Electrostatic interactions play an essential role in DNA repair and cold-adaptation of Uracil DNA glycosylase

Life has adapted to most environments on earth, including low and high temperature niches. The increased catalytic efficiency and thermoliability observed for enzymes from organisms living in constantly cold regions when compared to their mesophilic and thermophilic cousins are poorly understood at the molecular level. Uracil DNA glycosylase (UNG) from cod (cUNG) catalyzes removal of uracil from DNA with an increased k_cat and reduced K_m relative to its warm-active human (hUNG) counterpart. Specific issues related to DNA repair and substrate binding/recognition (K_m) are here investigated by continuum electrostatics calculations, MD simulations and free energy calculations. Continuum electrostatic calculations reveal that cUNG has surface potentials that are more complementary to the DNA potential at and around the catalytic site when compared to hUNG, indicating improved substrate binding. Comparative MD simulations combined with free energy calculations using the molecular mechanics-Poisson Boltzmann surface area (MM-PBSA) method show that large opposing energies are involved when forming the enzyme-substrate complexes. Furthermore, the binding free energies obtained reveal that the Michaelis-Menten complex is more stable for cUNG, primarily due to enhanced electrostatic properties, suggesting that energetic fine-tuning of electrostatics can be utilized for enzymatic temperature adaptation. Energy decomposition pinpoints the residual determinants responsible for this adaptation. Figure Electrostatic isosurfaces of cod uracil DNA glycosylase in complex with double stranded DNA     

First principles calculations on the influence of water-filled cavities on the electronic structure of Prussian Blue

Prussian Blue is a paradigmatic mixed valence material and a parent compound to a broad family of electronically, optically, and magnetically active materials. Its exact composition varies greatly depending on the preparation route, leading to large variations in its electronic properties. The influence of water molecules on the structural and electronic properties of Prussian Blue were studied using state-of-the-art first principles calculations. Water-filled cavities were found to have a profound influence on the band gap and density of states of this material while simultaneously leaving many of its properties largely unchanged. The resulting model of an almost independent superimposition of dehydrated material and hydrated sites is briefly discussed. Unit cell of “insoluble” Prussian Blue used in calculations     

Molecular electrostatic potentials in aromatic substituted 4-hydroxyquino-2-lones: Glycine/NMDA receptor antagonists

Hydroxyquinolone derivatives have proven to be useful for inhibition at the glycine binding site of N-methyl-D-aspartate (NMDA) receptor. In this work the electronic structure, molecular electrostatic potential (MESP) and vibrational characteristics of a set of C₃ substituted 4-hydroxyquino-2-lone (HQ) derivatives, which act as Glycine/NMDA receptor antagonists, have been investigated using the density functional calculations. In the optimized structures a substituent at the C₃ site of HQ tends to adopt a helical structure. MESP investigations reveal that the ligands showing better inhibition activity should possess electron-rich regions extending over the substituent and carbonyl group of HQ. A correlation of inhibitory activity to the molecular electrostatic potential topography at the carbonyl oxygen as well as to the molecular electron density topography turns out to be a significant output of the investigation. Figure Quantam chemical approach has been employed to understand the reactivity of a set of hydroxyquinolone derivatives known for their inhibition activity towards Glycine/NMDA receptor. Molecular electrostatic potential topography has been used as a tool to understand the reactivity pattern     

Pattern recognition based on color-coded quantum mechanical surfaces for molecular alignment

A pattern recognition algorithm for the alignment of drug-like molecules has been implemented. The method is based on the calculation of quantum mechanical derived local properties defined on a molecular surface. This approach has been shown to be very useful in attempting to derive generalized, non-atom based representations of molecular structure. The visualization of these surfaces is described together with details of the methodology developed for their use in molecular overlay and similarity calculations. In addition, this paper also introduces an additional local property, the local curvature (C _L), which can be used together with the quantum mechanical properties to describe the local shape. The method is exemplified using some problems representing common tasks encountered in molecular similarity. Figure Molecular surfaces for Lorazepam (left) and Diazepam (right)     

