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ABSTRACTS – Symposia
in cellulose. Atomistic studies include Quantum Chemical
calculations, Replica Exchange Molecular Dynamics (MD)
and conventional MD simulations. Coarse-grained studies
include statistical mechanical and phenomenological models.
Importantly, our computations provide useful clues on
rational procedure for the efficient degradation of cellulose.
48 Computer Simulation of Lignocellulosic Biomass, LOU-
KAS PETRIDIS (Oak Ridge National Laboratory, 1 Bethel
Valley Rd, Oak Ridge TN 37919; petridisl@ornl.gov).
The temperature-dependent structure and dynamics of
individual softwood lignin polymers in aqueous solution
have been examined using extensive molecular dynamics
simulations. With decreasing temperature the lignins are
found to transition from mobile, extended to glassy, compact
states. The low-temperature collapse is thermodynamically
driven by the increase of the translational entropy and density
fluctuations of water molecules removed from the hydration
shell, thus distinguishing lignin collapse from enthalpically
driven coil-globule polymer transitions and providing a
thermodynamic role of hydration water density fluctuations
in driving hydrophobic polymer collapse. Lignin also forms
aggregates in vivo and poses a barrier to cellulosic ethanol
production. Neutron scattering experiments and molecular
dynamics simulations reveal that lignin aggregates are
characterized by a surface fractal dimension that is invariant
under change of scale from 1-1000Å . The simulations
also reveal extensive water penetration of the aggregates and
heterogeneous chain dynamics corresponding to a rigid core
with a fluid surface. Finally, the interaction of lignin with
cellulose is examined and differential binding to crystalline
and amorphous cellulose explained thermodynamically.
49 Identification of Conserved Binding Motifs for Cellulase
Enzymes and the Creation of a Novel Approach to Identifying
the Enzymatic Mode of Action, SAMBASIVARAO
V SOMISETTI (1613 Illinois Street, Golden, CO 80401;
somissv@tigermail.auburn.edu).
Docking calculations have been conducted between 30+
cellulase enzymes and cellobiose to determine the various
binding motifs and to create a model capable of predicting
the enzymatic mode of action (i.e., endo-, exo-, or mixed
endo-/exo-). It is found that the binding motifs between cellobiose
and cellulase enzymes are highly conserved across
species and between endocellulase and cellobiohydrolase
(exocellulase CBHI and CBHII) enzymes. The various binding
pose distributions have been classified into two dominant
structural features, a single maximum pyramidal distribution
that is indicative of cellobiohydrolase enzymes and a bimodal
distribution indicative of endocellulase enzymes. The
observed binding patterns are found to depend on a specific
number of critical enzyme-substrate interactions that are
highly conserved across species. Utilizing a coarse grained
technique to systematically and unambiguously interpret the
docking results has resulted in the ability to identify/predict
the enzyme mode of action based on the cellobiose-cellulase
binding poses. To gain further insights into the structural
requirements that determine the enzymatic mode of action, a
pattern recognition relationship (PRR) has been studied. The
PRR correlation for exo-cellulases resulted in an r 2 value of
0.96 showing good predictive performance with an adjusted
r 2 value of 0.81. The identified conserved docking poses and
the correlation of a PRR provide valuable insights into the
structure function relationship in cellulase enzymes while
also serving as a predictive tool for the implementation of
structure-based intelligent design of endo- and exocellulase
enzymes.
50 Biomass to Biofuels: Computer Modeling of Cellulose
and Cellulases, MICHAEL F CROWLEY 1 , GREGG
T BECKHAM 2,3 , LINTAO BU 2 , and JAMES F MAT-
THEWS 1 ( 1 Biosciences Center, National Renewable Energy
Laboratory, 15013 Denver West Parkway, Golden, CO;
2
National Bioenergy Center, National Renewable Energy
Laboratory, 15013 Denver West Parkway, Golden, CO;
3
Department of Chemical Engineering, Colorado School of
Mines, Golden, CO; michael.crowley@nrel.gov).
One of the important contributions to solving the
world’s energy needs for the future will come from the sustainable
use of biomass to produce fuels. These renewable
fuels are immediately essential as fungible replacements for
liquid transportation fuels but there is still much work that
can be done to improve the economic viability of the industrial
implementation. We will present our efforts to improve
enzymatic conversion of cellulosic biomass to sugars, which
can be easily converted to liquid fuels such as ethanol in
the present and more advanced, higher energy dense fuels
in the future. We present the computational modeling and
analysis of cellulose structure and thermodynamics, cellulase
structure and function, and cellulosome assembly and
interaction with biomass in the form of plant cell walls. We
use molecular dynamics simulations to extract the dynamical
and thermodynamic properties of cellulose in multiple
shapes and crystalline forms and its response to temperature
changes that occur in biomass pretreatment. We show the
dependence of the twisting behavior of cellulose on fiber
diameter and explain the origin of the twist. We use thermodynamic
sampling methods to determine the free energy
of decrystallization, enzyme binding affinities, and product
expulsion energies of both native and mutated cellulases.
Our computer simulations inform the molecular biologists
of possible improvements that can be made to enzymes and
biomass for cheaper biofuels.
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