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Research Abstracts Online
January 2009 - March 2010

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University of Minnesota Twin Cities
College of Pharmacy
Department of Medicinal Chemistry

PI: Carston R. Wagner, Associate Fellow
Co-PI: Donald G. Truhlar, Fellow

Design and Modeling of Protein-Protein Interfaces

In an effort to develop stable, self-assembled protein nanostructures, these researchers have synthesized a homobifunctional small molecule consisting of two methotrexate molecules tethered together with a methylene linker (bis-MTX). This small molecule is capable of inducing the reversible dimerization of two dihydrofolate reductase (DHFR) monomers. Further expansion of this strategy has led to the construction of similarly homobifunctional DHFR fusion proteins, tethered together with 1, 3, 7, and 13 amino acid linkers (1-, 3-, 7-, and 13DD, respectively). Treatment of DHFR fusion proteins with bis-MTX yields the formation of an assortment stable protein structures ranging from a dimeric protein "square” to larger, octameric protein nanorings. To exert a level of control over this protein assembly, the researchers seek to modulate protein dimer stability via the introduction of dimer interfacial mutations. Key to this method is the engineering of a protein heterodimer that is lower in average free energy than either of the complementary homodimers. Initial progress in the laboratory has proven encouraging; however, the group’s crude protein modeling did not correlate well with experimental data. They are developing a computational model of the protein interface that will predict the effects of various interfacial mutations on homodimer and heterodimer stability. They are currently exploring the viability of MM-GBSA, Steered Molecular Dynamics, and modified umbrella sampling as methods for establishing this computational model. Additionally, they are characterizing the binding between mutant SHFR enzymes and the bis-MTX dimerizer in an effort to explain the differences present between experimental dimerization assays at high and low concentrations.

Group Members

Sanaa Bardaweel, Graduate Student
Matt Cuellar, Research Associate
Adrian Fegan, Research Associate
Amit Ganger, Graduate Student
Peter Huynh, Undergraduate Student
Yan Jia, Graduate Student
Brandie Kovaleski, Research Associate
Sidath Kumarapperuma, Research Associate
Qing Li, Graduate Student
Brian White, Graduate Student
Xin Zhou, Graduate Student