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