature, they can be found in every organism and that perhaps is the reason that their sequence shows amazingly high homology and similarity. Allosteric mechanisms govern their functions and that makes them very interesting and hard to investigate at the same time. In medicine, chaperone proteins are of extreme interest since they are related to various diseases including neurodegerative diseases such as Alzheimers disease, Pick’s disease and Parkinsons disease. Various forms of cancer also relate to the chaperone proteins. Hence the investigation of various small molecules that could up/down-regulate this system is of great biomedical relevance. In this dissertation we explored a member of the chaperone family that is constitutively expressed in every mammalian cell, the cognate Hsp70 (Hsc70). More specifically, we investigate the interactions of its ATPase domain with various small molecules that either act as inhibitors or enhancers of the protein’s activity. For example, we found that the compound MKT-077 blocks the Hsc70 ATPase activity by binding in a negatively charged cleft with its positive charge. This was identified with the use of chemical shift mapping experiments, NOE experiments and AUTODOCK simulations. MKT-077 binds only to the ADP form of the protein elucidating an amazing mechanism for the inhibition of the protein. Another inhibitor, methylene blue, binds to another locus of the ATPase. Interestingly, both of these molecules reduce the levels of tau in cell-based models of Alzheimers disease. This would suggest that the use of compounds that bind to Hsc70 at two separate sites could modulate Hsp70 activity in cells in a synergistic fashion.Ph.D.BiophysicsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/86521/1/rousaki_1.pdf