Molecular dynamics of the pyridoxine derivative in the acetylcholinesterase active cavity

Acetylcholinesterase (AChE) is a key enzyme in central nervous system, responsible for the regulation of nerve impulse transmission through the rapid hydrolysis of the acetylcholine neurotransmitter. In recent years, the issue of AChE specific interaction with ligands to regulate its activity becomes more and more popular. In particular, it is necessary to develop specific AChE inhibitors - potential new drugs for the treatment of neurodegenerative diseases, which will have a greater efficacy and fewer side effects. Currently, the methods of molecular modeling are actively used for the development of new drugs. In this paper we studied the insilico structure of a mouse AChE, since the study of enzyme activity in preclinical tests was carried out on mice. Pyridoxine derivative was used as ligands for which anticholinesterase symptoms were shown during the initial experiments invivo, and its position in the active center during the docking was similar acetylcholinesterase inhibitors used in medicine nowadays (proserin, physostigmine). The use of molecular dynamic simulation method allowed to evaluate the drug potential of inhibitors by the most cost -effective way. The study was conducted using the software package NAMD 2.8 and the force field AMBER 99. The study showed that the spatial position of ligand is favorable for AChE inhibiting. As the result of the molecular dynamics, the distance between the oxygen of the hydroxyl group Ser203 and the carbon atom of derived pyridoxine fragment carbamylation decreased from 6.4 Å to 3.8 Å, which contributes to their interaction to form a bond. The spatial position of the ligand is supported by the weak link between the tertiary nitrogen of carbamylation fragment and the oxygen of hydroxyl group Tyr124 AChE. Moreover, the ligand is held in an active cavity of the enzyme by hydrophobic interaction of its heterogenic cycle with Trp86 AChE. This state of the ligand structure may provide a long-term anticholinesterase of pyridoxine effect producers

The fluctuation analysis of conformational mobility for pyridoxine derivatives in the active site of acetylcholinesterase

© 2016, International Journal of Pharmacy and Technology. All rights reserved.Acetylcholinesterase (AChE) is the main enzyme of the nervous system that is responsible for the regulation of a nerve impulse transfer by a rapid hydrolysis of the neurotransmitter - acetylcholine. The most important aspect in the studies related to AChE is the issue of specific interaction with ligands for its activity regulation. In most cases it is necessary for AChE site-specific inhibitors design for development of potential new drugs for the treatment of neurodegenerative diseases with more efficiency and less side effects. Currently the methods of molecular modeling are widely used for new drugs design. In this study AChE structure of 2JEY mouse served as biological target. The derivatives of pyridoxine were used as ligands, with anticholinesterase effect shown in vivo. Moreover the position of these ligands in AChE active center during docking was similar to AChE inhibitors used in medicine (proserin, physostigmine). A combination of molecular docking and Molecular Dynamics methods allowed us to estimate the drug potential of inhibitors more efficiently. The study was carried out using the following software packages: AutoDock.1.5.6 (Vina application) and NAMD 2.8 with AMBER 99 force field. The result showed that the ligand position in the active cavity of an enzyme may vary significantly even for related compounds and these positions depend on ligand modification. The analysis of molecular dynamics revealed that the ligand mobility and respective inhibitory activity depend on an inhibitor size and on ligand affinity to AChE. The number of interatomic interactions between molecules and probabilities of their interactions in an active site of the enzyme were used for analysis. It was shown that the molecules with a high affinity for the enzyme active cavity not always will be able to get into active cavity by reason of their size. The hydrophobic interactions of ligands with uncharged amino acid residues allows them to bind more efficiently to the active center of AChE. Thus the structuralfeatures of the ligand exactly define long-term anticholinesterase effect

Prediction of the three-dimensional structure of the protein SaHPF and analysis of its molecular dynamics

© 2016, International Journal of Pharmacy and Technology. All rights reserved.SaHPF is the protein of gram-positive bacterium Staphylococcus aureus, which is causesa variety of diseases (pneumonia, meningitis, endocarditis, etc.), including nosocomial infections. SaHPF ishibernation-promoting factor, presumably interacts with the 30S subunit the ribosome and alters its conformation, and this results binding together of two ribosomes. Such ribosomal dimers do not perform protein synthesis, and this allows the cell to survive the unfavorable environmental conditions.The understanding of SaHPF-ribosome interaction mechanisms will allow to develop new antibacterial drugs. Protein structure was predicted using Robetta, Quark, I-Tasser, SWISS-MODEl and Phyre2 software, which used methods: homology, threading and ab initio. In total 24 protein models were built. Quality assessment of the obtained protein structures models was performed by Qmean program. Among the predicted structures, the most qualitative assessment was obtained model of the protein built in Robetta program, which builds the models by combining the methods of homology and ab initio. This model of the protein was analyzed by equilibrium molecular dynamics method in NAMD program, using Charmmforce field. The analysis of molecular dynamics trajectories using principal component and normal mode methods revealed a special mobility of the loop and the C-terminal domain of the protein, which may complicate the resolution of SaHPF structure by experimental methods (crystallography and NMR)

