Fusion Peptide Interaction with Lipid Bilayer: Modeling with Monte Carlo Simulation and Continuum Electrostatics Calculation

Abstract

Conformation of 20-residue peptide E5, an analog of the fusion peptide of influenza virus hemagglutinin, was explored by Monte-Carlo technique starting with the fully buried in the membrane ideal α-helix. The lipid bilayer (of 30 Å width) together with surrounding water were modeled by the atomic solvation parameters. During the simulation, residues 2–18 of the peptide retained α-helical conformation, and the peptide was found to be partially immersed into the bilayer. In the resulting low-energy conformers, the N-terminus was buried inside the membrane, its position with respect to the bilayer surface (Z_NT) being varied from 2.5 to 7.5 Å, and the orientation of the helical axis relative to the membrane plane (Θ) – from 10 to 35°. The low-energy conformers (below -200kcal/mol) were clustered in the space (Z_NT, Θ) into 4 groups. To select low-energy states of the peptide compatible with NMR data, we calculated pKa values of E5 ionizable groups and compared them with the experimental values. It was shown that the best correlation coefficient (0.87) and rmsd (0.68 in pH units) were obtained for the group of states which is characterized by Θ = 15–19° and Z_NT = 3.5–4.5Å.     

Interactions of Quinoxaline Antibiotic and DNA.: The Molecular Structure of a Triostin A—d(GCGTACGC) Complex

Abstract

The crystal structure of a DNA. octamer d(GCGTA.CGC) complexed to an antitumor antibiotic, triostin A, has been solved and refined to 2.2 Å resolution by x-ray diffraction analysis. The antibiotic molecule acts as a true bis intercalator surrouding the d(CpG) sequence at either end of the unwound right-handed DNA. double helix. A.s previously observed in the structure of triostin A.—d(CGTA.CG) complex (A.H.-J. Wang, et. al., Science, 225,1115–1121 (1984)), the alanine amino acid residues of the drug molecule form sequence-specific hydrogen bonds to guanines in the minor groove. The two central A · T base pairs are in Hoogsteen configuration with adenine in the syn conformation. In addition, the two terminal G · C base pairs flanking the quinoxaline rings are also held together by Hoogsteen base pairing. This is the first observation in an oligonucleotide of. Hoogsteen G · C base pairs where the cytosine is protonated. The principal functional components of a bis-intercalative compound are discussed.     

Cooperative Interactions of the Gene 5 Protein

Abstract

Using the refined molecular structure of the Gene 5 DNA Binding Protein (G5BP) and the mechanism of DNA binding deduced from a variety of experimental techniques (G. D. Brayer and A. McPherson, J. Mol. Biol. 169, 565, 1983; G. D. Brayer and A. McPherson, Biochemistry 23, 340, 1984), we have modeled the contiguous, linear aggregation of G5BP dimers along two opposing single strands of DNA. Using both automated graphics systems and systematic calculations of intermolecular contacts between adjacent units, we have optimized the fit of complementary protein surfaces in the presence of DNA. We propose that a minor conformational change involving residues 38–43, triggered by the binding of nucleic acid, relieves several critical steric contacts and permits otherwise extensively complementary surfaces to form an interface. The bonding between surfaces on adjacent G5BP units is the primary source of the cooperativity of binding observed for G5BP. The interacting amino acid residues at the interface are described.     

192 Computer-aided search for novel anti-HIV-1 agents presenting peptidomimetics of broadly neutralizing antibodies against the virus envelope GP120 V3 loop

Computer-aided search for novel anti-HIV-1 agents that are able to imitate the pharmacophore properties of the antigen-binding site of a broadly neutralizing mAb 3074 against the envelope gp120 V3 loop was carried out followed by evaluation of their potential inhibitory activity by molecular modeling. In doing so, the following problems were solved: (1) the mAb 3074 amino acid residues responsible for specific binding to the HIV-1 V3 loop were identified from the X-ray structures of this antibody Fab in complexes with the MN, UR29, and VI191 V3 peptides (Jiang et al., 2010); (2) using these data, 2039 possible mAb-3074 peptidomimetics were found by pepMMsMIMIC presenting a public, web-oriented virtual screening platform (Floris et al., 2011); (3) the complexes of these compounds with the above V3 peptides were built by molecular docking and, based on their analysis, the four molecules exhibiting a high affinity to V3 in the in silico studies were selected as the most probable peptidomimetics of mAb 3074 (Figure 1); and (4) stability of the complexes of these molecules with the MN, UR29, and VI191 V3 peptides was estimated by molecular dynamics and free energy simulations. As a result, a key role in specific binding of the selected compounds to the V3 loop was shown to belong to π-π interactions between their aromatic rings and the conserved Phe20 and/or Tyr21 of the V3 immunogenic crown. Similarly to mAb 3074, these compounds were found to block the tip of the V3 loop forming its invariant structural motif, which contains residues critical for cell tropism (Andrianov et al., 2011; Andrianov et al., 2012). In addition, the complexes of interest do not undergo significant changes within the molecular dynamics calculations, exhibiting the low values of free energy of their formation. In this context, the compounds given in Figure 1 are considered as the promising basic structures for the design of novel, potent, and broad anti-HIV-1 drugs.     

Monte Carlo Simulation of Hydration of the Guanine-Uracil Pairs with Guanine in Two Tautomeric Forms: Contribution of Water Bridging to Relative Stability of Mispairs

Abstract

Results are presented from Monte Carlo simulation of hydration of guanine-uracil mispairs by 25 and 50 water molecules. The hydration shells of three mispairs formed between “normal” dioxo form of uracil (U) and three forms of guanine (“normal” amino-oxo tautomer G and two rotamers of the “rare” amino-hydroxy tautomer G*) depend on the tautomeric forms of the guanine molecule. The simulation shows the important role of hydration effects on the relative stability of the mispairs.     

