Related ArticlesAn NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose.
Proteins. 2020 01;88(1):82-93
Authors: Turupcu A, Bowen AM, Di Paolo A, Matagne A, Oostenbrink C, Redfield C, Smith LJ
Abstract
The X-ray structure of lysozyme from bacteriophage lambda (? lysozyme) in complex with the inhibitor hexa-N-acetylchitohexaose (NAG6) (PDB: 3D3D) has been reported previously showing sugar units from two molecules of NAG6 bound in the active site. One NAG6 is bound with four sugar units in the ABCD sites and the other with two sugar units in the E'F' sites potentially representing the cleavage reaction products; each NAG6 cross links two neighboring ? lysozyme molecules. Here we use NMR and MD simulations to study the interaction of ? lysozyme with the inhibitors NAG4 and NAG6 in solution. This allows us to study the interactions within the complex prior to cleavage of the polysaccharide. 1 HN and 15 N chemical shifts of ? lysozyme resonances were followed during NAG4/NAG6 titrations. The chemical shift changes were similar in the two titrations, consistent with sugars binding to the cleft between the upper and lower domains; the NMR data show no evidence for simultaneous binding of a NAG6 to two ? lysozyme molecules. Six 150 ns MD simulations of ? lysozyme in complex with NAG4 or NAG6 were performed starting from different conformations. The simulations with both NAG4 and NAG6 show stable binding of sugars across the D/E active site providing low energy models for the enzyme-inhibitor complexes. The MD simulations identify different binding subsites for the 5th and 6th sugars consistent with the NMR data. The structural information gained from the NMR experiments and MD simulations have been used to model the enzyme-peptidoglycan complex.
[NMR paper] The Dynamics of Lysozyme from Bacteriophage Lambda in Solution Probed by NMR and MD Simulations.
The Dynamics of Lysozyme from Bacteriophage Lambda in Solution Probed by NMR and MD Simulations.
The Dynamics of Lysozyme from Bacteriophage Lambda in Solution Probed by NMR and MD Simulations.
Chembiochem. 2013 Jun 25;
Authors: Smith LJ, Bowen AM, Di Paolo A, Matagne A, Redfield C
Abstract
(15) N NMR relaxation studies, analyses of NMR data to include chemical shifts, residual dipolar couplings (RDC), NOEs and H(N) -H(?) coupling constants, and molecular dynamics (MD) simulations have been used to characterise the behaviour of...
nmrlearner
Journal club
0
06-27-2013 02:10 PM
[NMR paper] NMR assignment of the gpU tail protein from lambda bacteriophage.
NMR assignment of the gpU tail protein from lambda bacteriophage.
Related Articles NMR assignment of the gpU tail protein from lambda bacteriophage.
J Biomol NMR. 2005 May;32(1):91-2
Authors: Edmonds L, Thirumoorthy R, Liu A, Davidson A, Donaldson L
nmrlearner
Journal club
0
11-25-2010 08:21 PM
[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
nmrlearner
Journal club
0
11-25-2010 08:21 PM
[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...
nmrlearner
Journal club
0
11-24-2010 09:01 PM
[NMR paper] What is the average conformation of bacteriophage T4 lysozyme in solution? A domain o
What is the average conformation of bacteriophage T4 lysozyme in solution? A domain orientation study using dipolar couplings measured by solution NMR.
Related Articles What 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...
nmrlearner
Journal club
0
11-19-2010 08:32 PM
[NMR paper] NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of
NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif.
Related Articles NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine-rich motif.
Cell. 1998 Apr 17;93(2):289-99
Authors: Legault P, Li J, Mogridge J, Kay LE, Greenblatt J
The structure of the complex formed by the arginine-rich motif of the transcriptional antitermination protein N of phage lambda and boxB RNA was determined by heteronuclear magnetic resonance...
nmrlearner
Journal club
0
11-17-2010 11:06 PM
[NMR paper] A study of D52S hen lysozyme-GlcNAc oligosaccharide complexes by NMR spectroscopy and
A study of D52S hen lysozyme-GlcNAc oligosaccharide complexes by NMR spectroscopy and electrospray mass spectrometry.
Related Articles A study of D52S hen lysozyme-GlcNAc oligosaccharide complexes by NMR spectroscopy and electrospray mass spectrometry.
FEBS Lett. 1992 Jan 20;296(2):153-7
Authors: Lumb KJ, Aplin RT, Radford SE, Archer DB, Jeenes DJ, Lambert N, MacKenzie DA, Dobson CM, Lowe G
The production of a mutant hen lysozyme is described in which Asp-52, one of the catalytically important residues, is replaced by Ser. The mutant enzyme...
nmrlearner
Journal club
0
08-21-2010 11:41 PM
[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)...
An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose.
Linear Mode
