Nucleic Acid Structure Analysis

Transcription

1 Nucleic Acid Structure Analysis Dhananjay Bhattacharyya Biophysics Division, Saha Institute of Nuclear Physics, Kolkata and Manju Bansal Molecular Biophysics Unit, Indian Institute of Science, Bangalore

2 Nucleic Acid Backbone is Connected to Either of Four Different Bases

3 A C G T

4 C3 -endo C2 -endo

5 pseudorotation cycle of furanose ring in nucleosides (Saenger, 1984) tan P = {(τ 4 + τ 1 ) (τ 3 + τ )} / 2 * τ 2 *(sin 36 o + sin 72 o ) τ I+2 = τ max cos (P+ i * 144 o ) τ max = τ / cosp

6 Distribution of pseudorotation phase angle (P) calculated from B-DNA crystal structures

7 Torsion angles of DNA models α β γ δ ε ζ χ P A-DNA B-DNA C-DNA D-DNA

8 minor groove major groove minor groove major groove

9 Netropsin like drugs bind in the B-DNA narrow and deep minor groove

10 Actinomycin D like drugs make their place in between two stacked base pairs by distorting the DNA double helix

11 DNA kinks by 9 o at the dyad location while binding to two subunits of Catabolite Activator Protein (CAP)

12 TATA-box binding protein transforms the interfacing DNA region to A-DNA like structure

13 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

14 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)

15 Standard Reference frame of a Watson- Crick base pair

16 Definition and Nomenclature of Base Pair Doublet Parameters

17 Calculation of Base Pair parameters by NUPARM Local Step Parameters: Mean Local Helix Axis: Zm = Xm Ym, where Xm = Xaxis 1 + Xaxis 2 and Ym = Yaxis 1 + Yaxis 2 Y2 X2 X1 M is Base Pair Center to Center Vector Y1 Tilt : 2. * sin -1 ( -Zm Y1) Roll: 2. * sin -1 ( Zm X1) Twist: cos -1 (( X1 Zm) ( X2 Zm)) Shift (Dx) M Xm Slide(Dy) M Ym Rise(Dz) M Zm

18 Base Pair parameters of DNA models Tilt Roll Twist Shift Slide Rise Prop. A-DNA B-DNA C-DNA D-DNA

19 Local Helical Parameters: Local Helix Axis: Z* = X* Y*, where X* = Xaxis 1 - Xaxis 2 and Y* = Yaxis 1 - Yaxis 2 M is Base Pair Center to Center Vector Inclination : 2. * sin -1 ( -Z* Y1) Tip: 2. * 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* 3.3A 2.6A A-DNA structural Parameters: Roll ~ 12; Inclination ~2 Slide ~ -1.5; X-translation ~ -4. Rise ~ 3.2; Helical Rise ~2.6

20 Relation between the two frames ( ) ( ) ( ) { } ( ) ( ) ( ) { } ) / ( sin T and ) / ( sin R where RT ) T R T R / T cot / ) sin( RT T R T R / T cot / ) sin( / / τ = ρ = Ω = θ Ω = η η=inclination; θ=tip; τ=tilt; ρ=roll; Ω=Twist

21 Base Pair step parameters of B-DNA crystal structures (1BNA.pdb) Tilt of Dickerson Dodecamer (1BNA.pdb) Twist NUPARM CURVES X3DNA NUPARM CURVES X3DNA Roll Slide NUPARM CURVES X3DNA NUPARM CURVES X3DNA

22 Base pair doublet parameters of A-DNA structure (2ANA.pdb) Roll of A-DNA structure (2ANA.pdb) Twist of 2ANA NUPARM CURVES X3DNA NUPARM CURVES X3DNA Slide 1.5 Tilt NUPARM CURVES X3DNA -1-2 NUPARM CURVES X3DNA

23 Base pair doublet parameters of TATAbox DNA-TBP complex (PDT12), calculated by 3DNA (Lu & Olson 23)

24 Roll of 1CGP Residue no. Twist

25 Roll of TBP bound TATA box Nuparm Curves X3DNA Twist Nuparm Curves X3dna Slide Nuparm Curves X3dna

26 Tilt and Roll of nucleosomal DNA (1M1A)

27 Distribution of base-pair step parameters in high resolution DNA crystal structures Tilt Roll Twist Shift Red: A-DNA Slide Green:B-DNA Rise

