PSAFEProtein Structure And Function Exploration

for Undergraduate Biochemistry Students

 

The Goals

• Expand access to computational tools for UVA students

• Introduce undergraduate students to state-of-the-art molecular modeling software

• Encourage students to think critically, creatively and independently about biochemical research

• Showcase the work of undergraduates within UVA and beyond

Key Contributors

• Reg Garrett, Professor of Biology

• Elizabeth Magnotti, B.S. Chem, UVa, 2011

• Amanda Mullen, B.S. Chem, UVa, 2012

• Erna Kukic, B.S. Chem, UVa, 2013

• Sarah Smith, B.S. Chem, B.A. Biol, UVa, 2014

• Yitna Firdyiwek, Instructional Technology Advisor, ITS

The PSAFE Project

• PSAFE is a part of BIOL 5010 and CHEM 4410, both biochemistry lecture courses

• Each student is assigned a biomolecular structure

• For a semester-long project, done outside of class

• The structure is typically a protein, but sometimes a nucleic acid or a protein-nucleic acid complex

• Students study their structures all semester and become intimately acquainted with them

• Final project is a “molecular document” that showcases the structure and function of their molecular complex and provides multiple interactive views and animations of the structure

Guidance for Students

• A “head TA” is chosen from the previous year’s class

• This TA meets weekly with students to discuss aspects of the project and advise students

• The head TA also supervises grading of project milestones

• Students also have access to a library of project documents online on Collab

• Students also learn to explore a variety of databases online to learn about their structure

The Software

• Molecular documents are created using software from Molsoft LLC (La Jolla, California)

• Molsoft has graciously provided this sophisticated software to UVA students and faculty free for 4 years

• The software lets students describe their structure in text on the left side of the screen

• Hyperlinks in the text control graphic manipulations on the right side of the screen

Archiving the Student Projects

• We are generating 250 projects each year

• Students are eager to preserve and display their work

• Many have asked one and two years later

• Two strategies:• Cengage (publishers of Biochemistry by Garrett and

Grisham) have placed 140 of the 2010 projects on the textbook website – an arduous editing project

• We have developed a UVA (Collab) website to display the collected projects with a shorter turn-around time

The PSAFE Website

• The PSAFE website has been built on Collab – the eventual website will be psafe.us

• The principal challenge has been to transfer so many projects – 650 now, with many more to come

• Each project consists of several files managed by the Molsoft software via a home page (which we can call index.html) and all contained in a folder (directory)

• Yitna Firdyiwek has written a javascript to load the projects onto Collab

• The script allows projects to be searched according to student name, protein name, or chapter number

How it works

• The folders are named according to the convention:

• ChXX__StudentLastName__FirstInitial__ProteinName, followed in some cases by additional information

• The folder name is decomposed into three parts:• Chapter number

• Student name

• Protein name

• This allows each project to be listed either by chapter number, student name or protein name

• The hyperlinked lists that result open the index.html file

Thanks to:

• Yitna Firdyiwek

• Sarah Smith and the previous head TAs

• Reg Garrett

• Collab developers and support staff

• Andy Orry, Molsoft LLC and his colleagues

• Our students!