Modeling studies of chromatin fiber structure as a function of DNA linker length Supplemental material

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1 Modeling studies of chromatin fiber structure as a function of DNA linker length Supplemental material Ognjen Perišić a,,rosanacollepardo-guevara a,, Tamar Schlick a,b, a Department of Chemistry, New York University, 100 Washington Square East, New York, New York b Courant Institute of Mathematical Sciences, New York University, 251 Mercer Street, New York, New York 10012, Tel.: ; fax: These authors contributed equally to the work Corresponding author address: schlick@nyu.edu (Tamar Schlick) Preprint submitted to Journal of Molecular Biology July 24, 2010

2 q l (e) x y z (nm) q l (e) x y z (nm) q l (e) x y z (nm) q l (e) x y z (nm) Table S1: Nucleosome pseudo-charges and relative postions on the nucleosome surface at C S obtained with the DiSCO approach. 2 =0.15M

3 Parameter Description Value T Temperature K C S Monovalent salt concentration (NaCl) 0.15 M l 0 Equilibrium DNA segment length 3.0 nm L p Persistence length of linker DNA in monovalent salt 50 nm h Stretching rigidity of linker DNA 100k B T/lo 2 g Bending rigidity of linker DNA L p k B T/l o s Torsional rigidity constant of linker DNA erg.nm θ 0 Angular separation between linker segments at core 108 2w 0 Width of wound DNA supercoil 3.6 nm r 0 Radius of wound DNA supercoil 4.8 nm σ tt Excluded vol. distance for tail/tail interactions 1.8 nm σ tc Excluded vol. distance for tail/core interactions 1.8 nm σ cc Excluded vol. distance for core/core interactions 1.2 nm σ tl Excluded volume distance for tail/linker DNA interactions 2.7 nm σ cl Excluded vol. distance for core/linker DNA interactions 2.4 nm σ glhc Excluded vol. distance for globular link. hist./core interactions 2.2 nm σ glh1 Excluded vol. distance for globular link. hist./link.dna interactions 3.4 nm σ clhc Excluded vol. distance for C-term. link. hist./core interactions 2.4 nm σ clh1 Excluded vol. distance for C-term. link. hist./link.dna interactions 3.6 nm k ev Excluded vol. energy param for all components except for tail beads k B T k evt Tail/tail excluded volume interaction energy parameter 0.1 k B T q glh Charge on the globular linker histone bead 13.88e q clh Charge on the C-terminal linker histone bead 25.62e σ LHLH Excluded volume distance for link.histone/link.histone interactions 2.0 nm Table S2: Parameters employed in mesoscale modeling/simulation. 3

4 Bond k b Average SD Tail i-j (kcal/mol/aa) [Å] [Å] N-ter H N-ter H N-ter H2A C-ter H2A N-ter H2B Table S3: Protein bead stretching parameters. Angle k θ Average SD Tail i-j (kcal/mol/aa) [Å] [Å] N-ter H N-ter H N-ter H2A C-ter H2A N-ter H2B Table S4: Protein bond-angle parameters. 4

5 (a) Interdigitated solenoid (b) zigzag Figure S1: Initial configurations and their interaction patterns. 5

6 kcal/mol (a) Energy, 182 bp zigzag start solenoid start (b) Bending angle, 182 bp (c) Triplet angle, 182 bp (d) Dihedral angle, 182 bp million MC steps million MC steps (e) Energy, 218bp (f) Bending angle, 218 bp kcal/mol (g) Triplet angle, 218 bp (h) Dihedral angle, 218 bp million MC steps million MC steps Figure S2: Convergence of different quantities for 24-core 182-bp (top half) and 218-bp (bottom half) oligonucleosome trajectories simulated with LH. 6

7 j I (i,j) i 0 Figure S3: Internucleosome interaction matrix I (i, j). 7

8 Figure S4: Triplet, dihedral, and bending angles cartoons. 8

9 CS = 0.01 M without LH CS = 0.15 M without LH CS = 0.15 M with LH CS = 0.2 M with LH CS = 0.15 M with Mg and LH Short NRL Medium NRL Long NRL Figure S5: Space filling model for representative 48-core arrays (short NRL: 173 bp, medium NRL: 209 bp, and long NRL: 226 bp) at different salt concentrations. Nucleosomes, DNA linkers, and LH are colored as in Figure 2. 9

10 Figure S6: Description of the fiber axis calculation for 24-unit oligonucleosome. (a) Cyan - nucleosome cores, Red lines - connections between consecutive nucleosomes, Green line - fiber axis, as estimated by the least squares procedure; (b) Fiber axis decomposition into three separate curves for three vectors (x, y, and z); Blue dots - nucleosome centers, Green line - fiber axis, Reddots-separatorsbetweenlinesegmentsofthe fiber axis. 10

11 Figure S7: Geometry of the mesoscale oligonucleosome showing (a) assembly of oligonucleosome components into a chain, (b) entering/exiting linker DNA, and (c) individual coordinate systems for the linker DNA beads and nucleosome core, and Euler angle β depicting the linker DNA bending. For nucleosome core i, a i and b i lie in the nucleosome core plane, with a i pointing along the tangent at the attachment site of the entering DNA, and b i in the direction normal to this tangent. For linker DNA bead i, thevectora i points from the geometric center of i to either the center of the following DNA bead or to the attachment point in points from the attachment point of the exiting linker DNA to the center of the following DNA linker bead. The vectors a + i and a i represent the local tangents on the nucleosome cores at the exiting and entering points of attachment, respectively. the nucleosome (if i +1isacore). Thevectora DNA i 11