How does the protein environment optimize the thermodynamics of thiol sulfenylation? Insights from model systems to QM/MM calculations on human 2-Cys peroxiredoxin

Protein thiol/sulfenic acid oxidation potentials provide a tool to select specific oxidation agents, but are experimentally difficult to obtain. Here, insights into the thiol sulfenylation thermodynamics are obtained from model calculations on small systems and from a quantum mechanics/molecular mechanics (QM/MM) analysis on human 2-Cys peroxiredoxin thioredoxin peroxidase B (Tpx-B). To study thiol sulfenylation in Tpx-B, our recently developed computational method to determine reduction potentials relatively compared to a reference system and based on reaction energies reduction potential from electronic energies is updated. Tpx-B forms a sulfenic acid (R-SO^?) on one of its active site cysteines during reactive oxygen scavenging. The observed effect of the conserved active site residues is consistent with the observed hydrogen bond interactions in the QM/MM optimized Tpx-B structures and with free energy calculations on small model systems. The ligand effect could be linked to the complexation energies of ligand L with CH₃S^? and CH₃SO^?. Compared to QM only calculations on Tpx-B’s active site, the QM/MM calculations give an improved understanding of sulfenylation thermodynamics by showing that other residues from the protein environment other than the active site residues can play an important role.     

The Correlation between Rates of Cancer and Autism: An Exploratory Ecological Investigation

Background

Autism is associated with high rates of genomic aberrations, including chromosomal rearrangements and de novo copy-number variations. These observations are reminiscent of cancer, a disease where genomic rearrangements also play a role. We undertook a correlative epidemiological study to explore the possibility that shared risk factors might exist for autism and specific types of cancer.

Methodology/Principal Findings

To determine if significant correlations exist between the prevalence of autism and the incidence of cancer, we obtained and analyzed state-wide data reported by age and gender throughout the United States. Autism data were obtained from the U.S. Department of Education via the Individuals with Disabilities Education Act (IDEA) (2000–2007, reported annually by age group) and cancer incidence data were obtained from the Centers for Disease Control and Prevention (CDC) (1999–2005). IDEA data were further subdivided depending on the method used to diagnose autism (DSM IV or the Code of Federal Regulations, using strict or expanded criteria). Spearman rank correlations were calculated for all possible pairwise combinations of annual autism rates and the incidence of specific cancers. Following this, Bonferroni''s correction was applied to significance values. Two independent methods for determining an overall combined p-value based on dependent correlations were obtained for each set of calculations. High correlations were found between autism rates and the incidence of in situ breast cancer (p≤10⁻¹⁰, modified inverse chi square, n = 16) using data from states that adhere strictly to the Code of Federal Regulations for diagnosing autism. By contrast, few significant correlations were observed between autism prevalence and the incidence of 23 other female and 22 male cancers.

Conclusions

These findings suggest that there may be an association between autism and specific forms of cancer.     

Conformational Analysis of the 3′-5′-Cyclic Dinucleotide d<pApA> by Means of Molecular Mechanics

Abstract

The conformational properties of the cyclic dinucleotide d<(pApA)> were studied by means of molecular mechanics calculations in which a multiconformation analysis was combined with minimum energy calculations. In this approach models of possible conformers are built by varying the torsion angles of the molecule systematically. These models are then subjected to energy minimization; in the present investigation use was made of the AMBER Force field. It followed that the lowest energy conformer has a pseudo-two-fold axis of symmetry. In this conformer the deoxyribose sugars adopt a N-type conformation. The conformation of the sugar-phosphate backbone is determined by the following torsion angles: α⁺, β¹, γ⁺, ?¹ and ζ⁺. The conformation of this ringsystem corresponds to the structure derived earlier by means of NMR spectroscopy and X-ray diffraction. The observation of a preference for N-type sugar conformations in this molecule can be explained by the steric hindrance induced between opposite H3′ atoms when one sugar is switched from N- to S-type puckers. The sugars can in principle switch from N- to S-type conformations, but this requires at least the transition of γ⁺ to γ^?. In this process the molecule obtains an extended shape in which the bases switch from a pseudo-axial to a pseudo-equatorial position. The calculations demonstrate that, apart from the results obtained for the lowest energy conformation, the 180° change in the propagation direction of the phosphate backbone can be achieved by several different combinations of the backbone torsion angles. It appeared that in the low energy conformers five higher order correlations are found. The combination of torsion angles which are involved in changes in the propagation direction of the sugar-phosphate backbone in DNA-hairpin loops and in tRNA are found in the dataset obtained for cyclic d<(pApA)>. It turns out that in the available examples, 180° changes in the backbone direction are localized between two adjacent nucleotides.     

