Molecular Biophysics: Understanding How the Arrangement of Atoms in Protein Gives Rise to its Shape and Function

Faculty Advisor: Data Scientist; PhD, Molecular Biophysics, The University of Texas Southwestern Medical Center

Research Program Introduction

Molecular biophysics is a rapidly growing field of biomedical research that plays a vital role in studying life's molecules and the relationship between their structure and function. We will study molecules, including proteins, DNA, RNA, and pharmaceuticals. Our primary goal is to learn how to discover and use a molecule's three-dimensional structure to understand its function in the body.

We will begin with an introduction to organic chemistry and biochemistry, focusing on the structure of molecules. We will discuss how the amino acid sequence that makes up a protein gives rise to a protein’s 3-dimensional shape, and we will study how changes in a protein’s 3-dimensional shape may change its function.

We will discuss how structural biologists collect the experimental data they use to build 3D structures and how computational methods have been developed to construct 3D structures without reliance on laboratory data. Our survey will cover successive levels of complexity, from atoms to molecules to basic structures to more complex systems. Students may choose a protein they are interested in (e.g., a protein relevant to cardiology, psychiatry, or oncology) and review what is known about its structure. We can use that information to understand the mechanisms of how molecules work together or how we could use that information to design a novel drug to treat a disease.

Students will also learn general and subject-specific research and academic writing methods used in universities and scholarly publications and generate their own work products upon completion of the program.

Potential Topics for Final Project:

• Choose a protein(s) from a disease or condition and discuss its structure and how this data could be used to understand the biology behind it.

• Choose a family of similar proteins and compare how the 3D structures solved by experimental data differ from those predicted by algorithms.

• Describe the experimental protocol that would be used to collect the crystals used in X-ray crystallography to gather the data used to solve a structure.

• Compare and contrast some of the techniques used in solving 3D structures. What are their strengths and limitations?

• Consider a protein in a disease or condition that a lab animal may have. How similar is the animal’s protein to the human’s, and how might that influence how you interpret results using that animal model?

• Consider a biochemical pathway and the structures of the proteins in the pathway. Are the proteins modified in any way? How do these potential modifications help propagate a signal down that pathway?

• Other professor-approved research topics in this subject area that you are interested in

Program Details

• Cohort size: 3 to 5 students

• Workload: Around 4 to 5 hours per week (including class and homework time)

• Target students: 9 to 12th graders interested in biochemistry, organic chemistry, and/or pursuing a medical or life science research career.

• Schedule: TBD. Meetings will take place for around one hour per week, with a weekly meeting day and time to be determined one week before the class start date.