pumpkin c entre for m embrane p umps in c ells and d isease dynamics of multi-domain proteins going...
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PUMPkin
CENTRE FOR MEMBRANE PUMPS IN CELLS AND DISEASE
www.pumpkin.au.dk
Dynamics of Multi-Domain Proteins Going from an All-Atom Representation
to a Protein-Domain Representation
References1 Marrink et al., J. Phys. Chem. B, 2007, 111, 7812–78242 Monticelli et al., J. Chem. Theory Comput. 2008, 4, 819–8343 Periole et al., J. Chem. Theory Comput. 2009, 5, 2531-2543
IWONA SIUDA1,2,3, CHRISTIAN N. S. PEDERSEN1,3, LEA THØGERSEN1,2,3
1Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Denmark 2Bioinformatics Research Centre, C. F. Møllers Allé 8, DK-8000 Aarhus C, Denmark
3Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10C, DK-8000 Aarhus C, Denmark
Bioinformatics Research Centre | C. F. Møllers Allé 8 | DK-8000 Aarhus C | Denmark
Test Set9AAT1AMA 1USK 1USG
1L5B 1L5E 2EZA
3EZA
1B47 2CBL
4CTS 1CTS
1E8B 1E88
2HMI 1HVU
PDB PDB RMSD [Å] Domain average RMSD[Å]
1USK 1USG 7.04 0.681AMA 9AAT 1.66 0.984CTS 1CTS 2.37 1.381E8B 1E88 2.79 1.142EZA 3EZA 1.86 1.151L5B 1L5E 6.51 1.091B47 2CBL 1.87 0.542HMI 1HVU 5.73 1.41
The Pump Perspective
The domELNEDIN Model
ELNEDIN Model domELNEDIN ModelCG ModelAA Model
• Atomic details
• Time scale ≈ 100 ns
• Residue details• Time scale ≈ 1 μs
• Structure collapse
• Residue details• Time scale ≈ 1 μs• Structure stable
• Residue details• Time scale ≈ 1 μs• Structure stable• Conformational changes allowed
• Conformational changes not allowed
Established Models New Model
÷
+
Coarse Grained RepresentationsAll Atom (AA)
Model
Adding elastic network
Coarse Grained (CG)Model
Mapping atoms into beads
ELNEDIN Model domELNEDIN Model
Overall Inside domains only
Periplasmic Leucine-Binding Proteinpdb: 1USG
• Test set with protein structures resolved for at least two conformations.• RMSD between same domains in different conformations is on average 1.1 ± 0.3 Å.• Thus, it seems fair to restrain internal domain dynamics while modeling domain movements.
• Molecular dynamics modeling is highly valuable as a test ground for hypotheses in close interplay with wet-lab experiments.• Models with atomic resolution suffer from hard time scale limitations, but are very well established.• Models with residue resolution access the microsecond time scale1,2, but suffer from artificial restrictions to the structure and dynamics3.• The domELNEDIN model maintains the residue resolution, but restrictions are released to allow for domain movements.
PDB PDB RMSD [Å] Domain average RMSD[Å]
1T5S 2C88 10.2 2.0 (1.1)1T5S 3B9B 11.3 1.7 (0.8)2C88 3B9B 6.4 1.7 (1.1)
E2-ATPpdb 2C88
Ca2E1~P-ADPpdb 1T5S
E2Ppdb 3B9B
• The P-type ATPases consist of well defined protein domains. For the sarcoplasmic reticulum Ca2+-ATPase (SERCA), structures have been solved for several conformations.• SERCA is therefore a unique test case for the application of the domELNEDIN model to membrane proteins in general and to ATPase pumps in particular.
SERCA Structures
• With domELNEDIN molecular dynamics simulations of the ATPases, we would be able to model hypotheses involving conformational changes, which is currently not possible.