Research Poster 36 x 48 - A

1
Molecular Dynamics Simulations of M37 Lipase from
Psychrophilic Photobacterium lipolyticum in
Water and Methanol
Rhiannon Jacobs and Harish Vashisth Department
of Chemical Engineering, University of New
Hampshire, Durham, NH 03824
ABSTRACT
MOLECULAR DYNAMICS
METHODS
SYSTEMS
Enzyme activity is particularly promoted by
higher temperatures and the aqueous environment.
The M37 lipase from the Psychrophilic
Photobacterium lipolyticum is an enzyme that can
function in cold water conditions from 0 to 30C.
The Photobacterium lypolyticum species was
discovered from a sediment sample in the Yellow
Sea, which allowed for the isolation of M37
lipase. Surprisingly, the M37 lipase retains its
stability in methanol environments and therefore
has been used for biodiesel production. The
lipase characterization, reactivity, and
stability have been previously studied
experimentally, but a structural explanation of
lipase function in a methanol environment and at
cold temperatures is missing. Through the use of
molecular dynamics (MD) simulations in water,
methanol, and water/methanol environments, the
structure and dynamics of this lipase enzyme were
analyzed to further understand its functionality
so that the enzyme can be better optimized for
use in industrial applications.
Molecular dynamics are a computer based approach
to statistical mechanics which allows for an
estimation of equilibrium and dynamic properties
of a complex system that cannot be done
analytically. Molecular Dynamics is an approach
to evolve positions of a system of particles in
time, where particles interact with each other
under a complex potential function. MD
simulations are run on the principle of classical
mechanics where Fma. This equation is then
applied amongst the varying forces. MD displays
the atoms continuously interacting with each
other. Software Visualization software is
Visual Molecular Dynamics (VMD) which displays,
animates, and analyzes biomolecular systems using
3D graphics. Simulation software is NAMD
software which is distinctly designed for high
performance simulation of biomolecular systems.
Structure file obtained from Protein Data Bank
(2ORY) determined from crystalline
structure. Protein structure visualized in VMD
and solvated in water using the solvate function.
The water box converted to methanol box. NAMD
used to run simulations.
APPLICATIONS

• Biodiesel/biofuels production
• Medical/pharmaceutical
• Synthesis of fine chemicals
• Food Industry
• Environmental applications

Figure 1 Lid domain of the lipase used in
simulation highlighted in blue. Catalytic triad
(SER 174 ASP 236 HIS 312) highlighted in red.
CONCLUSIONS
RESULTS

• Proteins could be solvated in both water and
  methanol solutions but methanol and water boxes
  proved difficult to simulate.
• Further quantitative analysis will provide
  optimum conditions for the enzyme activity.
• Data is consistent with previous simulation on
  enzyme.
• 4. RMSD values consistent with values for short
  simulations on small proteins.

ACKNOWLEDGEMENTS
LIPASES
Figure 2 Lipase solvated in water box (left) lid
domain (blue) and catalytic triad (red)
highlighted.
Figure 3 Lipase solvated in methanol box (right)
lid domain (red) and catalytic triad (yellow)
highlighted.
Figure 4 RMSD versus simulation time (ns) for
different temperatures 288 K (red), 298 K
(green) and 313 K (blue).
Harish Vashisth, Ph.D, Faculty Mentor University
of New Hampshire Dept. of Chemical
Engineering Gregory Samuel Summer Teacher
Researcher
Lipases are biological catalysts that catalyze
the hydrolysis of triacylgylcerols (glycerols and
fatty acids) and possess catalytic properties of
the degradation of lipids. Lipases are found in
plants, animals, microorganisms, and more
recently bacteria and fungi. COLD ACTIVATED
LIPASES Wider oxyanion hole, increased
flexibility, and weakening of hydrophobic
clusters.
t0 ns t3 ns t6 ns t8 ns
REFERENCES
1 Hasan, Fariha, Aamer Ali Shah, and Abdul
Hameed. "Industrial Applications of Microbial
Lipases." Enzyme and Microbial Technology 39.2
(2006) 235-51. Web. 2 Joseph, Babu, Pramod W.
Ramteke, and George Thomas. "Cold Active
Microbial Lipases Some Hot Issues and Recent
Developments." Biotechnology Advances 26.5
(2008) 457-70. Web. 3 Jung, Suk-Kyeong, Dae
Gwin Jeong, Mi Sook Lee, Jung-Kee Lee, and
Hyung-Kwoun Kim. "Structural Basis for the Cold
Adaptation of Psychrophilic M37 Lipase from
Photobacterium Lipolyticum." Proteins(2008)
476-84. Web. 4 Yang, Kyung Seok, Jung-Hoon
Sohn, and Hyung Kwoun Kim. "Catalytic Properties
of a Lipase from Photobacterium Lipolyticum for
Biodiesel Production Containing a High Methanol
Concentration." Journal of Bioscience and
Bioengineering 107.6 (2009) 599-604. Web.
Figure 5 Snapshots of simulation run at 288 K
for 8 nanoseconds in water.