Supporting information to: Time-resolved observation of protein allosteric communication. Sebastian Buchenberg, Florian Sittel and Gerhard Stock 1
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1 Supporting information to: Time-resolved observation of protein allosteric communication Sebastian Buchenberg, Florian Sittel and Gerhard Stock Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79 Freiburg, Germany April, 7 To whom correspondence should be addressed S
2 CIS TRANS FIG. S: Secondary structure content of PDZS in (top) cis and (bottom) trans state for the equilibrium MD simulations. The content of β-sheet (red), α-helical (blue) and -helical conformations of the individual residues are shown obtained by DSSP (W. Kabsch and C. Sander, Biopolymers, 77-7 (98)). S
3 S i S j i j P type α α Gln-7 Thr-77. HB mc α α Ala-7 Leu-78. HB mc α α Val-7 Arg-79. HB mc α α Val-7 Leu HB mc α β -β Cys-7 Ser-7 -. α β -β Leu-78 Lys- -. α β -β Leu-78 Leu np α β Val-7 Val- -. np α β Arg-79 Cys-. α β Ala-7 Ile-.7 np α β Leu-78 Ile-. np α β Thr-77 Val-. α β Leu-78 Val-8 -. np α β -α Gln-7 Ala-9. α β -α Ala-7 Ala-9. np α β -α Val-7 Leu- -. np α β -α Thr-77 Leu-. β -α β Gly-8 Ser-. HB sc β C Glu-9 Gln-9.8 β -β β -β Lys- Asp- -.8 β -β β -β Lys- Ser-7. β -β β -β Asn- Ser-7. HB mc β -β α -β Asn- Gln-8 -. β -β β -β Gly- Gly- -. β -β β -α His- Glu-7. β -β C Val- Ser-9.8 β -β C Val- Pro-9. β β -α Ile- Ala-9 -. np β β -α Ile- Thr β C Tyr- Ser-9. α -β C Gly- Gln-9. α -β C Gly- Ser-9. β β -α Arg-7 Glu-7. β α -β Val- Thr-8. TABLE S: Contacts between residue i in segment S i and residue j in segment S j that change significantly ( P ij.) upon cis-trans isomerization of PDZS, where P ij = Pij trans Pij cis denotes the change of the contact probability. Here Pij cis or Pij trans denote the probability that the minimal distance between residue i and j in PDZS-cis or -trans, respectively, is below. nm. The last column indicates whether a given contact is a H bond within the main chain (HB mc ), a H bond between the main and a side chain (HB sc ), or a contact between two hydrophobic residues (np). In line with the discussion, the upper part of the table describes contact changes at the α side and the lower part changes at the β side of the binding pocket. S
4 Residue rmsd(nm) Region cis trans d i,i+ (nm) s Gly-. N δ δ, P II, ɛ.(±.) Lys-. β, P II, ζ, δ P II.(±.) Asn-. P II, α, P II, (β) β, (P II, α).(±.) Asp-. β β α, β, γ, δ δ.(±.7) - Asn-. α, β, P II, δ, δ δ, α.77(±.) - Gly-9.9 δ, P II δ.9(±.) Gly-.7 β, P II, α, P II, ɛ, δ P II, (P II, ɛ).(±.) - Val-. β, P II, (α) β, P II, δ, (α).(±.) - Asn-7. P II, α, δ δ, (β, P II ).(±.) Thr-8. β β β, P II, α β, (P II, α, δ ).(±.) Ser-9. α, δ, (P II ) α, δ, P II.(±.8) Arg-. α, δ, (P II ) β, δ, α, γ.7(±.) Gly-.9 P II, ɛ, α, δ, P II P II, ɛ, α, δ, P II, (ɛ).8(±.) - Gly-. P II, P II, ɛ P II, P II, (ɛ).(±.7) - Lys-. α β P II, α P II, (α).(±.78) Leu-. α, (β) α.(±.8) - Glu-7. P II, α α, (P II ).(±.) - Gly-8. β α α, δ, γ α, δ, (γ).9(±.) - Ala-9. β, P II, (α) β, P II.(±.) Thr-7.7 P II, α, δ P II.(±.) His-7. α, (β, P II ) α.(±.7) Cys-7.98 α δ, α α.(±.) Asn-8.7 α, γ γ, (α, β).8(±.) - Gly-9. C P II, (P II ) P II, α, δ.