Proteomics

Proteomics is one of the most rapidly growing areas of modern molecular biology. Currently, there is only a scant knowledge of the proteome (the set of PROTEins encoded by the genOME) and its involvement in biological processes. The proteome, unlike the genome is not a fixed attribute of an organism, but varies during development and among different cell types. In addition, the proteome is far more complex than the genome as a result of a host of post-translational modifications. The proteome also depends on the environment of a cell, and changes in different disease states. By analyzing the patterns of protein expression, proteomics seeks to correlate disease states with changes in specific protein expression or modification. Proteomics research employs three basic technologies: two-dimensional gel electrophoresis for protein separation, mass spectrometry for protein characterization, and/or Edman degradation for protein identification.

In addition to describing the proteome, there is also a need to characterize interactions among the components of the protein network, including protein-protein interactions, the assembly of protein complexes, receptor-ligand interactions, and protein-DNA interactions.

We are interested in the development and application of high sensitivity methods for the characterization of the proteome and for studies of protein-protein interactions and protein chemical modification.

Protein Structure, Stability, and Dynamics

Current research is directed towards characterization of the dynamic properties of proteins and, in particular, glass transition behavior in proteins and its implications for protein function, stability and folding. Dry globular proteins are rigid (glassy) but are plasticizer by water and undergo a transition from a rigid to a flexible state as the hydration level or temperature is increased. In addition to its fundamental interest, an understanding of this behavior is also important in many biotechnological applications of proteins and in the development of strategies for the stabilization and purification of proteins. Research projects in this area include:

• Definition of the hydration dependence of the glass transition with positron annihilation lifetime and CP-MAS solid state ¹³C NMR spectroscopies.
• CP-MAS solid state ¹³C NMR studies of the effects of polyols such as glycerol and sucrose on dehydration-induced conformational changes and the protection of proteins during lyophilization.
• Studies of organic ligand-protein matrix coprecipitates used in protein separations.
• Characterization of dynamically distinct regions of the protein interior using molecular modeling tools and analysis of protein structure and sequence databases.

Positron Annihilation Lifetime Spectroscopy

We are also interested in the development and application of positron annihilation lifetime spectroscopy to analytical problems in chemistry and biochemistry. When positrons from a radioactive source such as ²²Na enter condensed molecular matter they rapidly slow down to thermal energies through collisions and ionization processes. Once thermalized, some positrons may combine with electrons to form positronium (Ps). The triplet or o-Ps species has a lifetime of 140 ns in vacuo, but in condensed matter this lifetime is greatly reduced as a result of “pick-off” annihilation with an electron from its local environment. In solids, o-Ps localizes in cavities and regions of free volume. In liquids, o-Ps forms bubbles. There is a strong correlation between the “pick-off” lifetime and the size of the bubbles or cavities in which o-Ps traps. Positron annihilation lifetime spectroscopy may therefore be used to determine pore sizes and surface areas in porous materials, to characterize defect populations and free volumes in solids and to follow phase changes and glass transitions. Research projects in this area include:

• PAL spectroscopy studies of glass transitions in proteins as a function of hydration.
• Determination of pore size distributions in porous silicas and zeolites employed in separations and catalysis.
• Characterization of liquids confined in cavities in porous media.

Selected Publications

1. Roh, J. H., Novikov, V. N., Gregory, R. B., Curtis, J. E., Chowdhuri, Z. & Sokolov, A. P. Onsets of anharmonicity in protein dynamics. Physical Review Letters 95 (2005).

2. R.B. Gregory. Protein Hydration and Glass Transitions. In The Properties of Water in Foods, D. S. Reid, Ed.; Chapman Hall, 1997.

3. R. B. Gregory. Protein Hydration and Glass Transition Behavior. In Protein-Solvent Interactions, R. B. Gregory, Ed.; Marcel Dekker Inc:New York, 1995; pp 191-264.

4. R. B. Gregory, M. Gangoda, R. K. Gilpin and W. Su. Influence of Hydration on the Conformation of Lysozyme Studied by Solid-State ¹³C NMR Spectroscopy. Biopolymers 33, 1993, 513-519.

 

Last Updated: 12 June 2006