University of Minnesota
University Relations

Minnesota Supercomputing Institute

Log out of MyMSI


Research Abstracts Online
January 2008 - March 2009

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. Recent work has shown that the MMFF94 force field, with or without CM4 charges substituted for the force field’s default charges, provides the most accurate model for methotrexate. Based upon these results, the group has now begun to examine the efficacy of umbrella sampling in directly calculating the free energy of binding at the chemically induced DHFR-DHFR dimer interface. Calculated results will be compared to existing experimental data, and the method extended into a predictive model of the effects of mutation at the DHFR dimer interface.

Group Members

Sanaa Bardaweel, Graduate Student
Adrian Fegan, Research Associate
Chunqi Hu, Graduate 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