Related ArticlesSolution structural characteristics of cyanometmyoglobin: resonance assignment of heme cavity residues by two-dimensional NMR.
Biochemistry. 1990 Feb 13;29(6):1545-56
Authors: Emerson SD, La Mar G
Steady-state nuclear Overhauser effects (NOE), two-dimensional (2D) nuclear Overhauser effect spectroscopy (NOESY), and 2D spin correlation spectroscopy (COSY) have been applied to the fully paramagnetic low-spin, cyanide-ligated complex of sperm whale ferric myoglobin to assign the majority of the heme pocket side-chain proton signals and the remainder of the heme signals. It is shown that the 2D NOESY map reveals essentially all dipolar connectivities observed in ordinary 1D NOE experiments and expected on the basis of crystal coordinates, albeit often more weakly than in a diamagnetic analogue. For extremely broad (approximately 600-Hz) and rapidly relaxing (Tf1 approximately 3 ms) signals which show no NEOSY peaks, we demonstrate that conventional steady-state NOEs obtained under very rapid pulsing conditions still allow detection of the critical dipoar connectivities that allow unambiguous assignments. The COSY map was found to be generally less useful for the hyperfine-shifted residues, with cross peaks detected only for protons greater than 6 A from the iron. Nevertheless, numerous critical COSY cross peaks between strongly hyperfine-shifted peaks were resolved and assigned. In all, 95% (53 of 56 signals) of the total proton sets within approximately 7.5 A of the iron, the region experiencing the strongest hyperfine shifts and paramagnetic relaxation, are now unambiguously assigned. Hence it is clear that the 2D methods can be profitably applied to paramagnetic proteins. The scope and limitations of such application are discussed. The resulting hyperfine shift pattern for the heme confirmed expectations based on model compounds. In contrast, while exhibiting fortuitous 1H NMR spectral similarities, a major discrepancy was uncovered between the hyperfine shift pattern of the axially bound (F8 histidyl) imidazole in the protein and that of the imidazole in a relevant model compound [Chacko, V.P., & La Mar, G. N. (1982) J. Am. Chem. Soc. 104, 7002-7007], providing direct evidence for a protein-based deformation of axial bonding in the protein.
Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data
Protein side-chain resonance assignment and NOE assignment using RDC-defined backbones without TOCSY data
Abstract One bottleneck in NMR structure determination lies in the laborious and time-consuming process of side-chain resonance and NOE assignments. Compared to the well-studied backbone resonance assignment problem, automated side-chain resonance and NOE assignments are relatively less explored. Most NOE assignment algorithms require nearly complete side-chain resonance assignments from a series of through-bond experiments such as HCCH-TOCSY or HCCCONH. Unfortunately, these TOCSY...
nmrlearner
Journal club
0
06-27-2011 04:30 AM
[NMR paper] High-throughput 3D structural homology detection via NMR resonance assignment.
High-throughput 3D structural homology detection via NMR resonance assignment.
Related Articles High-throughput 3D structural homology detection via NMR resonance assignment.
Proc IEEE Comput Syst Bioinform Conf. 2004;:278-89
Authors: Langmead CJ, Donald BR
One goal of the structural genomics initiative is the identification of new protein folds. Sequence-based structural homology prediction methods are an important means for prioritizing unknown proteins for structure determination. However, an important challenge remains: two highly...
nmrlearner
Journal club
0
11-24-2010 09:25 PM
[NMR paper] An efficient high-throughput resonance assignment procedure for structural genomics a
An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR.
Related Articles An efficient high-throughput resonance assignment procedure for structural genomics and protein folding research by NMR.
Biochemistry. 2001 Dec 11;40(49):14727-35
Authors: Bhavesh NS, Panchal SC, Hosur RV
Sequence specific resonance assignment is the primary requirement for all investigations of proteins by NMR methods. In the present postgenomic era where structural genomics and protein folding have...
nmrlearner
Journal club
0
11-19-2010 08:44 PM
[NMR paper] NMR evidence for slow collective motions in cyanometmyoglobin.
NMR evidence for slow collective motions in cyanometmyoglobin.
Related Articles NMR evidence for slow collective motions in cyanometmyoglobin.
Nat Struct Biol. 1997 Apr;4(4):292-7
Authors: Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH
Residual dipolar couplings observed in NMR spectra at very high magnetic fields have been measured to a high degree of accuracy for the paramagnetic protein cyanometmyoglobin. Deviations of these measurements from predictions based on available crystallographic and solution structures are largely systematic...
nmrlearner
Journal club
0
08-22-2010 03:31 PM
[NMR paper] NMR evidence for slow collective motions in cyanometmyoglobin.
NMR evidence for slow collective motions in cyanometmyoglobin.
Related Articles NMR evidence for slow collective motions in cyanometmyoglobin.
Nat Struct Biol. 1997 Apr;4(4):292-7
Authors: Tolman JR, Flanagan JM, Kennedy MA, Prestegard JH
Residual dipolar couplings observed in NMR spectra at very high magnetic fields have been measured to a high degree of accuracy for the paramagnetic protein cyanometmyoglobin. Deviations of these measurements from predictions based on available crystallographic and solution structures are largely systematic...
nmrlearner
Journal club
0
08-22-2010 03:03 PM
[NMR paper] NMR study of the structural characteristics of variants of yeast iso-1-cytochrome c i
NMR study of the structural characteristics of variants of yeast iso-1-cytochrome c in which unvaried aromatic residues have been substituted.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles NMR study of the structural characteristics of variants of yeast iso-1-cytochrome c in which unvaried aromatic residues have been substituted.
Eur J Biochem. 1991 Dec 5;202(2):339-47
Authors: Thurgood AG, Davies AM, Greenwood C, Mauk AG, Smith M,...
nmrlearner
Journal club
0
08-21-2010 11:12 PM
[NMR paper] NMR study of the structural characteristics of variants of yeast iso-1-cytochrome c i
NMR study of the structural characteristics of variants of yeast iso-1-cytochrome c in which unvaried aromatic residues have been substituted.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_FREE_120x27.gif Related Articles NMR study of the structural characteristics of variants of yeast iso-1-cytochrome c in which unvaried aromatic residues have been substituted.
Eur J Biochem. 1991 Dec 5;202(2):339-47
Authors: Thurgood AG, Davies AM, Greenwood C, Mauk AG, Smith M,...