Professor of Biology
Chaired Constellation Professor in Biocomputation and Bioinformaics

Education and Training

B.S., Georgia State University
Biophysics

Ph.D., Moscow Physico-Technical Institute
Biophysical Chemistry and Structural Biology

Dr. Makhatadze completed his postdoctoral work at the Department of Biology at the Johns Hopkins University before moving to his first faculty position in the Department of Chemistry and Biochemistry at Texas Tech University.  After three years at Texas Tech he moved to the Penn State University College of Medicine, where he was Professor at the Department of Biochemistry and Molecular Biology and directed a graduate program in Chemical Biology.  Dr. Makhatadze joined Rensselaer in 2007 as a Constellation Professor in Biocomputation and Bioinformatics.

Dr. Makhatadze is on the editorial boards of the Journal of Biological Chemistry, Biochemica et Biophysica Acta, and Protein Engineering, Design and Selection. He is a member of the American Chemical Society, the American Society for Biochemistry and Molecular Biology, the Biophysical Society, the Federation of American Societies for Experimental Biology, and the Protein Society.  He is also a past and present member of the scientific review committees for the National Institutes of Health (NIH) and the National Science Foundation (NSF).

Contact

E-mail: makhag@rpi.edu
Tel: (518) 276-4417
Fax: (518) 276-2851

Office: Center for Biotechnology and Interdisciplinary Studies Rm. 3244A

Rensselaer Polytechnic Institute
110 8th Street
Troy, NY  12180-3590

Research Interests

Rational design of protein for thermostability, protein-protein and protein-ligand interactions, mechanism of adaptations to extreme conditions (thermophiles, psychrophiles, halophiles)

Research in the laboratory is directed towards understanding the structural and thermodynamic basis of the contributions of individual molecular components to the self-assembly of macromolecular complexes. In order to probe the role of different interactions in protein folding, stability and protein interactions with the ligands (ions, proteins, DNA, RNA, small effectors), a variety of experimental techniques as well as computational methods of analysis are used. Recombinant DNA technology is used to incorporate different amino acid residues into a given position in a protein sequence. The effect of these mutations on the overall energetics, structure and function of proteins is measured under different conditions such as salt concentration and ion type, temperature, and pH. Experimental techniques assessing energetics include scanning calorimetry, titration calorimetry, circular dichroism spectroscopy, and fluorescence spectroscopy. Structural information on the systems is obtained using multidimensional NMR spectroscopy or X-ray crystallography.

Three projects are under development in the laboratory.

The first project deals with the rational design of proteins for thermostability. The progress in understanding of forces responsible for the protein stability has been enormous, largely through the combination of experimental and theoretical approaches. It has been shown that hydrophobic effect, hydrogen bonding and packing interactions between residues buried in the protein interior are dominant factors that define protein stability. The role of surface residues for protein stability received much less attention. It was believed that surface residues are not important for protein stability particularly because their interactions with the solvent should be similar in the native and unfolded states. However, our experimental data using six different model proteins shows that the surface residues contribute to protein stability through a variety of factors. These factors can be operationally divided into long-range interactions (charge-charge interactions between ionizable groups) and short-range local interactions (salt-bridges, hydrophobicity and packing, peptide bond hydration, a-helical propensity, helix capping). We develop quantitative computational analyses of the contribution of these different factors to the protein stability and experimentally test their applicability to the design of the thermostable proteins.

The second project studies functional role of the S100 family of human Ca²⁺-binding proteins. Changes in the expression levels of these proteins in different disease states (cancer and neurodegenerative diseases in particular) are well documented, however, the biological role of S100 proteins remains largely unknown. We recently cloned S100Z a new member of this family that, in difference to the majority of S100 proteins, is located not on the chromosome 21 but on the chromosome 5. We are currently characterizing interaction of this protein with several potential interacting proteins that were identified using yeast two hybrid screen and various bioinformatics tools. A detailed understanding of S100 function in molecular terms, specifically in terms of proteins which may transduce its signal, may provide new substrates for the development of more effective therapies for cancer.

The third project studies the role of specific interactions for the initiation,propagation and termination of a-helices in proteins and the role of a-helices in mediating protein-protein interactions. The model systems for this study are the a-helices of ubiquitin and human pancreatic polypeptide, as well as short synthetic peptides. We use a variety of non-natural amino acid substitutions (D-amino acids, norvaline, norleucine, aminobutyric acid, etc) that allow us to expend beyond the 20 natural amino acid residues and alter specific types of interactions at given positions in the protein sequence. The rules derived from this study will provide an important background for biotechnological design of new more efficient biocatalytic molecules with the new or improved biological function.

Selected Publications

Protein Design

Makhatadze, G.I., Loladze, V.V., Ermolenko, D.N., Chen, X. & Thomas, S.T. (2003). - Contribution of surface salt bridges to protein stability: guidelines for protein engineering. - J Mol Biol 327, 1135-1148.

Strickler, S.S., Gribenko, A.V., Gribenko, A.V., Keiffer, T.R., Tomlinson, J., Reihle, T., Loladze, V.V. & Makhatadze, G.I. (2006). - Protein stability and surface electrostatics: a charged relationship. - Biochemistry 45, 2761-2766.

Gribenko, A.V. & Makhatadze, G.I. (2007). - Role of the Charge-Charge Interactions in Defining Stability and Halophilicity of the CspB Proteins. - J Mol Biol. 366, 842-856.

S100 Proteins

Brokx, R.D., Lopez, M.M., Vogel, H.J. & Makhatadze, G.I. (2001). - Energetics of target peptide binding by calmodulin reveals different modes of binding. - J Biol Chem 276, 14083-14091.

Gribenko, A.V., Hopper, J.E. & Makhatadze, G.I. (2001). - Molecular characterization and tissue distribution of a novel member of the S100 family of EF-hand proteins. - Biochemistry 40, 15538-15548.

Lee, Y.C., Volk, D.E., Thiviyanathan, V., Kleerekoper, Q., Gribenko, A.V., Zhang, S., Gorenstein, D.G., Makhatadze, G.I. & Luxon, B.A. (2004). - NMR structure of the Apo-S100P protein. - J Biomol NMR 29, 399-402.

a-Helices

Makhatadze, G.I. (2005). - Thermodynamics Of alpha-Helix Formation. - Adv Protein Chem 72, 199-226.

Richardson, J.M., Lopez, M.M. & Makhatadze, G.I. (2005). - Enthalpy of helix-coil transition: missing link in rationalizing the thermodynamics of helix-forming propensities of the amino acid residues. - Proc Natl Acad Sci U S A 102, 1413-1418.

Bang, D., Gribenko, A.V., Tereshko, V., Kossiakoff, A.A., Kent, S.B. & Makhatadze, G.I. (2006). - Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis. – Nature CB 2, 139-143.

Streicher, W.W. & Makhatadze, G.I. (2006). - Calorimetric evidence for a two-state unfolding of the beta-hairpin peptide trpzip4. - J Am Chem Soc 128, 30-31.