We developed in recent years the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS is a two-body coupled rotator model which accounts rigorously for mode-coupling between the global motion of the protein and the local motion of the spin-bearing probe and allows for general properties of the second rank tensors involved. We showed that a general tool of data analysis requires both capabilities. Several important functionalities were missing in our previous implementations of SRLS in data fitting schemes, and in some important cases, the calculations were tedious. Here we present a general implementation which allows for asymmetric local and global diffusion tensors, distinct local ordering and local diffusion frames, and features a rhombic local potential which includes Wigner matrix element terms of ranks 2 and 4. A recently developed hydrodynamics-based approach for calculating global diffusion tensors has been incorporated into the data-fitting scheme. The computational efficiency of the latter has been increased significantly through object-oriented programming within the scope of the C++ programming language, and code parallelization. A convenient graphical user interface is provided. Currently autocorrelated 15N spin relaxation data can be analyzed effectively. Adaptation to any autocorrelated and cross-correlated relaxation analysis is straightforward. New physical insight is gleaned on largely preserved local structure in solution, even in chain segments which experience slow local motion. Prospects associated with improved dynamic models, and new applications made possible by the current implementation of SRLS, are delineated.

General Theoretical/Computational Tool for Interpreting NMR Spin Relaxation in Proteins

ZERBETTO, MIRCO;POLIMENO, ANTONINO;
2009

Abstract

We developed in recent years the slowly relaxing local structure (SRLS) approach for analyzing NMR spin relaxation in proteins. SRLS is a two-body coupled rotator model which accounts rigorously for mode-coupling between the global motion of the protein and the local motion of the spin-bearing probe and allows for general properties of the second rank tensors involved. We showed that a general tool of data analysis requires both capabilities. Several important functionalities were missing in our previous implementations of SRLS in data fitting schemes, and in some important cases, the calculations were tedious. Here we present a general implementation which allows for asymmetric local and global diffusion tensors, distinct local ordering and local diffusion frames, and features a rhombic local potential which includes Wigner matrix element terms of ranks 2 and 4. A recently developed hydrodynamics-based approach for calculating global diffusion tensors has been incorporated into the data-fitting scheme. The computational efficiency of the latter has been increased significantly through object-oriented programming within the scope of the C++ programming language, and code parallelization. A convenient graphical user interface is provided. Currently autocorrelated 15N spin relaxation data can be analyzed effectively. Adaptation to any autocorrelated and cross-correlated relaxation analysis is straightforward. New physical insight is gleaned on largely preserved local structure in solution, even in chain segments which experience slow local motion. Prospects associated with improved dynamic models, and new applications made possible by the current implementation of SRLS, are delineated.
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Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/11577/2441071
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