Exhaustive conformational search for transition states: the case of catechol O-methyltransferase active site
A combination of the common quantum mechanics based transition state theory and exhaustive conformational search for the modeling of difficult reactions with hundreds of competing transition states is proposed. This approach is applied to study all transition state conformations of a reaction occurring in the catechol O-methyltransferase (COMT) active site in the absence of a major part of the enzyme, and the results are compared to the recent QM/MM modeling of this reaction within the enzyme. The main points of the method are (i) constraining of forming bonds upon conformer generation and (ii) preliminary constrained optimizations of located conformations to minima using a quantum mechanical method. Importantly, this methodology is applicable to the quantum mechanical part in QM/MM calculations and can reduce demand for large sampling in difficult cases.
The method ofWave Packet Molecular Dynamics Method (WPMD) is a promising replacement of the classical molecular dynamics for the simulations of many-electron systems including nonideal plasmas. In this contribution we report on a packet splitting technique where an electron is represented by multiple Gaussians, with mixing coefficients playing the role of additional dynamic variables. It provides larger flexibility and better accuracy than the original WPMD with a single Gaussian per electron. As a test case we consider ionization of hydrogen atom in a short laser pulse, where the split packets provide a basis for quantum branching.
The wave packet molecular dynamics (WPMD) method provides a variational approximation to the solution of the time-dependent Schr¨odinger equation. Its application in the field of high-temperature dense plasmas has yielded diverging electron width (spreading), which results in diminishing electron-nuclear interactions. Electron spreading has previously been ascribed to a shortcoming of the WPMD method and has been counteracted by various heuristic additions to the models used. We employ more accurate methods to determine if spreading continues to be predicted by them and how WPMD can be improved. A scattering process involving a single dynamic electron interacting with a periodic array of statically screened protons is used as a model problem for comparison. We compare the numerically exact split operator Fourier transform method, the Wigner trajectory method, and the time-dependent variational principle (TDVP). Within the framework of the TDVP, we use the standard variational form of WPMD, the single Gaussian wave packet (WP), as well as a sum of Gaussian WPs, as in the split WP method. Wave packet spreading is predicted by all methods, so it is not the source of the unphysical diminishing of electron-nuclear interactions in WPMD at high temperatures. Instead, the Gaussian WP’s inability to correctly reproduce breakup of the electron’s probability density into localized density near the protons is responsible for the deviation from more accurate predictions. Extensions of WPMD must include a mechanism for breakup to occur in order to yield dynamics that lead to accurate electron densities.
Helical segments are common structural elements of membrane proteins. Dimerization and oligomerization of transmembrane (TM) α-helices provides the framework for spatial structure formation and protein-protein interactions. The membrane itself also takes part in the protein functioning. There are some examples of the mutual influence of the lipid bilayer properties and embedded membrane proteins. This work aims at the detail investigation of protein-lipid interactions using model systems: TM peptides corresponding to native protein segments. Three peptides were considered corresponding to TM domains of human glycophorin A (GpA), epidermal growth factor receptor (EGFR) and proposed TM-segment of human neuraminidase-1 (Neu1). A computational analysis of structural and dynamical properties was performed using molecular dynamics method. Monomers of peptides were considered incorporated into hydrated lipid bilayers. It was confirmed, that all these TM peptides have stable helical conformation in lipid environment, and the mutual adaptation of peptides and membrane was observed. It was shown that incorporation of the peptide into membrane results in the modulation of local and mean structural properties of the bilayer. Each peptide interacts with lipid acyl chains having special binding sites on the surface of central part of α-helix that exist for at least 200 ns. However, lipid acyl chains substitute each other faster occupying the same site. The formation of a special pattern of protein-lipid interactions may modulate the association of TM domains of membrane proteins, so membrane environment should be considered when proposing new substances targeting cell receptors.
This paper describes the surface environment of the dense plasma arcs that damage rf accelerators, tokamaks, and other high gradient structures. We simulate the dense, nonideal plasma sheath near a metallic surface using molecular dynamics (MD) to evaluate sheaths in the non-Debye region for high density, low temperature plasmas. We use direct two-component MD simulations where the interactions between all electrons and ions are computed explicitly. We find that the non-Debye sheath can be extrapolated from the Debye sheath parameters with small corrections. We find that these parameters are roughly consistent with previous particle-in-cell code estimates, pointing to densities in the range 10^24–10^25 m^3. The high surface fields implied by these results could produce field emission that would short the sheath and cause an instability in the time evolution of the arc, and this mechanism could limit the maximum density and surface field in the arc. These results also provide a way of understanding how the properties of the arc depend on the properties (sublimation energy, for example) of the metal. Using these results, and equating surface tension and plasma pressure, it is possible to infer a range of plasma densities and sheath potentials from scanning electron microscope images of arc damage. We find that the high density plasma these results imply and the level of plasma pressure they would produce is consistent with arc damage on a scale 100 nm or less, in examples where the liquid metal would cool before this structure would be lost. We find that the submicron component of arc damage, the burn voltage, and fluctuations in the visible light production of arcs may be the most direct indicators of the parameters of the dense plasma arc, and the most useful diagnostics of the mechanisms limiting gradients in accelerators.
