center for biological physics* arjan van der vaart – studying the conformational changes of...

Center for Biological Physics*Center for Biological Physics*

Arjan van der VaartArjan van der Vaart – studying the – studying the conformational changes of proteins asconformational changes of proteins asthey interact with other moleculesthey interact with other moleculesBanu OzkanBanu Ozkan – studying the mechanism – studying the mechanism of protein foldingof protein foldingMichael ThorpeMichael Thorpe – studying geometric – studying geometric conformation changes based on flexibility conformation changes based on flexibility and rigidity of biological moleculesand rigidity of biological molecules

Summary of Research Group WorkSummary of Research Group Work

Math and Science Teachers Fellows

van der Vaart - Ozkan - Thorpe

Jeff Toller, Mohave High SchoolBullhead City, Arizona

General Overview of Our General Overview of Our StudentsStudents

♦ ♦ Title I School – 75% qualify for free orTitle I School – 75% qualify for free or reduced lunch/breakfastreduced lunch/breakfast♦ ♦ A Minority Majority SchoolA Minority Majority School 45% Hispanic45% Hispanic 40% Caucasian40% Caucasian 8% African-American8% African-American 5% Native American5% Native American 2% Other2% Other♦ ♦ Transient SchoolTransient School

Tracy Blondis, Westwood High SchoolMesa, Arizona

Selected Research in Selected Research in LaboratoryLaboratory

♦ ♦ Identify fundamental structure of proteins to analyzeIdentify fundamental structure of proteins to analyze

protein folding. Concerned primarily with chemical protein folding. Concerned primarily with chemical

interaction of amino acid side chains.interaction of amino acid side chains.

♦ ♦ Recognize areas of rigidity and flexibility in proteins. Recognize areas of rigidity and flexibility in proteins.

Flexible areas interact with other molecules toFlexible areas interact with other molecules to

undergo chemical reactions. Great potential for undergo chemical reactions. Great potential for

combating disease as proteins could be manufacturedcombating disease as proteins could be manufactured

for use.for use.♦♦ Use of computer simulations in analyzing data and parameters. Use of computer simulations in analyzing data and parameters. Protein folding occurs within picoseconds. Computer modelingProtein folding occurs within picoseconds. Computer modeling allows for time manipulations when analyzing data.allows for time manipulations when analyzing data.

Our Curricular Tasks and Our Curricular Tasks and Methods of Proposed Instructional Delivery

♦ ♦ Introduce students to the four orders of protein structureIntroduce students to the four orders of protein structure Primary Structure – amino acid sequencePrimary Structure – amino acid sequence Secondary Structure – Secondary Structure – αα and and ββ helices helices Tertiary Structure – foldingTertiary Structure – folding Quaternary Structure – compacted subunitsQuaternary Structure – compacted subunits To do this,To do this, a PowerPoint presentation will be provided with integrated computer simulations and embedded short videos

♦ ♦ Have students evaluate regions of protein flexibility and rigidityHave students evaluate regions of protein flexibility and rigidity by examining computer models by examining computer models Students will use critical thinking to determine areas of flexibility and rigidity in molecules by analyzing video simulations of proteins. Students will assemble in small groups to brainstorm possibilities and support their conclusions. Then as a class, ideas will be written on white boards. Similar ideas between groups will be emphasized in the hopes that students will lead themselves to the correct answers.

♦ ♦ Students will determine properties of chemical bonding betweenStudents will determine properties of chemical bonding between amino side chains based on hydrophilic and hydrophobicamino side chains based on hydrophilic and hydrophobic regions.regions.

Plastic interactive models will be fabricated that students can

hold and manipulate. These models will have painted regions

indicating hydrophobic and hydrophilic areas. Students will be

asked to find a logical method for chemical bonding. Emphasis

will be given on size of their molecule where a smaller size

indicates a smaller energy state.

♦ ♦ Have students understand the mechanism of protein folding byHave students understand the mechanism of protein folding by using a modified protein modeling softwareusing a modified protein modeling software

TEALsim, a free protein software designed for low level under- standing of protein folding, will be demonstrated to students. This software includes a few basic proteins that students can manipulate to determine the known properties of protein folding.

Dr. Mike Thorpe, ASU Department of Physics

♦♦ Dr. Thorpe’s research is diverse and Dr. Thorpe’s research is diverse and includes an emphasis in the theory of includes an emphasis in the theory of flexibility and mobility in glassy networks.flexibility and mobility in glassy networks. During our MSTF summer program, During our MSTF summer program, Dr. Thorpe introduced the concept of Dr. Thorpe introduced the concept of flexible regions in proteins that is flexible regions in proteins that is determined by x-ray crystallography.determined by x-ray crystallography.

Dr. Arjan van der Vaart, Dept. of Chemistry & Biochemistry

♦♦ Dr. van der Vaart’s research is to better Dr. van der Vaart’s research is to better understand the fundamental principlesunderstand the fundamental principles that govern conformational behavior inthat govern conformational behavior in computational simulations. He hopescomputational simulations. He hopes to build predictive models for explainingto build predictive models for explaining how biological molecules interact.how biological molecules interact.

Dr. Banu Ozkan, ASU Dept. of Physics

♦♦ Dr. Ozkan’s research focuses on howDr. Ozkan’s research focuses on how amino acid sequence encodes for theamino acid sequence encodes for the specific function and structure of proteins.specific function and structure of proteins. Banu also hopes to find how proteins foldBanu also hopes to find how proteins fold and assemble into macromolecules.and assemble into macromolecules.

Jeff Toller and Tracy Blondis

“This Summer 2007 Math and Science Teaching Fellows has given us an insight into the rapidly changing method of conducting scientific research. What an awesome opportunity to learn cutting edge research and then have the ability to share it with our students.”

– Tracy Blondis and Jeff Toller

* Supported by * Supported by Science Foundation Arizona, National Science Foundation Arizona, National Science Foundation, and Arizona State University Science Foundation, and Arizona State University