Interaction of copper organometallic precursors with barrier layers of Ti, Ta and W and their nitrides: a first-principles molecular dynamics study

Processes for the deposition of copper films on transition metal barrier layers by means CVD using organometallic precursors are often found to lead to poor adhesion characteristics of the grown film. By means of first-principles molecular dynamics simulations, we show that the source of the problem is the strong reactivity of the surfaces toward the precursors, which decompose spontaneously upon contact with the surface leading to contamination of the interface. Our simulations consider Ti, Ta, and W as barrier layers, and Cu(hfac)-(tmvs) as precursor. In contrast, we show that surfaces of these metals properly passivated with nitrogen, in such a way that only N atoms are exposed on the surface, are much less active and do not lead to decomposition of the precursor. We propose this passivation procedure as a practical solution to the adhesion problem. Figure CupraSelect on the WN (100) surface     

Three-dimensional structure of the catalytic domain of the yeast β-(1,3)-glucan transferase Gas1: a molecular modeling investigation

The three-dimensional (3D) structure of the catalytic domain of Gas1p, a protein belonging to the only family of β-(1,3)-glucan transferases so far identified in yeasts and some pathogenic fungi (family GH-72), has been predicted by combining results derived from threading methods, multiple sequence alignments and secondary-structure predictions. The 3D model has allowed the identification of several residues that are predicted to play a crucial role in structural integrity, substrate recognition and catalysis. In particular, the model of the catalytic domain can be useful for designing site-directed mutagenesis experiments and for developing inhibitors of Gas1p enzymatic activity. Figure Three-dimensional models of the Gas1p catalytic domain as predicted using as template 7A3H (PDB code) protein Electronic Supplementary Material Supplementary material is available for this article at     

Non-empirical study of the phosphorylation reaction catalyzed by 4-methyl-5-β-hydroxyethylthiazole kinase: relevance of the theory of intermolecular interactions

The subject of this study was an analysis of the role of active site residues in the phosphoryl transfer reaction catalyzed by 4-methyl-5-β-hydroxyethylthiazole kinase (ThiK). The ThiK-catalyzed reaction is of special interest due to the lack of a highly conserved aspartate residue serving as a catalytic base. ONIOM(B3LYP:PM3) models of stationary points along the reaction pathway consisted of reactants, two magnesium ions and several highly conserved ThiK active site residues. The results indicate that an S_N2-like mechanism of ThiK, with γ-phosphate acting as an alcohol-activating base is reasonable. Geometries of substrates, transition state and products were utilized in the non-empirical analysis of the physical nature of catalytic interactions taking place in the ThiK active site. The role of particular residues was investigated in terms of their ability to preferentially stabilize the transition state relative to substrates (differential transition state stabilization, DTSS) or products (differential product stabilization, DPS). It seems that Mg2, Glu126 and Cys198 play a major catalytic role, whereas Mg1 and the same Cys198 are responsible for product release. It is remarkable that no dominant role of an electrostatic term in the interactions involved in catalytic activity is observed for product release. Determination of catalytic fields expressing differential electrostatic potential of the transition state with respect to substrates revealed the optimal electrostatic features of an ideal catalyst for the studied reaction. The predicted catalytic environment is in agreement with experimental data showing increased catalytic activity of ThiK upon mutation of Cys198 to aspartate. Figure Catalytic fields for ThiK-catalyzed reaction juxtaposed with the positions of active site residues of a model system. Magnesium ions are considered part of the transition state/reactants. The surface of constant electronic density is colored according to differential electrostatic potential of transition state with respect to reactants. The sign of the differential potential reflects the electrostatic properties of a complementary molecular environment. Red (green) color denotes regions where a negative (positive) charge would be optimal for catalytic activity     