Comparative analysis of mice acetylcholinesterases by functional amino acid residues and molecular screening

In this paper, we have measured the distances between the reference amino acid residues of the acetylcholinesterase (AChE) active site, which showed that the existing three-dimensional models either have no differences or have differences within the structures resolution. Using the method of molecular docking in AutoDock, we have carried out the AChE screening with ligands, which denied the result of a previous calculation and showed that the affinity energy of one ligand (e.g.: donepezil) with 23 structures of enzyme is in the range of -6 to -12 kcal/mol, which is impossible for those structures having no significant differences. Following this line of reasoning, we can make two different conclusions: firstly, the existing AChE models are similar in general, and the choice of a model for work shall be based on the structure resolution, and a variety of screening results are just special cases of interaction with the side radicals of amino acid residues; secondly, the amount of insignificant changes in the spatial structure of each protein contributes largely to the screening result

Gramm-software package for molecular dynamics on graphical processing units

© 2010, Pleiades Publishing, Ltd. This work describes the software package and algorithms for molecular dynamics using NVIDEA GPU G80, G84, and G92. All potentials needed for MM2 and AMBER force fields are implemented and the combination of different potentials is allowed. The performance comparison of different MD algorithms on GPU and CPU is presented. All software is available from www.gpamm.mntech.ru

Membrane thermostability and gene expression of small heat-shock protein (sHSP) in weat shoots exposed to elevated temperatures and water deficiency

The temperature dependence of the permeability of cell membranes was studied in the range of 49-57°C by the conductometric method recording of electrolyte exosmosis from intact plant leave tissues of 7-day seedlings of three spring wheat (Triticum aestivum L.) varieties grown under different conditions of heat shock (Hs) and drought. The samples were heated at a given temperature for 5 min and the following kinetic parameters of thermostability membranes were determined: threshold membrane damage temperature (TMDT), slope of the temperature curves, and membrane damage coefficients (MDK) characterizing the amplitude and speed of thermotropic transitions. We found variety-specific differences in these parameters that allowed us to range the wheat genotypes studied according to the heat-resistance. Gene expression of sHspl6.9B and sHspl7.3 was evaluated by the content of the mRNA transcripts using the methods of relative RT-PCR and northern blot hybridization. In control samples a weak constitutive gene expression was detected; however, under the stress conditions - combined action of Hs and preceding thermoadaptation or drought - an increase of gene expression was found, especially for gene sHspl7.3, suggesting that the activity of these genes is stress-regulated. More ponounced differences between varieties with contrasting thermostability were found by the northern blot analysis of the sHspl7.3 gene transcripts. Under stress conditions, higher amount of transcripts of this gene was observed in highly resistant plant varieties with enhanced thermal stability of membranes as compared with less resistant plants. These results suggest a variety-specific dependence of the gene sHspl7.3 activity and a direct correlation of its transcription with the thermal stability of membranes and resistance of plants to hypothermia. We assume that the induction of synthesis and accumulation of sHspl7.3 ensures a higher membrane thermostability due to better association of the membranes with a pool of this protein, which prevents fluidization and disintegration of the lipid bilayer during high-temperature stress and water deficit

An anti-DNA antibody prefers damaged dsDNA over native

© 2016 Informa UK Limited, trading as Taylor & Francis GroupDNA–protein interactions, including DNA–antibody complexes, have both fundamental and practical significance. In particular, antibodies against double-stranded DNA play an important role in the pathogenesis of autoimmune diseases. Elucidation of structural mechanisms of an antigen recognition and interaction of anti-DNA antibodies provides a basis for understanding the role of DNA-containing immune complexes in human pathologies and for new treatments. Here we used Molecular Dynamic simulations of bimolecular complexes of a segment of dsDNA with a monoclonal anti-DNA antibody’s Fab-fragment to obtain detailed structural and physical characteristics of the dynamic intermolecular interactions. Using a computationally modified crystal structure of a Fab–DNA complex (PDB: 3VW3), we studied in silico equilibrium Molecular Dynamics of the Fab-fragment associated with two homologous dsDNA fragments, containing or not containing dimerized thymine, a product of DNA photodamage. The Fab-fragment interactions with the thymine dimer-containing DNA was thermodynamically more stable than with the native DNA. The amino acid residues constituting a paratope and the complementary nucleotide epitopes for both Fab–DNA constructs were identified. Stacking and electrostatic interactions were shown to play the main role in the antibody–dsDNA contacts, while hydrogen bonds were less significant. The aggregate of data show that the chemically modified dsDNA (containing a covalent thymine dimer) has a higher affinity toward the antibody and forms a stronger immune complex. These findings provide a mechanistic insight into formation and properties of the pathogenic anti-DNA antibodies in autoimmune diseases, such as systemic lupus erythematosus, associated with skin photosensibilization and DNA photodamage

