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The deamination reaction of 8-oxoguanine (8-oxoG) catalyzed by 8-oxoguanine deaminase (8-oxoGD) plays a critically important role in the DNA repair activity for oxidative damage. In order to elucidate the complete enzymatic catalysis mechanism at the stages of 8-oxoguanine binding, departure of 2-hydroxy-1H-purine-6,8(7H,9H)-dione from the active site, and formation of 8-oxoxanthine, extensive combined QM(PM3)/MM molecular dynamics simulations have been performed. Computations show that the rate-limiting step corresponds to the nucleophilic attack from zinc-coordinate hydroxide group to free 8-oxoguanine. Through conformational analyses, we demonstrate that Trp115, Trp123 and Leu119 connect to O8@8-oxoguanine with hydrogen bonds, and we suggest that mutations of tryptophan (115 and 123) to histidine or phenylalanine and mutation of leucine (119) to alanine could potentially lead to a mutant with enhanced activity. On this ground, a proton transfer mechanism for the formation of 8-oxoxanthine was further discussed. Both Glu218 and water molecule could be used as proton shuttles, and water molecule plays a major role in proton transfer in substrate. On the other hand, comparative simulations on the deamination of guanine and isocytosine reveal that, for the helping of hydrogen bonds between O8@8-oxoguanine and enzyme, O8@8-oxoguanine is the fastest to be deaminated among the three substrates which are also supported by the experimental kinetic constants. Extensive combined QM(PM3)/MM molecular dynamics simulations have been performed on the deamination reaction of 8-oxoguanine (8-oxoG) catalyzed by 8-oxoguanine deaminase (8-oxoGD). Our results show that the nucleophilic attack from zinc-coordinate hydroxide group to free 8-oxoguanine is the rate-limiting step of the reaction. And we suggest that mutations of tryptophan (115 and 123) to histidine or phenylalanine and mutation of leucine (119) to alanine could potentially lead to an 8-oxoGD mutant with enhanced activity. [ABSTRACT FROM AUTHOR]

Extensive combined quantum mechanical (B3LYP/6-31G*) and molecular mechanical (QM/MM) molecular dynamics simulations have been performed to elucidate the hydrolytic deamination mechanism of cytosine to uracil catalyzed by the yeast cytosine deaminase (yCD). Though cytosine has no direct binding to the zinc center, it reacts with the water molecule coordinated to zinc, and the adjacent conserved Glu64 serves as a general acid/base to shuttle protons from water to cytosine. The overall reaction consists of several proton-transfer processes and nucleophilic attacks. A tetrahedral intermediate adduct of cytosine and water binding to zinc is identified and similar to the crystal structure of yCD with the inhibitor 2-pyrimidinone. The rate-determining step with the barrier of 18.0 kcal/mol in the whole catalytic cycle occurs in the process of uracil departure where the proton transfer from water to Glu64 and nucleophilic attack of the resulting hydroxide anion to C2 of the uracil ring occurs synchronously. © 2016 Wiley Periodicals, Inc. [ABSTRACT FROM AUTHOR]

How the protein−protein interactions affect the phase behaviour of protein complexes can afford technical support for the application of egg white protein in food industry. Here the drawing of phase diagram of ovalbumin-lysozyme (Ova-Lys) complexes was reported, and the effect of interaction between Ova and Lys on the phase behaviour of three phases (co-soluble polymers, insoluble complexes and soluble complexes) was investigated by combining experimental and computational approaches. The soluble and insoluble complexes displayed an amorphous pattern, with the insoluble complexes manifesting a cross-linked conformation. Ova and Lys exhibited strong co-localization within heteroprotein complexes, where Ova being the predominant component on the surface of the complexes. Electrostatic and hydrogen bonding interactions were the main driving forces to afford co-soluble polymers, while electrostatic, hydrogen bonding and hydrophobic interactions existed in insoluble and soluble complexes. The strong force facilitated to yield insoluble complexes, while the weak force favoured to give co-soluble polymers. [Display omitted] • Influence of Ova-Lys interactions on protein complex phase behaviour was studied. • The phases included co-soluble polymers, insoluble complexes, and soluble complexes. • Electrostatic interaction was the main driving force for the phase formation. • Ova and Lys exhibited strong co-localization within the heteroprotein complexes. [ABSTRACT FROM AUTHOR]

