Related ArticlesWhat is the average conformation of bacteriophage T4 lysozyme in solution? A domain orientation study using dipolar couplings measured by solution NMR.
J Mol Biol. 2001 May 11;308(4):745-64
Authors: Goto NK, Skrynnikov NR, Dahlquist FW, Kay LE
Lysozyme from T4 bacteriophage is comprised of two domains that are both involved in binding substrate. Although wild-type lysozyme has been exclusively crystallized in a closed form that is similar to the peptidoglycan-bound conformation, a more open structure is thought to be required for ligand binding. To determine the relative arrangement of domains within T4 lysozyme in the solution state, dipolar couplings were measured in several different dilute liquid crystalline media by solution NMR methods. The dipolar coupling data were analyzed with a domain orientation procedure described previously that utilizes high- resolution X-ray structures. The cleft between the domains is significantly larger in the average solution structure than what is observed in the X-ray structure of the ligand-free form of the protein (approximately 17 degrees closure from solution to X-ray structures). A comparison of the solution domain orientation with X-ray-derived structures in the protein data base shows that the solution structure resembles a crystal structure obtained for the M6I mutant. Dipolar couplings were also measured on the lysozyme mutant T21C/T142C, which was oxidized to form an inter-domain disulfide bond (T4SS). In this case, the inter-domain solution structure was found to be more closed than was observed in the crystal (approximately 11 degrees). Direct refinement of lysozyme crystal structures with the measured dipolar couplings using the program CNS, establishes that this degree of closure can be accommodated whilst maintaining the inter-domain cystine bond. The differences between the average solution conformations obtained using dipolar couplings and the crystal conformations for both forms of lysozyme investigated in this study illustrate the impact that crystal packing interactions can have on the arrangement of domains within proteins and the importance of alternative methods to X-ray crystallography for evaluating inter-domain structure.
[NMR paper] Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy.
Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy.
Related Articles Dynamics of xenon binding inside the hydrophobic cavity of pseudo-wild-type bacteriophage T4 lysozyme explored through xenon-based NMR spectroscopy.
J Am Chem Soc. 2005 Aug 24;127(33):11676-83
Authors: Desvaux H, Dubois L, Huber G, Quillin ML, Berthault P, Matthews BW
Wild-type bacteriophage T4 lysozyme contains a hydrophobic cavity with binding properties that have been...
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[NMR paper] NMR solution structure of the monomeric form of the bacteriophage lambda capsid stabi
NMR solution structure of the monomeric form of the bacteriophage lambda capsid stabilizing protein gpD.
Related Articles NMR solution structure of the monomeric form of the bacteriophage lambda capsid stabilizing protein gpD.
J Biomol NMR. 2005 Apr;31(4):351-6
Authors: Iwai H, Forrer P, Plückthun A, Güntert P
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[NMR paper] NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme
NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains.
Related Articles NMR structure of Citrobacter freundii AmpD, comparison with bacteriophage T7 lysozyme and homology with PGRP domains.
J Mol Biol. 2003 Apr 4;327(4):833-42
Authors: Liepinsh E, Généreux C, Dehareng D, Joris B, Otting G
AmpD is a bacterial amidase involved in the recycling of cell-wall fragments in Gram-negative bacteria. Inactivation of AmpD leads to derepression of beta-lactamase expression, presenting a major...
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[NMR paper] Conformation of the cytoplasmic domain of phospholamban by NMR and CD.
Conformation of the cytoplasmic domain of phospholamban by NMR and CD.
Related Articles Conformation of the cytoplasmic domain of phospholamban by NMR and CD.
Mol Membr Biol. 1994 Oct-Dec;11(4):263-9
Authors: Hubbard JA, MacLachlan LK, Meenan E, Salter CJ, Reid DG, Lahouratate P, Humphries J, Stevens N, Bell D, Neville WA
Nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy have been used to characterize the conformation of the putative cytoplasmic domain of phospholamban (PLB), an oligomeric membrane-bound protein which...
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[NMR paper] Exploring the DNA binding domain of gene V protein encoded by bacteriophage M13 with
Exploring the DNA binding domain of gene V protein encoded by bacteriophage M13 with the aid of spin-labeled oligonucleotides in combination with 1H-NMR.
Related Articles Exploring the DNA binding domain of gene V protein encoded by bacteriophage M13 with the aid of spin-labeled oligonucleotides in combination with 1H-NMR.
Biochemistry. 1993 Sep 14;32(36):9407-16
Authors: Folkers PJ, van Duynhoven JP, van Lieshout HT, Harmsen BJ, van Boom JH, Tesser GI, Konings RN, Hilbers CW
The DNA binding domain of the single-stranded DNA binding protein...
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[NMR paper] The influence of hydration on the conformation of lysozyme studied by solid-state 13C
The influence of hydration on the conformation of lysozyme studied by solid-state 13C-NMR spectroscopy.
Related Articles The influence of hydration on the conformation of lysozyme studied by solid-state 13C-NMR spectroscopy.
Biopolymers. 1993 Apr;33(4):513-9
Authors: Gregory RB, Gangoda M, Gilpin RK, Su W
13C proton decoupled cross-polarization magic-angle spinning nmr spectra of lysozyme are reported as a function of hydration. Increases in hydration level enhance the resolution of the spectra, particularly in the aliphatic region, but has no...
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[NMR paper] Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spi
Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spin-spin coupling constants.
Related Articles Analysis of phi and chi 1 torsion angles for hen lysozyme in solution from 1H NMR spin-spin coupling constants.
Biochemistry. 1991 Jan 29;30(4):986-96
Authors: Smith LJ, Sutcliffe MJ, Redfield C, Dobson CM
Three-bond 3JHN alpha coupling constants have been determined for 106 residues and 3J alpha beta coupling constants have been measured for 57 residues of the 129-residue protein hen egg white lysozyme. These NMR...
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[NMR paper] Assignment of the backbone 1H and 15N NMR resonances of bacteriophage T4 lysozyme.
Assignment of the backbone 1H and 15N NMR resonances of bacteriophage T4 lysozyme.
Related Articles Assignment of the backbone 1H and 15N NMR resonances of bacteriophage T4 lysozyme.
Biochemistry. 1990 Jul 10;29(27):6341-62
Authors: McIntosh LP, Wand AJ, Lowry DF, Redfield AG, Dahlquist FW
The proton and nitrogen (15NH-H alpha-H beta) resonances of bacteriophage T4 lysozyme were assigned by 15N-aided 1H NMR. The assignments were directed from the backbone amide 1H-15N nuclei, with the heteronuclear single-multiple-quantum coherence (HSMQC)...