DFT study of the interaction of cytidine and 2′-deoxycytidine with Li, Na, and K: effects of metal cationization on sugar puckering and stability of the N-glycosidic bond

Density functional theory (DFT) calculations were performed at the B3LYP level with a 6-311++G(d,p) basis set to systematically explore the geometrical multiplicity and binding strength for complexes formed by Li⁺, Na⁺, and K⁺ with cytidine and 2′-deoxycytidine. All computational studies indicate that the metal ion affinity (MIA) decreases from Li⁺ to Na⁺ and K⁺ for cytosine nucleosides. For example, for cytidine the affinity for the above metal ions are 79.5, 55.2, and 41.8 and for 2′-deoxycytidine, 82.8, 57.4, and 42.2 kcal/mol, respectively. It is also interesting to mention that linear correlations between calculated MIA values and the atomic numbers (Z) of the above metal ions were found. The influence of metal cationization on the coordination modes and the strength of the N-glycosidic bond in cytosine nucleosides have been studied. In all cases, the N1-C1′ bond distance changes upon introducing a positive charge in the nucleosides. It has been found that metal binding significantly changes the values of the phase angle of pseudorotation P in the sugar unit of these nucleosides. With respect to the sugar ring, metal binding changes the values of the glycosyl torsion angle and sugar ring conformation. The present calculations in the gas phase provide the first clues on the intrinsic chemistry of these systems and may be of value for studies of the influence of metal cations on the conformational behavior and function of nucleic acids.     

Electrostatic Potential of B-DNA: Effect of Interionic Correlations

Modified Poisson-Boltzmann (MPB) equations have been numerically solved to study ionic distributions and mean electrostatic potentials around a macromolecule of arbitrarily complex shape and charge distribution. Results for DNA are compared with those obtained by classical Poisson-Boltzmann (PB) calculations. The comparisons were made for 1:1 and 2:1 electrolytes at ionic strengths up to 1 M. It is found that ion-image charge interactions and interionic correlations, which are neglected by the PB equation, have relatively weak effects on the electrostatic potential at charged groups of the DNA. The PB equation predicts errors in the long-range electrostatic part of the free energy that are only ∼1.5 kJ/mol per nucleotide even in the case of an asymmetrical electrolyte. In contrast, the spatial correlations between ions drastically affect the electrostatic potential at significant separations from the macromolecule leading to a clearly predicted effect of charge overneutralization.     

Chiroptical properties of S-proline conformational isomers

The chiroptical properties of S-proline conformational isomers are examined on a theoretical model in which electronic wave functions are obtained from semiempirical molecular orbital calculations. The CNDO/S molecular orbital model is used to perform SCF-MO calculations on ground state electronic structure and excited states are constructed in the virtual orbital-configuration interaction approximation. Electronic rotatory strengths and dipole strengths are calculated directly from the complete (but approximate) molecular electronic wave functions. Zwitterionic, cationic, and anionic S-proline structures are studied twotypes of conformational variables are represented in the calculations: (1) pyrrolidine ring conformation; and (2) rotation about the C^α-COO^? bond. Rotatory strengths are found to be somewhat sensitive to rotational isomerism about the C^α-COO^? bond, but are found to be rather insensitive to conformational changes within the pyrrolidine ring. The CD spectrum of zwitterionic S-proline down to ～160 nm appears to be well accounted for by the theoretically calculated results if conformational preferences with respect to rotation about the C^α-COO^? bond can be assumed to exist in solution media. Furthermore, spectra-structure correlations are offered for the anionic and cationic forms of S-proline in solution.     

On the computation of molecular surface correlations for protein docking using fourier techniques

The computation of surface correlations using a variety of molecular models has been applied to the unbound protein docking problem. Because of the computational complexity involved in examining all possible molecular orientations, the fast Fourier transform (FFT) (a fast numerical implementation of the discrete Fourier transform (DFT)) is generally applied to minimize the number of calculations. This approach is rooted in the convolution theorem which allows one to inverse transform the product of two DFTs in order to perform the correlation calculation. However, such a DFT calculation results in a cyclic or "circular" correlation which, in general, does not lead to the same result as the linear correlation desired for the docking problem. In this work, we provide computational bounds for constructing molecular models used in the molecular surface correlation problem. The derived bounds are then shown to be consistent with various intuitive guidelines previously reported in the protein docking literature. Finally, these bounds are applied to different molecular models in order to investigate their effect on the correlation calculation.     

