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At least 1,369 records · Page 76Linked to original sources
PubMed2003

Probing the conformational and dynamical effects of O-glycosylation within the immunodominant region of a MUC1 peptide tumor antigen.

MUC1 mucin is a large transmembrane glycoprotein, the extracellular domain of which is formed by a repeating 20 amino acid sequence, GVTSAPDTRPAPGSTAPPAH. In normal breast epithelial cells, the extracellular domain is densely covered with highly branched complex carbohydrate structures. However, in neoplastic breast tissue, the extracellular domain is under-glycosylated, resulting in the exposure of a highly immunogenic core peptide epitope (PDTRP in bold above), as well as in the exposure of normally cryptic core Tn (GalNAc), STn (sialyl alpha2-6 GalNAc) and TF (Gal beta1-3 GalNAc) carbohydrates. Here, we report the results of 1H NMR structural studies, natural abundance 13C NMR relaxation measurements and distance-restrained MD simulations designed to probe the structural and dynamical effects of Tn-glycosylation within the PDTRP core peptide epitope. Two synthetic peptides were studied: a nine-residue MUC1 peptide of the sequence, Thr1-Ser2-Ala3-Pro4-Asp5-Thr6-Arg7-Pro8-Ala9, and a Tn-glycosylated version of this peptide, Thr1-Ser2-Ala3-Pro4-Asp5-Thr6(alphaGalNAc)-Arg7-Pro8-Ala9. The results of these studies show that a type I beta-turn conformation is adopted by residues PDTR within the PDTRP region of the unglycosylated MUC1 sequence. The existence of a similar beta-turn within the PDTRP core peptide epitope of the under-glycosylated cancer-associated MUC1 mucin protein might explain the immunodominance of this region in vivo, as the presence of defined secondary structure within peptide epitope regions has been correlated with increased immunogenicity in other systems. Our results have also shown that Tn glycosylation at the central threonine within the PDTRP core epitope region shifts the conformational equilibrium away from the type I beta-turn conformation and toward a more rigid and extended state. The significance of these results are discussed in relation to the possible roles that peptide epitope secondary structure and glycosylation state may play in MUC1 tumor immunogenicity.

Amino Acid Sequence↗
PubMed2004

Self-assembly and properties of diblock copolymers by coarse-grain molecular dynamics.

Block-copolymer amphiphiles have been observed to assemble into vesicles and other morphologies long known for lipids but with remarkably different properties. Coarse-grain molecular dynamics (CG-MD) is used herein to elaborate the structures and properties of diblock copolymer assemblies in water. By varying the hydrophilic/hydrophobic ratio of the copolymer in line with experiment, bilayer, cylindrical and spherical micelle morphologies spontaneously assemble. Varying the molecular weight (MW) with hydrophilic/hydrophobic ratio appropriate to a bilayer yields a hydrophobic core thickness that scales for large MW as a random coil polymer, in agreement with experiment. The extent of hydrophobic-segment overlap in the core increases nonlinearly with MW, indicative of chain entanglements and consistent with the dramatic decrease reported for lateral mobility in polymer vesicles. Calculated trends with MW as well as hydrophilic/hydrophobic ratio thus agree with experiment, demonstrating that CG-MD simulations provide a rational design tool for diblock copolymer assemblies.

Computer Simulation↗
PubMed2002

Loss of a metal-binding site in gelsolin leads to familial amyloidosis-Finnish type.

Mutations in domain 2 (D2, residues 151-266) of the actin-binding protein gelsolin cause familial amyloidosis-Finnish type (FAF). These mutations, D187N or D187Y, lead to abnormal proteolysis of plasma gelsolin at residues 172-173 and a second hydrolysis at residue 243, resulting in an amyloidogenic fragment. Here we present the structure of human gelsolin D2 at 1.65 A and find that Asp 187 is part of a Cd2+ metal-binding site. Two Ca2+ ions are required for a conformational transition of gelsolin to its active form. Differential scanning calorimetry (DSC) and molecular dynamics (MD) simulations suggest that the Cd2+-binding site in D2 is one of these two Ca2+-binding sites and is essential to the stability of D2. Mutation of Asp 187 to Asn disrupts Ca2+ binding in D2, leading to instabilities upon Ca2+ activation. These instabilities make the domain a target for aberrant proteolysis, thereby enacting the first step in the cascade leading to FAF.

