Designing and Building the Cellular
Machinery with a Bottom-Up Strategy
C. Butler (BMEN), A. Chang-Gonzalez (BMEN), C. Chitrakar (BMEN), S. Kim (OCEN) , A. L. Liao (MSEN), Dr. W. Teizer (PHYS), Dr. W. Hwang (BMEN)
MATRIX METALLOPROTEINASE
(MMP-2)
Key Functions
∙ Protein associated with
metastasis and fibrosis
∙ Catalyzes extracellular
matrix degradation
∙ Degrades type-IV collagen
Figure 1: The MMP-2 enzyme with main
domains highlighted. Purple: Catalytic domain.
Yellow: Fib II domains. Green: Propeptide. Blue:
Hemopexin domain.
A simulation was performed
on MMP-2 using TAMU
supercomputing
service.
Energy minimization of MMP2 was followed by the heat
treatment at 300 K for 100 ps.
RESEARCH PURPOSE
The proteins studied are major components of key
processes that occur in the body such as tumor
invasion, angiogenesis, cell migration, regulation of
cytokinesis, and remodeling of the extracellular
matrix. Once the proteins are built, simulations on
these proteins can be performed to analyze static and
dynamic properties, thus elucidating how their
dynamic motion and mechanics are related to their
cellular function.
METHODS
∙ RCSB is a protein data bank “repository
for 3-dimensional structural data of large
biological molecules”
∙ 1976: 13 files
∙ 2014: 105,732 files
PROTEIN REQUIRED FOR
CYTOKINESIS-1 (PRC-1)
Key Functions
∙ Non motor microtubule-associated protein
∙ Key regulator of cytokinesis
∙ Essential for controlling formation of spindle
midzone during anaphase of cell mitosis in
eukaryotes
d
Figure 6: Two conformations of
PRC-1 homodimer as PRC-1
dynamically rearranges when at a
constant temperature of 300 K
with main domains highlighted.
Green: Dimerization domains.
Red: Rod domains. Blue: Spectrin
domains.
C-terminal
not
visualized.
∙ The PDB file is retrieved from RCSB
database and provides “cor” and “psf”
files
Figure 2: Degradation of collagen fibers involves
cleavage of fibrils by collagenolytic enzymes and
uptake of collagen fragments by macrophages and
fibroblasts or further cleavage by gelatinases. MMP,
matrix metalloproteinase. Mckleroy, W., T.-H. Lee, and K.
Atabai. "Always Cleave up Your Mess: Targeting Collagen Degradation to
Treat Tissue Fibrosis." AJP: Lung Cellular and Molecular Physiology 304.11
(2013): L709-721. Web.
∙ CHARMM provides a method to modify
the “cor” and “psf” files so that varying
conditions such as heat fluctuations,
energy minimization, and dynamic
vibrations can be modeled for analysis of
static and dynamic properties
DISCOIDIN DOMAIN
RECEPTOR (DDR-2)
Key Functions
∙ Receptor activated with a triple-helical
collagen binding to the extracellular
discoidin domain
∙ Plays a key role in communication of
cells and controls cell behavior: cell
growth, differentiation, and metabolism
∙ VMD is used for molecular modeling
and includes tools for working with
volumetric and sequence data
Figure 7: Distance measurements between PRC-1 spectrin domains during
molecular dynamics simulation using FACTS. Peaks represent extended PRC-1 while
valleys represent folded PRC-1. The distance being measured is labeled as “d” in
Figure 1.
Figure 3: DDR-2 receptor bound to a collagen molecule.
Blue: Collagen peptide. Red: Discoidin domain.
FUTURE WORK
∙ Run all-atom, explicit water simulations
∙ Calculate binding energy, force, and other
physical quantities to be able to understand the
mechanism of causing disease
∙ Measure binding energy, conformational, and
mechanical properties to be able to understand
their mechanism in health and disease.
Figure 4: Process of modeling proteins.
CHARMM provides the source code to
generateS the proteins and run further
simulations while VMD is used to
visualize the simulations.
Figure 5: Collagen triple helices visualized in VMD. All four
images are various representations of the same collagen protein
generated with VMD. VMD can visualize a protein backbone,
atomic structure, or bond locations among other
characteristics.
ACKNOWLEDGEMENTS
We would like to thank Dr. Wonmuk Hwang, Dr.
Winfried Teizer, and Andrew Liao for their
dedication and guidance in this project.
A molecular dynamics simulation was performed
on PRC-1 using TAMU Supercomputers. An
energy-minimized PRC-1 molecule was heated up
to 300 K, and allowed to continue dynamic
movement for 7 ns.
CITATIONS
∙ RCSB Protein Data Bank - RCSB PDB - 1CK7 Structure Summary." RCSB Protein
Data Bank - RCSB PDB - 1CK7 Structure Summary. N.p., n.d. Web. 26 Apr. 2015.
∙ Morgunova, Ekaterina, Ari Tuuttila, Ulrich Bergmann, Mikhail Isupov, Ylva Lindqvist,
Gunter Schneider, and Karl Tryggvason. "Structure of Human Pro-Matrix
Metalloproteinase-2: Activation Mechanism Revealed." Science284.5420 (1999): 1667670. Web.