Inverse Association between Air Pressure and Rheumatoid Arthritis Synovitis

Rheumatoid arthritis (RA) is a bone destructive autoimmune disease. Many patients with RA recognize fluctuations of their joint synovitis according to changes of air pressure, but the correlations between them have never been addressed in large-scale association studies. To address this point we recruited large-scale assessments of RA activity in a Japanese population, and performed an association analysis. Here, a total of 23,064 assessments of RA activity from 2,131 patients were obtained from the KURAMA (Kyoto University Rheumatoid Arthritis Management Alliance) database. Detailed correlations between air pressure and joint swelling or tenderness were analyzed separately for each of the 326 patients with more than 20 assessments to regulate intra-patient correlations. Association studies were also performed for seven consecutive days to identify the strongest correlations. Standardized multiple linear regression analysis was performed to evaluate independent influences from other meteorological factors. As a result, components of composite measures for RA disease activity revealed suggestive negative associations with air pressure. The 326 patients displayed significant negative mean correlations between air pressure and swellings or the sum of swellings and tenderness (p = 0.00068 and 0.00011, respectively). Among the seven consecutive days, the most significant mean negative correlations were observed for air pressure three days before evaluations of RA synovitis (p = 1.7×10⁻⁷, 0.00027, and 8.3×10⁻⁸, for swellings, tenderness and the sum of them, respectively). Standardized multiple linear regression analysis revealed these associations were independent from humidity and temperature. Our findings suggest that air pressure is inversely associated with synovitis in patients with RA.     

Assessment of the isodesmic method in the calculation of standard reduction potential of copper complexes

Molecular phenomena involving electron transfer and reduction/oxidation processes are of the utmost importance in chemistry. However, accurate computational calculations of standard reduction potentials (SRPs) for transition metal complexes are still challenging. For this reason, some computational strategies have been proposed in order to overcome the main limitations in SRP calculations for copper complexes. However, these strategies are limited to particular coordination spheres and do not represent a general methodology. In this work, we present standard reduction potential calculations for copper complexes in aqueous solution covering a wide range of coordination spheres. These calculations were performed using the M06-2X density functional, and by employing the direct and isodesmic approaches. Result analysis reveals that values obtained with the use of the isodesmic method are in better agreement with experimental values than those obtained from the direct method (mean unsigned error 0.39 V with the direct and 0.08 V with the isodesmic method). This approach provides values with errors comparable to the experimental uncertainty due to the proper cancellation of computational errors. These results strongly suggest the isodesmic approach as an adequate methodology for the calculation of SRPs for copper complexes with diverse coordination spheres.

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Graphical Abstract Comparison between direct and isodesmic methods in the calculation of standard reduction potentials for copper complexes using DFT methods.

     

Chemical bonding in carborane/aromatic co-polymers: a first-principles analysis of experimental photoemission spectra

First-principles density functional theory calculations have been used to study the relative stability and analyse the chemical bonding of novel cross-linked carborane polymers. Atomic charges with several population analysis methods based on fully relaxed structures were calculated to interpret the chemical binding energy shifts of XPS spectra of these boron carbide polymers. The results indicate that a base structure with one aromatic linking unit with carborane is energetically favoured. The linear relationship between experimental core-level photoemission binding energies and computational partial atomic charges from four population analysis methods (Mulliken, Hirshfeld, atoms-in-molecules (AIM) and natural bond order (NBO)) were analysed and the results indicate that cross-linking occurs at icosahedral B sites non-adjacent to icosahedral carbon sites, in agreement with recently reported experimental results. The role of basis set size in determining partial atomic charges was found to vary with population analysis method. Best linear correlations were identified with the more robust population analysis methods (Hirshfeld, AIM and NBO) with the AIM methods noted as being particularly sensitive to basis set size.     

Mechanism of Inhibition of the Human Sirtuin Enzyme SIRT3 by Nicotinamide: Computational and Experimental Studies

Sirtuins are key regulators of many cellular functions including cell growth, apoptosis, metabolism, and genetic control of age-related diseases. Sirtuins are themselves regulated by their cofactor nicotinamide adenine dinucleotide (NAD⁺) as well as their reaction product nicotinamide (NAM), the physiological concentrations of which vary during the process of aging. Nicotinamide inhibits sirtuins through the so-called base exchange pathway, wherein rebinding of the reaction product to the enzyme accelerates the reverse reaction. We investigated the mechanism of nicotinamide inhibition of human SIRT3, the major mitochondrial sirtuin deacetylase, in vitro and in silico using experimental kinetic analysis and Molecular Mechanics-Poisson Boltzmann/Generalized Born Surface Area (MM-PB(GB)SA) binding affinity calculations with molecular dynamics sampling. Through experimental kinetic studies, we demonstrate that NAM inhibition of SIRT3 involves apparent competition between the inhibitor and the enzyme cofactor NAD⁺, contrary to the traditional characterization of base exchange as noncompetitive inhibition. We report a model for base exchange inhibition that relates such kinetic properties to physicochemical properties, including the free energies of enzyme-ligand binding, and estimate the latter through the first reported computational binding affinity calculations for SIRT3:NAD⁺, SIRT3:NAM, and analogous complexes for Sir2. The computational results support our kinetic model, establishing foundations for quantitative modeling of NAD⁺/NAM regulation of mammalian sirtuins during aging and the computational design of sirtuin activators that operate through alleviation of base exchange inhibition.     

