pumpkin c entre for m embrane p umps in c ells and d isease dynamics of multi-domain proteins going...

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.