An easy way to include weak alignment constraints into NMR structure calculations |
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Authors: | Hans-Jürgen Sass Giovanna Musco Stephen J. Stahl Paul T. Wingfield Stephan Grzesiek |
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Affiliation: | (1) Department of Structural Biology, Biozentrum, University of Basel, CH-4056 Basel, Switzerland;(2) Department of Biological and Technological Research, c/o S.Raffaele Hospital Neuroscience Department, 20132 Milano, Italy;(3) National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, 20892-2350, U.S.A |
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Abstract: | We have recently shown that an energy penalty for the incorporation of residual tensorial constraints into molecular structure calculations can be formulated without the explicit knowledge of the Saupe orientation tensor (Moltke and Grzesiek, J. Biomol. NMR, 1999, 15, 77–82). Here we report the implementation of such an algorithm into the program X-PLOR. The new algorithm is easy to use and has good convergence properties. The algorithm is used for the structure refinement of the HIV-1 Nef protein using 252 dipolar coupling restraints. The approach is compared to the conventional penalty function with explicit knowledge of the orientation tensor's amplitude and rhombicity. No significant differences are found with respect to speed, Ramachandran core quality or coordinate precision. |
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Keywords: | orientation protein pseudo-inverse residual tensorial coupling structure calculation |
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