Journal of Magnetic Resonance 154, 28–45 (2002) doi:10.1006/jmre.2001.2454, available online at http://www.idealibrary.com on Specification and Visualization of Anisotropic Interaction Tensors in Polypeptides and Numerical Simulations in Biological Solid-State NMR Mads Bak, Robert Schultz, Thomas Vosegaard, and Niels Chr. Nielsen 1 Laboratory for Biomolecular NMR Spectroscopy, Department of Molecular and Structural Biology, University of Aarhus, DK-8000 Aarhus C, Denmark Received May 12, 2001; revised October 3, 2001; published online November 29, 2001 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 for- mat 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 ad- vanced solid-state NMR experiments on typical nuclear spin inter- actions 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 se- quences 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 uniaxi- ally oriented bacteriorhodopsin and rhodopsin under conditions of finite RF pulses and multiple spin interactions. C  2002 Elsevier Science INTRODUCTION Numerical simulations play an increasingly important role in the development and application of solid-state NMR methods for determination of the structure and dynamics of biological macromolecules immobilized by size, aggregation, or mem- brane association. This is ascribed to the fact that most solid- state NMR experiments used for this purpose strongly depend on manipulation of anisotropic interactions to obtain evolu- tion under well-defined isotropic or anisotropic parts of the Hamiltonian. Based on advanced RF irradiation schemes, of- ten in concert with sample spinning, a large number of pulse sequences have been devised to accomplish specific coher- 1 To whom correspondence should be addressed. E-mail: ncn@imsb.au.dk. ence transfers or measurement of specific structural parame- ters. Typically, these elements have been developed on basis of one- or two-spin systems using analytical tools such as aver- age Hamiltonian theory (1, 2) to tailor the effective Hamiltonian to the appropriate form. Subsequently, the elements have been tested by numerical simulations and by experiments on model systems and finally verified in real peptide applications either directly or as elements in more advanced pulse schemes. Thus, in the development process numerical simulations have primar- ily been used for verification while they so far have only been used sparsely for direct design of pulse sequences (3, 4). In con- trast, numerical simulations in combination with iterative fitting are regarded as being almost indispensable for the extraction of structural parameters from experimental spectra (5–15). Considering the increasing use of uniformly or extensively 13 C, 15 N-labeled samples, it becomes exceedingly important that the pulse sequence elements work appropriately in multiple-spin systems with characteristics potentially being far from the sim- ple one- or two-spin cases typically considered in the design of these elements. Under multiple-spin conditions vital coher- ences may leak to undesired spins which may cause a signifi- cant reduction in the sensitivity, wrong assignment of multiple- dimensional spectra, and wrong interpretations of anisotropic interactions in terms of structure and dynamics. Obviously, this problem may scale dramatically with the number of di- mensions and coherence transfer steps involved in the pulse sequence. This is an important issue since current remedies to the resolution problem of biological solid-state NMR, in addition to uniformly labeled samples, appear to involve in- creasingly sophisticated combinations of pulse sequence build- ing blocks in multiple-dimensional experiments. An important ingredient in the solution of this problem may be to investi- gate in detail the performance of the available pulse schemes on multiple-spin systems closely reflecting the conditions in relevant peptide structures. This may provide optimized ex- perimental procedures, motivate the design of new procedures on a multiple-spin basis, or result in the recommendation of alternative isotope labeling procedures (16) being optimally compatible with state-of-the-art solid-state NMR technology. 28 1090-7807/02 $35.00 C  2002 Elsevier Science All rights reserved.