Related ArticlesInter-domain dynamics explored by paramagnetic NMR.
J Am Chem Soc. 2013 Oct 11;
Authors: Russo L, Maestre-Martínez M, Wolff S, Becker S, Griesinger C
Abstract
An ensemble-based approach is presented to explore the conformational space sampled by a multi-domain protein showing moderate inter-domain dynamics in terms of translational and rotational motions. The strategy was applied on a complex of calmodulin (CaM) with the IQ-recognition motif from the voltage-gated calcium channel Cav1.2 (IQ), which adopts three different inter-domain orientations in the crystal. The N60D mutant of calmodulin was used to collect pseudocontact shifts (pcs's) and paramagnetically induced residual dipolar couplings (RDC's) for six different lanthanide ions. Then, starting from the crystal structure, pools of conformations were generated by free MD. We found the three crystal conformations in solution, but four additional MD derived conformations had to be included into the ensemble to fulfill all the paramagnetic data and cross validate optimally against unused paramagnetic data. Alternative approaches lead to similar ensembles. Our "ensemble" approach is a simple and efficient tool to probe and describe the inter-domain dynamics and represents a general method that can be used to provide a proper ensemble description of multi-domain proteins.
PMID: 24111622 [PubMed - as supplied by publisher]
Paramagnetic tagging for protein structure and dynamics analysis
Paramagnetic tagging for protein structure and dynamics analysis
Publication year: 2011
Source:Progress in Nuclear Magnetic Resonance Spectroscopy, Volume 58, Issues 1–2</br>
Peter H.J. Keizers, Marcellus Ubbink</br>
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03-09-2012 09:16 AM
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
Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains
Narrowing the conformational space sampled by two-domain proteins with paramagnetic probes in both domains
Abstract Calmodulin is a two-domain protein which in solution can adopt a variety of conformations upon reorientation of its domains. The maximum occurrence (MO) of a set of calmodulin conformations that are representative of the overall conformational space possibly sampled by the protein, has been calculated from the paramagnetism-based restraints. These restraints were measured after inclusion of a lanthanide binding tag in the C-terminal domain to supplement the data obtained...
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08-13-2011 02:47 AM
Reaction Pathways of Proton Transfer in Hydrogen-Bonded Phenol–Carboxylate Complexes Explored by Combined UV–Vis and NMR Spectroscopy
Reaction Pathways of Proton Transfer in Hydrogen-Bonded Phenol–Carboxylate Complexes Explored by Combined UV–Vis and NMR Spectroscopy
Benjamin Koeppe, Peter M. Tolstoy and Hans-Heinrich Limbach
http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jacsat/0/jacsat.ahead-of-print/ja201113a/aop/images/medium/ja-2011-01113a_0002.gif
Journal of the American Chemical Society
DOI: 10.1021/ja201113a
http://feeds.feedburner.com/~ff/acs/jacsat?d=yIl2AUoC8zA
http://feeds.feedburner.com/~r/acs/jacsat/~4/QUQwn6dGPs4
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05-03-2011 05:18 AM
[NMR paper] Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy.
Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy.
Related Articles Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy.
J Am Chem Soc. 2005 Aug 24;127(33):11676-83
Authors: Desvaux H, Dubois L, Huber G, Quillin ML, Berthault P, Matthews BW
Wild-type bacteriophage T4 lysozyme contains a hydrophobic cavity with binding properties that have been...
[NMR paper] NMR analysis of CYP1(HAP1) DNA binding domain-CYC1 upstream activation sequence inter
NMR analysis of CYP1(HAP1) DNA binding domain-CYC1 upstream activation sequence interactions: recognition of a CGG trinucleotide and of an additional thymine 5 bp downstream by the zinc cluster and the N-terminal extremity of the protein.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--highwire.stanford.edu-icons-externalservices-pubmed-custom-oxfordjournals_final_free.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles NMR analysis of CYP1(HAP1) DNA binding domain-CYC1 upstream...
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08-22-2010 05:08 PM
Paramagnetic tagging for protein structure and dynamics analysis
Paramagnetic tagging for protein structure and dynamics analysis
Publication year: 2010
Source: Progress in Nuclear Magnetic Resonance Spectroscopy, In Press, Accepted Manuscript, Available online 12 August 2010</br>
Peter H.J., Keizers , Marcellus, Ubbink</br>
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