What can you learn from molecular modeling?

© www.digitalworldbiology.com

Molecular Modeling Bioinforma7cs, & Digital Biology

Sandra Porter, PhD

President, Digital World Biology LLC Adjunct Shoreline Community College,

Aus7n Community College

co-‐PI Bio-‐Link, Bio-‐Link.org


Bio-‐Link and Biotech-‐Careers.org

• Bio-‐Link is a na7onwide consor7um of biotechnology educa7on programs at colleges that offer 2 yr degrees. – hJp://bio-‐link.org

• Bio-‐Link is commiJed to helping students gain the skills needed to enter the biotech/life science workforce.

• Course-‐in-‐a-‐Box -‐ pedagogy, informa7on for teaching biotech courses

• Biotech-‐Careers.org -‐ all about biotech careers – hJp://biotech-‐careers.org

http://Biotech-Careers.org

http://Biotech-Careers.org

http://biotech-careers.org


Bioinforma7cs for Biotech Students

Shoreline Community College

1 month (5 weeks) Hybrid – in person

Students – • from new to college to bachelors’ degrees,

• some non-‐na7ve English speakers

Aus7n Community College

1 semester (16 weeks) On-‐line

Students – • from new to college to bachelors’ degrees,

• some non-‐na7ve English speakers


Bioinforma7cs for Biotech Students

1. Molecular Structures – Chemical Bonds – Physical proper7es of amino acids, protein structure

2. Molecular Sequences – BLAST, alignments, evolu7on, sequence conserva7on – mRNA vs genomic sequences

3. Gene7c Varia7on – stop codon, subs7tu7on, frameshi_ – Effects of muta7ons – how might muta7ons change func7on

4. Variable – microarrays, RNA-‐Seq, gene annota7on


Challenges with Cn3D

• Not user friendly

• No color keys or chemical names

• All atoms same size

• Can only view files from MMDB, no PubChem or PDB

• No op7ons for mobile devices

• Not easy to capture & label images


3 Apps in iTunes, one in progress

• Molecule World -‐ iPad • Molecule World DNA Binding Lab -‐iPad

• Molecule World for iPhone (no sequences)


Molecule World DNA-‐binding lab


Gel electrophoresis lab -‐ in progress


What is Molecule World?

• App for molecular modeling, Digital World Biology LLC – slightly different versions for iPad & iPhone, the iPad version shows

sequences

• User-‐friendly – color keys, image capture, control by touch

• Can use structures from different databases – NCBI, PDB, PubChem

• Uses updated informa7on – atoms shown with different sizes – Newer hydrophobicity data

• Sequence viewer in iPad version



Molecule World


Compare elements

What can we do with molecular modeling?


Demonstrate presence of similar elements - CO2, H2O, Glucose, Fructose, and Sucrose



Small chemicals vs. biopolymers (protein, DNA, RNA)



Visualize shape: Molecules are not flat



Visualize chemical & sequence properties



Illustrate molecular interactions



Explore rela7onship between structure & func7on

• Learn about func7on by exploring structures – Capsaicin & wasabi receptors

• Visualize how a muta7on can affect func7on

– Breast cancer (BRCA1), drug resistance

• Protein interac7ons – Ebola Virus & an7bodies


Addi7onal resources – DWB Community Page

Bio-‐ITEST Gene7c Tes7ng Curriculum

– BRCA1 – case study, bioethics, BLAST to learn who has muta7on, iden7fy changed amino acid

Amgen Materials on PTC tas7ng & evolu7on

– Are non-‐human primates tasters or non-‐tasters?


Learn More

• Molecule World iPad and iPhone versions, and the Molecule World DNA Binding Lab can be found in the iTunes store

• Sign up for our newsleJer

• Visit DigitalWorldBiology.com

http://DigitalWorldBiology.com


BRCA1 M1775 & CTIP protein – bio-‐ITEST


BRCA1 – M1775 & CTIP protein phenyalanine


BRCA1 – M1775 & CTIP protein – bio-‐ITEST


BRCA1 – M1775 alone – bio-‐ITEST


BRCA1 – M1775 > R muta7on bio-‐ITEST


Taste receptors – capsaicin, element coloring

capsaicin


Taste receptors – capsaicin, charge coloring


Taste receptors – capsaicin, spider toxin


Taste receptors – capsaicin


Taste receptors – wasabi, charge coloring

Allyl isothiocyanate

What can you learn from molecular modeling?

Education

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