Structural biology should be computable!
• Protein structures determined by amino acid sequences
• Protein structures and complexes correspond to global free energy minima
• Fundamental test of understanding and huge practical relevance
Model of energetics of inter and intramolecular
interactions
Design(Given Structure, OptimizeSequence)
Prediction(Given Sequence, OptimizeStructure)
Ab initio structure Protein Structure Protein designprediction
Protein-protein docking Protein-protein Interface design interactions
ROSETTA
Model of macromolecular interactions
• Removal of single methyl groups can destabilize proteins --> jigsaw puzzle-like packing crucial
• Buried polar atoms almost always hydrogen bonded --> treat hydrogen bonding as accurately as possible
• Exposed charge substitutions generally have little effect --> damp long range elctrostatics
• Focus on short range interactions!
Random Start
Low-Resolution Monte Carlo Search
(integrate out sidechain degrees of
freedom)
High-Resolution Refinement with full atomic detail
105
Predictions
Conformational sampling
Select lowest energy models
Jeff Gray (Hopkins),Ora Furman (Hebrew University), Chu Wang
Docking Low-Resolution Search
• Monte Carlo Search• Rigid body translations and
rotations• Residue-scale interaction
potentials
Protein representation: backbone atoms + average centroids
N
O
OO
N
O
N
O
N
N
O
......
Docking Protocol
(Target 12: cohesin-dockerin; unbound-bound) 1. Initial Search 2. Refinement
RMSD to arbitrary starting structure
Ene
rgy
RMSD to starting structure of refinement
(Å)
red,orange– xrayblue – model; green – unbound
0.46Å interface rmsd 87% native contacts 6% wrong contacts
Target 12Cohesin-Dockerin
Side Chain Flexibility
dockerin
cohesinOra Furman,Chu Wang
Details of T12 Interface
D39
N37
S45
L83
E86
Y74
L22
R53
dockerin
cohesin
red,orange– xrayblue - model
red,orange– xrayblue - model
0.23Å interface rmsd
Target 15immunity protein D-colicin D tRNase
Accurate Side Chain Modeling
colicin
immunity proteinScience 310, 638-642
Details of T15 Interface
H611
red,orange– xrayblue - model
E56
K610K608
K607
E68
E59D61
colicin
immunity protein
red,orange– xrayblue – model; green – unbound
2.34Å interface rmsd 36% native contacts
Target 20HemK-RF1
Modeling Backbone Movement
RF1
HemK
Loop with methylated Gln
Chu Wang
QuickTime™ and aYUV420 codec decompressor
are needed to see this picture.
CASP6 T0198: PhoU domain repeat
Model 2: 4A over 210 rsds
(Model 1: 3.94 over 198)
Phil Bradley
CASP6 T0212
Model 2: 3.97 over 109 rsds(Model 1: 4.0 over 104)
QuickTime™ and aDV/DVCPRO - NTSC decompressor
are needed to see this picture.
T0281 ab initio prediction (1.59Å)Phil Bradley
1r69
1ubq
Science 309, 1868-1871
2REB
Boinc.bakerlab.org/rosettaDavid Kim
High resolution ab initio structure prediction from single sequences by enhanced diversity “barcode” directed samplingOutreach!
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
High Resolution Refinement of CASP target 199 - remote homology model
Calculations performed on SDSC teragrid clustersBin Qian
High Resolution NMR Model Refinement
Vatson Raman
Disulfide Bond Formation Protein
Blue - X-ray structure Green - NMR models Red - Rosetta models
Computing Structural Biology• Free energy function reasonable => Computing simple
protein structures and interactions now appears to be within reach
• Implications for structural genomics? • More cpu power => more accurate predictions for larger
proteins• For larger complexes, experimental data essential (low
resolution electron density!).• Symmetry helps!
Modeling accuracy also illustrated by structures of designed proteins
Top7 X-ray structure has correct topology. Backbone RMSD to design only 1.2Å!!
C- Backbone Overlay
Red : X-ray structure
Blue : Design modelBrian Kuhlman, Gautam Dantas;Science 302 1364-8
Design of novel H bond network
interface
G177
Q51
Q180
Q169
Y35
G177Q180
Q169
Q51
Y35
G177
Y35
Design X-ray
Lukasz Joachimiak
Design of new protein functions
• Design of new protein-protein interactions• Design of enzymes catalyzing novel
chemical reactions • Design of new transcription factor and
endonuclease specificities• Design of HIV vaccine
HIV vaccine design
• Present HIV coat protein epitopes locked into conformation observed in complexes with neutralizing antibodies using designed scaffolds
• Preliminary results: designed proteins fold and bind neutralizing antibodies (5nM affinity). One design confirmed crystallographically.
Bill Schief in collaboration with Peter Kwong
Crystal structure of Mab 2F5in complex with its HIV epitope
Model of non-HIV scaffold-epitope (red)
Computational design of non-HIV immunogens to elicit broadly-neutralizing antibodies
Bill Schief
WT-WT Design-WT
WT-Design Design-Design
Redesign ofDNA cleavage specificity of MsoIhoming endonuclease using ROSETTA
Justin Ashworth,Jim HavranekNature in press
Specific DNA cleavage by designed nuclease
wild-type I-Mso
Design
-1/2n1
wild-type
design
wild-type
design
Cleavage
targets
½ ¼
-
1/29
5uMnuclease
Acknowledgements
Design• Brian Kuhlman (UNC)• Gautam Dantas• Justin Ashworth• Jim Havranek
Robetta.bakerlab.org
prediction and design server: David Kim (domain parsing, boinc) and Dylan Chivian
Rosetta software freely available for academic use
Boinc.bakerlab.org/rosetta
Protein structure prediction• Phil Bradley (MIT) • Rhiju Das• Lars Marlstrom• Bin Qian• Vatson RamanProtein-protein docking• Ora Furman (Hebrew
University)• Chu Wang• Jeff Gray (Johns
Hopkins)
