Structure determination of turkey egg-white lysozyme using Laue diffraction data

Abstract

The three-dimensional structure of turkey egg-white lysozyme (TEWL) has been solved and refined at 2.5 A~ resolution using X-ray data collected by the Laue method. This is the first protein structure determination undertaken using Laue diffraction data. A re-examination of the existing structure of TEWL was necessary when attempts to refine an atomic model based on the C,~ positions in the Protein Data Bank (entry 1LZ2) failed. The correct orientation and position of the turkey lysozyme molecules within the crystallographic unit cell were determined by molecular replacement using a refined model of the homologous hen egg-white lysozyme crystal structure. After modification of the model to reflect the differences in amino-acid sequence between the chicken and turkey enzymes, the structure was subjected to crystallographic refinement using the simulated-annealing refinement technique and conventional least-squares refinement. This yielded a final residual of R = 20.7%. This crystal form is of potential interest for time-resolved crystallographic studies since the amino-acid residues involved in

Comparative Protein Structure Modeling Using MODELLER

“…Comparative modeling is often an efficient way to obtain useful information about the protein of interest. For example, comparative models can be helpful in designing mutants to test hypotheses about the protein's function (Wu et al, 1999;Vernal et al, 2002); in identifying active and binding sites (Sheng et al, 1996); in searching for, designing, and improving ligand binding strength for a given binding site (Ring et al, 1993;Li et al, 1996;Selzer et al, 1997;Enyedy et al, 2001;Que et al, 2002); modeling substrate specificity (Xu et al, 1996); in predicting antigenic epitopes (Sali and Blundell, 1993); in simulating protein-protein docking (Vakser, 1995); in inferring function from calculated electrostatic potential around the protein (Matsumoto et al, 1995); in facilitating molecular replacement in X-ray structure determination (Howell et al, 1992); in refining models based on NMR constraints (Modi et al, 1996); in testing and improving a sequence-structure alignment (Wolf et al, 1998); in annotating single nucleotide polymorphisms (Mirkovic et al, 2004;Karchin et al, 2005); in structural characterization of large complexes by docking to low-resolution cryo-electron density maps (Spahn et al, 2001;Gao et al, 2003); and in rationalizing known experimental observations. Fortunately, a 3-D model does not have to be absolutely perfect to be helpful in biology, as demonstrated by the applications listed above.…”

“…The alignments on which these models are based generally contain almost no errors. Models with such high accuracy have been shown to be useful even for refining crystallographic structures by the method of molecular replacement (Howell et al, 1992;Baker and Sali, 2001;Jones, 2001;Claude et al, 2004;Schwarzenbacher et al, 2004). Figure 5.6.15 Accuracy and application of protein structure models.…”

Comparative Protein Structure Modeling Using MODELLER

“…Comparative modeling is often an efficient way to obtain useful information about the protein of interest. For example, comparative models can be helpful in designing mutants to test hypotheses about the protein's function (Wu et al, 1999;Vernal et al, 2002); in identifying active and binding sites (Sheng et al, 1996); in searching for, designing, and improving ligand binding strength for a given binding site (Ring et al, 1993;Li et al, 1996;Selzer et al, 1997;Enyedy et al, 2001;Que et al, 2002); modeling substrate specificity (Xu et al, 1996); in predicting antigenic epitopes (Sali and Blundell, 1993); in simulating protein-protein docking (Vakser, 1995); in inferring function from calculated electrostatic potential around the protein (Matsumoto et al, 1995); in facilitating molecular replacement in X-ray structure determination (Howell et al, 1992); in refining models based on NMR constraints (Modi et al, 1996); in testing and improving a sequence-structure alignment (Wolf et al, 1998); in annotating single nucleotide polymorphisms Karchin et al, 2005); in structural characterization of large complexes by docking to low-resolution cryo-electron density maps (Spahn et al, 2001;Gao et al, 2003); and in rationalizing known experimental observations. Fortunately, a 3-D model does not have to be absolutely perfect to be helpful in biology, as demonstrated by the applications listed above.…”

Homology modeling a fast tool for drug discovery: Current perspectives

“…The importance of homology modeling is increasing as the number of available crystal structures increases. There are several other common applications of homology models: (1) studying the effect of mutations[111]; (2) identifying active and binding sites on protein (useful for ligand design)[112]; (3) searching for ligands of a given binding site (database mining)[113]; (4) designing novel ligands of a given binding site; (5) modeling substrate specificity[114]; (6) predicting antigenic epitopes[115]; (7) protein-protein docking simulations[116]; (8) molecular replacement in X-ray structure refinement[117]; (9) rationalizing known experimental observations[118] and (10) planning new computational experiments with the provided models. Typical applications of a homology model in drug discovery require a very high accuracy of the local side chain positions in the binding site.…”