The effect of internal motion on the quality of a protein structure derived from nuclear magnetic resonance (NMR) cross relaxation has been investigated experimentally. Internal rotation of the tyrosine-31 ring of turkey ovomucoid third domain was found to mediate magnetization transfer; the effect led to underestimation of proton-proton distances in its immediate neighborhood. Experimental methods that distinguish pure cross relaxation from chemical exchange mediated cross relaxation were used to separate true distances from distorted ones. Uncorrected and corrected sets of distances, where the corrections took internal motion into account, each were used as input to a distance geometry program for structural modeling. Each set of distances yielded a family of similar (converged) structures. The two families of structures differed considerably (2 A) in the region of tyrosine-31. In addition, differences as large as 1 A were observed at other positions throughout the structure. These results emphasize the importance of analyzing the effects of internal motions in order to obtain more accurate NMR solution structures.
[NMR paper] Carbonyl CSA restraints from solution NMR for protein structure refinement.
Carbonyl CSA restraints from solution NMR for protein structure refinement.
Related Articles Carbonyl CSA restraints from solution NMR for protein structure refinement.
J Am Chem Soc. 2001 Nov 7;123(44):11065-6
Authors: Lipsitz RS, Tjandra N
nmrlearner
Journal club
0
11-19-2010 08:44 PM
[NMR paper] Refinement of the protein backbone angle psi in NMR structure calculations.
Refinement of the protein backbone angle psi in NMR structure calculations.
Related Articles Refinement of the protein backbone angle psi in NMR structure calculations.
J Biomol NMR. 2000 Jan;16(1):47-58
Authors: Sprangers R, Bottomley MJ, Linge JP, Schultz J, Nilges M, Sattler M
Cross-correlated relaxation rates involving the Calpha-Halpha dipolar interaction and the carbonyl (C') chemical shift anisotropy (CSA) have been measured using two complementary 3D experiments. We show that the protein backbone angle psi can be directly refined...
nmrlearner
Journal club
0
11-18-2010 09:15 PM
[NMR paper] NMR exchange broadening arising from specific low affinity protein self-association:
NMR exchange broadening arising from specific low affinity protein self-association: analysis of nitrogen-15 nuclear relaxation for rat CD2 domain 1.
Related Articles NMR exchange broadening arising from specific low affinity protein self-association: analysis of nitrogen-15 nuclear relaxation for rat CD2 domain 1.
J Biomol NMR. 1999 Aug;14(4):307-20
Authors: Pfuhl M, Chen HA, Kristensen SM, Driscoll PC
Nuclear spin relaxation monitored by heteronuclear NMR provides a useful method to probe the overall and internal molecular motion for...
nmrlearner
Journal club
0
11-18-2010 08:31 PM
[NMR paper] 800 MHz 1H NMR solution structure refinement of oxidized cytochrome c7 from Desulfuro
800 MHz 1H NMR solution structure refinement of oxidized cytochrome c7 from Desulfuromonas acetoxidans.
Related Articles 800 MHz 1H NMR solution structure refinement of oxidized cytochrome c7 from Desulfuromonas acetoxidans.
Eur J Biochem. 1998 Sep 1;256(2):261-70
Authors: Assfalg M, Banci L, Bertini I, Bruschi M, Turano P
The solution structure of Desulfuromonas acetoxidans cytochrome c7 has been refined by using 1H-NMR spectra recorded at 800 MHz and by using pseudocontact shifts in the final energy minimization procedure. The protein,...
nmrlearner
Journal club
0
11-17-2010 11:15 PM
[NMR paper] Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of
Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm.
Biochemistry. 1997 Feb 25;36(8):2132-8
...
nmrlearner
Journal club
0
08-22-2010 03:31 PM
[NMR paper] Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of
Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--pubs.acs.org-images-acspubs.jpg Related Articles Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm.
Biochemistry. 1997 Feb 25;36(8):2132-8
...
nmrlearner
Journal club
0
08-22-2010 03:03 PM
[NMR paper] Localized solution structure refinement of an F45W variant of ubiquitin using stochas
Localized solution structure refinement of an F45W variant of ubiquitin using stochastic boundary molecular dynamics and NMR distance restraints.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Localized solution structure refinement of an F45W variant of ubiquitin using stochastic boundary molecular dynamics and NMR distance restraints.
...
nmrlearner
Journal club
0
08-22-2010 03:41 AM
[NMR paper] Protein structure refinement based on paramagnetic NMR shifts: applications to wild-t
Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www.pubmedcentral.nih.gov-corehtml-pmc-pmcgifs-pubmed-pmc.gif Related Articles Protein structure refinement based on paramagnetic NMR shifts: applications to wild-type and mutant forms of cytochrome c.
Protein Sci. 1995 Feb;4(2):296-305
...
Refinement of the NMR solution structure of a protein to remove distortions arising f
Linear Mode
