Related ArticlesWhat are the methodological and theoretical prospects for paramagnetic NMR in structural biology? A glimpse into the crystal ball.
J Magn Reson. 2019 09;306:173-179
Authors: Ravera E, Parigi G, Luchinat C
Abstract
NMR spectroscopy is very sensitive to the presence of unpaired electrons, which perturb the NMR chemical shifts, J splittings and nuclear relaxation rates. These paramagnetic effects have attracted increasing attention over the last decades, and their use is expected to increase further in the future because they can provide structural information not easily achievable with other techniques. In fact, paramagnetic data provide long range structural restraints that can be used to assess the accuracy of crystal structures in solution and to improve them by simultaneous refinements with the X-ray data. They are also precious for obtaining information on the conformational variability of biomolecular systems, possibly in conjunction with SAXS and/or DEER data. We foresee that new tools will be developed in the next years for the simultaneous analysis of the paramagnetic data with data obtained from different techniques, in order to take advantage synergistically of the information content of all of them. Of course, the use of the paramagnetic data for structural purposes requires the knowledge of the relationship between these data and the molecular coordinates. Recently, the equations commonly used, dating back to half a century ago, have been questioned by first principle quantum chemistry calculations. Our prediction is that further theoretical/computational improvements will essentially confirm the validity of the old semi-empirical equations for the analysis of the experimental paramagnetic data.
Molecular details of protein reveal glimpse into how kidney stones form - Phys.Org
Molecular details of protein reveal glimpse into how kidney stones form - Phys.Org
Molecular details of protein reveal glimpse into how kidney stones form Phys.OrgKidney stones—solid, pebble-like grit that forms when too much of certain minerals like calcium are in the urine—can strike men, women, and increasingly, ...
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01-07-2019 05:49 AM
[NMR paper] Beyond Structural Biology to Functional Biology: Solid-State NMR Experiments and Strategies for Understanding the M2 Proton Channel Conductance.
Beyond Structural Biology to Functional Biology: Solid-State NMR Experiments and Strategies for Understanding the M2 Proton Channel Conductance.
Related Articles Beyond Structural Biology to Functional Biology: Solid-State NMR Experiments and Strategies for Understanding the M2 Proton Channel Conductance.
J Phys Chem B. 2017 Apr 20;:
Authors: Qin H, Miao Y, Cross TA, Fu R
Abstract
In terms of structural biology, solid-state NMR experiments and strategies have been well established for resonance assignments leading to the...
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04-21-2017 03:35 PM
Crystal and NMR structures of a Trp-cage [Biophysics and Computational Biology]
Crystal and NMR structures of a Trp-cage
Scian, M., Lin, J. C., Le Trong, I., Makhatadze, G. I., Stenkamp, R. E., Andersen, N. H....
Date: 2012-07-31
To provide high-resolution X-ray crystallographic structures of a peptide with the Trp-cage fold, we prepared a cyclized version of this motif. Cyclized Trp-cage is remarkably stable and afforded two crystal forms suitable for X-ray diffraction. The resulting higher resolution crystal structures validate the prior NMR models and provide explanations for experimental observations that could not be rationalized by NMR structural data,...
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07-31-2012 08:27 PM
Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR.
Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR.
Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR.
Proc Natl Acad Sci U S A. 2011 May 31;108(22):E169-76
Authors: Takayama Y, Clore GM
Abstract
The intra- and intermolecular translocation processes whereby the bi-domain transcription factor Oct1 searches for its specific DNA target site have been investigated by...
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08-25-2011 07:02 AM
Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR [Biophysics and Computational Biology]
Intra- and intermolecular translocation of the bi-domain transcription factor Oct1 characterized by liquid crystal and paramagnetic NMR
Takayama, Y., Clore, G. M....
Date: 2011-05-31
The intra- and intermolecular translocation processes whereby the bi-domain transcription factor Oct1 searches for its specific DNA target site have been investigated by residual dipolar coupling (RDC) and paramagnetic relaxation enhancement (PRE) measurements. The RDC data show that the orientation of the POUS and POUHD domains of Oct1 relative to the long axis of the DNA is the same for specific and...
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05-31-2011 11:41 PM
[NMRwiki tweet] nmrwiki: Software to calculate theoretical second moment from crystal structure data?
nmrwiki: Software to calculate theoretical second moment from crystal structure data?http://qa.nmrwiki.org/question/180/
nmrwiki: Software to calculate theoretical second moment from crystal structure data?http://qa.nmrwiki.org/question/180/
Source: NMRWiki tweets
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09-29-2010 10:24 AM
[Question from NMRWiki Q&A forum] Free program to calculate the theoretical second moment from crystal structure data?
Free program to calculate the theoretical second moment from crystal structure data?
Does anyone know of a free, available program I can use to calculate the theoretical second moment from crystal structure data? I was only able to find one online, written in a mix of FORTRAN 77/90. The current limitations of the program can't accommodate my system (big unit cell and lots of atoms), and FORTRAN coding really isn't my fortay.
Ideally, the program would be able to simulate second moment(s) by defining specific rotational axes, and modeling different rotational rates and hopping angles...
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09-29-2010 10:24 AM
Prospects for lanthanides in structural biology by NMR
Prospects for lanthanides in structural biology by NMR
Gottfried Otting
Journal of Biomolecular NMR; 2008; 42(1); pp 1-9
Abstract:
The advent of different lanthanide-binding reagents has made site-specific labelling of proteins with paramagnetic lanthanides a viable proposition. This brings many powerful techniques originally established and demonstrated for paramagnetic metalloproteins into the mainstream of structural biology. The promise is that, by exploiting the long-range effects of paramagnetism, lanthanide labelling will allow the study of larger proteins and protein–ligand...
What are the methodological and theoretical prospects for paramagnetic NMR in structural biology? A glimpse into the crystal ball.
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