Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein

The c-Fos–c-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.

Elastic Properties of Boron Nitride Nanotubes and Their Comparison with Carbon Nanotubes

Boron Nitride Nanotubes (BNNTs) have alternating boron and nitrogen atoms in graphite like network and are strongly polar in nature due to a large charge on boron and nitrogen atoms. Hence electrostatic interactions are expected to play an important role in determining the elastic properties of BNNTs. In the absence of specific partial atomic charge information for boron and nitrogen, we have studied the elastic properties BNNTs varying the partial atomic charges on boron and nitrogen. We have computed Young modulus (Y) and Shear modulus (G) of BNNT as a function of the tube radius and number of walls using molecular mechanics calculation. Our calculation shows that Young modulus of BNNTs increases with increase in magnitude of the partial atomic charge on B and N and can be larger than the Young modulus of CNTs of same radius. This is in contrast to the earlier finding that CNTs has the largest tensile strength (PRL, 80, 4502, 1998). Shear modulus, on the other hand depends weakly on the magnitude of partial atomic charge and is less than the shear modulus of the CNT. The values obtained for Young modulus and Shear modulus are in excellent agreement with the available experimental results.

Roofed polyquinanes: synthesis and electronic structure

Starting from readily available norbornenobenzoquinone 7 and employing a photothermal metathesis reaction as the main strategy, novel "roofed" polyquinane bisenones 3 and 13 have been synthesized. Among these, the former is potentially serviceable for further elaboration to dodecahedrane 1. Catalytic hydrogenation of 3 provided the dione 12, which fully inscribes the circumference of dodecahedrane sphere. The "roofed" C-16-bisenone 3 has been successfully annulated to C19-bisenone 24 and C19-trisenone 26 by employing the Greene methodology and Pauson-Khand reaction, respectively. The molecular structures of 3 and 13 were computed using molecular mechanics and semiempirical MO methods. The nonbonded distances between the double bonds vary strongly with the method employed. The interactions between the pi-MO's were, therefore, probed by means of photoelectron (PE) spectroscopy. Comparison with the PE spectra of a series of model systems with increasing complexity enabled an unambiguous assignment of the observed peaks. The symmetric and antisymmetric combinations of the pi-MO's of the enone moieties of 3 and 13 show large splittings, characteristic of propano-bridged systems in which through-space and through-bond effects act in concert.

Modelling studies on neurodegenerative disease causing triplet repeat sequences d(CGG/GCC) and d(CAG/CTG): Duplexes vs Quadruplexes

Model building and molecular mechanics studies have been carried out to examine the potential structures for d(GGC/GCC)5 and d(CAG/CTG)5 that might relate to their biological function and association with triplet repeat expansion diseases. Model building studies suggested that hairpin and quadruplex structures could be formed with these repeat sequences. Molecular mechanics studies have demonstrated that the hairpin and hairpin dimmer structures of triplet repeat sequences formed by looping out of the two strands are as favourable as the corresponding B-DNA type hetero duplex structures. Further, at high salt condition, Greek key type quadruplex structures are energetically comparable with hairpin dimer and B-DNA type duplex structures. All tetrads in the quadruplex structures are well stacked and provide favourable stacking energy values. Interestingly, in the energy minimized hairpin dimer and Greek key type quadruplex structures, all the bases even in the non-G tetrads are cyclically hydrogen bonded, even though the A, C and T-tetrads were not hydrogen bonded in the starting structures.

Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

Conformational Polymorphism in G-tetraplex Structures: Strand Reversal by Base Flipover or Sugar Flipover

Guanine rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosidic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanine tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanines along a strand and different possible orientations of guanine strands in a G-tetraplex structure. It is found that for an oligo G stretch per se, a parallel four stranded structure with all guanines in anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanines along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosidic conformation and the inverted stacking arrangement arising from base flipover, in antiparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover

Guanlne rich sequences adopt a variety of four stranded structures, which differ in strand orientation and conformation about the glycosldic bond even though they are all stabilised by Hoogsteen hydrogen bonded guanlne tetrads. Detailed model building and molecular mechanics calculations have been carried out to investigate various possible conformations of guanlnes along a strand and different possible orientations of guanlne strands In a G-tetraplex structure. It is found that for an ollgo G stretch per se, a parallel four stranded structure with all guanines In anti conformation is favoured over other possible tetraplex structures. Hence an alternating syn-anti arrangement of guanlnes along a strand is likely to occur only in folded back tetraplex structures with antiparallel G strands. Our study provides a theoretical rationale for the observed alternation of glycosldic conformation and the inverted stacking arrangement arising from base filpover, In antlparallel G-tetraplex structures and also highlights the various structural features arising due to different types of strand orientations. The molecular mechanics calculations help in elucidating the various interactions which stabilize different G-tetraplex structures and indicate that screening of phosphate charge by counterions could have a dramatic effect on groove width in these four stranded structures.

