Nucleic Acid Structure Analysis - Jawaharlal Nehru Centre ...€¦ · Nucleic Acid Structure...
Transcript of Nucleic Acid Structure Analysis - Jawaharlal Nehru Centre ...€¦ · Nucleic Acid Structure...
Nucleic Acid Structure AnalysisNucleic Acid Structure Analysis
Dhananjay Bhattacharyya
Biophysics Division, Saha Institute of
Nuclear Physics, Kolkata
and
Manju Bansal
Molecular Biophysics Unit, Indian
Institute of Science, Bangalore
Nucleic Acid Backbone is Connected to Nucleic Acid Backbone is Connected to
Either of Four Different BasesEither of Four Different Bases
A
G
T
C
C3’-endo
C2’-endo
pseudorotation cycle of furanose ring in nucleosides
(Saenger, 1984)
tan P = (ττττ4 + ττττ1) – (ττττ3 + ττττ0) / 2 * ττττ2 *(sin 36o + sin 72o)
ττττI+2 = ττττmax cos (P+ i * 144o)
ττττmax = ττττ0 / cosP
Distribution of pseudorotation phase
angle (P) calculated from B-DNA
crystal structures
Torsion angles of DNA models
αααα ββββ γγγγ δδδδ εεεε ζζζζ χχχχ P
-51.7 174.8 41.7 79.0 -147.6 -75.2 -157.2 7.8
-29.9 136.4 31.1 143.4 -140.8 -160.5 -98.0 153.9
-43.3 142.2 47.8 140.6 -148.7 -149.5 -96.7 165.8
-61.9 -152.1 69.0 156.2 141.7 -100.5 -96.6 -167.5D-DNA
C-DNA
B-DNA
A-DNA
minor
groovemajor
groove
minor
groovemajor
groove
Netropsin like drugs bind in the B-DNA
narrow and deep minor groove
Actinomycin D like drugs make their place in between two
stacked base pairs by distorting the DNA double helix
DNA kinks by
90o at the dyad
location while
binding to two
subunits of
Catabolite
Activator
Protein (CAP)
TATA-box
binding
protein
transforms the
interfacing
DNA region to
A-DNA like
structure
Base Centered Parameters
• Torsion angles can not indicate structural features
• Torsion Angles are measured from dynamic backbone atoms
• Bases are more rigid and well defined in terms of thermal motion
• Axis system easily can be defined with respect to a base pair
Softwares for Calculation of Base
Pair Parameters
• NEWHELIX or FREEHELIX (Dickerson)
• NUPARM (1 & 2) (Bansal & Bhattacharyya)
• CURVES (Lavery)
• X3DNA (Olson)
• CEHS (Xiang-Jun Lu)
• CompDNA NGEOM (Zhurkin & Olson)
Standard Reference frame of a WatsonStandard Reference frame of a Watson--
Crick base pairCrick base pair
Definition and Nomenclature of Base Definition and Nomenclature of Base
Pair Doublet ParametersPair Doublet Parameters
Calculation of Base Pair Calculation of Base Pair
parameters by NUPARMparameters by NUPARM
Local Step Parameters:
Mean Local Helix Axis: Zm = Xm ×××× Ym,
where Xm = Xaxis1 + Xaxis2 and Ym = Yaxis1 + Yaxis2
M is Base Pair Center to Center Vector
Tilt : 2.0 * sin-1 ( -Zm • Y1) Roll: 2.0 * sin-1 ( Zm • X1)Twist: cos-1 (( X1 ×××× Zm) • ( X2 ×××× Zm)) Shift (Dx) M • XmSlide(Dy) M • YmRise(Dz) M • Zm
Y1
Y2
X1
X2
Base Pair parameters of DNA models
Tilt Roll Twist Shift Slide Rise Prop.
