The conformational properties of Glu 35 and Asp 52 of lysozyme active center

Godjayev, N. M.; Akyüz, Sevim; Ismailova, L. I.

doi:10.1007/s007770050032

Cited by 3 publications

(4 citation statements)

References 14 publications

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“…The atomic charges from dyn MP (r) [and dyn IAM (r) as well] follow chemical expectations, with positively charged C atoms and negatively charged O atoms and NH groups. These properties are essentially different from the theoretical electron densities of Godjayev et al (1998), who proposed a negatively charged C atom of the carboxyl group of Asp52 along with positively charged O atoms (Table 4). Although not impossible in principle, the present experimental electron densities lead to the scenario of O atoms of the carboxyl group that possess negative charges.…”

Section: Reaction Mechanismcontrasting

confidence: 82%

“…Wang et al (2007) have noticed that HEWL is rather rigid for a crystallized protein molecule, but that it nevertheless Table 4 Net atomic charges Q of Glu35 and Asp52 from dynamic densities and from quantum-chemical calculations (Godjayev et al, 1998 contains disordered parts for about 35% of the structure. Here, we have found that the ADPs of atoms within ordered parts of the structure have magnitudes that are larger than the magnitudes of the ADPs of small molecules in their crystallized state at room temperature, despite the nominal temperature of 100 K of HEWL (Fig.…”

Section: Reaction Mechanismmentioning

confidence: 99%

“…Since this proton is an essential proton for the Phillips mechanism (Phillips, 1966), the chemical characters of Glu35 and Asp52 of the present structure of HEWL are consistent with both the Phillips mechanism (Phillips, 1966) and the Koshland mechanism (Koshland, 1953), prohibiting a clear approval of one or the other reaction mechanism. Wang et al (2007) have noticed that HEWL is rather rigid for a crystallized protein molecule, but that it nevertheless Table 4 Net atomic charges Q of Glu35 and Asp52 from dynamic densities and from quantum-chemical calculations (Godjayev et al, 1998) contains disordered parts for about 35% of the structure.…”

Section: Reaction Mechanismmentioning

confidence: 99%

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The active site of hen egg-white lysozyme: flexibility and chemical bonding

Held¹,

Smaalen²

2014

Acta Crystallogr D Biol Crystallogr

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Chemical bonding at the active site of hen egg-white lysozyme (HEWL) is analyzed on the basis of Bader's quantum theory of atoms in molecules [QTAIM;Bader (1994), Atoms in Molecules: A Quantum Theory. Oxford University Press] applied to electron-density maps derived from a multipole model. The observation is made that the atomic displacement parameters (ADPs) of HEWL at a temperature of 100 K are larger than ADPs in crystals of small biological molecules at 298 K. This feature shows that the ADPs in the cold crystals of HEWL reflect frozen-in disorder rather than thermal vibrations of the atoms. Directly generalizing the results of multipole studies on small-molecule crystals, the important consequence for electron-density analysis of protein crystals is that multipole parameters cannot be independently varied in a meaningful way in structure refinements. Instead, a multipole model for HEWL has been developed by refinement of atomic coordinates and ADPs against the X-ray diffraction data of Wang and coworkers [Wang et al. (2007), Acta Cryst. D63, 1254-1268], while multipole parameters were fixed to the values for transferable multipole parameters from the ELMAM2 database [Domagala et al. (2012), Acta Cryst. A68, 337-351] . Static and dynamic electron densities based on this multipole model are presented. Analysis of their topological properties according to the QTAIM shows that the covalent bonds possess similar properties to the covalent bonds of small molecules. Hydrogen bonds of intermediate strength are identified for the Glu35 and Asp52 residues, which are considered to be essential parts of the active site of HEWL. Furthermore, a series of weak C-HÁ Á ÁO hydrogen bonds are identified by means of the existence of bond critical points (BCPs) in the multipole electron density. It is proposed that these weak interactions might be important for defining the tertiary structure and activity of HEWL. The deprotonated state of Glu35 prevents a distinction between the Phillips and Koshland mechanisms.

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Section: Reaction Mechanismcontrasting

confidence: 82%

Section: Reaction Mechanismmentioning

confidence: 99%

Section: Reaction Mechanismmentioning

confidence: 99%

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The active site of hen egg-white lysozyme: flexibility and chemical bonding

Held¹,

Smaalen²

2014

Acta Crystallogr D Biol Crystallogr

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“…Furthermore, AuO and ThT tend to associate with the IB domain of BSAN (the residues L115, P117, L122, E125, F133, K136, Y137, E140, Y160, R185) and the active center of LzN (the residues I58, N59, W62, W63, I98, D101, N103, A107, W108) [40,41]. Interestingly, Mudliar et al reported AuO binding to the hydrophobic IIA domain of BSA, i.e.…”

Section: Resultsmentioning

confidence: 99%

Auramine O as Potential Amyloid Marker: Fluorescence and Molecular Docking Studies

Vus

Tarabara

Semenova

et al. 2017

EEJP

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The applicability of Auramine O to the detection and characterization of lysozyme and serum albumin amyloid fibrils has been assessed using the fluorimetric titration and molecular docking. The parameters of the dye binding to native and fibrillar proteins were estimated in terms of the Langmuir adsorption model. It was found that Auramine O displays the high affinity for amyloid fibrils, being of the same order of magnitude as that of the classical amyloid markers. The dye also showed greater fluorescence response to lysozyme fibrils and lower sensitivity to the native protein, than Thioflavin T. Furthermore, unlike Thioflavin T, Auramine O was able to detect the morphological differences between lysozyme and albumin fibrils due to the shifts in the position of the emission maxima of the fibril-incorporated fluorophore. The molecular docking studies revealed that Auramine O and Thioflavin T form the most stable complexes with the G54_L56/S60_W62 groove of lysozyme fibrils, running parallel to the fibril axis. The results obtained suggest the contribution of both hydrophobic and electrostatic interactions to the stabilization of the dye complexes with amyloid fibrils.

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