[en] The X-ray structure of lysozyme from bacteriophage lambda (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 lambda lysozyme molecules. Here we use NMR and MD simulations to study the interaction of lambda 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) H(N) and (15) N chemical shifts of lambda 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 lambda lysozyme molecules. Six 150 ns MD simulations of lambda 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.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Turupcu, Aysegul
Bowen, Alice M.
Di Paolo, Alexandre
Matagne, André ; Université de Liège - ULiège > Département des sciences de la vie > Enzymologie et repliement des protéines
Oostenbrink, Chris
Redfield, Christina
Smith, Lorna J.
Language :
English
Title :
An NMR and MD study of complexes of bacteriophage lambda lysozyme with tetra- and hexa-N-acetylchitohexaose.
Publication date :
2019
Journal title :
Proteins
ISSN :
0887-3585
eISSN :
1097-0134
Publisher :
Wiley-Liss Inc, United States - New York
Volume :
88
Issue :
1
Pages :
82-93
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
(c) 2019 The Authors. Proteins: Structure, Function, and Bioinformatics published by Wiley Periodicals, Inc.
Holtje JV. From growth to autolysis - the murein hydrolases in Escherichia-Coli. Arch Microbiol. 1995;164:243-254.
Bienkowskaszewczyk K, Lipinska B, Taylor A. The R-gene product of bacteriophage lamda is the murein transglycosylase. Mol Gen Genet. 1981;184:111-114.
Evrard C, Fastrez J, Declercq JP. Crystal structure of the lysozyme from bacteriophage lambda and its relationship with V and C-type lysozymes. J Mol Biol. 1998;276:151-164.
Smith LJ, Bowen AM, Di Paolo A, Matagne A, Redfield C. The dynamics of lysozyme from bacteriophage lambda in solution probed by NMR and MD simulations. Chembiochem. 2013;14:1780-1788.
Smith LJ, van Gunsteren WF, Hansen N. Characterization of the flexible lip regions in bacteriophage lambda lysozyme using MD simulations. Eur Biophys J. 2015;44:235-247.
Leung AKW, Duewel HS, Honek JF, Berghuis AM. Crystal structure of the lytic transglycosylase from bacteriophage lambda in complex with hexa-N-acetylchitohexaose. Biochemistry. 2001;40:5665-5673.
Di Paolo A, Duval V, Matagne A, Redfield C. Backbone H-1, C-13, and N-15 resonance assignments for lysozyme from bacteriophage lambda. Biomol NMR Assign. 2010;4:111-114.
Vranken WF, Boucher W, Stevens TJ, et al. The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins. 2005;59:687-696.
Williamson MP. Using chemical shift perturbation to characterise ligand binding. Prog Nucl Magn Reson Spectrosc. 2013;73:1-16.
Schumann FH, Riepl H, Maurer T, Gronwald W, Neidig KP, Kalbitzer HR. Combined chemical shift changes and amino acid specific chemical shift mapping of protein-protein interactions. J Biomol NMR. 2007;39:275-289.
Schmid N, Christ CD, Christen M, Eichenberger AP, van Gunsteren WF. Architecture, implementation and parallelisation of the GROMOS software for biomolecular simulation. Comput Phys Commun. 2012;183:890-903.
Reif MM, Hunenberger PH, Oostenbrink C. New interaction parameters for charged amino acid side chains in the gromos force field. J Chem Theory Comput. 2012;8:3705-3723.
Pol-Fachin L, Rusu VH, Verli H, Lins RD. GROMOS 53A6(GLYC), an improved GROMOS force field for hexopyranose-based carbohydrates. J Chem Theory Comput. 2012;8:4681-4690.
Turupcu A, Oostenbrink C. Modeling of oligosaccharides within glycoproteins from free-energy landscapes. J Chem Inf Model. 2017;57:2222-2236.
The Pymol Molecular Graphics System, Version 1.6.0.0 Schrödinger, LLC.
Berendsen HJC, Postma JPM, van Gunsteren WF, Hermans J. Interaction models for water in relation to protein hydration. In: Pullman B, ed. Intermolecular Forces. Dordrecht, The Netherlands: Reidel; 1981:331-342.
Berendsen HJC, Postma JPM, van Gunsteren WF, Dinola A, Haak JR. Molecular dynamics with coupling to an external bath. J Chem Phys. 1984;81:3684-3690.
