Supplementary Material Consistsof the Following Files

SUPPLEMENTARY MATERIAL CONSISTSOF THE FOLLOWING FILES:

figureS1A-G.jpg7 parts of the Figure S1.

figureS2A-B.jpg2 parts of the Figure S2.

figureS3.jpgFigure S3.

C1.pdb

C2.pdb

C3.pdb

C4.pdb

C1-L-M.pdb

K-M-L-M.pdb

Fdiag-M.pdb

Fdiag -L-M.pdb

Ndiag -M.pdb

The names of the PDB files correspond to the abbreviations of the structure. Files C1 – C4 (structures that came from CICADA conformational search) contain the structures which consist of only one thymine loop (T5-T8) and adjacent guanine tetrade. Structures C1 – C4 are based on CICADA conformational search and include only one thymine loop and the adjacent guanine quartet. Files that came from the Files based on MD simulations contain whole quadruplex with 3 ions in the channel – averaged along last 500ps of the trajectory.

FIGURE CAPTIONS

FigureS1:

Time development of inter-thymine H-bonds: (A) simulation C1-M, (B) simulation C2-M, (C) simulation C3-M, (D) simulation C1-L, (E) simulation C1-L-M, (F) simulation K-M, (G) simulation K-M(K+). See Table S1 for H-bond type.

Figure S2:

Development of  angle of nucleotides T6 (A) and T7 (B) during the LES run C1-L, all copies A - E.

Figure S3

Interconversion of C1C1-L structures. Locally Enhanced Sampling started from the quadruplex with both loops identical and within. In the course of theLES trajectory theloops passed through different geometries (3 ns intermediate) and felt to approximatellywhile at the end they adopted essentially the same geometry.

Table S1 a) Lateral thymidine loop H-bonds seen in the course of the present paper. Numbers in parentheses correspond to analogous bases in the second loop T17-T20.

a)

ID / Atom 1 / Atom2
I / T5(17): O4 / T7(19): H3
II / T5(17): H3 / T7(19): O2
III / T5(17): O2 / T8(20): H3
IV / T5(17): H3 / T8(20): O4
V / T5(17): H3 / T8(20): O2
VI / T5(17): O4 / T8(20): H3
VII / T5(17): H3 / T7(19): O4
VIII / T5(17): O2 / T7(19): H3

MM-PBSA: comparison of parm94 and parm99 data

In order to complete the data, we re-evaluated all the MM-PBSA energies with the parm99 parametrization. In absolute values, it has changed the free energies by ca 35 kcal/mol. However, the changes of relative free energy differences of the individual structures are small. Albeit it has reduced the key free energy difference between Fdiag-L-M and Ndiag-M structures by ca 3 kcal/mol, the change is too small to affect any conclusion of this paper. The free energy balance between Fdiag-L-M and C1-L-M stuctures is almost unaffected.

Table S2 – the same as TABLE 3 in the paper, but with PARM 99. Free energies (G total taken from MM-PBSA analysis, last 2 ns snapshots average)

Simulation /

G(TOTAL)

/ G(Stem+L1) / G(Stem+L2) / G(Stem) / G(L1) § / G(L2) §
LATERAL
K-M / -5126 / -4488 / -4482 / -3844 / -644 / -638
K-M(K+) / -5109 / -4472 / -4465 / -3827 / -645 / -639
C1-M / -5082 / -4447 / -4458 / -3821 / -625 / -637
C2-M / -5130 / -4491 / -4487 / -3847 / -644 / -639
C3-M / -5129 / -4478 / -4477 / -3826 / -652 / -652
C1-L-M / -5165 / -4513 / -4511 / -3858 / -654 / -652
C4-M / -5130 / -4493 / -4493 / -3855 / -638 / -638
K-M-L-M / -5160 / -4508 / -4518 / -3865 / -643 / -653
DIAGONAL
Fdiag-L-M / -5167 / -4512 / -4519 / -3864 / -649 / -655
Fdiag-M / -5150 / -4505 / -4504 / -3858 / -647 / -646
Ndiag-M / -5155 / -4507 / -4509 / -3860 / -647 / -649

§Contributions of L1 and L2 are extracted from the preceding four columns as specified in the text. Solute entropy term is not included in this Table.

Table S3 – the same as TABLE 4 in the paper, but with PARM 99. Free energies (G total taken from MM-PBSA analysis, last 0.5 ns snapshots average)

Simulation /

G(TOTAL)

/ G(Stem+L1) / G(Stem+L2) / G(Stem) / G(L1) § / G(L2) §
LATERAL
K-M / -5126 / -4490 / -4483 / -3845 / -645 / -637
K-M(K+) / -5107 / -4471 / -4463 / -3826 / -645 / -637
C1-M / -5084 / -4447 / -4459 / -3822 / -625 / -637
C2-M / -5138 / -4495 / -4496 / -3852 / -643 / -644
C3-M / -5135 / -4481 / -4482 / -3828 / -653 / -654
C1-L-M / -5168 / -4519 / -4513 / -3863 / -656 / -650
C4-M / -5136 / -4497 / -4498 / -3859 / -638 / -639
K-M-L-M / -5162 / -4509 / -4520 / -3866 / -643 / -654
DIAGONAL
Fdiag-L-M / -5174 / -4519 / -4523 / -3867 / -652 / -656
Fdiag-M / -5147 / -4504 / -4503 / -3858 / -646 / -644
Ndiag-M / -5157 / -4509 / -4509 / -3861 / -648 / -648

§ Contributions of L1 and L2 are extracted from the preceding four columns as specified in the text. Solute entropy term is not included in this Table.