title: Specification and visualization of anisotropic interaction tensors in polypeptides and numerical simulations in biological solid-state NMR.
abstract: 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.
authors.affiliation: Laboratory for Biomolecular NMR Spectroscopy, Department of Molecular and Structural Biology, University of Aarhus, DK-8000 Aarhus C, Denmark.
authors.forename: Mads
authors.initials: M
authors.lastname: Bak
authors.forename: Robert
authors.initials: R
authors.lastname: Schultz
authors.forename: Thomas
authors.initials: T
authors.lastname: Vosegaard
authors.forename: Niels Chr
authors.initials: NC
authors.lastname: Nielsen
mesh_terms: D016880:Anisotropy; D003198:Computer Simulation; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D010455:Peptides / Q000737:chemistry*; D012984:Software
chemical_list: D010455:Peptides