Proton transfer in some periodic molecular systems

The electronic structure of representative hydrogen bonded systems: hydrogen cyanide, imidazole and malonic acid have been studied at the non-empirical level. The role of the dimensionality on the potential barrier for the proton transfer has been examined. It was shown that it depends on the crystal structure and only in some cases like hydrogen cyanide or imidazole the relevant crystals may be considered as one-dimensional. However, for more complicated crystallographic structures, e.g. malonic acid, the evaluated barrier is strongly dependent on the dimensionality taken into account in our calculations. Figure Density of states for the imidazole dimer: MD-EQ- standard proton position (black line), MD-TR- proton position in the middle of the hydrogen bond (red line)     

CoMFA study of distamycin analogs binding to the minor-groove of DNA: a unified model for broad-spectrum activity

A 3D-QSAR analysis has been carried out by comparative molecular field analysis (CoMFA) on a series of distamycin analogs that bind to the DNA of drug-resistant bacterial strains MRSA, PRSP and VSEF. The structures of the molecules were derived from the X-ray structure of distamycin bound to DNA and were aligned using the Database alignment method in Sybyl. Statistically significant CoMFA models for each activity were generated. The CoMFA contours throw light on the structure activity relationship (SAR) and help to identify novel features that can be incorporated into the distamycin framework to improve the activity. Common contours have been gleaned from the three models to construct a unified model that explains the steric and electrostatic requirements for antimicrobial activity against the three resistant strains. Figure A unified CoMFA model for broad-spectrum DNA minor-groove binders     

DFT tests for group 8 transition metal carbonyl complexes

The applicability of several popular density functionals in predicting the geometrical parameters and energetics of transition metal carbonyl complexes of iron, ruthenium and osmium has been studied. The methods tested include pure GGA functionals (BLYP, BP86, OPBE, HCTH, PBE, VSXC) and hybrid GGA functionals (B3PW91, B3LYP, PBE1PBE, MPW1K, B97-2, B1B95, PBE1KCIS). The effect of changing the metal basis set from Huzinaga’s all-electron basis to SDD scECP basis was also studied. The results show, that hybrid functionals are needed in order to describe the back-bonding ability of the carbonyl ligands as well as to deal with metal-metal bonds. The best general performance, when also the computational cost was considered, was obtained with hybrid functionals B3PW91 and PBE1PBE, which therefore provide an efficient tool for solving problems involving large or medium sized transition metal carbonyl compounds. Figure Optimized structure for one of the test molecules, the Ru₃(CO)₁₂ cluster, showing the staggered conformation of the carbonyl ligands     

3D-QSAR and docking studies of 3-arylquinazolinethione derivatives as selective estrogen receptor modulators

3D-QSAR and molecular docking analysis were performed to explore the interaction of estrogen receptors (ERα and ERβ) with a series of 3-arylquinazolinethione derivatives. Using the conformations of these compounds revealed by molecular docking, CoMFA analysis resulted in the first quantitative structure-activity relationship (QSAR) and first quantitative structure-selectivity relationship (QSSR) models predicting the inhibitory activity against ERβ and the selectivity against ERá. The q² and R² values, along with further testing, indicate that the obtained 3D-QSAR and 3D-QSSR models will be valuable in predicting both the inhibitory activity and selectivity of 3-arylquinazolinethione derivatives for these protein targets. A set of 3D contour plots drawn based on the 3D-QSAR and 3D-QSSR models reveal modifications of substituents at C2 and C5 of the quinazoline which my be useful to improve both the activity and selectivity of ERβ/ ERα. Results showed that both the steric and electrostatic factors should appropriately be taken into account in future rational design and development of more active and more selective ERβ inhibitors for the therapeutic treatment of osteoporosis. Figure Structures of ERβ binding with compounds 1aar, 1ax and 1aag obtained from molecular docking     

3D-QSAR studies of Dipeptidyl peptidase IV inhibitors using a docking based alignment

