The study of halogen bonds (X-bonds) is growing in nearly all fields of chemistry and material science. In biology and biochemistry, X-bonds have great potential to facilitate the rational design of new halogenated inhibitors against enzyme targets. This project applies a comprehensive strategy to study how structure affects the energy of biomolecular X-bonds in DNA and proteins. This project is developing a unique computational tool that can be used by biologists, biochemists and chemical biologists to rationally design new inhibitors against important enzymes. The tool would also be used to aid design of new biologically-based materials. The impact of this project on society is to improve the scientific literacy of the future workforce by engaging students at the K-12 level with experiential learning through an educational outreach project. This outreach project is introducing high school students to two important concepts in structural biology: 1) the fundamentals of 3-dimensional protein structures and 2) how those structures are experimentally determined. Finally, research training is provided to diverse groups of students, ranging from high school to postdoctoral levels, inclusive of gender, ethnicity and economic background.
The driving hypothesis of the proposed studies is that a force field for biological halogen bonds (ffBXB), once incorporated into a molecular mechanics/dynamics program, can be accurately and efficiently applied to design novel halogenated molecules for bioengineering applications. The project implements and tests the ffBXB in a standard molecular simulation program. The program is tested for its ability to accurately model the structures and energies of X-bonds that involve formally negatively charged oxygen acceptors in a previously-characterized experimental model DNA junction. The new program is independently cross-validated for its ability to accurately model the structures and energies of X-bonds that involve formally neutral oxygen acceptors in the model DNA junction and in T4 lysozyme. The validation studies are performed by X-ray crystallographic atomic level structure determination of these molecular systems and measuring their energies of interaction by differential scanning calorimetry (DSC) in solution. Free energy perturbation methods are used to study the effects of engineered X-bonds on the conformational and solvent dynamics of a biological system. The primary hypothesis is tested by applying the ffBXB to design new protein-protein interfaces. A coiled-coil polypeptide model system has been designed in which halogenated amino acids are introduced to serve as X-bond donating "knobs" that fit into engineered acceptor "holes". The resulting "X-Zipper" serves as a proof of concept that X-bonds can be used to facilitate specific assembly of proteins in a rational manner.