-0.05 13.15 30.04 0.06 -1.22 3.34 -10.64
-0.02 2.22 35.93 0.05 0.56 3.35 -15.14
0.43 -4.16 38.38 0.1 1.09 3.46 -11.09
0 -13.01 44.08 0 0.59 3.3 -7.97
A-DNA
B-DNA
C-DNA
D-DNA
Local Helical Parameters:
Local Helix Axis: Z* = X* ×××× Y*,
where X* = Xaxis1 - Xaxis2 and Y* = Yaxis1 - Yaxis2
M is Base Pair Center to Center Vector
Inclination : 2.0 * sin-1 ( -Z* • Y1) Tip: 2.0 * sin-1 ( Z* • X1)Twist: cos-1 (( X1 ×××× Z*) • ( X2 ×××× Z*)) X-translation (dx): M • X*Y-translation (dy): M • Y*Helical Rise(dz): M • Z*
A-DNA structural Parameters:
Roll ~ 12; Inclination ~20
Slide ~ -1.5; X-translation ~ -4.0
Rise ~ 3.2; Helical Rise ~2.63.3A
2.6A
Relation between the two frames
( ) ( ) ( ) ( ) ( ) ( )
)/(sinT
and
)/(sinR
where
RT)TRTR/cotT/)sin(
RTTRTR/cotT/)sin(
/
/
2
2
411221
411221
2
2
212
212
τ=
ρ=
−−−−−−Ω=θ
−−−−−−Ω=η
η=Inclination; θ=Tip; τ=Tilt; ρ=Roll; Ω=Twist
Base Pair step parameters of B-DNA
crystal structures (1BNA.pdb)
Tilt of Dickerson Dodecamer (1BNA.pdb)
-6
-4
-2
0
2
4
6
1 2 3 4 5 6 7 8 9 10 11
NUPARM
CURVES
X3DNA
Roll
-15
-10
-5
0
5
10
15
1 2 3 4 5 6 7 8 9 10 11
NUPARM
CURVES
X3DNA
Twist
25
30
35
40
45
1 2 3 4 5 6 7 8 9 10 11
NUPARM
CURVES
X3DNA
Slide
-1.5
-1
-0.5
0
0.5
1
1 2 3 4 5 6 7 8 9 10 11
NUPARM
CURVES
X3DNA
Base pair doublet parameters of A-DNA
structure (2ANA.pdb)
-2.5
-2
-1.5
-1
-0.5
0
0.5
1
1 2 3 4 5 6 7 NUPARM
CURVES
X3DNA
Roll of A-DNA structure (2ANA.pdb)
0
2
4
6
8
10
12
1 2 3 4 5 6 7
NUPARM
CURVES
X3DNA
Twist of 2ANA
26
31
36
41
1 2 3 4 5 6 7
NUPARM
CURVES
X3DNA
Slide
-3
-2
-1
01 2 3 4 5 6 7
NUPARM
CURVES
X3DNA
Tilt
Base pair doublet
parameters of TATA-
box DNA-TBP complex
(PDT012), calculated by
3DNA (Lu & Olson
2003)
Roll of 1CGP
-20
-10
0
10
20
30
40
50
16 18 20 22 24 26 28 30 32 34 36 38 40 42
Residue no.
Twist
20
25
30
35
40
45
16 18 20 22 24 26 28 30 32 34 36 38 40 42
Roll of TBP bound TATA box
-20
0
20
40
60
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Nuparm
Curves
X3DNA
Twist
0
10
20
30
40
50
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Nuparm
Curves
X3dna
Slide
-2
-1
0
1
2
3
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
Nuparm
Curves
X3dna
Tilt and Roll of
nucleosomal DNA (1M1A)
RiseSlideShift
TwistRollTilt
Distribution of base-pair step parameters in high
resolution DNA crystal structures
Red: A-DNA Green:B-DNA
Roll Variation in Crystal Structures
Roll of d(AA).d(TT) doublets
0
10
20
30
-15 -10 -5.4 -0.9 3.72 8.29 12.9
Roll
Oc
cu
rre
nc
e
Roll of d(CG).d(CG) doublets
0
10
20
30
40
-17 -10 -4.3 1.78 7.87 14 20.1
Roll
Oc
cu
rre
nc
e
Roll of d(GC).d(GC) doublets
0
5
10
15
20
-27 -21 -12 -5.4 1.15 7.68 14.2
Roll
Occu
rren
ce
Steric clash between
Purines of successive base
pairs can cause non-
parallel base pair
orientations (Calladine &
Drew 1982)
Minor Groove Width
Definition of Intra Base Pair
Parameters (IUPAC-IUB)
Definition of Intra Base Pair Definition of Intra Base Pair
Parameters (IUPACParameters (IUPAC--IUB)IUB)
Base pair parametersBase pair parameters
Buckle = 2 sin-1( Zm . Y1)
Opening = 2 sin-1( Zm . X1)
Propeller = cos-1 (( X1× Zm) . ( X
2× Zm))
Shear = -Xm . M
Stagger = Ym . M
Stretch = Zm . M
Xm = (XXXX1111 + XXXX2222) / | (XXXX1111 + XXXX2222) |
Ym = (YYYY1111 + YYYY2222) / | (YYYY1111 + YYYY2222) |
Zm = (XXXX1111 + XXXX2222) x (YYYY1111 + YYYY2222)/ | (XXXX1111 + XXXX2222) | | (YYYY1111 + YYYY2222) |
Y1
Y2 X2
X1
Base Pair Parameters of Dickerson DodecamerBuckle
-15
-10
-5
0
5
10
15
1 2 3 4 5 6 7 8 9 10 11 12
NUPARM
CURVES
X3DNA
Open Angle
-10
-5
0
5
10
15
1 2 3 4 5 6 7 8 9 10 11 12
Nuparm
Curves
X3dna
Propeller
-25
-20
-15
-10
-5
0
5
1 2 3 4 5 6 7 8 9 10 11 12Nuparm
Curves
X3dna
Stagger
-0.5
0
0.5
1
1 2 3 4 5 6 7 8 9 10 11 12
Nuparm
Curves
X3dna
Shear
-1
-0.5
0
0.5
1 2 3 4 5 6 7 8 9 10 11 12Nuparm
Curves
X3dna
Stretch
-1
0
1
2
3
4
1 2 3 4 5 6 7 8 9 10 11 12
Nuparm
Curves
X3dna
Possibility of Unusual Base
Pairing in RNA
Possibility of Unusual Base
Pairing in RNA
Unusual Basepairs Observed By Leontis (Leontis
et al., Nucl. Acids Res., 2003, 31, 3450.)
