1 / 8

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.

Download Presentation

Project #2: Develop atomistic molecular models of

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  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)

More Related