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Unformatted text preview: Research in Structural Bioinformatics and Molecular Biophysics OUTLINE:
• What is it and why is it useful?
• a. Biomolecular surface story.
• b. Improving enzyme s function.
• c. Folding proteins. Alexey Onufriev, Dept of Computer Science and Physics, Virginia Tech The emergence of in virtuo Science.
in vitro in virtuo Biological function = f( 3D molecular structure )
…A T G C …
structure Key challenges:
Biomolecular structures are
complex (e.g. compared to crystal solids).
Biology works on many time scales.
Experiments can only go so far.
A solution: Computational methods. Bilogical
function Why bother? Example: rational drug design.
If you block the enzymes
function – you kill
the virus. e.g:viral endonuclease
(cuts DNA, RNA) Drug
agent Example of successful computer-aided (rational) drug design:
One of the drugs that helped slow down the AIDS epidemic
(part of anti-retro viral cocktail). The drug blocks the function of a key viral protein. To
design the drug, one needs a precise 3D structure of that protein. Molecular shape DOES matter.
One can learn a lot from appropriate shape analysis. Example of a computer-science challenge:
molecular surface and volume
Need a SIMPLE, EFFICIENT approximation for volume and surface: water Molecular
1.4 A surface => no water
within. 1.4 A Grid
A possibility, but not a good
idea if speed
is a factor. water 1.4 A 1.4 A A typical PDB entry (header)
C O M P N D
M O L E C U L E :
M Y O G L O B I N ;
C O M P N D
C H A I N :
N U L L ;
C O M P N D
E N G I N E E R E D :
S Y N T H E T I C
G E N E ;
C O M P N D
M U T A T I O N :
I N S ( M 0 ) ,
F 4 6 V ,
D 1 2 2 N
S O U R C E
T I S S U E :
S K E L E T A L
M U S C L E ;
S O U R C E
C E L L U L A R _ L O C A T I O N :
C Y T O P L A S M ;
E X P D T A
X - R A Y
D I F F R A C T I O N
AUTHOR R.D.SMITH,J.S.OLSON,G.N.PHILLIPS JUNIOR Key Part: atomic coordiantes (x,y,z)
XY Z ATOM
from this? Meaningful visualization helps.
Examples. The surface of a short DNA
fragment which binds to a
drug dimer (chromomyosin) is
shown color coded on the left
by curvature and on the right
by B value (structural
flexibility). The latter are
propagated to the surface
from the B values of the atoms
below. The drug molecule is
represented in stick mode.
Note that where the drug
binds the DNA has
significantly lower B values,
indicating it is less mobile.
Also note from the left hand
surface that the effect of
binding the drug is to cause
the surface of the major
groove to "flex" outward,
while the minor groove
widens. Molecular surface
of acetyl choline
Sussman et al.)
color coded by
view is directly
into the active site
and acetyl choline
is present in a
Note the depth of
the pocket, its
the postive charge
on the acetyl
worm-like thing Active site in
group. We can do the same thing, but much much faster, based on the
virtual water ideas.
Example: potential of α-helix dipole. DelPhi (grid-based traditional method) GEM (our analytical method)
Developed in CS6104 Spring 04 The surface of the
active site of acetly
seen from two
color coded by
potential. Note the
potential gets more
negative the deeper
in one goes. Also
note that one view
of the surface is lit
from the inside, the
other from the
outside, i.e the
latter is the former
… As if this this was not already complex enough…
the molecules are ALIVE (i.e. they move). Everything that living things do …
…can be explained by the wiggling and jiggling of atoms.
Suggests the approach: model what nature does, i.e. let the
molecule evolve with time according to underlying physics laws. Everything that living things do… can be reduced to wiggling and jiggling of atoms R. Feynmann Suggests the approach: model what nature does, i.e. let the
molecule evolve with time according to underlying physics laws. Principles of Molecular Dynamics (MD):
nd Each atom moves by Newton s 2 Law: F = ma F = dE/dr
System s energy - + Bond
Bond stretching + A/r12 – B/r6 VDW interaction + Q1Q2/r
Electrostatic forces +… Now we
time. Can compute
Etc. Computational advantages of representing water implicitly, via the ``virtual water model Implicit water as dielectric continuum (currently being developed in my group at VT) Explicit water (traditional) Low computational cost. Fast dynamics. No need to track individual water molecules
No drag of viscosity
Large computational cost. Slow dynamics. An industrial application: improving the function of a commercial enzyme.
Collaboration with the Third Wave Technologies, Inc. Madison, WI Enzyme 5 specific flap endonuclease Cleaved DNA DNA Active site Problem: to understand the mechanism, need structure
of the enzyme-DNA complex (unavailable from experiment). Solution: model the structure using
molecular dynamics (and other) computational techniques Our Model The DNA The enzyme Result: On the basis of the model, mutations were
introduced that improved the enzyme s function. So, molecular volume changes with time.
How does that help?
Resolves the problem with oxygen uptake
by myoglobin. How oxygen gets inside myoglobin? Single vs. multiple channels. Myoglobin – protein responsible for oxygen transport ? ? ? ? ? ? Holes in the protein as a function of time How do we explain the specific location of the pathways? Dynamic pathways occur in the loose space in-between
the helices and in the loop regions. THEME I. Protein folding. Amino-acid sequence – translated genetic code. MET—ALA—ALA—ASP—GLU—GLU--…. How? Experiment: amino acid sequence uniquely determines protein s 3D shape (ground state). Nature does it all the time. Can we? Complexity of protein design Example: PCNA – a human DNA-binding protein. Single amino-acid
(phenilalanin) Drawn to scale The magnitude of the protein folding challenge: A small protein is a chain of ~ 50 mino acids (more for most ). Assume that each amino acid has only 10 conformations (vast underestimation) Total number of possible conformations: 1050 Say, you make one MC step per femtosecond. Exhaustive search for the ground state will take 1027 years. Why bother: protein s shape determines its biological function. Research in Structural Bioinformatics: SUMMARY:
Through a combination of novel computational approaches we
can gain insights into aspects of molecular function inaccessible
to experiment and traditional (sequence) bioinformatics, and
make contributions to both the applied and
fundamental science. ...
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This note was uploaded on 01/23/2012 for the course CS 3824 taught by Professor Staff during the Fall '08 term at Virginia Tech.
- Fall '08
- Computer Science