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Geometric and Kinematic Models of Proteins. Study of movement independent of the forces that cause them. What is Kinematics?. Protein. Long sequence of amino-acids (dozens to thousands), also called residues from a dictionary of 20 amino-acids. Role of Geometric and Kinematic Models. - PowerPoint PPT Presentation
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Geometric and Kinematic Geometric and Kinematic Models of ProteinsModels of Proteins
What is Kinematics?
Study of movement independent of the forces that cause them
Protein Long sequence of amino-acids (dozens to thousands), also
called residues from a dictionary of 20 amino-acids
Role of Geometric and Kinematic Models
Represent the possible shapes of a protein (compare/classify shapes, find motifs)
Answer proximity queries: Which atoms are close to a given atom? (computation of energy)
Compute surface area (interaction with solvent)
Find shape features, e.g., cavities (ligand-protein interaction)
What are the issues? Large number of atoms
Combinatorial problems Large number of degrees of freedom
Large-dimensional conformation space Need to efficiently update information during
simulation (surface area, proximity among atoms):• What is the position of every atom in some given
coordinate system?• Which atoms intersect a given atom?• What atoms are within some distance range from another
one?
Complex metric in conformational space Many shape matching issues
Geometric Models of Bio-Molecules
Hard-sphere model (van der Waals radii) Van der Waals surface
Van der Waals Potential
12-6 Lennard-Jones potential
The van der Waals force is the force to which the gecko's unique ability to cling to smooth surfaces is attributed!
Van der Waals interactions between twoatoms result from induced polarization effect (formation of electric dipoles). Theyare weak, except at close range.
Geometric Models of Bio-Molecules
Hard-sphere model (van der Waals radii) Van der Waals surface
H C N O F P S Cl
1.2
1.7
1.5
1.4
1.35
1.9
1.85
1.8
Van der Waals radii in Å
Geometric Models of Bio-Molecules
Hard-sphere model (van der Waals radii) Van der Waals surface Solvent- accessible surface Molecular surface
Computed Molecular Surfaces
Probe of 1.4Å Probe of 5Å
Computation of Hard-Sphere Surface
(Grid method [Halperin and Shelton, 97])
Each sphere intersects O(1) spheres
Computing each atom’s contribution to molecular surface takes O(1) time
Computation of molecular surface takes Θ(n) time
Why?
Computation of Hard-Sphere Surface
(Grid method [Halperin and Shelton, 97])
Each sphere intersects O(1) spheres
Computing each atom’s contribution to molecular surface takes O(1) time
Computation of molecular surface takes Θ(n) time
Why?
D. Halperin and M.H. Overmars Spheres, molecules, and hidden surface removal Computational Geometry: Theory and Applications 11 (2), 1998, 83-102.
Trapezoidal Trapezoidal DecompositionDecomposition
Trapezoidal Trapezoidal DecompositionDecomposition
D. Halperin and C.R. Shelton A perturbation scheme for spherical arrangements with application to molecular modeling Computational Geometry: Theory and Applications 10 (4), 1998, 273-288.
Possible project: Design software to update surface area during molecule motion
Other approach: Alpha shapes http://biogeometry.duke.edu/software/alphashapes/pubs.html
Simplified Geometric Models
United-atom model: non-polar H atoms are incorporated into the heavy atoms to which they are bonded
Lollipop model: the side-chains are approximated as single spheres with varying radii
Bead model: Each residue is modeled as a single sphere
Visualization Models
Stick (bond) model
Visualization Models
Visualization Models
Stick (bond) model
Small-sphere model
Kinematic Models of Bio-Molecules
Atomistic model: The position of each atom is defined by its coordinates in 3-D space
(x4,y4,z4)
(x2,y2,z2)(x3,y3,z3)
(x5,y5,z5)
(x6,y6,z6)
(x8,y8,z8)(x7,y7,z7)
(x1,y1,z1)
p atoms 3p parameters
Drawback: The bond structure is not taken into account
Peptide bonds make proteins into long kinematic chains
The atomistic model does not encode
this kinematic structure ( algorithms must maintain appropriate bond
lengths)
NN
NN
C’
C’
C’
C’
O
O O
O
C
C
C
C
C
C C
C
Resi Resi+1 Resi+2 Resi+3
Kinematic Models of Bio-Molecules
Atomistic model: The position of each atom is defined by its coordinates in 3-D space
Linkage model: The kinematics is defined by internal coordinates (bond lengths and angles, and torsional angles around bonds)
Linkage Model
T?
T?