The interaction of zein and β-lactoglobulin (β-LG) was explored by experiments combined with molecular dynamics simulation method. The results showed that the particle sizes of β-LG-Zein complex nanoparticles enhanced from 69.5 nm to 153.5 nm when the β-LG/zein mass ratio changed from 9:1 to 2:8. The complex nanoparticles exhibited better stability after 30 d of storage. Transmission electron microscope (TEM) showed that the β-LG-Zein nanoparticles dispersed evenly with high β-LG concentration. Fourier transform infrared spectroscopy (FTIR) and dissociation test experiments elucidated that hydrogen bonding, hydrophobic and electrostatic interactions were important for preparing β-LG-Zein complex nanoparticles. The conformational model of zein was constructed through homology modeling, and the structure of β-LG-Zein complex was obtained via molecular docking. Molecular dynamics simulation (MD) results clarified that β-LG firmly grasped zein like a clamp, taking the P68 and G88 residues of zein as the supporting point, and the binding Gibbs free energy reached −39.81 kcal/mol. In addition, the residues of V64, P65, P68, I69, G74, G75, G77 and G88 in zein and the residues of P54, L103 and A104 in β-LG played critical roles for the binding of zein to β-LG. This work can provide a theoretical foundation for the applications of β-LG-Zein complexes in food industry. [Display omitted] • The β-LG-Zein complex nanoparticles were fabricated by pH-shifting method. • The electrostatic, hydrogen bonding and hydrophobic interactions were the main driving forces. • The β-LG-Zein complex nanoparticles exhibited excellent storage stability. • Key residues with big energy contribution were recognized through MD simulations. [ABSTRACT FROM AUTHOR]

pH values have an important influence on the aggregation state of β-lactoglobulin (β-LG), which affects its ligand-binding properties. In this study, the pH-dependent interaction mechanisms between β-LG and epigallocatechin-3-gallate (EGCG) were explored by multi-spectroscopy and molecular dynamics simulation. Compared to β-LG, the increasing absorbance and blue shift of the maximum wavelength in UV–Vis spectroscopy confirmed the formation of β-LG-EGCG complexes. Fluorescence data showed that the quenching of β-LG by EGCG was mainly static quenching at different pH values, and the interaction between β-LG and EGCG was endothermic and spontaneously driven by hydrophobic interactions. Fourier transform infrared spectroscopy (FTIR) and circular dichroism (CD) studies demonstrated that the interactions between EGCG and β-LG caused slight changes to the secondary structure of β-LG. Molecular dynamics (MD) simulation elucidated that EGCG preferred to bind to the pocket of β-LG at pH 7.0 (dimer) and 5.3 (tetramer), which consisted of two I lamellae and an α-helix. However, the binding site of EGCG at pH 2.5 (monomer) was located on the outer surface of β-LG due to the closure of β-barrel structure of β-LG. Moreover, the binding free energies had a trend of pH 7.0 > pH 5.3 > pH 2.5, which was consistent with the trend of thermodynamic data. This study revealed the interaction mechanisms between EGCG and β-LG at different pH, which has great significance to further develop dairy products as EGCG delivery system. [Display omitted] • The pH-dependent interaction mechanisms between EGCG and β-LG were investigated. • The formation of β-LG-EGCG complexes was analysed by multi-spectroscopy. • EGCG preferred to bind to the β-LG pocket at pH 7.0 (dimer) and 5.3 (tetramer). • The binding site located at the outer surface of β-LG at pH 2.5 (monomer) for EGCG. [ABSTRACT FROM AUTHOR]