RNA structures show wide
variability of Base Pairing Types
• Some of these base pairs are significantly different from standard Watson-Crick types
• These unusual base pairs are also seen in DNA, such as in G-quadrates or triple helices
• Standard reference frame (axis system) applicable to WC type does not give meaningful results
Base Pair FinderBase Pair FinderBase Pair Finder
Took a base edge
Identify the H-bonding centers (N3G & N2G)
Look for H-bond partner through distance
calculation (N6A & N7A)
Calculate pseudo-angles (such as C6G-N3G-
N6A, N3G-N6A-N1A, N1G-N2G-N7A, N2G-
N7A-N9A in figure) for
planarity
Confirm orientation through angle calculation
Calculate E=Σi(di-3.0)2 + ½Σk(θk-π)2; i are for
two H-bond distances and k are for four pseudo
angles
Gives rise to:
6959 A:U W-W(C);
21965 G:C W-W(C) and
2786 G:U W-W(C) base pairs
G:U W:W Cis (2769)
U:U W:W Cis (360)
A:G W:W Cis (404)
A:G H:S Trans (2323)
A:U H:W Trans (1193)
A:A H:H Trans (437)
Axis System of Bases
G:C Base Pair Using W:W base edges in Cis Orientation
Buckle
0
1000
2000
3000
4000
5000
-48 -31 -13 4.83 22.6 40.4
Open
0
1000
2000
3000
4000
5000
-16 -11 -5.1 0.37 5.89 11.4 16.9
Propeller
0
1000
2000
3000
4000
5000
-42 -28 -13 1.13 15.5 29.9
Shear
0
2000
4000
6000
8000
-1.6 -1.3 -0.9 -0.6 -0.3 0.01 0.33 0.65 0.97 1.29 1.61
Stagger
0
2000
4000
6000
-2 -1.6 -1.3 -0.9 -0.5 -0.1 0.3 0.69 1.08 1.47 1.86
Stretch
0
2000
4000
6000
2.26 2.45 2.65 2.84 3.04 3.23 3.43
Distribution of Base Pair Parameters for A:U Distribution of Base Pair Parameters for A:U Distribution of Base Pair Parameters for A:U Distribution of Base Pair Parameters for A:U
HHHH----W (Trans) Base Pair (freq: 1164)W (Trans) Base Pair (freq: 1164)W (Trans) Base Pair (freq: 1164)W (Trans) Base Pair (freq: 1164)
Buckle
0
50
100
150
200
250
-71 -51 -31 -11 9.53 29.8 50
Open
0
100
200
300
-30 -21 -11 -1.9 7.63 17.1 26.6
Propeller
050
100150200250
-45 -32 -19 -5.3 7.97 21.3 34.5
Shear
0100200300400
-1.9 -1.3 -0.6 0.05 0.7 1.36 2.01
Stagger
050
100150200250300
-2.1 -1.2 -0.4 0.47 1.31 2.16
Stretch
0
100
200
300
2 2.26 2.52 2.78 3.04 3.3 3.56
Telomeric DNA (PDB ID: 1JPQ)
Tilt Roll Twist Shift Slide Rise Cup
--------------------------------------------------------------------------------
LC 1 G:G 19 27.23 -10.46 166.15 1.78 -0.28 2.97 -3.59 W:H C
LC 2 G:G 20 3.15 7.09 -112.63 -5.31 0.18 3.61 -7.16 H:W C
LC 3 G:G 21 3.19 3.74 76.95 -0.29 -5.42 3.20 31.84 W:H C
LC 4 G:G 12 29.27 35.74 102.57 4.26 1.34 6.44 17.26 W:H C
LC 5 T: 0 -16.15 35.76 64.60 -0.51 2.68 -4.74 0.00 :
