project #2: develop atomistic molecular models of
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
Activity: Computational Biology and Data AnalysisStructural Computational Biology Team
First Meeting, Philadelphia, September 29, 2007Attending:John BradyJiancong Xu
Mike CrowleyPavan Ghatty
Hong GuoMike HimmelMark Nimlos
Loukas PetridisMoumita Saharay
Jeremy SmithEd Uberbacher
Project #2: Develop atomistic molecular models of cellulosomal cellulases working on insoluble cellulose substrates.
Leader: Mark NimlosContributors: 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 wallLeader: Jeremy Smith
Contributors: Brady, Crowley, Himmel, Petridas, Uberbacher, York
Project #4a (was 3b): Investigate microfibril dynamics.
Leader: Jeremy SmithContributors: Brady, Crowley, Himmel, Petridis, Uberbacher
Project #4b: Model plant cell wall
Leader: Jeremy SmithContributors: Brady, Crowley, Himmel, Petridis, Uberbacher, York
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.
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.
- 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.
Lignin and Biomass Recalcitrance
Matrix polysaccharide coated on cellulose microfibrils Prevents enzymes (cellulases) from accessing cellulose Heterogeneus structure (different composiiton and linkages)
Loukas Petridis - Center for Molecular Biophysics, ORNL
Investigate how two forms of lignin interact with cellulose Guaiacy: two coniferyl alcohols with C-CC-C linkage
model of branched lignin found in more recalcitrant primary wall Syringyl: coniferyl and sinapyl alcohol linked via -O-4’-O-4’
model of linear lignin found in less recalcitrant secondary wall
Obtain force field for model lignin compounds
Build cellulose microfibril (36 chains about 90k atoms)
Lignin:
Lignin and Biomass Recalcitrance
Matrix polysaccharide coated on cellulose microfibrils Prevents enzymes (cellulases) from accessing cellulose Heterogeneus structure (different composiiton and linkages)
Loukas Petridis - Center for Molecular Biophysics, ORNL
Guaiacy: two coniferyl alcohols with C-CC-C linkage
model of branched lignin found in more recalcitrant primary cell wall Syringyl: coniferyl and sinapyl alcohol linked via -O-4’-O-4’
model of linear lignin found in less recalcitrant secondary cell wall
Obtain force field for model lignin compounds
Build cellulose microfibril (amorphous + crystalline part)
Lignin
toughens
cellulose
hydrolysis
Investigate how two forms of lignin interact with
cellulose
Examine on molecular level the heat treatment of lignocellulose
biomass (lignin detaching from cellulose surface, amorphous part becomes
larger)