Dipeptidyl peptidase IV (DPP-IV) deactivates the incretin hormones GLP-1 and GIP by cleaving the penultimate proline or alanine from the N-terminal (P1-position) of the peptide. Inhibition of this enzyme will prevent the degradation of the incretin hormones and maintain glucose homeostasis; this makes it an attractive target for the development of drugs for diabetes. This paper reports 3D-QSAR analysis of several DPP-IV inhibitors, which were aligned by the receptor-based technique. The conformation of the molecules in the active site was obtained through docking methods. The QSAR models were generated on two training sets composed of 74 and 25 molecules which included phenylalanine, thiazolidine, and fluorinated pyrrolidine analogs. The 3D-QSAR models are robust with statistically significant r², q², and values. The CoMFA and CoMSIA models were used to design some new inhibitors with several fold higher binding affinity. Figure The CoMFA contours around molecule D1T155 (a) steric contours - favored (green); disfavored (yellow) (b) electrostatic contours - electropositive (blue); electronegative (red)     

A three-dimensional model of the human transglutaminase 1: insights into the understanding of lamellar ichthyosis

The stratum corneum, the outer layer of the epidermis, serves as a protective barrier to isolate the skin from the external environment. Keratinocyte transglutaminase 1 (TGase 1) catalyzes amide crosslinking between glutamine and lysine residues on precursor proteins forming the impermeable layers of the epidermal cell envelopes (CE), the highly insoluble membranous structures of the stratum corneum. Patients with the autosomal recessive skin disorder lamellar ichthyosis (LI) appear to have deficient cross-linking of the cell envelope due to mutations identified in TGase 1, linking this enzyme to LI. In the absence of a crystal structure, molecular modeling was used to generate the structure of TGase 1. We have mapped the known mutations of TGase 1 from our survey obtained from a search of PubMed and successfully predicted the impact of these mutations on LI. Furthermore, we have identified Ca²⁺ binding sites and propose that Ca²⁺ induces a cis to trans isomerization in residues near the active site as part of the enzyme transamidation activation. Docking experiments suggest that substrate binding subsequently induces the reverse cis to trans isomerization, which may be a significant part of the catalytic process. These results give an interpretation at the molecular level of previously reported mutations and lead to further insights into the structural model of TGase 1, providing a new basis for understanding LI. Figure Ribbon image of the model of the human TGase 1 structure. The side chains of residues reported to be mutated in patients with LI (34 amino acid mutation sites) are shown as spheres. This paper is dedicated to the memory of Dr. Peter M. Steinert (April 7, 2003).     

Aromaticity and electronic properties of Heterosuperbenzene (Heterohexabenzocoronene)

A global electrophilicity parameter and the aromaticity of some heterocyclic polyaromatic hydrocarbons were evaluated on the basis of DFT calculations. The substitution of carbon atoms by nitrogen atoms dramatically changes the global electrophilicity of the molecules, with the fully substituted molecule being the most electrophilic with a reactivity very close to that of fullerene. Figure Fully substituted heterohexabenzocoronene Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Cold-active enzymes studied by comparative molecular dynamics simulation

Enzymes from cold-adapted species are significantly more active at low temperatures, even those close to zero Celsius, but the rationale of this adaptation is complex and relatively poorly understood. It is commonly stated that there is a relationship between the flexibility of an enzyme and its catalytic activity at low temperature. This paper gives the results of a study using molecular dynamics simulations performed for five pairs of enzymes, each pair comprising a cold-active enzyme plus its mesophilic or thermophilic counterpart. The enzyme pairs included α-amylase, citrate synthase, malate dehydrogenase, alkaline protease and xylanase. Numerous sites with elevated flexibility were observed in all enzymes; however, differences in flexibilities were not striking. Nevertheless, amino acid residues common in both enzymes of a pair (not present in insertions of a structure alignment) are generally more flexible in the cold-active enzymes. The further application of principle component analysis to the protein dynamics revealed that there are differences in the rate and/or extent of opening and closing of the active sites. The results indicate that protein dynamics play an important role in catalytic processes where structural rearrangements, such as those required for active site access by substrate, are involved. They also support the notion that cold adaptation may have evolved by selective changes in regions of enzyme structure rather than in global change to the whole protein. Figure Collective motions in C^α atoms of the active site of cold-active xylanase Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