Topographic components analysis of evoked potentials: estimation of model parameters and evaluation of parameter uniqueness

The purpose of this paper is to evaluate the practicability of the ‘topographic components model’ proposed by Möcks¹ for the spatio-temporal characterization of multi-channel evoked potentials (EP), and to present a complete and detailed algorithm for this method of analysis. Details of the algorithm are discussed along with various computational issues, especially with regard to contrasts with traditional principal components analysis. The algorithm is applied to multi-channel pattern-shift visual EP data obtained from normal subjects, and the model is demonstrated to provide data reduction of 71% with a relative mean-squared error (MSE) of 2%. Obvious features of the data are seen to be reflected in the estimated model parameters, lending support to the appropriateness of the model. The results also demonstrate that although the model parameters are uniquely identifiable in theory¹, care must be taken when fitting the model to insure that the MSE is not so insensitive to perturbations in the model parameters that they are rendered ‘non-unique’ for all practical purposes. The proper selection of model order is shown to play a critical role in avoiding this problem. Finally, a theoretical analysis is presented which evaluates the relationship between parameter ‘uniqueness’, model order, and the non-orthogonality of the model components.     

Immunophysical properties and prediction of activities for vaccinia virus complement control protein and smallpox inhibitor of complement enzymes using molecular dynamics and electrostatics

We present immunophysical modeling for VCP, SPICE, and three mutants using MD simulations and Poisson-Boltzmann-type electrostatic calculations. VCP and SPICE are homologous viral proteins that control the complement system by imitating, structurally and functionally, natural regulators of complement activation. VCP and SPICE consist of four CCP modules connected with short flexible loops. MD simulations demonstrate that the rather complex modules of VCP/SPICE and their mutants exhibit a high degree of intermodular spatial mobility, which is affected by surface mutations. Electrostatic calculations using snapshots from the MD trajectories demonstrate variable spatial distribution of the electrostatic potentials, which suggests dynamic binding properties. We use covariance analysis to identify correlated modular oscillations. We also use electrostatic similarity indices to cluster proteins with common electrostatic properties. Our results are compared with experimental data to form correlations between the overall positive electrostatic potential of VCP/SPICE with binding and activity. We show how these correlations can be used to predict binding and activity properties. This work is expected to be useful for understanding the function of native CCP-containing regulators of complement activation and receptors and for the design of antiviral therapeutics and complement inhibitors.     

Molecular interactions of alcohols with zeolite BEA and MOR frameworks

Zeolites can adsorb small organic molecules such as alcohols from a fermentation broth. Also in the zeolite-catalyzed conversion of alcohols to biofuels, biochemicals, or gasoline, adsorption is the first step. Several studies have investigated the adsorption of alcohols in different zeolites experimentally, but computational investigations in this field have mostly been restricted to zeolite MFI. In this study, the adsorption of C1–C4 alcohols in BEA and MOR was investigated using density functional theory (DFT). Calculated adsorption geometries and the corresponding energies of the designed cluster models were comparable to periodic calculations, and the adsorption energies were in the same range as the corresponding computational and experimental values reported in the literature for zeolite MFI. Thus, BEA and MOR may be good adsorption materials for alcohols in the field of downstream processing and catalysis. Aside from the DFT calculations, adsorption isotherms were determined experimentally in this study from aqueous solutions. For BEA, the adsorption of significant amounts of alcohol from aqueous solution was observed experimentally. In contrast, MOR was loaded with only a very small amount of alcohol. Although differences were found between the affinities obtained from gas-phase DFT calculations and those observed experimentally in aqueous solution, the computational data presented here represent molecular level information on the geometries and energies of C1–C4 alcohols adsorbed in zeolites BEA and MOR. This knowledge should prove very useful in the design of zeolite materials intended for use in adsorption and catalytic processes, as it allows adsorption behavior to be predicted via judiciously designed computational models.     

THE EFFECT OF AERATION ON THE GROWTH OF SPARTINA ALTERNIFLORA LOISEL.

