Biomimetics
2013
GOAL: Design biomimetics for artificial photosynthesis. In the crystal structure of Photosystem 2, there are two symmetrical tyrosines. One of them oxidizes water, the other does not. The one that oxidizes water is special in that it has a very tight, strained hydrogen bond with the histidine next to it. Can we create this strained hydrogen bond in small protein, a model system? If so, it would be the first step towards a biomimetic system that performs photosynthesis.
APPROACH: How do we do it? Three steps: (1) Find a protein that will serve as a template, a protein scaffold, for building the active site. This is a computational project involving database searches using geometric hashing. this project. (2) Model the active site. We will use the MOE software to design an active site that holds the histidine and tyrosine together. (3) Synthesize the protein in the lab. This step involves PCR, cloning and protein purification using standard methods.
WHO CAN DO THIS PROJECT (1) If you are a computer science major or have good programming skills, you can do part 1 of this project. (2) If you are a chemistry or BCBP major and you can do part 2 of this project. (3) If you are a biology, BCBP or BFMB major you can do part 3 of this project.
This project is a collaboration with the K.V. Lakshmi lab in Chemistry.
Lab Database
2012
GOAL: We have a web-accessible MySQL database that contains entries for samples, including plasmids, fragments, cell, and protein. We need to add features, such as a back button, mouseover information and a login page. A new database containing lab protocols can be added and linked to people and samples. Also, there is inventory work to be done.
APPROACH: Learn how to make entries in MySQL. Learn how to make/manage a web-base server page.
WHO CAN DO THIS PROJECT: Any undergraduate with programming experience and basic knowledge of molecular biology. The student should be skilled in Unix systems, HTML, and MySQL, or must be willing to learn.
CURRENT STATUS (Feb 2013): Jacob Tivin took on this project during the spring of 2012 and constructed the database and interface. The database now needs a better interface and a search function. Anyone up for this?
Contraceptive vaccine
2012
GOAL: Preliminary evidence suggests that antibodies against a calcium channel called CatSper, located in the tail of the sperm, may block capacitation and slow motility. If so, we can use CatSper to make a contraceptive vaccine. Help this collaborative project by constructing and synthesizing antigenic proteins for testing in a collaborator's lab.
APPROACH: Cloning, protein purification.
WHO CAN DO THIS PROJECT: Any undergraduate who has completed coursework in molecular biology and biochemistry.
CURRENT STATUS (Feb 2013): Danielle Basore took on the project and is well on the way to having protein for testing.
GFP-based biosensors
2012
GOAL: We use the Leave-One-Out technique to modify green fluorescent protein (GFP) in a way that creates a binding site for a peptide. LOO-GFP glows only in the presence of the peptide. Several projects exist relating to GFP biosensors, from computational design using the Rosetta suite of programs, to cloning and screening, to protein purification, to biophysical characterization, to crystallization and X-ray structure solution.
APPROACH: Cloning, protein purification, biophysics. Computational methods.
WHO CAN DO THIS PROJECT: Any undergraduate who has completed coursework in molecular biology and biochemistry. PSD students preferred.
CURRENT STATUS (Feb 2013): Undergrads Angela Choi and Rachel Alschuler are expressing and purifying LOO-GFP clones and GFP-based indole biosensors for biophysical assays
Protein design
2012
GOAL: Computational protein design may be used to create binding protein that can be then incorporaed into biosensors. Choose what you want to detect, then use Rosetta and in-house tools to design a protein that binds your target. Add your own programs!
APPROACH: Computational biology.
WHO CAN DO THIS PROJECT: Computer science students and any student with good programming skills and a willingness to learn about protein structure.
The phone cord effect
2012
GOAL: We are curious about why there is a prediminance of right-handedness in helical crossover structures in protein structures. Our theory is that helix formation generates torque on the chain, trapping crossovers in the right-handed state. To investigate this hypothesis, we have constructed circular peptides with helix-forming sequences. How fast do they fold when circularized? We can determine the rate by NMR. Work with a grad student to help complete this fascinating project, which includes a compuational component and a biophysics component.
APPROACH: Computational biology. Biochemistry, biophysics (NMR).
WHO CAN DO THIS PROJECT: Any undergraduate who has completed coursework in molecular biology and biochemistry. PSD students preferred. For the computational part, the student must know Unix and how to program.
Mon Sep 3 11:21:22 EDT 2012