LC 6 T: 0 -22.93 -47.04 32.85 -3.12 -1.74 6.70 0.00 :
LC 7 T: 0 13.70 49.51 -26.95 -5.01 2.20 -6.66 4.15 :
LC 8 G:G 22 4.93 -0.61 77.93 -0.08 -6.03 3.48 5.51 W:H C
LC 9 G:G 13 -2.23 2.03 -23.71 -0.30 1.56 3.45 -12.68 W:H C
LC 10 G:G 20 -9.71 5.20 76.81 -0.58 -5.84 3.51 18.36 W:H C
LC 11 G:G 15 5.29 10.56 41.20 1.51 -3.27 11.16 -10.69 W:H C
LC 12 G:G 8 10.97 -6.79 167.70 1.28 0.00 3.13 -6.78 W:H C
LC 13 G:G 9 5.44 8.01 -112.14 -5.24 0.18 3.57 -6.16 H:W C
LC 14 G:G 10 48.09 -10.89 164.64 2.30 0.23 2.65 0.48 W:H C
LC 15 G:G 11 32.96 5.30 12.22 -1.75 2.36 5.49 17.91 H:W C
LC 16 T: 0 -14.90 39.32 66.47 -0.81 3.01 -4.72 0.00 :
LC 17 T: 0 -25.02 -45.62 48.09 -2.27 -0.58 6.85 0.00 :
LC 18 T: 0 -119.01 -37.81 19.04 0.52 7.74 2.68 -3.17 :
LC 19 G:G 1 6.30 -5.64 -102.33 -0.18 -6.97 3.62 6.03 H:W C
LC 20 G:G 10 9.11 14.38 156.06 0.55 9.80 2.20 4.72 H:W C
LC 21 G:G 3 -5.30 -4.41 -101.92 0.38 -6.79 3.43 -11.89 H:W C
LC 22 G:G 8
Inter Base Pair parameters of 1JPQ
Buckle Open Propel Stagger Shear Stretch
--------------------------------------------------------------------
BL 1 G:G 19 -0.75 -2.56 4.64 0.06 2.50 2.86 W:H C
BL 2 G:G 20 -4.34 -2.52 -2.46 -0.25 -2.43 2.83 H:W C
BL 3 G:G 21 -11.50 -3.93 2.12 -0.07 2.41 2.95 W:H C
BL 4 G:G 12 20.34 -4.54 -0.60 -0.23 2.44 2.91 W:H C
BL 5 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :
BL 6 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :
BL 7 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :
BL 8 G:G 22 0.39 -4.33 -6.90 0.08 2.43 2.89 W:H C
BL 9 G:G 13 5.90 -6.09 -3.94 -0.12 2.37 2.95 W:H C
BL 10 G:G 20 -6.78 -3.20 -7.45 0.02 2.46 2.86 W:H C
BL 11 G:G 15 11.58 -7.34 -15.29 -0.52 2.38 3.03 W:H C
BL 12 G:G 8 0.88 -4.43 6.63 -0.01 2.46 2.86 W:H C
BL 13 G:G 9 -5.90 -6.09 -3.94 -0.12 -2.37 2.95 H:W C
BL 14 G:G 10 -12.06 -6.09 1.20 -0.15 2.37 2.90 W:H C
BL 15 G:G 11 -11.58 -7.34 -15.29 -0.52 -2.38 3.03 H:W C
BL 16 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :
BL 17 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :
BL 18 T: 0 0.00 0.00 0.00 0.00 0.00 0.00 :
BL 19 G:G 1 0.75 -2.56 4.64 0.06 -2.50 2.86 H:W C
BL 20 G:G 10 6.78 -3.20 -7.45 0.02 -2.46 2.86 H:W C
BL 21 G:G 3 11.50 -3.93 2.12 -0.07 -2.41 2.95 H:W C
BL 22 G:G 8 -0.39 -4.33 -6.90 0.08 -2.43 2.89 H:W C
Intra Base Pair Parameters of 1JQP
Twist
Slide
ShearPropeller
Open angle
Thanks
• Dr. Sudip Kundu (CU)
• Anirban Ghosh (IISc)
• Shayantani Mukherjee (SINP)
• Jhuma Das (SINP)
• Arvind Marathe (IISc)
• Sukanya Halder (SINP)
http://www.saha.ac.in/biop/bioinformatics.html