What can you learn from molecular modeling?

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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  

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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  

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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

©  www.digitalworldbiology.com

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

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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

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3  Apps  in  iTunes,  one  in  progress

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

• Molecule  World  for  iPhone  (no  sequences)  

©  www.digitalworldbiology.com

Molecule  World  DNA-­‐binding  lab

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Gel  electrophoresis  lab  -­‐  in  progress

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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

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What  is  Molecule  World?

   Molecule  World

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Compare elements

What can we do with molecular modeling?

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

What can we do with molecular modeling?

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

What can we do with molecular modeling?

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Visualize shape: Molecules are not flat

What can we do with molecular modeling?

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Visualize chemical & sequence properties

What can we do with molecular modeling?

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Illustrate molecular interactions

What can we do with molecular modeling?

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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

©  www.digitalworldbiology.com

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?

©  www.digitalworldbiology.com

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

©  www.digitalworldbiology.com

What  is  Molecule  World?

©  www.digitalworldbiology.com

BRCA1          M1775  &  CTIP  protein  –  bio-­‐ITEST

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BRCA1  –  M1775  &  CTIP  protein  phenyalanine

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BRCA1  –  M1775  &  CTIP  protein  –  bio-­‐ITEST  

©  www.digitalworldbiology.com

BRCA1  –  M1775  alone  –  bio-­‐ITEST  

©  www.digitalworldbiology.com

BRCA1  –  M1775  >  R  muta7on                bio-­‐ITEST  

©  www.digitalworldbiology.com

Taste  receptors  –  capsaicin,  element  coloring

capsaicin

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Taste  receptors  –  capsaicin,  charge  coloring

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Taste  receptors  –  capsaicin,  spider  toxin

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Taste  receptors  –  capsaicin

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Taste  receptors  –  capsaicin

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Taste  receptors  –  wasabi,  charge  coloring

Allyl  isothiocyanate