Specification and visualization of anisotropic interaction tensors in polypeptides and numerical simulations in biological solid-state NMR.
Software facilitating numerical simulation of solid-state NMR experiments on polypeptides is presented. The Tcl-controlled SIMMOL program reads in atomic coordinates in the PDB format from which it generates typical or user-defined parameters for the chemical shift, J coupling, quadrupolar coupling, and dipolar coupling tensors. The output is a spin system file for numerical simulations, e.g., using SIMPSON (Bak, Rasmussen, and Nielsen, J. Magn. Reson. 147, 296 (2000)), as well as a 3D visualization of the molecular structure, or selected parts of this, with user-controlled representation of relevant tensors, bonds, atoms, peptide planes, and coordinate systems. The combination of SIMPSON and SIMMOL allows straightforward simulation of the response of advanced solid-state NMR experiments on typical nuclear spin interactions present in polypeptides. Thus, SIMMOL may be considered a "sample changer" to the SIMPSON "computer spectrometer" and proves to be very useful for the design and optimization of pulse sequences for application on uniformly or extensively isotope-labeled peptides where multiple-spin interactions need to be considered. These aspects are demonstrated by optimization and simulation of novel DCP and C7 based 2D N(CO)CA, N(CA)CB, and N(CA)CX MAS correlation experiments for multiple-spin clusters in ubiquitin and by simulation of PISA wheels from PISEMA spectra of uniaxially oriented bacteriorhodopsin and rhodopsin under conditions of finite RF pulses and multiple spin interactions.
Bak
Mads
M
Laboratory for Biomolecular NMR Spectroscopy, Department of Molecular and Structural Biology, University of Aarhus, DK-8000 Aarhus C, Denmark.
Schultz
Robert
R
Vosegaard
Thomas
T
Nielsen
Niels Chr
NC
D016880:Anisotropy; D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D012984:Software
D010455:Peptides