title: Computer Modeling of Spin Labels: NASNOX, PRONOX, and ALLNOX.
abstract: Measurement of distances between spin labels using electron paramagnetic resonance with the double electron-electron resonance (DEER) technique is an important method for evaluation of biomolecular structures. Computation of interlabel distances is of value for experimental planning, validation of known structures using DEER-measured distances, and determination of theoretical data for comparison with experiment. This requires steps of building labels at two defined sites on proteins, DNA or RNA; calculation of allowable label conformers based on rotation around torsional angles; computation of pairwise interlabel distances on a per conformer basis; and calculation of an average distance between the two label ensembles. We have described and validated two programs for this purpose: NASNOX, which permits computation of distances between R5 labels on DNA or RNA; and PRONOX, which similarly computes distances between R1 labels on proteins. However, these programs are limited to a specific single label and single target types. Therefore, we have developed a program, which we refer to as ALLNOX (Addition of Labels and Linkers), which permits addition of any label to any site on any target. The main principle in the program is to break the molecular system into a "label," a "linker," and a "target." The user can upload a "label" with any chemistry, define a "linker" based on a SMILES-like string, and then define the "target" site. The flexibility of ALLNOX facilitates theoretical evaluation of labels prior to synthesis and accommodates evaluation of experimental data in biochemical complexes containing multiple molecular types.
authors.affiliation: Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA.
authors.forename: Kathleen N
authors.initials: KN
authors.lastname: Beasley
authors.affiliation: Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA.
authors.forename: Brian T
authors.initials: BT
authors.lastname: Sutch
authors.affiliation: Department of Laboratory Medical Sciences, Faculty of Allied Health Sciences, Hashemite University, Zarqa, Jordan.
authors.forename: Ma'mon M
authors.initials: MM
authors.lastname: Hatmal
authors.affiliation: Department of Biochemistry, University of Southern California, Los Angeles, California, USA.
authors.forename: Ralf
authors.initials: R
authors.lastname: Langen
authors.affiliation: Department of Chemistry and Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.
authors.forename: Peter Z
authors.initials: PZ
authors.lastname: Qin
authors.affiliation: Department of Pharmacology & Pharmaceutical Sciences, University of Southern California, Los Angeles, California, USA; Department of Biochemistry, University of Southern California, Los Angeles, California, USA. Electronic address: ihaworth@usc.edu.
authors.forename: Ian S
authors.initials: IS
authors.lastname: Haworth
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D011506:Proteins / Q000737:chemistry*; D013113:Spin Labels
chemical_list: D011506:Proteins; D013113:Spin Labels; D004247:DNA
keywords: ALLNOX; Computation; Conformation; Distance; Flexibility; Spin label