Plasmatic membranes contain high amount of membrane proteins. They perform vital functions of life, so any disruptions in their structure result in pathologies and diseases. Studies of these proteins with experimental methods are very complicated and expensive, as they require the membrane environment. Despite considerable progress achieved so far in methods of structure determination and property analysis, many computational methods are developing to predict the structural and dynamical parameters of proteins in membranes. Among the algorithms of modeling are the homology analysis, de novo structure prediction, molecular dynamics simulations and other. With growing computational capabilities, sophisticated techniques are developed taking into account more environmental factors. Combined approaches with different levels of approximation of intermolecular interactions are widely used. The major interest in studies of membrane proteins is focused on their transmembrane domains that are fundamental structural elements and are constituted by α-helices or helical bundles incorporated into lipid bilayer in most cases. Therefore, the fundamental problem of interaction of a pair of helices in membrane arises: the exact mechanism of this process is still not so clear. In place of the prevailing concept of dimerization motifs that states the importance of protein-protein contacts, a new model of the membrane as an adaptable lipid matrix is proposed. It states that biological membrane can adjust its properties around proteins and also modulates their activity. This mechanism of the mutual influence of two components is challenging modern computational methods of membrane model- ing because these systems are quite large and include many components to be treated accurately. Nowadays, investigations of the complex multi-component model systems become possible with modern methods of computational experiment.
Transmembrane α-helical domains are common structural elements in membrane proteins structure. They are involved into functioning of receptors and ion channels. Protein-protein interactions in lipid environment underlie the function of the most membrane systems. The properties of lipid environment can modulate the activity of membrane proteins, such as receptor tyrosine kinases. Glycophorin A is a glycoprotein that forms a very stable dimer. Its transmembrane domain is known as a good model system to study dimerization of α-helices. The major mechanism of the disturbance of a dimer by point mutations is thought to be a change of protein-protein contacts, but the role of the membrane is not well understood. In present work we study the behavior of transmembrane segment of human glycophorin A and two mutant forms G83A and T87V using molecular dynamics simulations in lipid environment. The free energy of dimerization has been estimated and the analysis of lipid properties was done. We propose different mechanisms for each mutation: T87V strongly changes protein-protein contacts. For G83A we demonstrate with the decomposition approach the major contribution of non-favorable protein-lipid contacts coupled with the redistribution interfacial protein-protein interactions. For monomers and dimers of all three forms of glycophorin A we found lipid binding sites near the interface of dimerization in the hydrophobic region of the bilayer. Surprisingly, in the case of monomers lipid acyl chains bind to the interfacial residues. Thus, the membrane plays an active role in dimer formation.
We have performed a comparative analysis of the bio-oil produced by thermal liquefaction of microalgae in different solvents using high-resolution Orbitrap mass spectrometry and GC-MS approach. Water, methanol, ethanol, butanol, isopropanol, acetonitrile, toluene, and hexane were used as solvents in which the liquefaction was performed. It was observed that all resulting oils demonstrate a considerable degree of similarity. For all samples, compounds containing 1 and 2 nitrogen atoms dominated in the positive ESI spectra, while a relative contribution of other compounds was small. In negative ESI mode, compounds having 2 to 7 oxygens were observed. Statistical analysis revealed that products can be combined in two groups depending on the solvent used for the liquefaction. To the first group, we can attribute the products obtained by using protic (alcohols) and to the second by using aprotic (acetonitrile, toluene) solvents. Nevertheless, based on our results, we concluded that solvent possesses a minor impact on molecular composition of bio-oil. We suggested that the driving force of the liquefaction reaction is the thermal dehydration of the carbohydrate in algae, resulting in water formation, which could be the trigger of the producing of bio-oil. To prove this hypothesis, we performed the reaction with the dry algae in the absence of the solvent and observed the formation of bio-oil.
This volume, being the 55th of this Series, contains a wealth of information on bioactive natural products. In Chapter 1, Watson and colleagues have discussed the synthesis of monoterpene indole alkaloids, an important class of structurally diverse natural products, with respect to conventional and biomimetic synthetic approaches.
