Overall Research Goals
Although proteins are often depicted as static structures, it is well-known that these molecules experience significant conformational fluctuations. As a result of these fluctuations, proteins in solution exist as ensembles of closely related, transient and interconverting conformational microstates which, on average, describe the crystal structure. Research in our lab is centered on characterizing the conformational ensembles of proteins and elucidating the complex interplay between local conformational fluctuations, global stability, and function (i.e. catalysis, allosterism, signal transduction).
We believe it is important to employ a diversity of approaches and to adopt multiple viewpoints to address this complex problem. As such, the lab is engaged in projects that range from the development of theoretical models to the experimental determination of the effects of environmental perturbations and mutations on various biophysical and functional properties. Current projects in the lab fall into four main research areas.
Research Project I
Development and Refinement of a Structure-based Model of the
Protein
Ensemble (COREX/BEST).
Model development, which is intimately tied to the experimental studies in our lab, is geared toward the design and refinement of a structure-based model for conformational fluctuations.
However, whereas classic model development approaches seek to quantitatively capture a particular phenomena of interest, our unique approach is targeted toward the development of a model that possesses the properties of being; 1) simple, 2) experimentally verifiable, and 3) capable of unifying seemingly disparate observations within the context of a single formalism. This approach, which often requires unorthodox assumptions and the development of novel testing strategies, has allowed us to unify the description of a vast array of phenomena, ranging from site-site communication, to cooperativity in cold denaturation, to pH dependent fluctuations.
Hilser, V.J. (2001) Modeling the Native State Ensemble. In Protein Structure, Stability and Folding. Methods in Molecular Biology. Ed. K. Murphy. Humana Press, Totowa, NJ, 93-115.
Research Project II
Experimental Characterization of Conformational Fluctuations.
We use various biophysical techniques (including isothermal
titration (ITC) and differential scanning calorimetry (DSC), NMR chemical
shift perturbation, 15N relaxation, and hydrogen-deuterium exchange) to
investigate the role of conformational fluctuations in determining stability
and binding energetics in several model proteins in the lab. We currently
have ongoing projects with dihydrofolate reductase (DHFR) and SEM5 SH3 domain. 
Research Project III
Experimental Determination of Conformational Bias in the Denatured
State
Ensemble.
We are interested in the thermodynamic origins and consequences
of conformational preferences in the denatured states of proteins, in particular
the preference for the left-handed poly-proline II (PII) conformation.
We harness the ability of SH3 domains to bind peptides that adopt the PII
conformation in order to probe for residual PII content in unstructured peptides.
By monitoring the effects of perturbants and mutations on the thermodynamics
of binding, we can investigate the underlying thermodynamic bases for the
observed preferences, and use this information to develop a more accurate
model of the denatured states of proteins. 
Research Project IV
Thermodynamic Classification of Protein Fold Space.
Using the ensemble-based model of proteins developed and validated in our lab, we are focused on characterizing proteins in energetic, rather than structural terms. We are interested in the underlying thermodynamic rules that relate sequence to fold, as well as thermodynamic homology between different folds. To date, we have shown that proteins can be represented in purely thermodynamic terms, that this representation is sufficient for fold recognition, and that energetic building blocks in proteins can be identified and used as the basis of a purely thermodynamic classification of protein fold space.