Diastereospecific Coupling of Imines by Low-Valent Titanium: An Experimental and Computational Study

The reaction of phenylsilane (PhSiH3) and titanium(IV) isopropoxide Ti(OiPr)(4)] generates low-valent titanium alkoxides that reduce and reductively couple imines. The C-C coupling reaction is diastereospecific, with exclusive formation of the (+/-)-isomer. The yield is dependent on the concentration of titanium(IV) isopropoxide used. Using imines with varying electronic demand revealed that the coupling is most efficient for unsubstituted imines. The involvement of a trimeric titanium biradical species is invoked to explain the observed concentration dependence and diastereospecificity in the reaction. Multilayer ONIOM (''our own n-layered integrated molecular orbital and molecular mechanics'') calculations were carried out on the plausible intermediates involved by using the Guassian 09 suite of programs. Formation of the trimeric biradical species leading to the formation of the (+/-)-isomer is more favored than formation of the trimeric biradical species, which leads to the meso-isomer. Similar calculations with dimeric intermediates do not predict the (+/-)-selectivity. Mass spectral analysis of the reaction mixture indicates the presence of a trimeric titanium alkoxide species.

Analysis of geometric and strain effects in homo-Diels-Alder reactions

Molecular mechanics calculations have been carried out to quantify the key geometric and strain effects which are likely to control the homo-Diels-Alder reactivity of 1,4-dienes. The criteria considered include C1..C5 and C2..C4 distances in the diene, twist angle of the two pi units, and the magnitude of strain increase as a result of cycloaddition. By first considering these factors in a number of non-conjugated dienes with known reactivity, the ranges of values within which the reaction is favoured are proposed. Calculations are also reported on several substrates which have not been investigated so far. Promising systems for experimental study are suggested which, in addition to being intrinsically interesting, would place the present proposals on a firm basis.

Docking and free energy simulations to predict conformational domains involved in hCG-LH receptor interactions using recombinant antibodies

Single chain fragment variables (ScFvs) have been extensively employed in studying the protein-protein interactions. ScFvs derived from phage display libraries have an additional advantage of being generated against a native antigen, circumventing loss of information on conformational epitopes. In the present study, an attempt has been made to elucidate human chorionic gonadotropin (hCG)-luteinizing hormone (LH) receptor interactions by using a neutral and two inhibitory ScFvs against hCG. The objective was to dock a computationally derived model of these ScFvs onto the crystal structure of hCG and understand the differential roles of the mapped epitopes in hCG-LH receptor interactions. An anti-hCG ScFv, whose epitope was mapped previously using biochemical tools, served as the positive control for assessing the quality of docking analysis. To evaluate the role of specific side chains at the hCG-ScFv interface, binding free energy as well as residue interaction energies of complexes in solution were calculated using molecular mechanics Poisson-Boltzmann/surface area method after performing the molecular dynamic simulations on the selected hCG-ScFv models and validated using biochemical and SPR analysis. The robustness of these calculations was demonstrated by comparing the theoretically determined binding energies with the experimentally obtained kinetic parameters for hCG-ScFv complexes. Superimposition of hCG-ScFv model onto a model of hCG complexed with the 51-266 residues of LH receptor revealed importance of the residues previously thought to be unimportant for hormone binding and response. This analysis provides an alternate tool for understanding the structure-function analysis of ligand-receptor interactions. Proteins 2011;79:3108-3122. (C) 2011 Wiley-Liss, Inc.

Self-Assembly of Metallamacrocycles Using a Dinuclear Organometallic Acceptor: Synthesis, Characterization, and Sensing Study

A dinuclear organometallic acceptor 4,4'-bis[trans-Pt(PEt(3))(2)(O(3)SCF(3))(ethynyl)]biphenyl (1) containing Pt-ethynyl functionality is synthesized. Multinuclear NMR ((1)H, (31)P, and (13)C), infrared (IR), and electrospray ionization mass spectrometry (ESI-MS) including single-crystal X-ray diffraction analysis established the formation of 1. Equimolar treatment of acceptor 1 separately with three different ``clip'' type ditopic donors (L(a)-L(c)) yielded [2 + 2] self-assembled three metallamacrocycles 2a-2c, respectively. These macrocycles were characterized by various spectroscopic techniques, and their sizes/shapes were obtained through geometry optimization using molecular mechanics universal force field (MMUFF) simulations. Attachment of unsaturated ethynyl functionality to biphenyl building unit helped to make the macrocycles (2a-2c) pi-electron rich and thereby fluorescent in nature. Furthermore, 2c in solution has been examined to be suitable for sensing electron-deficient nitroaromatic like picric acid, which is often considered as a secondary chemical explosive. The fluorescence study of 2c showed a marked quenching of initial emission intensity upon titrating with picric acid (PA), and it exhibited the largest fluorescence quenching response with high selectivity among various other electron deficient aromatic compounds tested.