(±.) - TABLE S: Residues i showing large changes in their main chain conformations between cis and trans state and extent of changes. The latter is quantified in terms of the rmsd between the average structures of the residues in the cis and trans state. Only residues with rmsd values above.8 nm are listed. Corresponding motifs in the cis and trans state are given in the nomenclature proposed by Hollingsworth and Karplus (Bioimol. Concepts, 7-8 ()). Brackets indicate motifs that are only weakly populated. In addition, changes in the C α distances between corresponding neigboring residues i and i+, d i,i+, are given. The rightmost column, s, indicates whether the changes are within the statistical error (s = ), or, if not, indicating that residue i is a hinge residue, it yields the sign of d i,i+. Thus, s < or s > means that the C α distance between residues i and i + is reduced or increased, respectively. S
5 residue x x x x x x x7 FIG. S: (Top) Influence of the 9 preselected dihedral angles on the first seven eigenvectors of dpca+ (see Methods section of main text). (Bottom) Distributions and time traces of the means and variances of principal components x x 7. S
6 FIG. S: Ramachandran plots of (top left) Asn in cis, (top right) Asn in trans, (bottom left) Ser 9 in cis, and (bottom right) Ser 9 in trans configuration. S
7 a b c d FIG. S: Ramacolor plots (F. Sittel and G. Stock, J. Chem. Theory Comp., - ()) for selected cis (b), NEQ (c), and trans (d) microstates. As displayed by the φ, ψ color space in (a), the plots give an impression of the structural differences of states and their respective secondary structure content. The x-axis gives the state while the y-axis denotes the index of a residue. The colors of the boxes are computed from the color code weighted by the intra state distribution in the Ramachandran plot. The typical secondary structure elements are highlighted by green (α-helix), red (β-sheet) and blue (left-handed α-helix). S7
8 State.8.. ca_dist_9_9 State.8.. ca_dist_9_9 State.8.. ca_dist_9_9 State.8.. ca_dist_9_ ca_dist ca_dist ca_dist ca_dist 7.. ca_dist_9_7.. ca_dist_9_7.. ca_dist_9_7.. ca_dist_9_7.... contact_dist.... contact_dist.... contact_dist.... contact_dist contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9... contact_dist 9... contact_dist 9... contact_dist 9... contact_dist 9.. contact_dist 9.. contact_dist 9.. contact_dist 9.. contact_dist contact_dist contact_dist contact_dist contact_dist 9 FIG. S: Distance distributions (in units of nm) of selected microstates ( of ). S8
9 State ca_dist_9_9 State ca_dist_9_9 State ca_dist_9_9 State ca_dist_9_ ca_dist ca_dist ca_dist ca_dist 7.. ca_dist_9_7.. ca_dist_9_7.. ca_dist_9_7.. ca_dist_9_7.... contact_dist.... contact_dist.... contact_dist.... contact_dist contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9 contact_dist 9... contact_dist 9... contact_dist 9... contact_dist 9... contact_dist 9.. contact_dist 9.. contact_dist 9.. contact_dist 9.. contact_dist contact_dist contact_dist contact_dist contact_dist 9 FIG. S: Distance distributions (in units of nm) of selected microstates ( of ). S9
10 # macrostates Qmin FIG. S: Number of macrostates as a function of the metastability Q min using a lag time of τ = ns. The macrostates are based on dynamical clustering using the Most Probable Path method by A. Jain and G. Stock (J. Chem. Theory Comp. 8, 8-89 ()). 8 7; 9 FIG. S7: Dynamical network of macrostates obtained for Q min =.7, placing the states according to their position in x -x space. Nodes are colored by their respective content of microstates identified as cis (blue), NEQ (green) or trans (red). Selected microstates are labeled at the macrostate they are part of. As in Fig. S, the macrostates and connections are based on dynamical clustering using the Most Probable Path method. S
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