Category Archives: Linus Pauling Institute

Elucidating protein structure with crystals

Kelsey in the lab pipetting one of her many buffers!

Proteins are the workhorse molecules of the cell, contributing to diverse processes such as eyesight, food breakdown, and disabling of pathogens. Although cells cannot function without helper proteins, they’re so small that it’s impossible to view them without the aid of special tools. Proteins are encoded by RNA, and RNA is encoded by DNA; when DNA is mutated, the downstream structure of the protein can be impacted. When proteins become dysfunctional as part of disease, understanding how and why they behave differently can lead to the development of a therapy. In Andy Karplus’ lab in the Department of Biochemistry & Biophysics, PhD candidate Kelsey Kean uses a technique known as protein x-ray crystallography to study the relationship between protein structure and function.

Protein crystals. On the left, each blade making up this cluster is an individual crystal that needs to be separated before we can use them.

Protein diffraction. An individual crystal is placed in front of an x-ray beam and we collect the diffraction resulting from the x-ray hitting each atom in the protein crystal . Using the position and darkness of each spot (along with some other information), we can figure out where each atom in the crystal was originally positioned.

An electron density map. After collecting and processing our diffraction images, we get an electron density map (blue)- this shows us where all the electrons for each atom in the protein are- and this guides us in building in the atomic coordinates (yellow) for each part of the protein. It’s like a puzzle!

Crystallization of protein involves many steps, each of which presents its own unique challenges. A very pure protein sample is required to form an ordered crystal lattice, and hundreds of different buffer solutions are tested to find the ideal crystallization conditions. Sometimes crystals can take weeks, months, or a year to grow: it all depends on the protein. Once a crystal is obtained, Kelsey ships it to the synchrotron at Lawrence Berkeley National Laboratory, which provides a source of ultra powerful x-ray light beams. Exposure of the protein crystal to x-ray light results in a diffraction pattern, which is caused by the x-ray light diffracting off of all the atoms in the crystal. A map of electron density is generated from the diffraction pattern, and then the electron density map is used to determine where the atoms are located in the protein, like a complex puzzle. X-ray protein crystallography is really amazing because it allows you to visualize proteins at the atomic level!

In addition to her lab work, Kelsey is extensively involved in teaching and STEM outreach. For the past 3 summers, she has organized a week-long summer biochemistry camp through STEM Academy, with the help of a group of biochemistry graduate students. Kelsey has also been involved in Discovering the Scientist Within, a program providing 150 middle school girls with the opportunity to perform science experiments, including isolation of strawberry DNA and working with mutant zebrafish.

Kelsey completed her undergraduate degree in biochemistry with a minor in math at the University of Tulsa, where she was also a Division I athlete in rowing. She attributes her work ethic and time management skills to her involvement in Division I athletics, which required a significant commitment of time and focus outside of lab and coursework. During one summer when she wasn’t busy with competitive rowing, she performed experiments related to protein crystallography at the Hauptman-Woodward Medical Research Institute associated with the University at Buffalo.

Kelsey knew she wanted to pursue science from an early age. She grew up surrounded by scientists: her mom is a biochemist and her dad is a software engineer! She recalls playing with Nalgene squirt bottles as a kid, and participated in the Science Olympiad in middle school, where she engineered a Rube Goldberg machine. She cites early exposure to science from her family as one reason why she feels strongly about STEM outreach to students who might not otherwise receive encouragement or support. In the future, Kelsey would like to teach at a primarily undergraduate institution.

Please join us this Sunday, April 23rd on KBVR Corvallis 88.7FM at 7 pm PST  to hear much more about x-ray protein crystallography, STEM outreach, and to hear an awesome song of Kelsey’s choosing! You can also stream this episode live at www.kbvr.com/listen.

Oops that’s a mistake.. No, that’s a new detox pathway!

It’s graduation season and for those folks who think grad school isn’t for them, take a look at this week’s guest who is one of the first to participate in the 4+1 Bioresource Research program in the College of Agricultural Sciences allowing students to complete their undergraduate and graduate degrees in 5 years! Taylor Hughes is an Oregonian native who grew up testing the river through his backyard for organic pollutants that would eventually lead him to Oregon State University scholarship. Like most recent graduates, high school and college alike, he didn’t know exactly which career path to take. He was looking towards environmental sciences after a pivotal class in high school that forced him identify an ecological system and develop a method to test a hypothesis; essentially he was a scientist in the making!

Chasing giant Fall Chinook on the Umpqua River in my hometown

Chasing giant Fall Chinook on the Umpqua River in my hometown

Fast-forward through the pre-requisite classes, and four years at OSU, and Taylor is now a recent graduate of the Bioresource Research degree focusing on toxicology. The degree requires some research hours where he worked on a senior thesis focusing on how naturally produced bodily chemicals were influencing our bodies’ endocannabinoid receptors system that work to keep our internal functions stable. This was Taylor’s first exposure to the “-omics” branch of science, some common examples include genomics and metabolomics.

This research focuses on biomolecules of specific functions or from specific species, however the vast number of molecules produced by our biology leads to massive datasets that tend to be hypothesis generating research rather than hypothesis driven research. What does this mean for the rest of us? It leads to unintended discoveries, answers to questions we didn’t know we had. Now that Taylor has returned to OSU and focusing on lipidomics, he has found as a potentially new detoxification pathway that has previously been unknown!

Tune in on tonight, June 5th at 7PM on 88.7FM or online to listen to us talk to the Roseburg-native Taylor Hughes about new understandings in how our bodies can remove toxic by-products.

Competing at a BBQ Cook-off fundraiser that raises money for Doernbecker's Children's hospital

Competing at a BBQ Cook-off fundraiser that raises money for Doernbecker’s Children’s hospital

Liver On The Edge

When thinking of the consequences of a diet high in fats, sugars, and cholesterol, many will think of weight gain and heart disease, but it may be the liver that suffers the most in the end. Non Alcoholic Fatty Liver Disease (NAFLD) affects as many as 35% of Americans and is caused by fat abnormally being stored in the liver. This disease can lead to irreversible scarring, inflammation, cancer, and even liver failure.

Healthy Mouse Liver

Healthy Mouse Liver

Currently, there is no known cure, but Kelli Lytle, RD, a Ph. D. student of Donald Jump in the department of Nutrition is looking for an answer; not with drugs, but with diet. If we change our diet to one that is low in fats, sugars, and cholesterol, can we nurse our livers back to health? By using a two-pronged approach with a mouse model and a cell culture model, she can better understand not only if restoration is possible, but how it works.

Diseased Mouse Liver. White circles indicate pockets of fat

Diseased Mouse Liver. White circles are pockets of fat

In this episode of our show, we will find out how Kelli found her passion for nutrition. We follow her journey from her beginnings studying Art History in Portland Community College, to becoming a registered dietician, and on to her five years at Oregon State University where she has not only published her work, but also communicated it to broad audiences in the three minute thesis competition.

So, tune in to hear Kelli’s passion for Science, Nutrition, and Science Communication on Sunday, January 31st at 7PM PST on 88.7FM or stream it live at http://kbvr.com/listen.

Photo credit: Kelli Lytle