Issues with Linkage Model
Update the position of each atom in world coordinate system
Determine which pairs of atoms are within some given distance(topological proximity along chain spatial proximitybut the reverse is not true)
Rigid-Body Transform
x
z
y
x
T
T(x)
2-D Case
x
y
2-D Case2-D Case
x
y
x
y
2-D Case2-D Case
x
y
x
y
2-D Case2-D Case
x
y
x
y
2-D Case2-D Case
x
y
x
y
2-D Case2-D Case
x
y
x
y
x
y
2-D Case2-D Case
x
y
tx
ty
cos -sin sin cos
Rotation matrix:
ij
x
y
2-D Case2-D Case
x
y
tx
ty
i1 j1i2 j2
Rotation matrix:
ij
x
y
2-D Case2-D Case
x
y
tx
ty
a
b
ab
v
a’b’ =
a’
b’
i1 j1i2 j2
Rotation matrix:
ij
Transform of a point?
Homogeneous Coordinate Homogeneous Coordinate MatrixMatrix
i1 j1 tx
i2 j2 ty
0 0 1
x’ cos -sin tx x tx + x cos – y sin y’ = sin cos ty y = ty + x sin + y cos 1 0 0 1 1 1
x
y
x
y
tx
ty
x’
y’
y
x
T = (t,R) T(x) = t + Rx
3-D Case3-D Case
1
2
?
Homogeneous Coordinate Homogeneous Coordinate Matrix in 3-DMatrix in 3-D
i1 j1 k1 tx
i2 j2 k2 ty
i3 j3 k3 tz
0 0 0 1
with: – i12 + i22 + i32 = 1– i1j1 + i2j2 + i3j3 = 0– det(R) = +1– R-1 = RT
x
z
y xy
z ji
k
R
ExampleExample
x
z
y
cos 0 sin tx
0 1 0 ty
-sin 0 cos tz
0 0 0 1
Rotation Matrix
R(k,) =
kxkxv+ c kxkyv- kzs kxkzv+ kys
kxkyv+ kzs kykyv+ c kykzv- kxs
kxkzv- kys kykzv+ kxs kzkzv+ c
where:
• k = (kx ky kz)T
• s = sin• c = cos• v = 1-cos
k
Homogeneous Coordinate Matrix in 3-D
x
z
y xy
z ji
k
x’ i1 j1 k1 tx xy’ i2 j2 k2 ty yz’ i3 j3 k3 tz z1 0 0 0 1 1
=(x,y,z)
(x’,y’,z’)
Composition of two transforms represented by matrices T1 and T2 : T2 T1
Questions?
What is the potential problem with homogeneous coordinate matrix?
Building a Serial Linkage Building a Serial Linkage ModelModel
Rigid bodies are:• atoms (spheres), or• groups of atoms
Building a Serial Linkage Building a Serial Linkage ModelModel
1. Build the assembly of the first 3 atoms:
a. Place 1st atom anywhere in spaceb. Place 2nd atom anywhere at bond length
Bond LengthBond Length
Building a Serial Linkage Building a Serial Linkage ModelModel
1. Build the assembly of the first 3 atoms:
a. Place 1st atom anywhere in spaceb. Place 2nd atom anywhere at bond lengthc. Place 3rd atom anywhere at bond length
with bond angle
Bond angleBond angle
Coordinate FrameCoordinate Frame
z
x
y
Building a Serial Linkage Building a Serial Linkage ModelModel
1. Build the assembly of the first 3 atoms:
a. Place 1st atom anywhere in spaceb. Place 2nd atom anywhere at bond lengthc. Place 3rd atom anywhere at bond length
with bond angle
2. Introduce each additional atom in the sequence one at a time
1 0 0 0 c -s 0 0 1 0 0 d
0 c -s 0 s c 0 0 0 1 000 s c 0 0 0 1 0 0 0 100 0 0 1 0 0 0 1 0 0 0 1
Ti+1 =
Bond LengthBond Length
z
x
y
1 0 0 0 c -s 0 0 1 0 0 d
0 c -s 0 s c 0 0 0 1 000 s c 0 0 0 1 0 0 0 100 0 0 1 0 0 0 1 0 0 0 1
Ti+1 =
Bond angleBond angle
z
x
y
Torsional (Dihedral) angle
z
x
y
1 0 0 0 c -s 0 0 1 0 0 d
0 c -s 0 s c 0 0 0 1 000 s c 0 0 0 1 0 0 0 100 0 0 1 0 0 0 1 0 0 0 1
Ti+1 =
Transform Ti+1
i-2
i-1
i
i+1Ti+1
d
1 0 0 0 c -s 0 0 1 0 0 d
0 c -s 0 s c 0 0 0 1 000 s c 0 0 0 1 0 0 0 100 0 0 1 0 0 0 1 0 0 0 1
Ti+1 =
z
x
y
x
y
z
Transform TTransform Ti+1i+1
i-2
i-1
i
i+1Ti+1
d
z
x
y
x
y
z
Readings:
J.J. Craig. Introduction to Robotics. Addison Wesley, reading, MA, 1989.