Amino Acid Substitution↗
PubMed2003

Pulling geometry defines the mechanical resistance of a beta-sheet protein.

Proteins show diverse responses when placed under mechanical stress. The molecular origins of their differing mechanical resistance are still unclear, although the orientation of secondary structural elements relative to the applied force vector is thought to have an important function. Here, by using a method of protein immobilization that allows force to be applied to the same all-beta protein, E2lip3, in two different directions, we show that the energy landscape for mechanical unfolding is markedly anisotropic. These results, in combination with molecular dynamics (MD) simulations, reveal that the unfolding pathway depends on the pulling geometry and is associated with unfolding forces that differ by an order of magnitude. Thus, the mechanical resistance of a protein is not dictated solely by amino acid sequence, topology or unfolding rate constant, but depends critically on the direction of the applied extension.

Anisotropy↗
PubMed2004

Structure and K+ ion-dependent stability of a parallel-stranded DNA quadruplex containing a core A-tetrad.

The c-MYC oncogene, containing the DNA 5'-GGAGG repeat sequence, is emerging as an attractive target for anti-cancer therapeutics with evidence to suggest that DNA quadruplex formation is involved in regulating gene transcription. We describe NMR studies and molecular dynamics (MD) simulations on intermolecular quadruplex structures containing the purine-rich GGAGG motif which we show readily assembles to form stable parallel-stranded quadruplexes containing A- and G-tetrads with evidence for weak sequence-specific K(+) ion binding at the 5'-GA step.

Antineoplastic Agents↗
PubMed2004

Preferred dimerization of tetra-tolyl- and tetra-tosylurea derivatives of flexible and rigidified calix[4]arenes.

The dimerization of tetratolyl- and tetratosyl-urea derivatives 1 and 2, derived from a tetrapentoxy calix[4]arene in the cone conformation and of the corresponding tetra-urea derivatives 3 and 4, in which the cone conformation is rigidified by the two crown-3 tethers, have been studied. All six possible equimolar mixtures were examined by 1H NMR using CDCl3 and CD2Cl2 as solvents. While no heterodimers are found for the combinations 1/3 and 2/4 in either solvent, all remaining combinations lead to the (exclusive) formation of heterodimers in CD2Cl2. In CDCl3 heterodimers are only observed for the combinations of 3 with 2 or 4. These results are discussed in terms of entropic and enthalpic contributions and compared with MD-simulations in a box of chloroform solvent molecules.

Calixarenes↗
PubMed2006

Be(II) in aqueous solution--an extended ab initio QM/MM MD study.

An ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation at double-zeta restricted Hartree-Fock (RHF) level was performed at 293.15 K, including first and second hydration shell in the QM region to study the structural and dynamical properties of the Be(II)-hydrate in aqueous solution. The first tetrahedrally arranged hydration shell, with the four water molecules located at a mean Be-O distance of 1.61 A, is highly inert with respect to ligand exchange processes. The second shell, however, consisting in average of approximately 9.2 water ligands at a mean Be-O distance of 3.7 A and the third shell at a mean Be-O distance of 5.4 A with approximately 19 ligands rapidly exchange water molecules between them and with the bulk, respectively. Other structural parameters such as radial and angular distribution functions (RDF and ADF) and tilt- and theta-angle distributions were also evaluated. The dynamics of the hydrate were studied in terms of ligand mean residence times (MRTs) and librational and vibrational frequencies. The mean residence times for second shell and third shell ligands were determined as 4.8 and 3.2 ps, respectively. The Be-O stretching frequency of 658 cm(-1), associated with a force constant of 147 N m(-1) could be overestimated but it certainly reflects the exceptional stability of the ion-ligand bond in the first hydration shell.

