This course will prepare students to understand and
incorporate 3D macromolecular structure into their research
The principles of protein structure will be
reviewed, including noncovalent bonds. Structural bioinformatics
and genomics will be introduced. Students will learn what
percentage of proteins have known 3D structures, and the
importance of crystallographic models compared to homology models, or
Using laptop computers, students will learn how to find 3D protein molecular models for proteins in their research, and how to use Proteopedia.Org and FirstGlance in Jmol (adopted by Nature Structure & Molecular Biology) to investigate key structural features.
|Protein structure will be related to function, evolutionary conservation and multiple-sequence alignments, and drug design. Specific oligomers will be constructed and visualized. Students will learn how to prepare customized publication-quality molecular images, animations for Powerpoint slides, and how to effectively and intuitively communicate function-structure relationships with online molecular scenes in the Proteopedia.Org wiki. Each student will prepare Powerpoint slides capturing examples of the skills they have learned. All the software is web browser-based, easy to use, works on Windows or Mac OS X, requires no installation, is free and open-source, and is expected to be available for years to come.|
Proteopedia: The best place to begin understanding a molecule's structure.
Protein Data Bank & PDB Codes
Finding published molecules of interest.
Begin Powerpoint Slides.
Review of Protein Chemistry and Structure.
Introduction to Structural Bioinformatics.
|IV. FirstGlance in Jmol for exploring any macromolecule.|
Introduction to Multiple Sequence Alignment (MSA) and Conservation
Structure of Atomic Coordinate ("PDB") Files
|Effect of mutation on protein function||Genetic consequence||Example|
mutation LOST from gene pool
mutation remains in gene pool
* in methyl CpG binding protein 2 (MeCP2),
ASASPKQRRS IIRDRGPMYD DPTLPEGWTR KLKQRKSGRS AGKYDVYLIN
PQGKAFRSKV ELIMYFEKVG DTSLDPNDFD FTVTGRGSPS RHHHHHH
** R133C causes Rett syndrome, a severe neurological disorder.
Gray: disordered in crystal, absent in model 3c2i.
Evolutionary Conservation with ConSurf-DB
Authoring Molecular Scenes in Proteopedia
Publication-Quality Images & Animations for Powerpoint
FirstGlance in Jmol -- Part III
Salt Bridges & Cation-Pi Orbital Interactions
Color by Uncertainty ("Temperature")
Gaps in the Model due to Disorder
Intrinsically Unstructured Proteins
Structural Bioinformatics and Genomics.
Homology (Comparative) Modeling
Assessing Model Quality
Publication Quality Images and Animations with Polyview-3D
Finishing Powerpoint Slides
Click on the above image for
a larger view and explanation.
Probably we will not have time in class to spend on these resources. Links are provided here in case you are interested to look at these later.
Simplified SV40 Virus Capsid.
Lac repressor bending the DNA operon. If this image is not moving, reload the page.