Zhang, M. and Kavraki, L. E.. A New Method for Fast and Accurate Derivation of Molecular Conformations. Journal of Chemical Information and Computer Sciences, 42(1):64–70, 2002.http://www.cs.rice.edu/CS/Robotics/papers/zhang2002fast-comp-mole-conform.pdf
1 0 0 0 c -s 0 0 1 0 0 d
0 c -s 0 s c 0 0 0 1 000 s c 0 0 0 1 0 0 0 100 0 0 1 0 0 0 1 0 0 0 1
Ti+1 =
Serial Linkage ModelSerial Linkage Model
-1
1
-2
0
T1
T2
Relative Position of Two Relative Position of Two AtomsAtoms
i
k
Tk(i) = Tk … Ti+2 Ti+1 position of atom k
in frame of atom i
Ti+1 Tki+1
k-1Ti+2
UpdateUpdate
Tk(i) = Tk … Ti+2 Ti+1
Atom j between i and k Tk
(i) = Tj(i) Tj+1 Tk
(j+1)
A parameter between j and j+1 is changed
Tj+1 Tj+1
Tk(i) Tk
(i) = Tj(i) Tj+1 Tk
(j+1)
Tree-Shaped LinkageTree-Shaped Linkage
Root group of 3 atoms
p atoms 3p 6 parameters
Why?
Tree-Shaped LinkageTree-Shaped Linkage
Root group of 3 atoms
p atoms 3p 6 parameters
world coordinate system
T0
Simplified Linkage ModelIn physiological conditions: Bond lengths are assumed constant
[depend on “type” of bond, e.g., single: C-C or double C=C; vary from 1.0 Å (C-H) to 1.5 Å (C-C)]
Bond angles are assumed constant[~120dg]
Only some torsional (dihedral) angles may vary
Fewer parameters: 3p6 p3
Bond Lengths and Angles Bond Lengths and Angles in a Proteinin a Protein
: C C: C C: N N
=
3.8Å
C
CN
C
Linkage Model
peptide group
side-chain group
Convention for Angles
is defined as the dihedral angle composed of atoms Ci-1–Ni–Ci–Ci
If all atoms are coplanar:
Sign of : Use right-hand rule. With right thumb pointing along central bond (N-C), a rotation along curled fingers is positive
Same convention for
C
CN
C
C
CN
C
Ramachandran MapsThey assign probabilities to φ-ψ pairs based on frequencies in known folded structures
φ
ψ
The sequence of N-C-C-… atoms is the backbone (or main chain)
Rotatable bonds along the backbone define the - torsional degrees of freedom
Small side-chains with degree of freedom
C
C
---- Linkage Model of Linkage Model of ProteinProtein
Side Chains with Multiple Torsional Degrees of Freedom
( angles)
0 to 4 angles: 1, ..., 4
Kinematic Models Kinematic Models of Bio-Moleculesof Bio-Molecules
Atomistic model: The position of each atom is defined by its coordinates in 3-D spaceDrawback: Fixed bond lengths/angles are encoded as additional constraints. More parameters
Linkage model: The kinematics is defined by internal parameters (bond lengths and angles, and torsional angles around bonds)Drawback: Small local changes may have big global effects. Errors accumulate. Forces are more difficult to express
Simplified (--) linkage model: Fixed bond lengths, bond angles and torsional angles are directly embedded in the representation.Drawback: Fine tuning is difficult
In linkage model a small local In linkage model a small local change may have big global change may have big global
effecteffect
Computational errors may accumulate
Drawback of Homogeneous Coordinate Matrix
x’ i1 j1 k1 tx xy’ i2 j2 k2 ty yz’ i3 j3 k3 tz z1 0 0 0 1 1
=
Too many rotation parameters Accumulation of computing errors along a
protein backbone and repeated computation Non-redundant 3-parameter representations
of rotations have many problems: singularities, no simple algebra A useful, less redundant representation of
rotation is the unit quaternion
Unit QuaternionUnit Quaternion
R(r,) = (cos /2, r1 sin /2, r2 sin /2, r3 sin /2)
= cos /2 + r sin /2
R(r,)
R(r,+2)
Space of unit quaternions:Unit 3-sphere in 4-D spacewith antipodal points identified
Operations on Operations on QuaternionsQuaternions
P = p0 + p
Q = q0 + q
Product R = r0 + r = PQ
r0 = p0q0 – p.q (“.” denotes inner product)
r = p0q + q0p + pq (“” denotes outer product)
Conjugate of P:P* = p0 - p
Transformation of a PointTransformation of a PointPoint x = (x,y,z) quaternion 0 + x
Transform of translation t = (tx,ty,tz) and rotation (n,)
Transform of x is x’
0 + x’ = R(n,) (0 + x) R*(n,) + (0 + t)