Pt-6(II) nanoscopic cages with an organometallic backbone as sensors for picric acid

An organometallic building block 1,3,5-tris(4-trans-Pt(PEt3)(2)I(ethynyl)phenyl)benzene (1) incorporating Pt-ethynyl functionality has been synthesized and characterized. 2 + 3] self-assembly of its nitrate analogue 1,3,5-tris(4-trans-Pt(PEt3)(2)(ONO2)(ethynyl)phenyl)benzene (2) with ``clip'' type bidentate donors (L-1-L-3) separately afforded three trigonal prismatic architectures (3a-3c), respectively. All these prisms were characterized and their shapes/sizes are predicted through geometry optimization employing molecular mechanics universal force field (MMUFF) simulation. The extended p-conjugation including the presence of Pt-ethynyl functionality makes them electron rich as well as luminescent in nature. Macrocycles 3b and 3c exhibit fluorescence quenching in solution upon addition of picric acid PA], which is a common constituent of many explosives. Interestingly, the non-responsive nature of fluorescent intensity towards other electron-deficient nitro-aromatic explosives (NAEs) makes them promising selective sensors for PA with a detection limit predicted to be ppb level. Furthermore, solid-state quenching of fluorescent intensity of the thin film of 3b upon exposure to saturated vapor of picric acid has drawn special attention for infield applications.

VIBRATIONAL CHARACTERISTICS OF ZIGZAG, ARMCHAIR AND CHIRAL CANTILEVER SINGLE-WALLED CARBON NANOTUBES

Finite element analysis has been performed to study vibrational characteristics of cantilever single walled carbon nanotubes. Finite element models are generated by specifying the C-C bond rigidities, which are estimated by equating energies from molecular mechanics and continuum mechanics. Bending, torsion, and axial modes are identified based on effective mass for armchair, zigzag and chiral cantilever single walled carbon nanotubes, whose Young's modulus is evaluated from the bending frequency. Empirical relations are provided for frequencies of bending, torsion, and axial modes.

A novel method for studying the buckling of nanotubes considering geometrical imperfections

Buckling of nanotubes has been studied using many methods such as molecular dynamics (MD), molecular mechanics, and continuum-based shell theories. In MD, motion of the individual atoms is tracked under applied temperature and pressure, ensuring a reliable estimate of the material response. The response thus simulated varies for individual nanotubes and is only as accurate as the force field used to model the atomic interactions. On the other hand, there exists a rich literature on the understanding of continuum mechanics-based shell theories. Based on the observations on the behavior of nanotubes, there have been a number of shell theory-based approaches to study the buckling of nanotubes. Although some of these methods yield a reasonable estimate of the buckling stress, investigation and comparison of buckled mode shapes obtained from continuum analysis and MD are sparse. Previous studies show that the direct application of shell theories to study nanotube buckling often leads to erroneous results. The present study reveals that a major source of this error can be attributed to the departure of the shape of the nanotube from a perfect cylindrical shell. Analogous to the shell buckling in the macro-scale, in this work, the nanotube is modeled as a thin-shell with initial imperfection. Then, a nonlinear buckling analysis is carried out using the Riks method. It is observed that this proposed approach yields significantly improved estimate of the buckling stress and mode shapes. It is also shown that the present method can account for the variation of buckling stress as a function of the temperature considered. Hence, this can prove to be a robust method for a continuum analysis of nanosystems taking in the effect of variation of temperature as well.

Electronically nonadiabatic decomposition mechanisms of clusters of zinc and dimethylnitramine

Electronically nonadiabatic decomposition mechanisms of dimethylnitramine (DMNA) in presence of zinc metal clusters are explored. Complete active space self-consistent field (CASSCF) calculation is employed for DMNA-Zn and ONIOM (Our own N-layered integrated molecular orbital and molecular mechanics) methodology is coupled with CASSCF methodology for DMNA-Zn-10 cluster. Present computational results show that DMNA-Zn clusters undergo electronically nonadiabatic reactions, rendering nitro-nitrite isomerization followed by NO elimination. The overall reactions are also found to be highly exothermic in nature. This is the first report on electronically nonadiabatic decomposition pathways of DMNA-Zn-n neutral clusters. (C) 2014 Elsevier B.V. All rights reserved.