My lab is concerned with understanding the relationship between primary sequence and 3-dimensional structure and function of proteins. We have two complementary programs. One is to study the structure and function of naturally occurring proteins using structural (NMR and crystallography) and biochemical methods. The other approach is protein design where we computationally predict novel sequences that will adopt desired folds or functions, and biophysically characterize the designed sequences to validate and improve the computational methods.
Chemokines and Viral Immunomodulatory Proteins. In our structure-function studies of naturally occurring proteins, we have been particularly interested in chemokines and their receptors. Chemokines are secreted proteins that function as the intercellular messengers that control migration and activation of leukocytes in response to signals associated with infection and injury. However chemokines are like a double edge sword because in addition to their protective role, abnormal production of chemokines is involved in a number of diseases including arthritis, arteriosclerosis, asthma, viral disease and cancer metastasis. We have solved chemokine structures by NMR and crystallography. We also use mutagenesis and functional assays to map out residues involved in binding and activation of receptors. In addition to providing structural and mechanistic information, our studies have lead to the identification of several mutant proteins that act as receptor antagonists and have great promise as therapeutic agents in the treatment of human disease. To gain further insight into the molecular basic of binding and signaling of the receptors, we are now pursuing the expression and reconstitution of chemokine receptors, ultimately for structural studies by 2D and 3D crystallographic methods and NMR. As G-protein coupled receptors, they represent one of the most important and abundant classes of membrane protein signaling molecules.<>Other structural targets include viral "immunomodulatory" proteins. These are proteins that viruses encode in order to suppress and evade the host immune response. Specific examples include soluble chemokine binding proteins that block the activity of chemokines, apoptosis inhibitory proteins that prevent apoptosis thereby allowing viruses to replicate, and other anti-inflammatory proteins. These viral proteins are particularly interesting structural targets because many of them have multiple functions and interact with a diversity of host proteins. From a fundamental standpoint, they are excellent systems for understanding specificity and molecular recognition. They also target some of the most important molecules in the host immune response.>
Protein Design. In addition to more traditional approaches for understanding the molecular basis of protein structure and function, we also take an engineering approach by designing new proteins. To this end we develop computational tools that enable us to predict novel sequences that fold into pre-defined 3-dimensional structures. Past work has involved the design and characterization of protein scaffolds. We are now developing methods for introducing binding and function into proteins, and generating new protein folds. From these studies we are learning fundamental principles of the sequence determinants of protein structure, stability, and dynamics. However, we also believe that computational protein design has the potential to revolutionize biotechnology and chemical biology with applications that have only begun to be explored.
Solution Structure and Dynamics of the Melanoma Inhibitory Activity Protein (MIA). [J.C. Lougheed, P.J. Domaille and T.M. Handel. (2002) Journal of Biomolecule NMR 22:211-223]
Protein Design: Where We Were, Where We Are, Where We're Going. [N. Pokala and T.M. Handel (2001) Journal of Structural Biology 134:269-281]
Identification of Surface Residues of the Monocyte Chemotactic Protein-1 that Affect Signaling through the MCP-1 Receptor, CCR2b. [K. Jarnagin, D. Grunberger, M. Mulkins, B.Wong, S. Hemmerich, C. Paavola, A.Bloom, S. Bhakta, R. Freedman, D. McCarley, I. Polsky, A. Ping-Tsou, A. Kosaka, T.M. Handel (1999) Biochemistry 38, 16167-16177]
Solution Structure and Dynamics of a Designed Hydrophobic Core Variant of Ubiquitin. [E.C. Johnson, G.A. Lazar, J.R. Desjarlais and T.M. Handel (1999) Structure with Folding and Design 7, 967-76]
Hydrophobic Core Design and Structure Prediction with Backbone Flexibility. [J.R. Desjarlais and T.M. Handel (1999) J. Molecular Biology 289, 305-318]
Monomeric Monocyte Chemoattractant Protein-1 (MCP-1) Binds and Activates the MCP-1 Receptor CCR2b. [C. Paavola, S. Hemmerich, D. Grunberger, I. Polsky, A. Bloom, R. Freedman, M. Mulkins, S. Bhakta, D. McCarley, L. Wiesent, B. Wong, K. Jarnagin, T.M. Handel (1998) J. of Biological Chemistry 273, 33157-33165]
De Novo Design of the Hydrophobic Core of Ubiquitin. [G. Lazar, J. R. Desjarlais, T. M. Handel (1997) Protein Science 6, 1167-1178]
De Novo Design of the Hydrophobic Cores of Proteins. [J. R. Desjarlais and T. M. Handel (1995) Protein Science 4, 2006-2018]
Last Updated 2004-09-20