Nonextensive Statistical Mechanics Application to Vibrational Dynamics of Protein Folding

The vibrational dynamics of protein folding is analyzed in the framework of Tsallis statistics. We employ exact expressions for classical harmonic oscillators by considering the unnormalized constraints. As q→1, we show that these approximations agree with the result of Gaussian network model.     

Polymer-attractive spherical cage system

We analyze the structural behavior of a single polymer chain inside an attractive sphere. Our model is composed of a coarse-grained polymer governed by Lennard-Jones interactions of the monomers and an attractive sphere potential which follows by integrating the monomer-monomer interaction over the (inner) surface of the sphere. By means of extensive multicanonical Monte Carlo simulations it is shown that the system exhibits a rich phase diagram in the adsorption strength-temperature (ε ? T) plane ranging from highly ordered and compact to extended and random coil structures and from desorbed to partially or even completely adsorbed conformations. These findings are identified with different energetic and structural observables. The resulting phase diagram in the ε ? T plane is compared with that for a polymer adsorbing to a plane, attractive substrate obtained previously by Möddel, Bachmann, and one of the authors.     

Comparison of the ELP and multicanonical methods in simulation of the heptapeptide deltorphin

To investigate the performance of the energy landscape paving (ELP) procedure for peptides, we apply it here to deltorphin, a linear heptapeptide with bulky side chains (H-Tyr¹-D-Met²-Phe³-His⁴-Leu⁵-Met⁶-Asp⁷-NH₂) and compare the results with the Multicanonical method (MUCA) in regard of finding the low-energy structures. Deltorphin is modeled in vacuum by the potential energy function ECEPP. Received 23 July 2002 / Received in final form 18 September 2002 Published online 31 December 2002     

Conformational properties of surfactant-like peptides with variable glycine tails

The three-dimensional structures of surfactant-like peptides containing 4-10 glycines as the components of the hydrophobic tails and aspartic acids as the hydrophilic heads (G₄D₂, G₆D₂, G₈D₂, G₁₀D₂) are investigated by using the multicanonical simulation procedure. The thermodynamically most stable low energy structures of the sequences are determined. Ramachandran plots are prepared and analyzed to predict the secondary structure motifs of the molecules.     

Searching low-energy conformations of two elastin sequences

The three-dimensional structures of two common repeat motifs Val¹-Pro²-Gly³-Val⁴-Gly⁵ and Val¹-Gly²-Val³-Pro⁴-Gly⁵-Val⁶-Gly⁷-Val⁸-Pro⁹ of tropoelastin are investigated by using the multicanonical simulation procedure. By minimizing the energy structures along the trajectory the thermodynamically most stable low-energy microstates of the molecule are determined. The structural predictions are in good agreement with X-ray diffraction experiments.Received: 12 December 2003, Published online: 15 March 2004PACS: 02.70.Lq 02.70.Lq Monte Carlo and statistical methods - 05.50. + q Lattice theory and statistics (Ising, Potts, etc.) - 82.20.Wt Computational modeling; simulation     

Exploring and exploiting the reactivity of glucuronic acid donors

The relative reactivity of glucuronic acid esters was established in a series of competition experiments, in which two thioglucoside and/or thioglucuronic acid ester donors competed for a limited amount of activator (NIS-TfOH). Although glucuronic acid esters are often considered to be of very low reactivity, the series of competition reactions revealed that the reactivity of the glucuronic acid esters studied is sufficient to provide productive glycosylation reactions. The latter is illustrated in the synthesis of two Streptococcus pneumoniae trisaccharides, in which the applicability of the two similarly protected frame-shifted thiodisaccharide donors, Glc-GlcA and GlcA-Glc, were compared. The Glc-GlcA disaccharide, featuring the glucuronic acid donor moiety, proved to be the most productive in the assembly of a protected S. pneumoniae trisaccharide.     

LASER PHOTOLYSIS OF 3-METHYLLUMIFLAVIN

Abstract— Using high-intensity actinic light, the chlorophyll a fluorescence transient from HCO^-₃-depleted chloroplasts shows a rapid initial rise (O → I) followed by a slow phase (I → P). In the presence of HCO^-₃, the O → I rise is delayed but the I → P phase is much more rapid. Using low-intensity actinic light, the chlorophyll a fluorescence transient from 3-(3,4-dichlorophenyl)-1,1 dimethylurea (DCMU)-treated chloroplasts is delayed in the presence of HCO^-₃. Bicarbonate increases the amount of delayed light emission from chloroplasts given 10 s illumination with weak blue light (0·4 W/m²). DCMU greatly increases the amount of delayed light seen in the presence of HCO^-₃ under these conditions but decreases the amount seen in the absence of HCO^-₃. It is suggested that HCO^-₃ may somehow form or stabilize, in the dark, a number of reaction centers corresponding to the S₁ state in the model of B. Forbush, B. Kok and M. McGloin ( Photochem. Photobiol. 14, 307–321, 1971).