Ifs and Buts of DEER. Likai Song, Ilker Sen, Marco Bonora, Florida State University, NHMFL
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1 Ifs and Buts of DEER Likai Song, Ilker Sen, Marco Bonora, P. Fajer Florida State University, NHMFL
2 1. X-band v. W-band: is bigger better? DEER STEPR 2. DEER Analysis: how not to over interpret the data? 3. Rotamers: is there H-bond? 4. Structure determination: EPR as a structural method? 11/06/09
3 W-band DEER T4L_21C65C X-band 0.26 W-band TnC_55C83C CDB3_142C CDB3_341C CDB3_342C
4 High frequency (W-band) DEER Likai Song, J. Zhou & P. Fajer GHz W-band v. X-band distances GHz us us nm nm Distance W-band (A) Band 3 DEER spectra Distance distribution Distance X-band (A) T4 Lysozyme Troponin C Excellent agreement between the X- and W-band determined distances on three different proteins.
5 Denysenkov, Prisner, Bennati, PNAS 06 Savitsky, Dubinskii, Flores, Lubitz, and K. Mbius, JPC 07 Polyhach, Godt, Bauer G. Jeschke, JMR 07 A B Dipolar frequency Dipolar frequency Orientational selectivity 22 o disorder
6 Pump-observe field scan T4L_65C89C + 35 G (0.021) + 30 G (0.026) + 25 G (0.023) + 15 G (0.048) + 10 G (0.062) Time (ns) - 30 G (0.012) - 20 G (0.016) - 10 G (0.037) Time (ns) No orientational selectivity observed
7 ST-EPR at W-band Spectral diffusion sensitivity Spectral diffusion is 4-fold greater at W-band than at X-band
8 W-band ST-EPR is 4 times more sensitive to slow motion (us ms)
9 DEER analysis DeFit Sen & Fajer EPR newsletter 09
10 F-test decision on # gaussians Excellent definition of complex distribution
11 Multiple populations
12 Add noise
13 Add error contours!
14 When two populations are different? Width (nm) Width (nm) Distance (nm)
15 Spin label rotamer simulation
16 No modelling EPR spin-spin (A) CW KCsA DEER apotnc DEER Ca TnC DEER troponin Ca T1 apotnc Cβ-Cβ (A) Multiple spin-spin distances observed for a single x- ray distance
17 Modelling Sale et al. JACS 2005, Fajer J. Phys EPR spin-spin (A) y = 0.93x R 2 = 0.93 CW KCsA DEER apotnc DEER Ca TnC DEER troponin Ca T1 apotnc T1 troponin Ca X-ray plus MD/MC (A) Adding modeling to x-ray structures now shows correlation between EPR and atomistic detail
18 Simulated Scaling Method Hongzhi Li, Mikolai Fajer, and Wei Yang, JCP 06 Potential energy is separated into a scaling portion (U s ) and an environment portion (U e ) Scaling factor λ m changes from 0 to 1 during simulation facilitating transitions 19
19 M. Fajer, JACS 07 Spin labels buried in protein interior Potential of Mean Force and X-ray Visualization SS correctly predicts the X tal conformation of a buried residue. 20
20 Distribution: model v. data MC/MD DEER MC/MD DEER observed distribution due to SL rotamer distribution observed distribution due to backbone distribution model to get insight what is rotamer and what is backbone heterogeneity
21 Hydrogen bonding in MTSSL?? Mchaourab & Hubbell 96, Columbus & Hubbell 02 : comparison of S-S and C-S linkages 22
22 χ 1 -χ 2 scan energy profile (χ 3 =90) basis set independent (PM3, PM3MM, HF 6-31*) 23
23 Molecular orbitals Lone pair of the S δ interacts with H of C α NBO deletion (HF, DFT): the global minimum rotamer has ~1 kcal/mol stabilization energy 24
24 QM rotamers and x-ray Guo, Hubbell Structure 08 Rotamer Energy S2-CaH S1-NH X-ray mm yes mt rare tp yes tm 2.0 yes 11/06/09
25 Other secondary structures Beta strand Rotamer Energy S2-CaH S1-NH tp mm tt 1.2 tm 1.4 Loop Rotamer Energy S2-CaH S1-NH mm tp tt 1.4 mp 1.3 mt 1.8 pt /06/09
26 From EPR to structure
27 DGEOM-lite - Monte Carlo/Simplex strategy Eulerian rotations + translation Scoring function is EPR distance distribution random starting position Monte Carlo iterations evaluation of distances with EPR penalty function simplex best agreement with experimental restraints Penalty manipulate few points (EPR spin labels) - use of DEER distance distributions Interspin Distance (Å) 29 Structure from EPR
28 6 restraints 11/06/09 DUAL Simplex 1K weighted rdn2 30
29 rotation 11/06/09 DUAL Simplex 1K weighted rdn2 31
30 rotation 11/06/09 DUAL Simplex 1K weighted rdn2 32
31 rotation 11/06/09 DUAL Simplex 1K weighted rdn2 33
32 translation 11/06/09 DUAL Simplex 1K weighted rdn2 34
33 Smooth muscle myosin
34 Position of the solutions with χ 2 min < χ 2 < 5 χ 2 min
35 Best solution χ 2 min = 1.2 EM our conformation DGEOM-lite reproduces the EM structure
36 monomers χ 2 <1.5 <1.4 <1.3 <1.25 χ 2 min monomers best fit Wendt et al. model
37 Best 20 solutions
38 Collaborators Likai Song (Harvard) Ilker Sen (A. Einstein U.) Wei Yang (FSU) Mikolai Fajer (now at UCSD) 41
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Molecular Modelling for Medicinal Chemistry (F13MMM) jonathan.hirst@nottingham.ac.uk Room A36 http://comp.chem.nottingham.ac.uk Assisted reading Molecular Modelling: Principles and Applications. Andrew