Related ArticlesComparing NMR and X-ray protein structure: Lindemann-like parameters and NMR disorder.
J Biomol Struct Dyn. 2017 Jul 17;:1-34
Authors: Faraggi E, Dunker K, Sussman J, Kloczkowski A
Abstract
Disordered protein chains and segments are fast becoming a major pathway for our understanding of biological function, especially in more evolved species. However, the standard definition of disordered residues: the inability to constrain them in X-ray derived structures, is not easily applied to NMR derived structures. We carry out a statistical comparison between proteins whose structure was resolved using NMR and using X-ray protocols. We start by establishing a connection between these two protocols for obtaining protein structure. We find a close statistical correspondence between NMR and X-ray structures if fluctuations inherent to the NMR protocol are taken into account. Intuitively this tends to lend support to the validity of both NMR and X-ray protocols in deriving biomolecular models that correspond to in-vivo conditions. We then establish Lindemann-like parameters for NMR derived structures and examine what order/disorder cutoffs for these parameters are most consistent with X-ray data and how consistent are they. Finally, we find critical value of $L=4$ for the best correspondence between X-ray and NMR derived order/disorder assignment, judged by maximizing the Matthews correlation, and a critical value $L=1.5$ if a balance between false positive and false negative prediction is sought. We examine a few non-conforming cases, and examine the origin of the structure derived in X-ray. This study could help in assigning meaningful disorder from NMR experiments.Running Title: NMR X-ray comparison.
PMID: 28714803 [PubMed - as supplied by publisher]
[NMR paper] Interpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH.
Interpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH.
Related Articles Interpretation of seemingly contradictory data: low NMR S2 order parameters observed in helices and high NMR S2 order parameters in disordered loops of the protein hGH at low pH.
Chemistry. 2017 May 15;:
Authors: Smith LJ, Athill R, van Gunsteren WF, Hansen N
Abstract
At low pH human growth hormone (hGH) adopts a partially folded state...
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Comparing and Contrasting Fluorotryptophan Substitutions for 19F Membrane Protein NMR Spectroscopy
Comparing and Contrasting Fluorotryptophan Substitutions for 19F Membrane Protein NMR Spectroscopy
Publication date: 3 February 2017
Source:Biophysical Journal, Volume 112, Issue 3, Supplement 1</br>
Author(s): Calem Kenward, Kyungsoo Shin, Muzaddid Sarker, Carley Bekkers, Jan K. Rainey</br>
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02-03-2017 09:55 PM
Structure from Disorder: Scripps Research Institute Scientists Find New Source ... - HealthCanal.com
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Structure from Disorder: Scripps Research Institute Scientists Find New Source ...
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Wright's laboratory and others have been studying these interactions using a technique called nuclear magnetic resonance (NMR) spectroscopy. However, E1A's intrinsic stickiness means that it tends to aggregate at NMR-friendly concentrations, rendering ...
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Structure from Disorder: Scripps Research Institute Scientists Find New Source ... - HealthCanal.com
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06-21-2013 12:16 AM
[NMR paper] Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
From Mendeley Biomolecular NMR group:
Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
Journal of biomolecular NMR (2012). Mark Berjanskii, Jianjun Zhou, Yongjie Liang, Guohui Lin, David S Wishart et al.
In protein X-ray crystallography, resolution is often used as a good indicator of structural quality. Diffraction resolution of protein crystals correlates well with the number of X-ray observables that are used in structure generation and, therefore, with protein coordinate errors. In protein NMR, there is no...
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01-02-2013 01:48 PM
[NMR paper] Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
From Mendeley Biomolecular NMR group:
Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
Journal of biomolecular NMR (2012). Mark Berjanskii, Jianjun Zhou, Yongjie Liang, Guohui Lin, David S Wishart et al.
In protein X-ray crystallography, resolution is often used as a good indicator of structural quality. Diffraction resolution of protein crystals correlates well with the number of X-ray observables that are used in structure generation and, therefore, with protein coordinate errors. In protein NMR, there is no...
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10-19-2012 10:22 AM
[NMR paper] Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
From Mendeley Biomolecular NMR group:
Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures.
Journal of biomolecular NMR (2012). Mark Berjanskii, Jianjun Zhou, Yongjie Liang, Guohui Lin, David S Wishart et al.
In protein X-ray crystallography, resolution is often used as a good indicator of structural quality. Diffraction resolution of protein crystals correlates well with the number of X-ray observables that are used in structure generation and, therefore, with protein coordinate errors. In protein NMR, there is no...
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08-24-2012 08:01 PM
Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures
Resolution-by-proxy: a simple measure for assessing and comparing the overall quality of NMR protein structures
<div class="Abstract" lang="en">Abstract <div class="normal">In protein X-ray crystallography, resolution is often used as a good indicator of structural quality. Diffraction resolution of protein crystals correlates well with the number of X-ray observables that are used in structure generation and, therefore, with protein coordinate errors. In protein NMR, there is no parameter identical to X-ray resolution. Instead, resolution is often used as a synonym of NMR model...
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06-11-2012 08:14 AM
[NMR paper] NMR structure of the LCCL domain and implications for DFNA9 deafness disorder.
NMR structure of the LCCL domain and implications for DFNA9 deafness disorder.
Related Articles NMR structure of the LCCL domain and implications for DFNA9 deafness disorder.
EMBO J. 2001 Oct 1;20(19):5347-53
Authors: Liepinsh E, Trexler M, Kaikkonen A, Weigelt J, Bányai L, Patthy L, Otting G
The LCCL domain is a recently discovered, conserved protein module named after its presence in Limulus factor C, cochlear protein Coch-5b2 and late gestation lung protein Lgl1. The LCCL domain plays a key role in the autosomal dominant human deafness...