Beryllium↗
PubMed2006

Orientational preferences of aromatic guests in dimeric capsules of tetraurea calix[4]arenes--MD and NMR studies.

Molecular dynamics (MD) simulations have been performed for complexes of a dimeric capsule of a tetraurea calixarene with a series of twelve aromatic guests. A distinct orientational preference and a restriction of the internal mobility was found which depend on the size and electronic properties of the guests. The results are in agreement with the CIS values obtained from (1)H NMR spectroscopic measurements and with complexation selectivities obtained by competition experiments.

Benzene Derivatives↗
PubMed2006

Formation of left-handed helices in hybrid peptide oligomers with cis beta-sugar amino acid and L-Ala as building blocks.

Residue based control of specific helical folding is explored in hybrid peptide oligomers consisting of alternating L-Ala and cis-beta-furanoid sugar amino acid (FSAA) residues as building blocks; two series of these hybrid oligomers are designed, synthesized and extensively characterized by using NMR, CD, FT-IR and MD simulation studies; results show the co-existence of left-handed 11- and 14/15-helical conformations in these short oligomers of Boc-(alpha/beta) and Boc-(beta/alpha) series.

Alanine↗
PubMed2004

The effects of solute-solvent electrostatic interactions on solvatochromic shifts in supercritical CO2.

Solvent clustering around attractive solutes is an important feature of supercritical solvation. We examine here the effects of the local density enhancement on solvatochromic shifts in electronic absorption and emission spectra in supercritical CO2. We use molecular dynamics (MD) simulation to study the spectral line shifts for model diatomic solutes that become more polar upon electronic excitation. The electronic transition is modeled as either a change from a quadrupolar to a dipolar solute charge distribution or as an increase in the magnitude of the solute dipole. Our main focus is on the density dependence of the line shifts at 320 K, which corresponds to about 1.05 times the solvent critical temperature, Tc, but results for higher temperatures are also obtained in order to determine the behavior of the line shifts in the absence of local density enhancement. We find that the extent of local density enhancement at 1.05Tc is strongly correlated with solute-solvent electrostatic attraction and that the density dependence of the emission line shifts resembles the behavior of the effective local densities, rho(eff), obtained from the first-shell coordination numbers. The differences that are seen are shown to be due to solute-solvent orientational correlations which provide an additional source of enhancement for electrostatic solvation energies and spectral line shifts.

Journal Article↗
PubMed2004

Theoretical studies of the kinetics of methane hydrate crystallization in external electromagnetic fields.

Nonequilibrium molecular-dynamics (MD) simulations have been performed for the growth and dissolution of a spherical methane hydrate crystallite, surrounded by a saturated water-methane liquid phase, in both the absence and presence of external electromagnetic (e/m) fields in the microwave to far infrared range (5-7500 GHz) at root-mean square (rms) electric field intensities of up to 0.2 V/A. A rigid/polarizable potential was used to model water and a rigid/nonpolarizable model was utilized for methane. In the absence of a field, it was found that the average growth rate of the crystallite was approximately 0.32 water and 0.045 methane molecules per picosecond, evaluated over a 500 ps NPT simulation for three different initial geometries. Upon the application of an e/m field, it was found that no significant deviations from the zero-field crystal growth patterns were observed for rms electric field intensities of less than about 0.1 V/A, regardless of the field frequency. At, and above, this "threshold" intensity, it was found that dissolution took place. The mobility of the molecules in the system was enhanced by the e/m field, to the greatest extent for frequencies of 50-100 GHz. Furthermore, it was observed that there was a systematic frequency variation in the pattern of dipole alignment with the external field and this led to marked differences in the rate of dissolution.

Journal Article↗
PubMed2004

Theoretical study of the local structure and Raman spectra of CaO-SiO2 binary melts.

