Supplementary Material: 2D-IR Spectroscopy of an AHA Labelled Photoswitchable PDZ2 Domain

Supplementary Material: 2D-IR Spectroscopy of an AHA Labelled Photoswitchable PDZ2 Domain Brigitte Stucki-Buchli, Philip Johnson, Olga Bozovic, Claudio Zanobini, Klemens Koziol, Peter Hamm Department of Chemistry, University of Zurich, Zurich, Switzerland and Adnan Gulzar, Steffen Wolf, Sebastian Buchenberg, Gerhard Stock Institute of Physics, Albert Ludwigs University, Freiburg, Germany I. AHA MD PARAMETERS AHA parameterization procedure Force field parameters for the azobenzene photoswitch and the attached cysteine side chains as well as for AHA labels were obtained with the Antechamber package.[1] For the determination of atomic charges, the structures of the switch with attached cysteine side chains in cis and trans conformations as well as the AHA labels were optimized on B3LYP/6-31G* level using the GAUSSIAN g9 program suite.[2] Atomic charges of the different conformers were then computed as Mulliken charges from HF/6-31G* single point calculations. Point charges for MD calculations were then obtained from multiconformational restrained electrostatic potential (RESP)[3] calculations. The Cβ partial charges of covalently attached Cys residues were constrained to the value given in the Amber99sb*ILDN force field. [ AHA ] [ atoms ] AHA parameters N N -.4157 1 H H.2719 2 CA CT.773 3 HA H1.795 4 CB CT -.1172 5 HB1 H1.5338 6 HB2 H1.5338 7 CG CT.1526 8 HG1 H1.612 9 HG2 H1.612 1 N1 Nah -.44965 11 N2 Nbh.288 12 N3 Nch -.6395 13 C C.5973 14 O O -.5679 15

2 [ bonds ] -C N N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG HG1 CG HG2 CG N1 N1 N2 N2 N3 C O [ impropers ] -C CA N H CA +N C O [ atomtypes ] [ bondtypes ] Nah 7 14.1. A 3.25e-1 7.1128e-1 Nbh 7 14.1. A 3.25e-1 7.1128e-1 Nch 7 14.1. A 3.25e-1 7.1128e-1 [ angletypes ] Nah CT 1.1477 26259. ; AHA side chain GAFF Nah Nbh 1.1216 71747. ; AHA side chain GAFF Nbh Nch 1.1124 9923. ; AHA side chain GAFF [ dihedraltypes ] CT CT Nah 1 19.5 555.64 ; CB-CG1-N1 AHA GAFF CT Nah Nbh 1 116.2 574.38 ;CG1-N1-N2 AHA GAFF Nah CT H1 1 19.6 412.21 ; N1-CG1-HG12 AHA GAFF Nah Nbh Nch 1 18. 566.1 ; N1-N2-N3 AHA GAFF CT CT CT Nah 3.6584 1.95253. -2.6338.. CT CT Nah Nbh 3...... CT Nah Nbh Nch 3...... Nah CT CT H1 3.6584 1.95253. -2.6338.. Nbh Nah CT H1 3......

3 II. SUPPLEMENTARY FIGURES 1 1517.51 N16AHA 1 1518.51 I2AHA 8 6 4 8 6 4 2 2 6 8 1 12 14 16 18 2 6 8 1 12 14 16 18 2 1 1544.1 S48AHA 1 1518.1 L66AHA Relative intensity (%) 8 6 4 8 6 4 2 2 6 8 1 12 14 16 18 2 6 8 1 12 14 16 18 2 1 1518.51 L78AHA 1 1517.51 N8AHA 8 6 4 8 6 4 2 2 6 8 1 12 14 16 18 2 Molecular Mass (Da) 6 8 1 12 14 16 18 2 Molecular mass (Da) FIG. S1: ESI-mass spectra of all mutants considered in this paper, evidencing the the excellent purity of the labelled and cross-linked protein.

4 1..8 no AHA trans no AHA cis.6.4.2..2 2 4 6 8 1..8 N16AHA trans N16AHA cis 1. I2AHA trans I2AHA cis.6.4.2.5...2 2 4 6 8.5 2 4 6 8 1. S48AHA trans S48AHA cis 1..8 L66AHA trans L66AHA cis.5..6.4.2..5 2 4 6 8.2 2 4 6 8 1..8 L78AHA trans L78AHA cis 1. N8AHA trans N8AHA cis.6.4.2.5...2 2 4 6 8.5 2 4 6 8 FIG. S2: Temperature-induced unfolding measured by CD in the two states of the photo-switch of the PDZ2 domain without AHA label (top), and all the mutants considered in this paper. The trans data have been measured for the dark-adapted protein, the cis data after illumination for 2 min at 37 nm from a cw diode laser (CrystaLaser CL-2). The data have been fit to a function 1/(1 + exp((t T m)/ T )) after subtraction of the background and normalisation. The fit results are summarized in Table 1.

5 214 N16AHA I2AHA S48AHA 21 probe (cm -1 ) 26 214 L66AHA L78AHA N8AHA 21 26 26 21 214 26 21 214 26 21 214 pump (cm -1 ) FIG. S3: Purely absorptive 2D IR spectra of the dark-adapted trans-state of all mutants considered in this study. The AHA signal can be recognized, but is sitting on a huge water background (which has not been measured independently and subtracted out, since that would require much larger sample amounts). The water background is positive (red, excited state absorption), while the AHA diagonal band is seen as negative dip. The relative contribution of the AHA varies, since the concentration varied between.6 mm and 1.1 mm, given by the solubility of the particular mutant.

6 1 1518.51 L78AHA dark 8 6 4 2 26 1 12 14 16 18 11 1 1518.51 L78AHA 3 min 8 6 4 2 1 12 14 16 18 11 1 1518.51 L78AHA 2 min 8 6 4 2 1 12 14 16 18 11 Molecular Mass (Da) FIG. S4: ESI-mass spectra of L78AHA (from a different batch than in Fig. S1) before illumination (top), and after 3 min (middle) or 2 min (bottom) of illumination at 37 nm from a cw diode laser (CrystaLaser CL-2). The first case coincides with the conditions used to measure the 2D IR difference spectra of Fig. 3, while the second case applied significantly more light. Even in the second case, still basically no changes in the chemical composition of the sample are detectable, in particular no reduction of the azido-group that would lower the mass by 26 Da due to the loss of a N 2 molecule. The corresponding peak is labelled in the top panel, is very small, and does not increase upon illumination.

7 a AHA b AHA FIG. S5: (a) Absolute FTIR spectrum of L78AHA with the buffer background subtracted; the inset focusing into the small AHA band. (b) Difference FTIR spectra of L78AHA. The black line shows the result when taking a background for the darkadapted protein in trans, and then switching to cis by illumination at 37 nm. The dip at 21 cm 1 indicates the loss of intensity of the AHA band. The red line shows the result when taking the cis configuration as background and then (partially) switching back to trans by illumination at 42 nm. The AHA band regains its intensity. Back-switching from cis to trans is not complete, since both the cis and the trans configuration absorb at 42 nm, thus establishing a photo-equilibrium (in contrast to trans-cis switching at 37 nm that can be performed to almost 1%). The results nevertheless show that back-switching is reversible.

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