Search results for "Biomolecules"

Solution NMR structure of aD,L-alternating oligonorleucine as a model of ?-helix

2001

beta-Helix structures are of particular interest due to their capacity to form transmembrane channels with different transport properties. However, the relatively large number of beta-helices configurations does not allow a direct conformational analysis of beta-helical oligopeptides. A synthetic alternating D,L-oligopeptide with twelve norleucines (XIIMe) has been used as a model to get insight in the conformational features of beta-helix structures. The spatial configuration of XIIMe in solution has been determined by NMR. An extensive set of distances (nuclear Overhauser effect) and dihedral (J coupling constants) constraints have been included in molecular dynamics calculations. The NMR…

The Transoid, Ortho, and Gauche Conformers of Decamethyl-n-tetrasilane, n-Si4Me10:  Electronic Transitions in the Multistate Complete Active Space Se…

2003

Multistate complete active space second-order perturbation theory (MS-CASPT2) is used to improve earlier descriptions of the low-energy valence excited states of the transoid, ortho, and gauche conformers of decamethyl-n-tetrasilane, n-Si4Me10, using a generally contracted basis set of atomic natural orbitals (ANOs) at a ground-state geometry optimized in the second-order Moller−Plesset perturbation theory (MP2) approximation with Dunning's correlation consistent triple-ζ basis set (cc-pVTZ) on the silicon atoms and the 6-31G* and 6-31G basis sets on the carbon and hydrogen atoms, respectively. Relative energies, relative free energies, and mole fractions of the transoid, ortho, and gauche …

Effective approach for calculations of absolute stability of proteins using focused dielectric constants

2009

The ability to predict the absolute stability of proteins based on their corresponding sequence and structure is a problem of great fundamental and practical importance. In this work, we report an extensive, refinement and validation of our recent approach (Roca et al., FEBS Lett 2007;581:2065-2071) for predicting absolute values of protein stability DeltaG(fold). This approach employs the semimacroscopic protein dipole Langevin dipole method in its linear response approximation version (PDLD/S-LRA) while using the best fitted values of the dielectric constants epsilon'(p) and epsilon'(eff) for the self energy and charge-charge interactions, respectively. The method is validated on a divers…

Molecular-dynamics simulation of a glassy polymer melt: Rouse model and cage effect

1999

We report results of molecular-dynamics simulations for a glassy polymer melt consisting of short, linear bead-spring chains. It was shown in previous work that this onset of the glassy slowing down is compatible with the predictions of the mode coupling theory. The physical process of `caging' of a monomer by its spatial neighbors leads to a distinct two step behavior in the particle mean square displacements. In this work we analyze the effects of this caging process on the Rouse description of the melt's dynamics. We show that the Rouse theory is applicable for length and time scales above the typical scales for the caging process. Futhermore, the monomer displacement is compared with si…

Formation of Micelles in Homopolymer-Copolymer Mixtures:  Quantitative Comparison between Simulations of Long Chains and Self-Consistent Field Calcul…

2006

Using Monte Carlo simulations of the bond fluctuation model and self-consistent field calculations, we study the formation of micelles in a mixture of homopolymers and asymmetric AB-diblock copolymers with composition, fA = 1/8. Both types of molecules are fully flexible and have identical length. We work in the semi-grand-canonical ensemble, i.e., we fix the monomer density and incompatibility, χN ≃ 100 (strong segregation regime), and control the composition of the mixture via the exchange chemical potential, δμ ≡ μAB − μB between the copolymers and homopolymers. The Monte Carlo simulation comprises moves that allow homopolymers to mutate into AB-diblock copolymers and vice versa. These m…

Anharmonic activations in proteins and peptide model systems and their connection with supercooled water thermodynamics

2016

International audience; — Proteins, the nano-machines of living systems, are highly dynamic molecules. The timescale of functionally relevant motions spans over a very broad range, from femtoseconds to several seconds. In particular, the pico-to nanoseconds region is characterized by side-chain and backbone anharmonic fluctuations that are responsible for many biological tasks like ligand binding, substrate recognition and enzymatic activity. Neutron scattering on hydrated protein powders reveals two main activations of anharmonic dynamics, characterized by different onset temperature and amplitude. Here we review our work on synthetic polypeptides, native proteins, and single amino acids t…

1988

Light scattering, neutron scattering and viscosity measurements on a nematic and a smectic polymethacrylate demonstrate the presence of molecularly disperse coils in solution. For the nematic polymer, toluene is a theta solvent, the behaviour familiar from conventional polymers (unperturbed coil conformation) being exhibited at the theta point. The isotropic melts likewise contain unperturbed coils; in the case of the nematic polymers, however, the coils in the melt have a radius of gyration which is about 30% smaller than that in solution at the theta point. In the liquid-crystalline phase, the mean radii of gyration in both cases are identical to the corresponding parameters in the isotro…

Feature selection on a dataset of protein families: from exploratory data analysis to statistical variable importance

2016

Proteins are characterized by several typologies of features (structural, geometrical, energy). Most of these features are expected to be similar within a protein family. We are interested to detect which features can identify proteins that belong to a family, as well as to define the boundaries among families. Some features are redundant: they could generate noise in identifying which variables are essential as a fingerprint and, consequently, if they are related or not to a function of a protein family. We defined an original approach to analyze protein features for defining their relationships and peculiarities within protein families. A multistep approach has been mainly performed in R …

Crystal structure of 1-ferrocenyl-2-(4-methyl-benzo-yl)spiro-[11H-pyrrolidizine-3,11'-indeno[1,2-b]quinoxaline].

2014

In the title compound the four-fused-rings system is approximately planar and the pyrrolidine rings of the pyrrolidizine fragment adopt a twist conformation. In the crystal, mol­ecules are linked by C—H⋯O hydrogen bonds and C—H⋯π inter­actions, forming double-chains parallel to the c axis.

Crystal structure of (1S,2R,4S)-1-[(morpholin-4-yl)methyl]-4-(prop-1-en-2-yl)cyclohexane-1,2-diol

2014

Besides intra­molecular O—H⋯N hydrogen bonds, the crystal structure displays inter­molecular O—H⋯O and C—H⋯O hydrogen bonds linking the mol­ecules into undulating layers parallel to the (01) plane.