Molecular dynamics of immune complex of photoadduct-containing DNA with Fab-Anti-DNA antibody fragment

© 2016, Pleiades Publishing, Inc.Antibodies to DNA play an important role in the pathogenesis of autoimmune diseases. The elucidation of structural mechanisms of both the antigen recognition and the interaction of anti-DNA antibodies with DNA will help to understand the role of DNA-containing immune complexes in various pathologies and can provide a basis for new treatment modalities. Moreover, the DNA-antibody complex is an analog of specific intracellular DNA-protein interactions. In this work, we used in silico molecular dynamic simulations of bimolecular complexes of the dsDNA segment containing the Fab fragment of an anti-DNA antibody to obtain the detailed thermodynamic and structural characteristics of dynamic intermolecular interactions. Using computationally modified crystal structure of the Fab-DNA complex (PDB ID: 3VW3), we studied the equilibrium molecular dynamics of the 64M-5 antibody Fab fragment associated with the dsDNA fragment containing the thymine dimer, the product of DNA photodamage. Amino acid residues that constitute paratopes and the complementary nucleotide epitopes for the Fab-DNA construct were identified. Stacking and electrostatic interactions were found to play the main role in mediating the most specific antibodydsDNA contacts, while hydrogen bonds were less significant. These findings may shed light on the formation and properties of pathogenic anti-DNA antibodies in autoimmune diseases, such as systemic lupus erythematosus associated with skin photosensitivity and DNA photodamage

Essential Dynamics of DNA-Antibody Complexes

© 2016, Springer Science+Business Media New York.Antibodies against double-stranded DNA play an important role in the pathogenesis of autoimmune diseases. Structural analysis of antibody-DNA complexes contributes to our understanding of the role of DNA-containing immune complexes in human pathologies and may help in designing novel treatments. In this paper, we study dynamics of the full-atomic structure of the molecular complexes formed by an antibody Fab fragment with double-stranded DNA, containing or not containing a thymine dimer. Molecular dynamics simulations are used in conjunction with the Principle Component Analysis technique. We found that removing a covalent bond from the thymine dimer results in changes of the structural dynamics of the light and heavy chains of Fab as well as in the DNA strands. A significant increase in mobility of the Fab light chain was observed throughout the entire simulation runs with a higher amplitude of fluctuations at the interface with DNA. Essential dynamics analysis of simulation trajectories of the antibody-dsDNA complexes shows that fluctuations in the low-frequency eigenvectors are localized at the ends of the DNA sequences, suggesting that these bending motions are important for the DNA-antibody interactions

An anti-DNA antibody prefers damaged dsDNA over native

© 2016 Informa UK Limited, trading as Taylor & Francis Group.DNA–protein interactions, including DNA–antibody complexes, have both fundamental and practical significance. In particular, antibodies against double-stranded DNA play an important role in the pathogenesis of autoimmune diseases. Elucidation of structural mechanisms of an antigen recognition and interaction of anti-DNA antibodies provides a basis for understanding the role of DNA-containing immune complexes in human pathologies and for new treatments. Here we used Molecular Dynamic simulations of bimolecular complexes of a segment of dsDNA with a monoclonal anti-DNA antibody’s Fab-fragment to obtain detailed structural and physical characteristics of the dynamic intermolecular interactions. Using a computationally modified crystal structure of a Fab–DNA complex (PDB: 3VW3), we studied in silico equilibrium Molecular Dynamics of the Fab-fragment associated with two homologous dsDNA fragments, containing or not containing dimerized thymine, a product of DNA photodamage. The Fab-fragment interactions with the thymine dimer-containing DNA was thermodynamically more stable than with the native DNA. The amino acid residues constituting a paratope and the complementary nucleotide epitopes for both Fab–DNA constructs were identified. Stacking and electrostatic interactions were shown to play the main role in the antibody–dsDNA contacts, while hydrogen bonds were less significant. The aggregate of data show that the chemically modified dsDNA (containing a covalent thymine dimer) has a higher affinity toward the antibody and forms a stronger immune complex. These findings provide a mechanistic insight into formation and properties of the pathogenic anti-DNA antibodies in autoimmune diseases, such as systemic lupus erythematosus, associated with skin photosensibilization and DNA photodamage