Biomolecular simulations and their computational challenges Bridging scales in time and space
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1 Biomolecular simulations and their computational challenges Bridging scales in time and space Ilpo Vattulainen Biological Physics & Soft Matter Team Dept of Physics, TUT & Dept of Applied Physics, HUT tfy.tkk.fi/bio/ Member of COMP Center of Excellence
2 INTRODUCTION: SCALES Challenge: modeling cells Complexity, Complexity, scales scales ~20 µ m
3 INTRODUCTION: SCALES A Sense of Scales
4 INTRODUCTION: SCALES Towards multi-scale modeling Mesoscale: Macroscale: effective interactions times ~1 s and collective phenomena long-range effects scales ~ 1µ large scales Different methods for different scales Main question is how to bridge them in a controlled and reliable fashion Coarse-graining Atomistic picture: microscopic accuracy interatomic forces intermolecular
5 TCSC mpere Centre for Scientific Computing Akaatti cluster Frontnode + Computing nodes. All together, approximately 200 cores for scientific computing Delivery of another 200 cores (Blade, infinityband) by the end of Nov Techila PC-grid Currently approximately 750 computing cores Web: Contact: Kari Suomela Mika Anttila Antti Saarinen Ilpo Vattulainen (TC
6 NTRODUCTION: LIPOPROTEINS Lipoproteins Carriers of cholestero Structure of lipoproteins not known: Functions not understood Cholesteryl esters in the interior of LDL. M. Heikelä, I. Vattulainen, M.T.Hyvönen, Biophys. J. 90 (2006) 2247; A. Koivuniemi et al. Biophys. J. LDL and HDL particles carrying cholesterol. Vuorela et al., under preparation (2009). Catte et al., Biophys. J. 94, 2306 (2008)
7 RESULTS: BAD CHOLESTEROL Lipoproteins, carriers of Chol Low density lipoprotein (LDL) bad cholesterol LDL is a pain for simulations. 1. LDL size ~25 nm, plus solvent 1. Time scales should be > 10 microseconds 1. Atomistic simulations would take roughly at least 3000 CPU-years. No chance. 1. Coarse-grained simulations feasible take only about 5 CPUyears per simulation. LDL structure determined through coarse-grained simulations. Murtola et al., manuscript under preraration (2009).
8 RESULTS: GOOD CHOLESTEROL HDL Good cholesterol High density lipoprotein (HDL) good cholesterol All-atom model 10 ns at 310K CoarseGrained model 1 µs at 310K Simulation results allow us to understand the functions of HDL, and later find treatments for diseases such as atherosclerosis Atomistic and coarse-grained modeling of model spheroidal HDL particles. A. Catte et al., Biophys. J. 94, 2306 (2008). Novel Changes in Discoidal High Density Lipoprotein Morphology: A Molecular Dynamics St udy. A. Catte et al., Biophys. J. 90, 4345 (2006). Models with: 2 ApoA-I proteins POPCs Cholesterol esters These are semi-ok
9 ESULTS: CHOLESTEROL IN LIPOPROTEINS HDL Good cholesterol Annular cholesterol esters (green) in contact with apoa-i: Almost 100% Packing of cholesterol esters (green) within POPCs Chol esters stabilizing apoa-i and thus HDL A. Catte et al., Biophys. J. 94, 2306 (2008). Almost 100% of chol esters are annular. Atomistic and CG models consistent regarding contacts, the minor differences due to the CG
10 ESULTS: CHOLESTEROL IN LIPOPROTEINS HDL Good cholesterol Full line: with ApoA-I Dashed: no ApoA-I T. Vuorela et al., Paper under preparation (2009) Full HDL with a realistic lipid composition Coarse-grained simulations over ~10 µ s each SUMMARIZING THE RESULTS: Triglycerides and Chol esters in the core, partly in the interface PCs, Chols at the surface ApoA-I s favor contacts with Chol and its esters, supporting the stabilization mechanism of Chol Three-layer model
11 ESULTS: CHOLESTEROL IN LIPOPROTEINS ystems biology bridged to simulations High density lipoprotein (HDL) good cholesterol Mass spectrometry: Lipid profiling for HDL composition from subjects with low and high HDL. Simulations: HDL structure for the different molecular compositions obtained from mass spec. Triglycerol distribution distinctly different in the HDL particles in subjects with two subject types. Lipid composition, structure and function of low and high HDL. Yetukuri, Soderlund, Koivuniemi, Seppanen-Laakso, Niemela, Hyvonen,
12 ESULTS: EFFECTS OF NANOMATERIALS ON CELLS Nanomaterials acting on membranes Fullerene Gallic acid What will happen when carbon nanoparticles act on cells together with phenolic acids such as the gallic acid? -Time Translocation of Fullerene Reveals Cell Contraction. alonen, S. Lin, M. L. Reid, M. Allegood, X. Wang, A. M. Rao, I. Vattulainen, P. C. Ke. ll 4, 1986 (2008).
13 ESULTS: EFFECTS OF NANOMATERIALS ON CELLS Nanomaterials acting on cells -Time Translocation of Fullerene Reveals Cell Contraction. alonen, S. Lin, M. L. Reid, M. Allegood, X. Wang, A. M. Rao, I. Vattulainen, P. C. Ke. ll 4, 1986 (2008).
