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Project #2: Develop atomistic molecular models of

Activity: Computational Biology and Data Analysis Structural Computational Biology Team First Meeting, Philadelphia, September 29, 2007 Attending: John Brady Jiancong Xu Mike Crowley Pavan Ghatty Hong Guo Mike Himmel Mark Nimlos Loukas Petridis Moumita Saharay Jeremy Smith Ed Uberbacher.

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Project #2: Develop atomistic molecular models of

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  1. Activity: Computational Biology and Data AnalysisStructural Computational Biology TeamFirst Meeting, Philadelphia, September 29, 2007Attending:John BradyJiancong XuMike CrowleyPavan GhattyHong GuoMike HimmelMark NimlosLoukas PetridisMoumita SaharayJeremy SmithEd Uberbacher

  2. Project #2: Develop atomistic molecular models of cellulosomal cellulases working on insoluble cellulose substrates. Leader: Mark Nimlos Contributors: Brady, Crowley, Guo, Himmel, Saharay, Smith Project #3a: Develop atomistic molecular models of C. thermocellum cellulosomes working on insoluble cellulose substrates. Leader: Mike Crowley Contributors: Brady, Jiancong Xu, Guo, Himmel, Saharay, Smith Project #3b (was 4a): Simulate microbe-cellulosome-biomass interface. Leader: Mike Crowley Contributors: Brady, Jiancong Xu, Gou, Himmel, Petridas, Smith, Uberbacher Project #4a (was 3b): Investigate microfibril dynamics. Leader: Jeremy Smith Contributors: Brady, Crowley, Himmel, Petridas, Uberbacher Project #4b: Model plant cell wall Leader: Jeremy Smith Contributors: Brady, Crowley, Himmel, Petridas, Uberbacher, York

  3. Project #4a (was 3b): Investigate microfibril dynamics. Leader: Jeremy Smith Contributors: Brady, Crowley, Himmel, Petridis, Uberbacher Project #4b: Model plant cell wall Leader: Jeremy Smith Contributors: Brady, Crowley, Himmel, Petridis, Uberbacher, York

  4. Towards a Simulation Model of the Plant Cell Wall Why do we want such a thing? Cell wall architecture and mechanics determines recalcitrance to hydrolysis.

  5. Steps to be Taken:Year One • Force field parameterization (cellulose (done); lignin (nearly done);hemicellulose pectins). • Simulation of crystalline cellulose, fibrils. • Simulation of lignin in solution.

  6. Amorphous and Crystalline Cellulose. • Simulation of lignin:hemicellulose:cellulose interaction. • Generation of Reliable Configurational Ensembles for Amorphous Polymer Systems. • Peta- and Exascale Supercomputing. • Coarse-grained modeling: REACH methodology. • Interaction with neutron and X-ray scattering experiment. • Role of Hydration. • Pretreatment (Heat/pH etc). Longer Term Goal: Interaction of Cellulases and Cellulosomes with Plant Cell Wall.

  7. Lignin and Biomass Recalcitrance Loukas Petridis - Center for Molecular Biophysics, ORNL • Matrix polysaccharide coated on cellulose microfibrils • Prevents enzymes (cellulases) from accessing cellulose • Heterogeneus structure (different composiiton and linkages) Lignin: Obtain force field for model lignin compounds Build cellulose microfibril (36 chains about 90k atoms) Investigate how two forms of lignin interact with cellulose • Guaiacy: two coniferyl alcohols with C-C linkage model of branched lignin found in more recalcitrant primary wall • Syringyl: coniferyl and sinapyl alcohol linked via b-O-4’ model of linear lignin found in less recalcitrant secondary wall

  8. Lignin and Biomass Recalcitrance Loukas Petridis - Center for Molecular Biophysics, ORNL • Matrix polysaccharide coated on cellulose microfibrils • Prevents enzymes (cellulases) from accessing cellulose • Heterogeneus structure (different composiiton and linkages) toughens cellulose hydrolysis Lignin Obtain force field for model lignin compounds Build cellulose microfibril (amorphous + crystalline part) Investigate how two forms of lignin interact with cellulose • Guaiacy: two coniferyl alcohols with C-C linkage model of branched lignin found in more recalcitrant primary cell wall • Syringyl: coniferyl and sinapyl alcohol linked via b-O-4’ model of linear lignin found in less recalcitrant secondary cell wall Examine on molecular level the heat treatment of lignocellulose biomass(lignin detaching from cellulose surface, amorphous part becomes larger)

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