Related ArticlesNMR structure of the protein NP_247299.1: comparison with the crystal structure.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1367-80
Authors: Jaudzems K, Geralt M, Serrano P, Mohanty B, Horst R, Pedrini B, Elsliger MA, Wilson IA, Wüthrich K
The NMR structure of the protein NP_247299.1 in solution at 313 K has been determined and is compared with the X-ray crystal structure, which was also solved in the Joint Center for Structural Genomics (JCSG) at 100 K and at 1.7 Å resolution. Both structures were obtained using the current largely automated crystallographic and solution NMR methods used by the JCSG. This paper assesses the accuracy and precision of the results from these recently established automated approaches, aiming for quantitative statements about the location of*structure variations that may arise from either one of the methods used or from the different environments in solution and in the crystal. To evaluate the*possible impact of the different software used for the crystallographic and the NMR structure determinations and analysis, the concept is introduced of reference structures, which are computed using the NMR software with input of upper-limit distance constraints derived from the molecular models representing the results of the two structure determinations. The use of this new approach is explored to quantify global differences that arise from the different methods of structure determination and analysis versus those that represent interesting local variations or dynamics. The near-identity of the protein core in the NMR and crystal structures thus provided a basis for the identification of complementary information from the two different methods. It was thus observed that locally increased crystallographic B values correlate with dynamic structural polymorphisms in solution, including that the solution state of the protein involves a slow dynamic equilibrium on a time scale of milliseconds or*slower between two ensembles of rapidly interchanging conformers that contain, respectively, the cis or trans form of the C-terminal proline and represent about 25 and 75% of the total protein.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Systematic comparison of crystal and NMR protein structures deposited in the protein data bank.
Open Biochem J. 2010;4:83-95
Authors: Sikic K, Tomic S, Carugo O
Nearly all the macromolecular three-dimensional structures deposited in Protein Data Bank were determined by either crystallographic (X-ray) or Nuclear Magnetic Resonance (NMR) spectroscopic methods. This paper reports a systematic comparison of the crystallographic and NMR results deposited in...
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[NMR paper] NMR structure of the HIV-1 regulatory protein Vpr in H2O/trifluoroethanol. Comparison
NMR structure of the HIV-1 regulatory protein Vpr in H2O/trifluoroethanol. Comparison with the Vpr N-terminal (1-51) and C-terminal (52-96) domains.
Related Articles NMR structure of the HIV-1 regulatory protein Vpr in H2O/trifluoroethanol. Comparison with the Vpr N-terminal (1-51) and C-terminal (52-96) domains.
Eur J Biochem. 2002 Aug;269(15):3779-88
Authors: Wecker K, Morellet N, Bouaziz S, Roques BP
The human immunodeficiency virus type 1, HIV-1, genome encodes a highly conserved regulatory gene product, Vpr (96 amino acids), which is...
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11-24-2010 08:58 PM
[NMR paper] Structure-based analysis of protein dynamics: comparison of theoretical results for h
Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data.
Related Articles Structure-based analysis of protein dynamics: comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data.
Proteins. 1999 Dec 1;37(4):654-67
Authors: Haliloglu T, Bahar I
An analytical approach based on Gaussian network model (GNM) is proposed for predicting the rotational dynamics of proteins. The method, previously shown to successfully...
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11-18-2010 08:31 PM
Comparison of NMR and crystal structures highlights conformational isomerism in prote
Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites.
Related Articles Comparison of NMR and crystal structures highlights conformational isomerism in protein active sites.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1393-405
Authors: Serrano P, Pedrini B, Geralt M, Jaudzems K, Mohanty B, Horst R, Herrmann T, Elsliger MA, Wilson IA, Wüthrich K
The JCSG has recently developed a protocol for systematic comparisons of high-quality crystal and NMR structures of proteins. In this...
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10-16-2010 03:56 PM
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Related Articles Comparison of NMR and crystal structures for the proteins TM1112 and TM1367.
Acta Crystallogr Sect F Struct Biol Cryst Commun. 2010 Oct 1;66(Pt 10):1381-92
Authors: Mohanty B, Serrano P, Pedrini B, Jaudzems K, Geralt M, Horst R, Herrmann T, Elsliger MA, Wilson IA, Wüthrich K
The NMR structures of the TM1112 and TM1367 proteins from Thermotoga maritima in solution at 298 K were determined following a new protocol which uses the software package UNIO for...
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[NMR paper] Crystal structure of the SH2 domain from the adaptor protein SHC: a model for peptide
Crystal structure of the SH2 domain from the adaptor protein SHC: a model for peptide binding based on X-ray and NMR data.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--linkinghub.elsevier.com-ihub-images-PubMedLink.gif Related Articles Crystal structure of the SH2 domain from the adaptor protein SHC: a model for peptide binding based on X-ray and NMR data.
J Mol Biol. 1995 Nov 17;254(1):86-95
Authors: Mikol V, Baumann G, Zurini MG, Hommel U
Src homology 2 domains (SH2) are protein molecules found within a wide variety of cytoplasmic...
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[NMR paper] Probing protein structure by solvent perturbation of NMR spectra. A comparison with p
Probing protein structure by solvent perturbation of NMR spectra. A comparison with photochemically induced dynamic nuclear polarization techniques applied to native alpha-lactalbumin.
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 Probing protein structure by solvent perturbation of NMR spectra. A comparison with photochemically induced dynamic nuclear polarization techniques applied to native alpha-lactalbumin.
Eur J Biochem. 1995 Jan 15;227(1-2):78-86...
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[NMR paper] Exploring the dynamic information content of a protein NMR structure: comparison of a
Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI.
http://www.ncbi.nlm.nih.gov/corehtml/query/egifs/http:--www3.interscience.wiley.com-aboutus-images-wiley_interscience_pubmed_logo_120x27.gif Related Articles Exploring the dynamic information content of a protein NMR structure: comparison of a molecular dynamics simulation with the NMR and X-ray structures of Escherichia coli ribonuclease HI.
Proteins. 1999 Jul 1;36(1):87-110
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