28 Roll Variation in Crystal Structures Roll of d(cg).d(cg) doublets Occurrence Roll of d(aa).d(tt) doublets Occurrence Roll Roll of d(gc).d(gc) doublets Roll Occurrence Roll

29 Steric clash between Purines of successive base pairs can cause nonparallel base pair orientations (Calladine & Drew 1982)

30 Minor Groove Width

31

32 Definition of Intra Base Pair Parameters (IUPAC-IUB) IUB)

33 Base pair parameters Buckle = 2 sin -1 ( Zm. Y 1 ) Opening = 2 sin -1 ( Zm. X 1 ) Propeller = cos -1 (( X 1 Zm). ( X 2 Zm)) Shear = -Xm. M Stagger = Ym. M Stretch = Zm. M Y2 Y1 X1 X2 Xm = (X 1 + X 2 ) / (X 1 + X 2 ) Ym = (Y 1 + Y 2 ) / (Y 1 + Y 2 ) Zm = {(X 1 + X 2 ) x (Y 1 + Y 2 )}/ { (X 1 + X 2 ) (Y 1 + Y 2 ) }

34 Base Pair Parameters of Dickerson Dodecamer Buckle Stagger Open Angle NUPARM CURVES X3DNA Shear Nuparm Curves X3dna Nuparm Curves X3dna Nuparm Curves X3dna -1-1 Propeller Stretch Nuparm Curves X3dna Nuparm Curves X3dna

35 Possibility of Unusual Base Pairing in RNA

36 Unusual Basepairs Observed By Leontis (Leontis et al., Nucl. Acids Res., 23, 31, 345.)

37 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

38 Base 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=Σ i (d i -3.) 2 + ½Σ k (θ k -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); G:C W-W(C) and 2786 G:U W-W(C) base pairs

39 G:U W:W Cis (2769) U:U W:W Cis (36) A:G W:W Cis (44)

40 A:U H:W Trans (1193) A:G H:S Trans (2323) A:A H:H Trans (437)

41 Axis System of Bases

42 G:C Base Pair Using W:W base edges in Cis Orientation Buckle Shear Open Stagger Propeller Stretch

43 Distribution of Base Pair Parameters for A:U H-W (Trans) Base Pair (freq: 1164) Buckle Open Shear Stagger Propeller Stretch

44 Telomeric DNA (PDB ID: 1JPQ)

45 Inter Base Pair parameters of 1JPQ Tilt Roll Twist Shift Slide Rise Cup LC 1 G:G W:H C LC 2 G:G H:W C LC 3 G:G W:H C LC 4 G:G W:H C LC 5 T: : LC 6 T: : LC 7 T: : LC 8 G:G W:H C LC 9 G:G W:H C LC 1 G:G W:H C LC 11 G:G W:H C LC 12 G:G W:H C LC 13 G:G H:W C LC 14 G:G W:H C LC 15 G:G H:W C LC 16 T: : LC 17 T: : LC 18 T: : LC 19 G:G H:W C LC 2 G:G H:W C LC 21 G:G H:W C LC 22 G:G 8

46 Intra Base Pair Parameters of 1JQP Buckle Open Propel Stagger Shear Stretch BL 1 G:G W:H C BL 2 G:G H:W C BL 3 G:G W:H C BL 4 G:G W:H C BL 5 T: : BL 6 T: : BL 7 T: : BL 8 G:G W:H C BL 9 G:G W:H C BL 1 G:G W:H C BL 11 G:G W:H C BL 12 G:G W:H C BL 13 G:G H:W C BL 14 G:G W:H C BL 15 G:G H:W C BL 16 T: : BL 17 T: : BL 18 T: : BL 19 G:G H:W C BL 2 G:G H:W C BL 21 G:G H:W C BL 22 G:G H:W C

47 Twist Slide Propeller Shear Open angle

48 Thanks Dr. Sudip Kundu (CU) Anirban Ghosh (IISc) Shayantani Mukherjee (SINP) Jhuma Das (SINP) Arvind Marathe (IISc) Sukanya Halder (SINP)