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      AI-designed NMR spectroscopy RF pulses for fast acquisition at high and ultra-high magnetic fields

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          Abstract

          Nuclear magnetic resonance (NMR) spectroscopy is a powerful high-resolution tool for characterizing biomacromolecular structure, dynamics, and interactions. However, the lengthy longitudinal relaxation of the nuclear spins significantly extends the total experimental time, especially at high and ultra-high magnetic field strengths. Although longitudinal relaxation-enhanced techniques have sped up data acquisition, their application has been limited by the chemical shift dispersion. Here we combined an evolutionary algorithm and artificial intelligence to design 1H and 15N radio frequency (RF) pulses with variable phase and amplitude that cover significantly broader bandwidths and allow for rapid data acquisition. We re-engineered the basic transverse relaxation optimized spectroscopy experiment and showed that the RF shapes enhance the spectral sensitivity of well-folded proteins up to 180 kDa molecular weight. These RF shapes can be tailored to re-design triple-resonance experiments for accelerating NMR spectroscopy of biomacromolecules at high fields.

          Abstract

          Here, the authors utilized an evolutionary algorithm and artificial intelligence to design new basic 2D biomolecular NMR experiments to accelerate the acquisition of large biomolecular spectra. The method enables recording the spectra of poorly soluble or unstable macromolecules and analyzing the kinetics of biomolecular aggregation and oligomerization. The authors laid the foundation for accelerating multidimensional NMR experiments at high and ultra-high magnetic fields.

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          Most cited references42

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          NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

          The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.
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            NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

            Summary: SPARKY (Goddard and Kneller, SPARKY 3) remains the most popular software program for NMR data analysis, despite the fact that development of the package by its originators ceased in 2001. We have taken over the development of this package and describe NMRFAM-SPARKY, which implements new functions reflecting advances in the biomolecular NMR field. NMRFAM-SPARKY has been repackaged with current versions of Python and Tcl/Tk, which support new tools for NMR peak simulation and graphical assignment determination. These tools, along with chemical shift predictions from the PACSY database, greatly accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format interconversion for interfacing with a variety of web servers including, PECAN , PINE, TALOS-N, CS-Rosetta, SHIFTX2 and PONDEROSA-C/S. Availability and implementation: The software package, along with binary and source codes, if desired, can be downloaded freely from http://pine.nmrfam.wisc.edu/download_packages.html. Instruction manuals and video tutorials can be found at http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm. Contact: whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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              Optimal control of coupled spin dynamics: design of NMR pulse sequences by gradient ascent algorithms.

              In this paper, we introduce optimal control algorithm for the design of pulse sequences in NMR spectroscopy. This methodology is used for designing pulse sequences that maximize the coherence transfer between coupled spins in a given specified time, minimize the relaxation effects in a given coherence transfer step or minimize the time required to produce a given unitary propagator, as desired. The application of these pulse engineering methods to design pulse sequences that are robust to experimentally important parameter variations, such as chemical shift dispersion or radiofrequency (rf) variations due to imperfections such as rf inhomogeneity is also explained.
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                Author and article information

                Contributors
                vegli001@umn.edu
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                12 July 2023
                12 July 2023
                2023
                : 14
                : 4144
                Affiliations
                [1 ]GRID grid.17635.36, ISNI 0000000419368657, Department of Biochemistry, Molecular Biology & Biophysics and Department of Chemistry, , University of Minnesota, ; Minneapolis, MN 55455 USA
                [2 ]GRID grid.4708.b, ISNI 0000 0004 1757 2822, Present Address: Department of Chemistry, , University of Milan, ; 20133 Milan, Italy
                Author information
                http://orcid.org/0000-0002-1374-2797
                http://orcid.org/0000-0001-6957-6743
                http://orcid.org/0000-0002-2795-6964
                Article
                39581
                10.1038/s41467-023-39581-4
                10338431
                37438347
                f1b46a3e-da83-4fe2-8bee-f46cd700aa52
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 4 May 2023
                : 20 June 2023
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000002, U.S. Department of Health & Human Services | National Institutes of Health (NIH);
                Award ID: HL144130
                Award ID: GM121735
                Award Recipient :
                Funded by: U.S. Department of Health & Human Services | National Institutes of Health (NIH)
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                © Springer Nature Limited 2023

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