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FlexWeb
Nassim Sohaee
FlexWeb
Proteins
• The ability of proteins to change their
conformation is important to their
function as biological machines.
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Protein Structure
• Experimental methods cannot operate at
the time scale necessary to record protein
folding and motions.
• Traditional methods are just good for
small peptide fragments.
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Protein Motion and Folding
1. Understanding the folding process can
give insight into how to develop better
structure prediction algorithms.
2. Some Diseases such as Alzheimer’s and
Mad Cow disease are caused by
misfolded proteins.
3. Many biochemical process are regulated
by protein switching from one shape to
another shape.
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Classic Method
• Molecular Dynamic Simulation: use
energy function and solve Newton’s
equation of motions for the atoms in
protein.
• Used in past 25 years.
– Computationally demanding (Many simulation
steps.)
– Developing need to look at large proteins, protein
complexes, viral capsids, etc.
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FIRST/FRODA
• The method is atom-led in the sense that
the principal variables are the atomic
positions rather than the dihedral angles.
• FIRST/FRODA is about 100 to 1000
times faster than previous methods, and
treats all atoms equivalently, whether they
are in rings or not, main-chain or sidechain.
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Review
• We consider a protein as a network in
which all covalent bond lengths and
angles are fixed (constrained), and the
covalent double bonds are locked
(constrained).
• Constraints are also assigned to
hydrophobic interactions and hydrogen
bonds, which are determined by using the
local chemistry and geometry as input.
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Review …
• Changes in the shape of the protein occur by
changes in dihedral angles of rotatable bonds.
• Rigidity analysis, using the pebble game and
FIRST, determines which dihedral angles are
rotatable and which are locked.
• The rigidity of the three-dimensional folded
protein is determined by the constraints
introduced by hydrogen bonds and hydrophobic
tethers (double bounds like C=N are considered
lock).
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Degree of Freedom
• Determining the rigidity of the protein is then a
matter of balancing degrees of freedom against
constraints.
• The pebble game is an algorithm for
distributing the degrees of freedom belonging
to the atoms (pebbles) over the bonds
(constraints) so as to determine the rigidity.
• In FIRST/FRODA a protein is treated as a
Body-Bar graph.
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Body-Bar Graph
• In the body–bar representation, rigid
bodies, each having six degrees of
freedom, define a set of vertices, and the
set of generic bars that connect those
bodies defines a network.
Example of Body-Bar graph.
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Body-Bar graph of Protein
• Each atomic site is a body with six
degrees of freedom
• Hydrophobic tether reduce the degree of
freedom by 2
• Single covalent bonds or Hydrogen bonds
by 5
• Locked bonds (double, peptide) by 6
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Pebble Game
Rigid graph, check with Pebble game.
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FIRST
• The flexibility analysis performed by
FIRST describes the rigidity of the
protein based on a given set of
hydrophobic and hydrogen bond
constraint.
• Sections of protein that are not mutually
rigid according to this analysis should be
able to move relative to each other.
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Example of First
An example of a rigid cluster decomposition using the
pebble game in FIRST, showing the largest rigid regions in
solid colors (blue, green and red).
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Not provided by FIRST
• flexibility and mobility are closely
connected concepts, but not identical.
• The rigidity analysis does not determine
the mobility or range of allowed motion
that follows from the flexibility.
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FRODA
• Framework Rigidity Optimized Dynamic
Algorithm: is a form of geometric
simulation which explores the allowed
motion of the protein on the basis of
rigidity analysis.
• In simulating the flexible motion of a
protein, we constrain bond lengths and
bond angles, while permitting some
dihedral angles to vary.
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How FRODA works?
• A conformer of the protein must obey
constraints on covalent bond length and
angles, hydrogen-bond length and angles
for those hydrogen bonds include in the
rigidity analysis, and hydrophobic tether.
• FRODA finds new conformers by
randomly displacing the atoms and then
applying an interactive fitting process
which enforce the constraints.
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WHATIF
By adding hydrogen atoms to the
structure and eliminated non-buried
water molecules from the structure,
produce a structure suitable for
rigidity analysis and geometric
simulation.
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In the result .pdb file
remove the water
molecules.
•Add Protons to the Structure
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Upload the
pdb file
Hydrogen bonds are identified with
an energy scale based on their
geometry, with energies ranging
from 0 down to - 10 (kcal/mol). A
user-defined energy cutoff
determines which bonds to include
and which not, with the default
being, - 1 (kcal/mol).
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Showing how the rigidity of
the protein depends on the
cutoff, with a lower cutoff
producing more and smaller
rigid clusters
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Results
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Plotting the mobility of each
residue, showing clearly that
FRODA captures the main
features of the mobility of the
protein, when compared with the
NMR data.
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