The structure of 5a,6–anhydrotetracycline and its Mg2+ complexes in aqueous solution

Semiempirical molecular orbital theory has been used for a systematic scan of the binding positions for a Mg²⁺ ion with 5a,6–anhydrotetracycline taking both conformational flexibility and possible different tautomeric forms into account. The magnesium ion has been calculated alone and with four or five complexed water molecules in order to simulate the experimental situation more closely. The results are analyzed by comparing the behavior of the title compound with that of tetracycline itself and possible causes for the stronger induction of the Tetracycline Receptor (TetR) by 5a,6–anhydrotetracycline than by tetracycline are considered. Energetically favored 3D -structure of the zwitteranionic 5a,6-anhydrotetracycline magnesium complex in solution Electronic Supplementary Material Supplementary material is available for this article at     

CHIH-DFT determination of the molecular structure and IR and UV spectra of solanidine

Solanidine is the steroidal aglycon of some potato glycoalkaloids and a very important precursor for the synthesis of hormones and some pharmacologically active compounds. In this work, we make use of a new chemistry model within Density Functional Theory, called CHIH-DFT, to calculate the molecular structure of solanidine, as well to predict its infrared and ultraviolet spectra. The calculated values are compared with the experimental data available for this molecule as a means of validation of our proposed chemistry model. Figure Molecular structure of solanidine calculated with the CHIH(small) model chemistry     

Modeling study of the influences of the aromatic transitions and the local environment on the far-UV rotational strengths in TEM-1 β-lactamase

Rotational strengths in the far-UV of TEM-1 β-lactamase have been investigated with two theoretical models based on the matrix method. The first model excludes, and a second includes, effects of the local electrostatic interactions on the chromophore energies. Special attention is given to the contributions of the aromatic side-chain chromophores, and the mechanisms of generation of rotational strengths are analyzed. The sensitivity of the computational models with respect to the structural changes of the protein are discussed. Figure Structure of TEM-1 β-lactamase. Both domains—α and αβ, the secondary structural elements and the aromatic and disulfide chromophores are shown     

Halogen bonding and the design of new materials: organic bromides, chlorides and perhaps even fluorides as donors

In some halides RX, the halogen X has a region of positive electrostatic potential on its outermost portion, centered around the extension of the R−X bond. The electrostatic attraction between this positive region and a lone pair of a Lewis base is termed halogen bonding. The existence and magnitudes of such positive potentials on some covalently bonded halogens, and the characteristic directionality of the interaction, can be explained in terms of the degree of sp hybridization and polarizability of X and the electronegativity of R. Halogen bonding increases in strength in the order Cl < Br < I; fluorine is frequently said to not form halogen bonds, although a notable result of the present study is computational evidence that it does have the capability of doing so, if R is sufficiently electron withdrawing. An increasingly important application of halogen bonding is in the design of new materials (e.g., crystal engineering). In this paper, we present the calculated energies of a series of halogen-bonding interactions that could be the basis for forming linear chains, of types X----X----X---- or X----Y----X----Y----. We focus upon chlorides and bromides, and nitrogen bases. The B3PW91/6-311G(3df,2p) and MP2/6-311++G(3df,2p) procedures were used. We show how the computed electrostatic potentials (B3PW91/6-31G**) can provide guidance in selecting appropriate halide/base pairs. Figure Computed electrostatic potential of CH₃CH₂Br on the molecular surface defined by the 0.001-au contour of the electronic density. The bromine is facing the reader, and has a small positive (green) region centered around the intersection of the C–Br axis with the surface     

Molecular dynamics study of the initial stages of catalyzed single-wall carbon nanotubes growth: force field development

Effective force fields for Ni-C interactions developed by Yamaguchi and Maruyama for the formation of metallofullerenes are modified to simulate the catalyzed growth of single-wall carbon nanotubes on Ni_n clusters with n >20, and the reactive empirical bond order Brenner potential for C-C interactions is also revised to include the effect of the metal atoms on such interactions. Figure Force field parameters for carbon-metal interactions obtained from DFT calculations in small clusters.