Hockney RW. Potential calculation and some applications. Methods Comput Phys. 1970;9:135-211.
Heinz TN, Hunenberger PH. A fast pairlist-construction algorithm for molecular simulations under periodic boundary conditions. J Comput Chem. 2004;25:1474-1486.
Tironi IG, Sperb R, Smith PE, van Gunsteren WF. A generalised reaction field method for molecular dynamics simulations. J Chem Phys. 1995;102:5451-5459.
Heinz TN, van Gunsteren WF, Hunenberger PH. Comparison of four methods to compute the dielectric permittivity of liquids from molecular dynamics simulations. J Chem Phys. 2001;115:1125-1136.
Ryckaert JP, Ciccotti G, Berendsen HJC. Numerical integration of cartesian equations of motion of a system with constraints - molecular dynamics of n-alkanes. J Comput Phys. 1977;23:327-341.
Eichenberger AP, Allison JR, Dolenc J, et al. GROMOS ++ software for the analysis of biomolecular simulation trajectories. J Chem Theory Comput. 2011;7:3379-3390.
Kabsch W, Sander C. Dictionary of protein secondary structure—pattern recognition of hydrogen bonded and geometrical features. Biopolymers. 1983;22:2577-2637.
van Gunsteren WF, Allison JR, Daura X, et al. Deriving structural information from experimentally measured data on biomolecules. Angew Chem Int Ed. 2016;55:15990-16010.
Arimori T, Kawamoto N, Shinya S, et al. Crystal structures of the catalytic domain of a novel glycohydrolase family 23 chitinase from ralstonia sp A-471 reveals a unique arrangement of the catalytic residues for inverting chitin hydrolysis. J Biol Chem. 2013;288:18696-18706.
Prlic A, Bliven S, Rose PW, et al. Pre-calculated protein structure alignments at the RSCB PDB website. Bioinformatics. 2010;26:2983-2985.
Andreeva A, Howorth D, Chandonia JM, et al. Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res. 2008;36:D419-D425.
Ye YZ, Godzik A. Flexible structure alignment by chaining aligned fragment pairs allowing twists. Bioinformatics. 2003;19:Ii246-Ii255.
Berman HM, Westbrook J, Feng Z, et al. The Protein Data Bank. Nucleic Acids Res. 2000;28:235-242.
Kim SJ, Chang J, Singh M. Peptidoglycan architecture of gram-positive bacteria by solid-state NMR. BBA-Biomembranes. 2015;1848:350-362.
Schumann P. Peptidoglycan structure. In: Rainey F, Oren A, eds. Methods in Microbiology, Vol 38: Taxonomy of Prokaryotes. Vol 38; London: Academic Press. 2011:101-129.
Meroueh SO, Bencze KZ, Hesek D, et al. Three-dimensional structure of the bacterial cell wall peptidoglycan. Proc Natl Acad Sci U S A. 2006;103:4404-4409.
Matter H, Szilagyi L, Forgo P, Marinic Z, Klaic B. Structure and dynamics of a peptidoglycan monomer in aqueous solution using NMR spectroscopy and simulated annealing calculations. J Am Chem Soc. 1997;119:2212-2223.
Rao R, Qasba PK, Balaji PV, Chandrasekaran R. Conformation of carbohydrates. Amsterdam, The Netherlands: Harwood Academuic Publishers; 1998.
Nakimbugwe D, Masschalck B, Deckers D, Callewaert L, Aertsen A, Michiels CW. Cell wall substrate specificity of six different lysozymes and lysozyme inhibitory activity of bacterial extracts. FEMS Microbiol Lett. 2006;259:41-46.
Cho S, Wang Q, Swaminathan CP, et al. Structural insights into the bactericidal mechanism of human peptidoglycan recognition proteins. Proc Natl Acad Sci U S A. 2007;104:8761-8766.
Kuroki R, Weaver LH, Matthews BW. A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme. Science. 1993;262:2030-2033.
Anderson WF, Grutter MG, Remington SJ, Weaver LH, Matthews BW. Crystallographic determination of the mode of binding of oligosaccharides to bacteriophage-T4 lysozyme—implications for the mechanism of catalysis. J Mol Biol. 1981;147:523-543.