Allowance for Spatial Dispersion of Dielectric Permittivity in Polyelectrolyte Model of DNA

Abstract

In order to allow for real dielectric properties of a solvent in calculating of electrostatic characteristics of strongly charged polyions such as DNA in salt solution we consider a simple model of linear dielectric response of a medium. The interactions between charged particles are treated in the framework of self-consistent-field approximation. The basic characteristic of the problem, electrostatic potential, can be found from the solution of non-linear integro-differential equation. Specifically we consider so-called quasimacroscopic model where dielectric response of a medium depends only on the distance from the polyion. Application of the approach for calculating of the B-to-Z free energy qualitatively retains the main conclusion obtained previously within the model with fixed dielectric constant: non-monotonous behavior of the free energy difference as a function of ionic strength. At the same time, essential sensitivity of the results to specific values of dielectric parameters is observed.     

144 Sculpting light with DNA origami

We used the DNA origami method (Rothemund, 2006) for the fabrication of self-assembled nanoscopic materials (Seeman, 2010). In DNA origami, a virus-based 8?kilobase-long DNA single-strand is folded into shape with the help of ～ 200 synthetic oligonucleotides. The resulting DNA nanostructures can be designed to adopt any three-dimensional shape and can be addressed through DNA hybridization or chemical modification with nanometer precision. We have realized that complex assemblies of nanoparticles, including magnetic, fluorescent, and plasmonic nanoparticles. Such nanoconstructs may exhibit striking optical properties such as strong optical activity in the visible range (Kuzyk et al., 2012). To this end, plasmonic particles were assembled in solution to form helices of controlled handedness. We achieved spatial control over particle placement better than 2?nm and attachment yields of 97% and above. As a collective optical response emerging from our dispersed nanostructures, we detected pronounced circular dichroism (CD) originating from the plasmon–plasmon interactions in the particle helices. In recent experiments, we were able to show that the optical response of chiral biomolecules can be transferred from the UV into the visible region in plasmonic hotspots. Thus, sensitive detection of chiral biomolecules may become feasible in the near future. We also found that the orientation of the helices in respect to the incoming light beam critically influences the resulting CD spectra. Our results can be explained with theoretical models based on plasmonic dipole interaction and demonstrate the potential of DNA origami for the assembly of metafluids with designed optical properties.     

Comparison of Complex DNA Mixtures with Generic Oligonucleotide Microchips

Abstract

The reproducibility of melting curves for repeated hybridizations of target DNA with generic oligonucleotide microchips is shown experimentally to depend on the character of matching between fragments of target DNA and immobilized oligonucleotides. The reproducibility of melting curves is higher for the perfect match duplexes and decreases as the number of mismatched pairs within duplexes increases. This effect was applied to the comparative analysis of complex DNA mixtures. We developed a scheme in which we can identify and discriminate between the probe oligonucleotides responsible for the distinctions between target DNA mixtures. A scheme is illustrated by comparing DNA mixtures corresponding to VD-J genes connected with populations of mRNAs CDR3 TCR Vb (T-cell receptor beta complementarity determining region 3) from the thymus and pancreas of NOD mice. Our results demonstrate that generic microchips can be applied efficiently to the analysis of DNA mixtures.     

Atomic Force Microscopy Imaging of Double Stranded DNA and RNA

Abstract

A procedure for imaging long DNA and double stranded RNA (dsRNA) molecules using Atomic Force Microscopy (AFM) is described. Stable binding of double stranded DNA molecules to the flat mica surface is achieved by chemical modification of freshly cleaved mica under mild conditions with 3-aminopropyltriethoxy silane. We have obtained striking images of intact lambda DNA, Hind III restriction fragments of lambda DNA and dsRNA from reovirus. These images are stable under repeated scanning and measured contour lengths are accurate to within a few percent. This procedure leads to strong DNA attachment, allowing imaging under water. The widths of the DNA images lie in the range of 20 to 80nm for data obtained in air with commercially available probes. The work demonstrates that AFM is now a routine tool for simple measurements such as a length distribution. Improvement of substrate and sample preparation methods are needed to achieve yet higher resolution.     

Melting of Cross-Linked DNA IV. Methods for Computer Modeling of Total Influence on DNA Melting of Monofunctional Adducts,Intrastrand and Interstrand Cross-Links Formed by Molecules of an Antitumor Drug

Abstract

A theoretical method is developed for calculation of melting curves of covalent complexes of DNA with antitumor drugs. The method takes into account all the types of chemical modifications of the double helix caused by platinum compounds and DNA alkylating agents: 1) monofunctional adducts bound to one nucleotide; 2) intrastrand cross-links which appear due to bidentate binding of a drug molecule to two nucleotides that are included into the same DNA strand; 3) interstrand cross-links caused by bidentate binding of a molecule to two nucleotides of different strands. The developed calculation method takes into account the following double helix alterations at sites of chemical modifications: 1) a change in stability of chemically modified base pairs and neighboring ones, that is caused by all the types of chemical modifications; 2) a change in the energy of boundaries between helical and melted regions at sites of chemical modification (local alteration of the factor of cooperativity of DNA melting), that is caused by all the types of chemical modifications, too; 3) a change in the loop entropy factor of melted regions that include interstrand cross-links; 4) the prohibition of divergence of DNA strands in completely melted DNA molecules, which is caused by interstrand cross-links only. General equations are derived, and three calculation methods are proposed to calculate DNA melting curves and the parameters that characterize the helix-coil transition.