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)