14 ESULTS: EFFECTS OF NANOMATERIALS ON CELLS Nanomaterials acting on membranes ects of fullerene and gallic acid on lipid membranes and membrane proteins. Monticelli, E. Salonen, P. C. Ke, Vattulainen. rk in progress ( ).
15 ESULTS: EFFECTS OF NANOMATERIALS ON CELLS Nanomaterials acting on membranes ects of fullerene and gallic acid on lipid membranes and membrane proteins. Monticelli, E. Salonen, P. C. Ke, Vattulainen. rk in progress ( ).
16 Thank you! Acknowledgments: Academy of Finland Center of Excellence funding European Union ESF, Nordita Helsinki Inst of Physics Bioindustry Finnish Foundations Center for Scientific Computing Collaborators (experiments, examples): Collaborators (theory, examples): Ole G. Mouritsen et al. (Odense) Elina Ikonen (Biomedicum, Hki) Petri Kovanen (Wihuri, Hki) Amy Rowat (Harvard) Peter Westh (Roskilde) Juha Holopainen (HUS, Hki) Susanne Wiedmert (Hki) Michael R. Morrow (Newfoundland) Filip Tuomisto (HUT) Paavo Kinnunen (Biomedicum, Hki) Martin Zuckermann (Vancouver) Roland Faller (UC Davis) Tapio Ala-Nissilä (HUT/COMP) Adam Foster (HUT/COMP) Kirsi Tappura et al. (VTT) P. Capkova (Prague) Aatto Laaksonen et al. (Stockholm) Kin Wah-Yu (Hong Kong) Alex Bunker (Viikki/Drug Design) Klaus Schulten et al. (Illinois) SJ Marrink (Groningen) AA Gurtovenko (UK) Networks: SimBioMa (ESF), MOLSIMU (COST), Nordita, Graduate Schools, etc.
17 Activities (examples) Peer-reviewed publications by the BIO Group: 20 articles in articles in articles in 2009 by now (+ 7 papers under review) Typical journals: PLoS, Small, JACS, JBC, PRL, JPCB, JCP Conferences (co)organized: ICBL2007, Sep 2007 Summer School, Sep 2007 Lipid Meeting, Sep 2008 NORDITA programme, Mar 2009 Networking: Graduate School Graduate School Graduate School SimBioMa (ESF), FuncDyn (COST), in Glycosciences in Nanosciences in Materials Physics NORDITA, MOLSIMU (COST), Funding: Center of Excellence status Academy of Finland projects Academy of Finland positions Graduate Schools EU FP7 TEKES/industry Foundations Tampere Univ of Tech
18 People BIO Group at HUT (Hki): Marja Hyvönen, PhD Giulia Rossi, PhD Sarah Overduin, PhD Olli Punkkinen, PhD Markus Miettinen, MSc Jelena Telenius, MSc Risto Mikkeli, student Ilpo Vattulainen BIO Group at TUT (Tre): Tomasz Rog, Academy Res Fellow Sami Paavilainen, PhD Oana Cramariuc, PhD Liam McWhirter, PhD Hector Martinez-Seara, PhD Samuli Ollila, MSc Anette Hall, MSc Artturi Koivuniemi, MSc Timo Vuorela, MSc Sanja Pöyry, MSc Karol Kaszuba. MSc Reinis Danne, MSc Antti Lamberg, DThesis student Adam Orlowski, student Maria Lehtivaara, student Matti Javanainen, student Eero Hytönen, student Juha Järvinen, student Henrik Hammaren, student Team at Wihuri Research Institute (Helsinki): Katariina Lähdesmäki, MSc Artturi Koivuniemi, MSc Marja Hyvönen, PhD Collaborat ors shown in red
19 Collaborators (w/ joint articles/projects) Experimental collaborators: Prof. Elina Ikonen - Biomedicum, Helsinki Prof. Kai Simons MPI Dresden Doc. Juha Holopainen Dept of Ophtalmology, Helsinki Univ Hospital Dr. Susanne Wiedmer Univ of Helsinki Prof. Matej Oresic VTT Systems Biology Dr. Matti Jauhiainen, THL Prof. Pu-Chun Ke Clemson University, USA Prof. Michael Morrow Newfoundland, Canada Prof. Matti Vuento Univ of Jyväskylä MEMPHYS Center for Biomembrane Physics, Odense, Denmark (J. Bernardino de la Serna, H. Kandela, O.G. Mouritsen et al.) Prof. Petri Kovanen Wihuri Research Institute, Helsinki Dr. Annele Virtanen Tampere Univ of Tech, Finland Dr. Filip Tuomisto Deprt of Applied Physics, Helsinki Univ of Tech Dr. Amy Rowat Harvard Univ, USA Prof. Peter Westh Roskilde Univ, Denmark Theory/Computational collaborators: Prof. Siewert-Jan Marrink Groningen, The Netherlands Prof. Mikko Karttunen Univ of Western Ontario, Canada Prof. Roland Faller UC Davis, USA Dr. Erik Lindahl Stockholm, Sweden Dr. Ramon Reigada Univ of Barcelona Dr. Andrei Gurtovenko - Bradford, UK Dr. Alex Bunker Viikki Biocenter, Helsinki Prof. Tapio Ala-Nissilä Dept of Applied Physics, HUT Dr. Adam Foster Dept of Applied Physics, Helsinki Univ of Tech Dr. Sergey Lyulin Russian Academy of Science, St Petersburg
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