Macromolecular Structures: A User’s Perspective Mike Word, Ph.D. GlaxoSmithKline & Duke University Biochemistry November, 2003
Jan 26, 2016
Macromolecular Structures:
A User’s PerspectiveMike Word, Ph.D.
GlaxoSmithKline & Duke University Biochemistry
November, 2003
Rational drug designwhat we want to be doing
4cox
Illustration by David Goodsell
Structure Function1aos
(urea cycle)
1dcn
(eye lens)
94% sequence identity
Structure not always unique
Prionprotein
SCOP classes All alpha proteins (138) All beta proteins (93) Alpha and beta proteins (/) (97)
– Mainly parallel beta sheets (beta-alpha-beta units)
Alpha plus beta proteins (+) (184)– Mainly antiparallel beta sheets (segregated alpha and beta regions)
Multi-domain proteins (28) Membrane and cell surface proteins and
peptides (11) Small proteins (54) Coiled coil proteins (5) Peptides (77)
http://scop.berkeley.edu/
~30%
??
Comparative Protein Modeling Aim - To gain structural insights for a
new protein sequence before experimental elucidation takes place
Method - Extrapolation of the new structure from that of related family members
Alternative: ab initio (or de novo ) modelingSequence + theory modelA range of techniques; mostly energy basedVery difficult to apply
Folds, families and motifs
Template Selection
Alignment Model Building
EvaluationFold
Assignment
Evolutionary patterns are critical for successful prediction of function
Templates
Atomic coordinates from X-ray or NMR Highest sequence homology Relevant domain fragment SWISS-MODEL “first approach”:
– Can the structure be modeled?
Template Selection
Alignment Model Building
EvaluationFold
Assignment
Target to template alignment
Should consider (2º) structure: domain boundaries, motifs, location of loops, active site residues, SS bonds...
Can’t recover from incorrect alignment!
Template Selection
Alignment Model Building
EvaluationFold
Assignment
Comparative modeling methods Manual model
building Satisfaction of
spatial restraints Template based
fragment assembly
Template Selection
Alignment Model Building
EvaluationFold
Assignment
Model Evaluation
Does the model match the template(s)? Is the stereochemistry good? Energy ok? Are amino acids in reasonable
environments? What parts are conserved in the
sequence alignment? What information can the model
provide?
Template Selection
Alignment Model Building
EvaluationFold
Assignment
All-Atom Small-Probe Contact Surface Analysis
Contact score:
score = e–(gap/err)2
+ 4 Vol(Hbonds)
- 10 Vol(Overlaps)
clsc = number(clashes > 0.4Å)/1000 atoms
Clash score:
[van der Waals contacts]
[hydrogen bonds]
[atomic clashes]
dots
MolProbity Structure
validation server
Add H’s, analyze contacts
http://kinemage. biochem.duke.edu/
CASP
Critical Assessment of Techniques for Protein Structure Prediction
Biannual contest to model proteins of unknown structure– While experimental structure
determination is still in progress Evaluates manual to completely
automated structure prediction http://predictioncenter.llnl.gov
Acknowledgements
Richardson Lab: Dave & Jane, Laura Weston, Ian Davis, Bryan Arendall, Shuren Wang, Jeremy Block, Michael Prisant, Simon Lovell, Thomas LaBean, Mike Zalis
GlaxoSmithKline Protein Bioinformatics: Nicolas Guex, Kristin Koretke
NIH GM15000 GlaxoSmithKline