Constellation Professor of Biocomputation and Bioinformatics
Professor, Department of Biology
Professor, Department of Chemistry and Chemical Biology
Education and Training
B.S., Georgia State University 1985
Ph.D., Moscow Physico-Technical Institute 1990
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 of Biocomputation and Bioinformatics.
Dr. Makhatadze is on the editorial boards of the Proteins: Structure, Function & Bioinformatics, Biophysical Journal, and Protein Engineering. 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).
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
Rational design of protein for thermostability, functional protein dynamics, protein-protein and protein-ligand interactions, mechanism of adaptations to extreme conditions (thermophiles, psychrophiles, halophiles, barophiles), bioinformatics, computer simulations of protein folding.
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, pressure-perturbation calorimetry, titration calorimetry, circular dichroism spectroscopy, fluorescence spectroscopy, stopped-flow kinetics, and analytical ultracentrifugation. Structural information on the systems is obtained using multidimensional NMR spectroscopy. Computer simulations are used to obtain atomistic details for individual model systems.
Four main 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 the 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 have developed 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 physico-chemical basis of adaptation of organisms to high hydrostatic pressure at the level of individual macromolecules. Pressure is an important environmental variable that plays an essential role in biological adaptation for many extremophilic organisms, so called barophiles (also called piezophiles). On Earth these organisms are generally populating the deep ocean floor where hydrostatic pressure can reach 110 MPa (~1,100 atm). Single cell organisms are not the only ones evolved to live under high hydrostatic pressure. The segmented microscopic animals tardigrades (“water bear”) can survive pressures up to 6,000 atm in the dormant state. Pompeii worms (Alvinella pompejana) are species of polychaete worms that live at high pressure and temperature near hydrothermal vents on the ocean floor. More recently, several species of nematoda were identified in the deep terrestrial subsurfaces. Bacterial species have been isolated from 1,350 meters into the Earth crust where temperature reaches 102°C and pressure is estimated to be in excess of 3,000 atm. There are also reports of prokaryotic organisms at the bottom of the oil well sediments and deep in the Arctic ice. All these examples suggest the possibility of life forms on other planets even though the temperature and pressure conditions can be dramatically different from those on the surface of Earth. Such different temperature and pressure conditions are expected to be found under the ice crust on Mars, Jupiter's moon Europa, and Saturn's moon Enceladus. Using a novel method of pressure-perturbation calorimetry combined with protein engineering methods, detailed computer simulations, and bioinformatics we are deciphering the role of different interactions in defining structural and functional state of proteins at high hydrostatic pressure.
The third project studies the 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 the 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 the 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 the 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 fourth project deals with the mechanisms by which a 39-residue peptide from human prostatic acidic phosphatase (PAPf39) forms amyloid fibrils that enhance HIV infectivity by several orders of magnitude. We use a battery of biophysical methods (ThT fluorescence, circular dichroisms and deep-UV resonance Raman spectroscopies, NMR, analytical ultracentrifugation, small angle X-ray scattering, hydrogen-deuterium exchange mass spectrometry), biochemical methods (protease protection, bacterial expression, isotopic labeling), and computational method (replica-exchange molecular dynamic simulations) to identify key elements that are involved in the amyloid structure formation. The ultimate goal is to develop small-molecule inhibitors that prevent interactions of viral particles with PAPf29 fibrils.
Last 3 years (2010-2012)
1. Wafer, LN, Streicher, WW, McCallum, SA, Makhatadze GI (2012) - Thermodynamic and Kinetics Analysis of Peptides Derived from CapZ, NDR, p53, HDM2, and HDM4 Binding to Human S100B. Biochemistry, in press
2. Scian M, Lin JC, Le Trong I, Makhatadze GI, Stenkamp RE, Andersen NH. (2012) - Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction. - Proc Natl Acad Sci U S A. 109:12521-12525.
3. Voepel, T. and Makhatadze, G.I. (2012) – Enzyme Activity in Crowded Milieu – PLoS ONE 7: e39418.
4. Jayasimha, P, Shanmuganathan, A, Suladze, S, Makhatadze GI. (2012) - Contribution of Buried Aspartic Acid to the Stability of the PDZ2 Protein - Journal of Chemical Thermodynamics, 52:64-68 Cover Illustration
5. Zarrine-Afsar, A, Zhang, Z, Schweiker, KL, Makhatadze, GI, Davidson, AR, Chan, HS. (2012). - Surface-exposed electrostatic interactions are less specific in the folding transition state than those in the folded state of the Fyn SH3 domain – Proteins 80:858-870.
6. Chan, CH, Wilbanks, CC, Makhatadze, GI, Wong, KB. (2011) - Electrostatic contribution of surface charge residues to the stability of a thermophilic protein: benchmarking experimental and predicted pKa values - PLoS ONE 7:e30296.
7. Loladze, VV, Makhatadze, GI. (2011). - Energetics of Charge-Charge Interactions between Adjacent in Sequence Residues - Proteins, 79:3494-34999
8. Juárez O, Shea ME, Makhatadze GI, Barquera B. (2011). - The role and specificity of the catalytic and regulatory cation binding sites of the Na+-pumping NADH:quinone oxidoreductase from Vibrio cholera - Journal of Biological Chemistry, 286:26383-26390.
9. Jimenez-Cruz CA, Makhatadze GI, Garcia, AE. (2011). - Protonation/Deprotonation effects on the stability of the Trp-Cage Miniprotein - Physical Chemistry Chemical Physics, 13:17056-17063.
10. Bush, J. Makhatadze GI. (2011). - Statistical Analysis of Protein Structures Suggests that Buried Ionizable Residues in Proteins are Hydrogen Bonded or Form Salt Bridges - Proteins, 79:2027-2032
11. Patel MM, Tzul, F, Makhatadze GI (2011). - Equilibrium and Kinetic Studies of Protein Cooperativity using Urea-Induced Folding/Unfolding of a Ubq-UIM Fusion Protein. - Biophysical Chemistry 159:58-65.
12. Patel MM, Sgourakis NG, Garcia AE, Makhatadze GI. (2010). - Experimental Test of the Thermodynamic Model of Protein Cooperativity Using Temperature-Induced Unfolding of a Ubq-UIM Fusion Protein. - Biochemistry. 49:8455-67
13. Tsamaloukas, AD, Pyzocha, NK, Makhatadze, GI. (2010). - Pressure Perturbation Calorimetry of Unfolded Proteins. - J Physical Chemistry B, 114(49):16166-70
14. Streicher, W. W. and Makhatadze, G. I. (2010) - Protein Heat Capacity. - In Heat Capacities: Liquids, Solutions and Vapours. Royal Society of Chemistry, London, UK. Cover Illustration
15. Streicher WW, Lopez MM, Makhatadze GI. (2010). - Modulation of quaternary structure of S100 proteins by calcium ions. - Biophys Chem. 151:181-186.
16. Sgourakis, NG., Patel, MM., Garcia, AE., Makhatadze, GI., McCallum, SA (2010) - Conformational Dynamics and Structural Plasticity Play Critical Roles in Ubiquitin Recognition of a UIM Domain. – J. Molecular Biology 396:1128-1144.
Wafer, L.N.R., Streicher, W. W., Makhatadze, G. I. (2010) - Thermodynamics of the Trp-cage Miniprotein Unfolding in Urea. – Proteins: Structure, Function, Bioinformatics. 78:1376-1381.