[NMR paper] Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme.
Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme.
Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme.
J Chem Phys. 2014 Nov 14;141(18):185101
Authors: Kanematsu Y, Tachikawa M
Abstract
Multicomponent quantum mechanical (MC_QM) calculation has been extended with ONIOM (our own N-layered integrated molecular orbital + molecular mechanics) scheme [ONIOM(MC_QM:MM)] to take account of both the nuclear quantum effect and the surrounding environment effect. The authors have demonstrated the first implementation and application of ONIOM(MC_QM:MM) method for the analysis of the geometry and the isotope shift in hydrogen-bonding center of photoactive yellow protein. ONIOM(MC_QM:MM) calculation for a model with deprotonated Arg52 reproduced the elongation of O-H bond of Glu46 observed by neutron diffraction crystallography. Among the unique isotope shifts in different conditions, the model with protonated Arg52 with solvent effect reasonably provided the best agreement with the corresponding experimental values from liquid NMR measurement. Our results implied the availability of ONIOM(MC_QM:MM) to distinguish the local environment around hydrogen bonds in a biomolecule.
PMID: 25399161 [PubMed - as supplied by publisher]
[NMR paper] Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates
Use of H/D isotope effects to gather information about hydrogen bonding and hydrogen exchange rates
Publication date: Available online 11 October 2013
Source:Journal of Magnetic Resonance</br>
Author(s): Mitsuhiro Takeda , Yohei Miyanoiri , Tsutomu Terauchi , Chin-Jiun Yang , Masatsune Kainosho</br>
Polar side-chains in proteins play important roles in formingand maintaining three-dimensional structures, and thus participate invarious biological functions. Until recently, most protein NMR studieshave focused onthe non-exchangeable protons of amino acid...
nmrlearner
Journal club
0
10-11-2013 10:43 AM
Comprehensive Determination of Protein Tyrosine pKa Values for Photoactive Yellow Protein Using Indirect 13C NMR Spectroscopy
Comprehensive Determination of Protein Tyrosine pKa Values for Photoactive Yellow Protein Using Indirect 13C NMR Spectroscopy
8 February 2012
Publication year: 2012
Source:Biophysical Journal, Volume 102, Issue 3</br>
</br>
Upon blue-light irradiation, the bacterium Halorhodospira halophila is able to modulate the activity of its flagellar motor and thereby evade potentially harmful UV radiation. The 14*kDa soluble cytosolic photoactive yellow protein (PYP) is believed to be the primary mediator of this photophobic response, and yields a UV/Vis absorption spectrum that...
nmrlearner
Journal club
0
02-03-2013 10:13 AM
[NMR paper] Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of
Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation.
Related Articles Molecular dynamics simulations of photoactive yellow protein (PYP) in three states of its photocycle: a comparison with X-ray and NMR data and analysis of the effects of Glu46 deprotonation and mutation.
Eur Biophys J. 2002 Dec;31(7):504-20
Authors: Antes I, Thiel W, van Gunsteren WF
Photoactive yellow protein (PYP) is a...
nmrlearner
Journal club
0
11-24-2010 08:58 PM
[NMR paper] NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of c
NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths.
Related Articles NMR of hydrogen bonding in cold-shock protein A and an analysis of the influence of crystallographic resolution on comparisons of hydrogen bond lengths.
Protein Sci. 2001 Sep;10(9):1856-68
Authors: Alexandrescu AT, Snyder DR, Abildgaard F
Hydrogen bonding in cold-shock protein A of Escherichia coli has been investigated using long-range HNCO spectroscopy. Nearly half of the...
nmrlearner
Journal club
0
11-19-2010 08:44 PM
[NMR paper] Probing the nature of the blue-shifted intermediate of photoactive yellow protein in
Probing the nature of the blue-shifted intermediate of photoactive yellow protein in solution by NMR: hydrogen-deuterium exchange data and pH studies.
Related Articles Probing the nature of the blue-shifted intermediate of photoactive yellow protein in solution by NMR: hydrogen-deuterium exchange data and pH studies.
Biochemistry. 2000 Nov 28;39(47):14392-9
Authors: Craven CJ, Derix NM, Hendriks J, Boelens R, Hellingwerf KJ, Kaptein R
The nature of the pB intermediate of photoactive yellow protein (PYP) from Ectothiorhodospira halophila has...
nmrlearner
Journal club
0
11-19-2010 08:29 PM
[NMR paper] NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the D
NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with target RNA fragments with site-specific uridine substitutions.
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 the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with...
nmrlearner
Journal club
0
08-22-2010 03:31 PM
[NMR paper] NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the D
NMR analysis of the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with target RNA fragments with site-specific uridine substitutions.
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 the hydrogen bonding interactions of the RNA-binding domains of the Drosophila sex-lethal protein with...
nmrlearner
Journal club
0
08-22-2010 03:03 PM
The impact of hydrogen bonding on amide 1H chemical shift anisotropy studied by cross
The impact of hydrogen bonding on amide 1H chemical shift anisotropy studied by cross-correlated relaxation and liquid crystal NMR spectroscopy.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-pubmed-acs_authorchoice.jpg http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles The impact of hydrogen bonding on amide 1H chemical shift anisotropy studied by cross-correlated relaxation and liquid crystal NMR spectroscopy.
J Am Chem Soc. 2010 Aug 11;132(31):10866-75
...
Theoretical analysis of geometry and NMR isotope shift in hydrogen-bonding center of photoactive yellow protein by combination of multicomponent quantum mechanics and ONIOM scheme.
Linear Mode