A procedure for the Raman spectra calculation of vitreous and molten silicates was presented in this paper. It includes molecular dynamics MD simulation for the generation of equilibrium configurations, Wilson's GF matrix method for the calculations of eigenfrequencies and corresponding vectors, electro-optical parameters method (EOPM) for the Raman intensity calculations, and the bond polarizability model (BPM) for the determination of polarizability and polarizability derivative. One of the most important characteristics of this procedure is the achievement of the partial Raman spectra of five tetrahedral units, as well as the total spectral envelope. In this paper, the calculation was carried out for the vitreous and molten calcium silicates with different compositions and at various temperatures. It is worthwhile to note that the calculation is based on statistical configurations distribution in the space and so it is not needed to artificially adjust the full width at half maximum (FWHM) of spectra. It was also tested through the good agreement of the calculated spectra with the experimental, including some regularity of spectral properties. According to the calculation, the symmetrical stretching of whole tetrahedral units, to which the stretching of Si-O(nb) bond gives the main contribution to intensity, is proven to be the dominance in the high-frequency range (800-1200 cm(-1)) and the symmetrical bending of Si-O(b)-Si, to which the stretching of Si-O(b) bond exhibits the main contribution, is the dominance in the medium-frequency range (400-700 cm(-1)). As the first theoretical results, the Raman scattering coefficient of each Q(i) was found little change along with the variation of composition and temperature.

Journal Article↗
PubMed2004

An application of coupled reference interaction site model/molecular dynamics to the conformational analysis of the alanine dipeptide.

We present an application of our recently proposed coupled reference interaction site model (RISM) molecular dynamics (MD) solvation free energy methodology [Freedman and Truong, Chem. Phys. Lett. 381, 362 (2003); J. Chem. Phys. 121, 2187 (2004)] to study the conformational stability of alanine dipeptide in aqueous solution. In this methodology, radial distribution functions obtained from a single MD simulation are substituted into a RISM expression for solvation free energy. Consequently, iterative solution of the RISM equation is not needed. The relative solvation free energies of seven different conformations of the alanine dipeptide in aqueous solution are calculated. Results from the coupled RISM/MD methodology are in good agreement with those from earlier simulations using the accurate free energy perturbation approach, showing that the alphaR conformation is most stabilized by solution. This study establishes a framework for applying this coupled RISM/MD method to larger biological systems.

Alanine↗
PubMed2005

The merits of the frozen-density embedding scheme to model solvatochromic shifts.

We investigate the usefulness of a frozen-density embedding scheme within density-functional theory [J. Phys. Chem. 97, 8050 (1993)] for the calculation of solvatochromic shifts. The frozen-density calculations, particularly of excitation energies have two clear advantages over the standard supermolecule calculations: (i) calculations for much larger systems are feasible, since the time-consuming time-dependent density functional theory (TDDFT) part is carried out in a limited molecular orbital space, while the effect of the surroundings is still included at a quantum mechanical level. This allows a large number of solvent molecules to be included and thus affords both specific and nonspecific solvent effects to be modeled. (ii) Only excitations of the system of interest, i.e., the selected embedded system, are calculated. This allows an easy analysis and interpretation of the results. In TDDFT calculations, it avoids unphysical results introduced by spurious mixings with the artificially too low charge-transfer excitations which are an artifact of the adiabatic local-density approximation or generalized gradient approximation exchange-correlation kernels currently used. The performance of the frozen-density embedding method is tested for the well-studied solvatochromic properties of the n-->pi(*) excitation of acetone. Further enhancement of the efficiency is studied by constructing approximate solvent densities, e.g., from a superposition of densities of individual solvent molecules. This is demonstrated for systems with up to 802 atoms. To obtain a realistic modeling of the absorption spectra of solvated molecules, including the effect of the solvent motions, we combine the embedding scheme with classical molecular dynamics (MD) and Car-Parrinello MD simulations to obtain snapshots of the solute and its solvent environment, for which then excitation energies are calculated. The frozen-density embedding yields estimated solvent shifts in the range of 0.20-0.26 eV, in good agreement with experimental values of between 0.19 and 0.21 eV.

Journal Article↗