MOLECULAR DYNAMICS SIMULATION STUDY OF MULTIMERIZATION OF THE MMS6 PROTEIN FROM MAGNETOSPIRILLUM MAGNETICUM STRAIN AMB-1 APS March Meeting March 17, 2009.

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Presentation transcript:

MOLECULAR DYNAMICS SIMULATION STUDY OF MULTIMERIZATION OF THE MMS6 PROTEIN FROM MAGNETOSPIRILLUM MAGNETICUM STRAIN AMB-1 APS March Meeting March 17, /12 Monica H. Lamm 2, Rastko Sknepnek 1, Lijun Wang 3, Marit Nilsen-Hamilton 3 1 Department of Physics and Astronomy 2 Department of Chemical and Biological Engineering 3 Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University and DOE Ames Laboratory

APS March Meeting March 17, /12 Motivation 500nm Magnetotactic bacteria - Magnetospirillum magneticum AMB-1 main structure of interest are magnetosomes: vesicles containing magnetite (Fe 3 O 4 ) nanocrystals nanocrystals ~50nm in length form a long linear chain (from T. Prozorov, et al. ACS Nano 1, 228 (2007)) B earth 1. Understand formation of magnetite nanocrystals. 2. Mimic it in the laboratory. 3. Control the self-assembly by organic (block copolymer) matrix. Talk Y Study Mms6 protein which appears to be crucial for nanocrystals formation

APS March Meeting March 17, /12 Experiments with Pluronic ® copolymers: Mms6 is crucial for growth of magnetite nanocrystals. (T. Prozorov, et al. ACS Nano 1, 228 (2007)) Experiments on bacteria show presence of Mms6 protein is in magnetosomes. (Arakaki et al., J. Biol. Chem., 278, 8745 (2003)) Mms6 protein Short protein: sequence: GGTIWTGKGLGLGLGLGLGAWGPIILGVVGAGAVYAYMKSRDIESAQSDEEVELRDALA 59 amino acids molecular weight: 5961 g/mol approximate diameter: 2.5 nm hydrophilic C 25 -terminus C 21 -terminus hydrophobic N-terminus Structure is at present not known. Number of subunits KCl (mM) His-Mms6ND~20-40ND C25Mms C21Mms6138ND Mms6 aggregates in a solution. Is this a membrane protein?

Modeling AdvantagesDisadvantages Reduce number of degrees of freedom Parameters tuned for narrow range of physical conditions Larger time step  longer simulations Work in real units (temperature, pressure, etc.) APS March Meeting March 17, /12 Atomistic simulations are not feasible: multimers contain tens of proteins relevant time scales are hundreds of nanoseconds protein structure is at present not known Use an intermediate level coarse grained model. Aggregation and interaction with a phospholipid bilayer.

APS March Meeting March 17, /12 Coarse-grained model Model by Shih, et al. J. Phys. Chem B 110, 3674 (2006). water L0L0L0L0 Model by Marrink et al. JPC-B 108, 750 (2004). ProteinDPPC phospholipid

APS March Meeting March 17, /12 Bonded interactions Harmonic bond: Angle interaction: Dihedral interaction: Nonbonded interactions q (e)  (nm)  r cut (nm)  mn (kJ/mol) IIIIIIIVV ±

Molecular dynamics Simulation parameters Ensemble NPT ( Berendsen thermo/barostat) Temperature K Salt concentration0 Pressure1 atm Number of beads25,000 to 80,000 Time step10-15fs Length (typical)100 – 300ns (10-20 million time steps) Simulations performed with LAMMPS (S. Plimpton, J. Comp. Phys. 117, 1 (1995); lammps.sandia.gov) Initial configurations build by CGBuilder Python toolkit. APS March Meeting March 17, /12

C 21 terminus after 300 ns (KSRDIESAQSDEEVELRDALA) APS March Meeting March 17, /12 Results - single chain studies negative positive polar nonpolar/apolar GGTIWTGKGLGLGLGLGLGAWGPIIL GVVGAGAV YAYMKSRDIESAQSDEEVELRDALA Mms6 after 300 ns

Results - multimerization studies 30 C 21 chains in a L=150A box after 170ns (water molecules not shown) APS March Meeting March 17, /12 negative positive polar nonpolar/apolar Number of subunits KCl (mM) His-Mms6ND~20-40ND C25Mms C21Mms6 13 8ND Two multimers of sizes 13 and 16!

APS March Meeting March 17, /12 negative positive polar nonpolar/apolar 30 Mms6 chains in a L=130A box after 175ns (water molecules not shown) One large aggregate!

Results – Mms6 in a DPPC bilayer APS March Meeting March 17, /12 negative positive polar nonpolar/apolar 10 Mms6 proteins and 1024 DPPC molecules after 180ns. (water not shown) Starting from a random configuration, bilayer with embedded proteins froms within approximately 60ns. Mms6 is likely to be a membrane protein

Summary and Conclusions APS March Meeting March 17, /12 Mms6 protein: small protein present in magnetosomes of magnetotactic bacteria plays major role in growth of magnetite nanocrystals forms multimers in a solution We have used an intermediate level coarse grained model to simulate assembly of multimers and interaction with a phospholipid bilayer. Coarse grained model qualitatively agrees with experiments. Recent experiments suggest that Mms6 binds iron III. Our model needs improvement to explain this phenomenon. Our simulation suggest that Mms6 is a membrane protein.