The interaction mechanism of zein and lysozyme was investigated via multiple analytical methods combining with molecular dynamics simulations in this study. The results showed that the zein-lysozyme complex nanoparticles with a ratio of 2:1 were stable at pH 4.0. The electrostatic and hydrophobic interactions were the main driving forces for the formation of zein-lysozyme complexes. Hydrogen bonding also existed in the nanoparticles, but not the main driving force. Images of transmission electron microscope (TEM) showed the aggregation of samples, and the field emission scanning electron microscopy (FE-SEM) images showed that the surface morphology changes from smooth to rough and irregular. Molecular dynamics simulations elucidated that lysozyme preferred to bind to the protruding area of zein. The residues of P192, A193, A194, Y195, L196, Q198, L199, N203, Q245, and L253 in zein and the residues of D49, Y63, W64, A108, W109, and V110 in lysozyme contributed the most. These results can provide a scientific guideline for the potential application of zein-lysozyme nanoparticles as delivery systems or emulsion stabilizers in food industry. [Display omitted] • The interaction mechanism of zein and lysozyme was investigated. • The electrostatic and hydrophobic interactions were the main driving forces. • MD simulations showed that lysozyme preferred to bind to the protruding area of zein. • Key residues with big energy contribution were recognized in both zein and lysozyme. [ABSTRACT FROM AUTHOR]

Abstract: Although various Trypanosoma vivax purine-specific inosine–adenosine–guanosine nucleoside hydrolase (IAG-NH) crystal structures have been determined and the chemical reaction mechanism of substrate hydrolysis has been studied recently, the mechanistic details for the release of base and ribose are still unclear. Herein molecular dynamics (MD) simulations combined with umbrella sampling technique were utilized to explore the regulation mechanisms of key residues and loops 1 and 2 for the base release. Our results have indicated that the base release process is not the rate-limiting step in the entire hydrolysis process, and the very low barrier of ~5.6kcal/mol can be washed out easily by the notable exothermicity from the substrate hydrolysis step. Moreover, the MD simulations have revealed that Glu82/Trp83 in loop 1 and His247/Arg252 in loop 2 are important to modulate the base release. The partial helix-to-coil change of loop 2 along with the base release process has been observed, showing good agreement with the IAG-NH crystal structures. The local binding site around the ribose after the base release is also discussed. [Copyright &y& Elsevier]

Although various T. vivaxpurine-specificinosine–adenosine–guanosinenucleoside hydrolase (IAG-NH) crystal structures were determined inrecent years, the mechanistic details for the cleavage of N-glycosidic bond and the release of base are still unclear.Herein, the irreversible hydrolysis reaction has been studied by abinitio QM/MM MD simulations, and the results indicate a highly dissociativeand concerted mechanism. The protonation of substrate at N7 of inosineis found to strongly facilitate the hydrolysis process, while thehydrolysis reaction is less sensitive to the protonation state ofAsp 40 residue. The proton-transfer channel and the dependence ofactivity on the anti/syn-conformation of substrate are also explored. [ABSTRACT FROM AUTHOR]

Zein as a kind of carrier material has attracted extensive interest, while the interaction mechanism between zein and nutrients is still elusive. In this work, the binding mechanism of zein with epigallocatechin-3-gallate (EGCG) was investigated via multi-spectroscopy and molecular dynamics (MD) simulation. The quenching of zein by EGCG is mainly static quenching, and the secondary structure of zein is slightly changed after the binding of EGCG to zein. The formation of Zein-EGCG complexes was confirmed by ultraviolet–visible (UV–Vis) spectroscopy, X-ray diffraction (XRD), and scanning electron microscopy (SEM). Molecular dynamics (MD) simulation clarified that the EGCG prefers to bind to the pocket of zein formed by residues Y171, Q174, L176 and L205. Electrostatic and van der Waals interactions played a dominant role for the binding of EGCG to zein, which was consistent with the results by fourier transform infrared spectroscopy (FTIR) and thermodynamic analysis. This study provides new insights into the interaction mechanism between zein and EGCG, which is very important to develop plant protein as tea polyphenol delivery system. [Display omitted] • Interaction mechanism between zein and EGCG was studied. • The quenching of zein by EGCG is mainly static quenching. • The formation of Zein-EGCG complexes was confirmed. • The van der Waals and electrostatic interactions played an important role in binding of EGCG to zein. [ABSTRACT FROM AUTHOR]