Titanocene(III) has been widely used in the synthesis of complex organic molecules and natural products including polyketides, phenylpropanoids, antibiotics, and alkaloids. Oltra and coworkers have provided a review on the stereoselective synthesis of natural products facilitated by titanocene(III) in Chapter 2.
About 70 biologically active macrocyclic bisbibenzyls (MBBs) have been isolated and structurally elucidated during the last 30 years. Song and Zhao, in Chapter 3, have provided a review on the synthesis of MBBs with diverse pharmacological properties.
Diabetes mellitus is the most common endocrine/metabolic disorder that poses a global health concern. Reyes and colleagues have discussed the hypoglycemic activity of some terrestrial and marine bioactive compounds with potential for treating type 2 diabetes in Chapter 4. In Chapter 5, Pietruszka and coworkers have highlighted the importance of some marine oxylipins that exhibit different bioactive properties.
Depression has become a psychiatric disorder, which leads to various disabilities. Natural compounds like polyphenols and terpenoids have antioxidant and neuroprotective properties and can be used for the treatment of depression. In Chapter 6, Rodrigues et al. review the clinical studies and trials on polyphenols and terpenoids for the treatment of various psychiatric disorders. The lipid A phosphate and their phosphorylated analogues found in Gram-negative bacteria are of major importance because they provide the host with defense against infections from various microorganisms. Paradies and Zimmermann have discussed physical characteristics, isolation, and bioactivity of lipopolysaccharides (lipid A) for developing new vaccines and therapeutics in Chapter 7.
Hydroxycinnamic acids (HCAs) are a group of phytonutrients with numerous beneficial effects on human health that are largely derived from plants. HCAs play important roles like defense against UV rays or pathogenic attack during growth and development of plants. In Chapter 8, El-Seedi and colleagues present a review focusing on the therapeutic effects of HCAs for the treatment of cancer, diabetes, pulmonary, hepatic, neuro-, and cardiovascular diseases. In Chapter 9, Pomilio and Mercader have presented the study of natural anthocyanins and other related flavonoids for the readers, highlighting their possible and preferable uses as health-protecting food dyes over synthetic ones. They have also discussed the anthocyanins isolated from Ipomoea cairica along with their QSAR studies.
Cardiovascular diseases are considered to be a major threat to health. Polyphenols and carotenoids are structurally diverse groups of bioactive compounds isolated from fruits and vegetables, carrying protective effects against endothelial dysfunction. These therapeutic effects have been explored by Yamagata in Chapter 10.
The roots of licorice and ivy leaves have been used in folk medicine and drugs since long. The biological activity of these complexes has been discussed by Yakovishin and Grishkovets in Chapter 11. In Chapter 12, the chemical and biological characteristics of amicoumacins and xenocoumacins are reviewed by Korshun et al. with reference to the preparation of antibiotics.
I hope that this volume will be received with the same enthusiasm as the earlier volumes of this long-standing series the first volume of which was published under my Editorship in 1988. I would like to express my gratitude to Ms. Taqdees Malik and Mr. Mahmood Alam for their assistance in the preparation of this volume.
The New Russian Encyclopedia is a fundamental reference publication in 18 volumes that characterizes nature, population, economy, history, science, art, technology and other important aspects. Contains about 60,000 articles, about 30,000 biographies, about 15,000 color illustrations, maps, charts, diagrams, tables. Leaves since 2003.
The hydrogenation of diphenylacetylene (DPA) on palladium–silver catalysts with a single-atom structure was investigated. It has been shown experimentally that the reaction rate of alkene to alkane hydrogenation is substantially lower than the rate of DPA semi-hydrogenation. The kinetic barriers of all stages of hydrogenation were calculated by the DFT method.
The swelling of a poly (methyl methacrylate) in supercritical carbon dioxide was studied by means of full atomistic classical molecular dynamics simulation. In order to characterize the polymer swelling, we calculated various properties related to the density, structure, and dynamics of polymer chains as a function of the simulation time, temperature, and pressure. In addition, we compared the properties of the macromolecular chains in supercritical CO2 with the properties of the corresponding bulk system at the same temperature and atmospheric pressure. It was shown that diffusion of CO2 molecules into the polymer led to a significant increase in the chain mobility and distances between them. Analysis of diffusion coefficients of CO2 molecules inside and outside the poly(methyl methacrylate) sample has shown that carbon dioxide actively interacts with the functional groups of poly (methyl methacrylate). Joint analysis of the radial distribution functions obtained from classical molecular dynamics and of the averaging interatomic distances from Car-Parrinello molecular dynamics allows us to make a conclusion about the possibility of formation of weak hydrogen bonds between the carbon dioxide oxygen atom and the hydrogen atoms of the polymer methyl groups.