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Title: Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences

Abstract

Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with bothmore » sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.« less

Authors:
; ; ;  [1];  [1]
  1. University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino (Finland) (Italy)
Publication Date:
OSTI Identifier:
22347708
Resource Type:
Journal Article
Journal Name:
Acta Crystallographica. Section D: Biological Crystallography
Additional Journal Information:
Journal Volume: 70; Journal Issue: Pt 4; Other Information: PMCID: PMC4306559; PMID: 24699641; PUBLISHER-ID: dz5299; OAI: oai:pubmedcentral.nih.gov:4306559; Copyright (c) Rinaldelli et al. 2014; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); Journal ID: ISSN 0907-4449
Country of Publication:
Denmark
Language:
English
Subject:
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND SUPERFLUIDITY; ATOMS; COUPLING; COUPLINGS; CRYSTALS; GEOMETRY; MATHEMATICAL SOLUTIONS; METALS; MOLECULES; NUCLEAR MAGNETIC RESONANCE; ORIENTATION; RELIABILITY; SOLIDS; SOLUTIONS; X RADIATION

Citation Formats

Rinaldelli, Mauro, Ravera, Enrico, Calderone, Vito, Parigi, Giacomo, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Murshudov, Garib N., E-mail: garib@mrc-lmb.cam.ac.uk, Luchinat, Claudio, and University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences. Denmark: N. p., 2014. Web. doi:10.1107/S1399004713034160.
Rinaldelli, Mauro, Ravera, Enrico, Calderone, Vito, Parigi, Giacomo, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Murshudov, Garib N., E-mail: garib@mrc-lmb.cam.ac.uk, Luchinat, Claudio, & University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino. Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences. Denmark. https://doi.org/10.1107/S1399004713034160
Rinaldelli, Mauro, Ravera, Enrico, Calderone, Vito, Parigi, Giacomo, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Murshudov, Garib N., E-mail: garib@mrc-lmb.cam.ac.uk, Luchinat, Claudio, and University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino. 2014. "Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences". Denmark. https://doi.org/10.1107/S1399004713034160.
@article{osti_22347708,
title = {Simultaneous use of solution NMR and X-ray data in REFMAC5 for joint refinement/detection of structural differences},
author = {Rinaldelli, Mauro and Ravera, Enrico and Calderone, Vito and Parigi, Giacomo and University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino and Murshudov, Garib N., E-mail: garib@mrc-lmb.cam.ac.uk and Luchinat, Claudio and University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino},
abstractNote = {Paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and diamagnetic residual dipolar couplings can now be used in the program REFMAC5 from CCP4 as structural restraints together with X-ray crystallographic data. These NMR restraints can reveal differences between solid state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. The program REFMAC5 from CCP4 was modified to allow the simultaneous use of X-ray crystallographic data and paramagnetic NMR data (pseudocontact shifts and self-orientation residual dipolar couplings) and/or diamagnetic residual dipolar couplings. Incorporation of these long-range NMR restraints in REFMAC5 can reveal differences between solid-state and solution conformations of molecules or, in their absence, can be used together with X-ray crystallographic data for structural refinement. Since NMR and X-ray data are complementary, when a single structure is consistent with both sets of data and still maintains reasonably ‘ideal’ geometries, the reliability of the derived atomic model is expected to increase. The program was tested on five different proteins: the catalytic domain of matrix metalloproteinase 1, GB3, ubiquitin, free calmodulin and calmodulin complexed with a peptide. In some cases the joint refinement produced a single model consistent with both sets of observations, while in other cases it indicated, outside the experimental uncertainty, the presence of different protein conformations in solution and in the solid state.},
doi = {10.1107/S1399004713034160},
url = {https://www.osti.gov/biblio/22347708}, journal = {Acta Crystallographica. Section D: Biological Crystallography},
issn = {0907-4449},
number = Pt 4,
volume = 70,
place = {Denmark},
year = {Tue Apr 01 00:00:00 EDT 2014},
month = {Tue Apr 01 00:00:00 EDT 2014}
}