Related ArticlesNMR trial models: experiences with the colicin immunity protein Im7 and the p85alpha C-terminal SH2-peptide complex.
Acta Crystallogr D Biol Crystallogr. 2001 Oct;57(Pt 10):1397-404
Authors: Pauptit RA, Dennis CA, Derbyshire DJ, Breeze AL, Weston SA, Rowsell S, Murshudov GN
Two cases of successful molecular replacement using NMR trial models are presented. One is the crystal structure of the Escherichia coli colicin immunity protein Im7; the other is a heretofore unreported crystal structure of a specific PDGF receptor-derived peptide complex of the carboxy-terminal SH2 domain from the p85alpha subunit of human phosphatidylinositol 3-OH kinase. In both cases, molecular replacement was non-trivial. Success was achieved using trial models that consisted of an ensemble of NMR structures from which the more flexible portions had been excised. Use of maximum-likelihood refinement proved critical to be able to refine the poor starting models. The challenges typical of the use of NMR trial models in molecular replacement are discussed.
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Combining NMR ensembles and molecular dynamics simulations provides more realistic models of protein structures in solution and leads to better chemical shift prediction
Abstract While chemical shifts are invaluable for obtaining structural information from proteins, they also offer one of the rare ways to obtain information about protein dynamics. A necessary tool in transforming chemical shifts into structural and dynamic information is chemical shift prediction. In our previous work we developed a method for 4D prediction of protein 1H chemical shifts in which molecular motions, the...
nmrlearner
Journal club
0
02-11-2012 10:31 AM
[NMR paper] High-quality homology models derived from NMR and X-ray structures of E. coli protein
High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
Related Articles High-quality homology models derived from NMR and X-ray structures of E. coli proteins YgdK and Suf E suggest that all members of the YgdK/Suf E protein family are enhancers of cysteine desulfurases.
Protein Sci. 2005 Jun;14(6):1597-608
Authors: Liu G, Li Z, Chiang Y, Acton T, Montelione GT, Murray D, Szyperski T
The structural...
nmrlearner
Journal club
0
11-25-2010 08:21 PM
[NMR paper] NMR solution structure of ImB2, a protein conferring immunity to antimicrobial activi
NMR solution structure of ImB2, a protein conferring immunity to antimicrobial activity of the type IIa bacteriocin, carnobacteriocin B2.
Related Articles NMR solution structure of ImB2, a protein conferring immunity to antimicrobial activity of the type IIa bacteriocin, carnobacteriocin B2.
Biochemistry. 2004 Sep 21;43(37):11740-9
Authors: Sprules T, Kawulka KE, Vederas JC
Bacteriocins produced by lactic acid bacteria are potent antimicrobial compounds which are active against closely related bacteria. Producer strains are protected against...
nmrlearner
Journal club
0
11-24-2010 10:01 PM
[NMR paper] Conformational changes of colicin Ia channel-forming domain upon membrane binding: a
Conformational changes of colicin Ia channel-forming domain upon membrane binding: a solid-state NMR study.
Related Articles Conformational changes of colicin Ia channel-forming domain upon membrane binding: a solid-state NMR study.
Biochim Biophys Acta. 2002 Apr 12;1561(2):159-70
Authors: Huster D, Yao X, Jakes K, Hong M
Channel-forming colicins are bactericidal proteins that spontaneously insert into hydrophobic lipid bilayers. We have used magic-angle spinning solid-state nuclear magnetic resonance spectroscopy to examine the conformational...
nmrlearner
Journal club
0
11-24-2010 08:49 PM
[NMR paper] NMR studies of metal ion binding to the Zn-finger-like HNH motif of colicin E9.
NMR studies of metal ion binding to the Zn-finger-like HNH motif of colicin E9.
Related Articles NMR studies of metal ion binding to the Zn-finger-like HNH motif of colicin E9.
J Inorg Biochem. 2000 Apr;79(1-4):365-70
Authors: Hannan JP, Whittaker SB, Hemmings AM, James R, Kleanthous C, Moore GR
The 134 amino acid DNase domain of colicin E9 contains a zinc-finger-like HNH motif that binds divalent transition metal ions. We have used 1D 1H and 2D 1H-15N NMR methods to characterise the binding of Co2+, Ni2+ and Zn2+ to this protein. Data for the...
nmrlearner
Journal club
0
11-18-2010 09:15 PM
[NMR paper] NMR study of Ni2+ binding to the H-N-H endonuclease domain of colicin E9.
NMR study of Ni2+ binding to the H-N-H endonuclease domain of colicin E9.
Related Articles NMR study of Ni2+ binding to the H-N-H endonuclease domain of colicin E9.
Protein Sci. 1999 Aug;8(8):1711-3
Authors: Hannan JP, Whittaker SB, Davy SL, Kühlmann UC, Pommer AJ, Hemmings AM, James R, Kleanthous C, Moore GR
Ni2+ affinity columns are widely used for protein purification, but they carry the risk that Ni2+ ions may bind to the protein, either adventitiously or at a physiologically important site. Dialysis against ethylenediaminetetraacetic acid...
nmrlearner
Journal club
0
11-18-2010 08:31 PM
[NMR paper] Orientational distribution of alpha-helices in the colicin B and E1 channel domains:
Orientational distribution of alpha-helices in the colicin B and E1 channel domains: a one and two dimensional 15N solid-state NMR investigation in uniaxially aligned phospholipid bilayers.
Related Articles Orientational distribution of alpha-helices in the colicin B and E1 channel domains: a one and two dimensional 15N solid-state NMR investigation in uniaxially aligned phospholipid bilayers.
Biochemistry. 1998 Jan 6;37(1):16-22
Authors: Lambotte S, Jasperse P, Bechinger B
Thermolytic fragments of the channel-forming bacterial toxins colicin...
nmrlearner
Journal club
0
11-17-2010 11:06 PM
[NMR paper] The secondary structure of the colicin E3 immunity protein as studied by 1H-1H and 1H
The secondary structure of the colicin E3 immunity protein as studied by 1H-1H and 1H-15N two-dimensional NMR spectroscopy.
Related Articles The secondary structure of the colicin E3 immunity protein as studied by 1H-1H and 1H-15N two-dimensional NMR spectroscopy.
Biochemistry. 1992 Jun 23;31(24):5578-86
Authors: Yajima S, Muto Y, Yokoyama S, Masaki H, Uozumi T
By performing 1H-1H and 1H-15N two-dimensional (2D) nuclear magnetic resonance (NMR) experiments, the complete sequence-specific resonance assignment was determined for the colicin E3...