A greenhouse experiment was designed to investigate the correlations between waterlogging and aeration, and associated changes in pH, redox potentials and sulfide concentrations, on the growth of Spartina alterniflora Loisel. Elemental concentrations of the aerial and root material were determined and used for correlations with growth response. Redox potentials adjusted to pH 7 (Eh 7) ranged from −184 mv to 5 mv and were highly correlated (r) with aerial and root dry weight biomass (.97 and .97, respectively) and plant height (1.0). The range of soil pH at the conclusion of the study was 6.07 to 6.74 and was negatively correlated with aerial and root dry weight biomass. Sulfide concentrations ranged from 10–² to 10–⁷ m and vorrelations with aerial and root dry weights and height were −.85, −.85 and −.87, respectively. High negative correlations were found between sodium and sulfur concentrations and S. alterniflora growth. Positive correlations between potassium, phosphorus, manganese, zinc, copper, iron and growth response were also observed. Correlations of elemental concentrations of the plants with redox potentials and/or pH suggest that these two physical variables may be responsible in part for the regulation of 5. alterniflora growth in nature by regulating availability of nutritional elements.     

Salt contribution to the flexibility of single‐stranded nucleic acid of finite length

Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this article, the salt effects on the flexibility of single‐stranded (ss) nucleic acid chain ranging from 12 to 120 nucleotides are investigated systematically by the coarse‐grained Monte Carlo simulations where the salt ions are considered explicitly and the ss chain is modeled with the virtual‐bond structural model. Our calculations show that, the increase of ion concentration causes the structural collapse of ss chain and multivalent ions are much more efficient in causing such collapse, and both trivalent/small divalent ions can induce more compact state than a random relaxation state. We found that monovalent, divalent, and trivalent ions can all overcharge ss chain, and the dominating source for such overcharging changes from ion‐exclusion‐volume effect to ion Coulomb correlations. In addition, the predicted Na⁺ and Mg²⁺‐dependent persistence length l_p’s of ss nucleic acid are in accordance with the available experimental data, and through systematic calculations, we obtained the empirical formulas for l_p as a function of [Na⁺], [Mg²⁺] and chain length. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 370–381, 2013.     

Molecular dynamics simulation of hydrated d(CGGGTACCCG)4 as a four-way DNA Holliday junction and comparison with the crystallographic structure

Molecular dynamics (MD) simulation of decamer sequence (CGGGTACCCG)₄ as a four-way Holliday junction is reported here for 15.0 ns at three different temperatures 100, 200 and 300 K, respectively, using AMBER force field. Particle mesh Ewald method has been utilised to deal long-range interaction potentials. After MD simulation, various parameters of the junction model including backbone and helical parameters have been worked out and the dynamical pathway is discussed. Structural analysis and geometrical calculations were carried out through X3DNA. The computational results obtained are compared with the previously reported crystallographic outcomes. The width and depth of the major and minor grooves of the duplex of the four arms of the DNA junction have been calculated. The variations in the C1′–C1′ distances between the two complementary strands are discussed in detail. A close observation of the results reveals that the conformation of the average simulated structure at low temperature is of ‘B’ form and the structural integrity of the DNA junction having a twofold sequence symmetry is temperature dependent. It also seems that besides the other parameters (i.e. presence of ions, solvents, etc.), temperature may be playing a key role in preserving the structural integrity of the DNA junction.     

On the stochastic dynamics of neuronal interaction

The response of many neurons in the nervous system is a nonlinear function of membrane potential. Nevertheless, if the membrane potentials are normally distributed then their covariance satisfies a linear equation. This suggests that information in the nervous system may be processed by correlations between membrane potentials, a hypothesis which is subject to direct experimental test. The acquisition, storage, and retrieval of information in the form of correlations is consistent with present knowledge of human information processing.     

Molecular dynamics simulations of membrane proteins

Membrane proteins control the traffic across cell membranes and thereby play an essential role in cell function from transport of various solutes to immune response via molecular recognition. Because it is very difficult to determine the structures of membrane proteins experimentally, computational methods have been increasingly used to study their structure and function. Here we focus on two classes of membrane proteins—ion channels and transporters—which are responsible for the generation of action potentials in nerves, muscles, and other excitable cells. We describe how computational methods have been used to construct models for these proteins and to study the transport mechanism. The main computational tool is the molecular dynamics (MD) simulation, which can be used for everything from refinement of protein structures to free energy calculations of transport processes. We illustrate with specific examples from gramicidin and potassium channels and aspartate transporters how the function of these membrane proteins can be investigated using MD simulations.