Biomedical subjects

S B Engelsen

Publications and source records attributed to S B Engelsen.

9 recordsLinked to original sources

PubMed2001

The diluted aqueous solvation of carbohydrates as inferred from molecular dynamics simulations and NMR spectroscopy.

The purpose of this paper is to review our understanding of the dilute hydration (aqueous solvation) behaviour of disaccharide compounds. To this end we discuss and scrutinize the results that have been obtained for the three model disaccharides: maltose, sucrose and trehalose from experimental NMR studies and from theoretical molecular dynamics studies in explicit aqueous solutions. The focus is on the description of molecular hydration features that will influence macroscopic entities such as diffusion and relaxation: residence times of hydration waters, hydration numbers and hydration densities. The principles of molecular dynamics simulation are briefly outlined while a detailed presentation is given of the key features that characterise hydration: the solvation of the glycosidic linkage, the radial hydration of the solute, the water density anisotropy around the solute, the residential behaviour of water molecules in the periphery of the solute, and rotational and translational diffusion coefficients. With respect to the use of NMR in characterising the structure and dynamics of the hydration, the hydrodynamic theory of rotational and translational diffusion of biomolecules as well as the use of pulse field gradient spin echo experiments are briefly presented. The NMR-defined rotational diffusion coefficients (D(r)) and the experimentally determined translational diffusion (D(t)) coefficients are reported for 4% (w/w) solutions of sucrose, trehalose and maltose. These results are compared with theoretical data obtained from molecular dynamics simulations of sucrose, trehalose and maltose under identical conditions (concentration, temperature, etc.). With our present level of knowledge we can propose that although carbohydrates share a number of hydration characteristics, evidence is accumulating in support of the notion that it is not the amount or overall hydration but rather the detailed individual carbohydrate-water interaction that is likely to determine carbohydrate structure and functionality.

Carbohydrate Conformation↗

PubMed2001

Evaluation of quality changes in walnut kernels (Juglans regia L.) by Vis/NIR spectroscopy.

Storage of walnut kernels in light and at room temperature, as is common practice, is detrimental to their sensory quality and shelf life. This study demonstrates that Vis/NIR spectroscopy, in combination with multivariate data analysis (chemometrics), is a most capable rapid method for monitoring the overall quality deterioration of walnut kernels. Spectral predictions of the sensory attributes nutty and rancid tastes by partial least-squares regression (PLSR) resulted in correlations (r(2)) of 0.77 and 0.86, respectively, whereas with PLSR prediction of the chemical parameter hexanal content a correlation (r(2)) of 0.72 was obtained. The study further establishes that storage in light results in pronounced oxidative changes, especially in walnuts stored at 21 degrees C, whereas dark storage at 5 degrees C results in walnuts without any trace of rancid taste during 25 weeks of storage at accelerated storage conditions (50% oxygen).

Food Handling↗

PubMed1999

The mean hydration of carbohydrates as studied by normalized two-dimensional radial pair distributions.

The hydration of carbohydrates plays a key role in many biological processes. Molecular dynamics simulations provide an effective tool for investigating the hydration of complex solutes such as carbohydrates. In this article we devise an algorithm for the calculation of two-dimensional radial pair distributions describing the probability of finding a water molecule in a site defined by two reference atoms. The normalized 2D radial pair distribution is proposed as an effective tool for investigating and comparing localized or ordered water sites around flexible molecules such as carbohydrates when analyzing molecular dynamics simulations and the utility of 2D radial pair distributions is demonstrated using sucrose as an example. In this relatively simple structure, 2D radial pair distributions were able to characterize and quantify the importance of two unique interresidue hydration sites in which a water molecule is forming a bridge between the glycopyranosyl and fructofuranosyl residues. The approach is proposed to be a valuable tool for comparing and understanding the hydration of flexible biomolecules such as carbohydrates.

Algorithms↗

PubMed1999

Presence and dehydration of ikaite, calcium carbonate hexahydrate, in frozen shrimp shell.

Ikaite, calcium carbonate hexahydrate, has by means of X-ray diffraction analyses of frozen samples been identified as the mineral component of the white spots formed in the shell of frozen shrimp during storage. When the shrimp thaw and the shell material is dried and kept at room temperature, ikaite rapidly transforms into a mixture of anhydrous calcium carbonate forms. X-ray diffraction analyses and Raman spectra of synthetic ikaite as well as the dehydration product confirm the assignments, and the rate constant for dehydration is approximately 7 x 10(-)(4) s(-)(1) at ambient temperature. Differential scanning calorimetry showed that dehydration of synthetic ikaite is an entropy-driven, athermal process and confirms that a single first-order reaction is rate-determining. Ikaite is found to be stable in aqueous solution at temperatures below 5 degrees C and in the shell of frozen shrimps but decomposes on thawing to form anhydrous calcium carbonates.

Animals↗

PubMed1997

Internal motions and hydration of sucrose in a diluted water solution.

This paper represents a synthesis of our most recent work on the hydration, internal and overall dynamics of sucrose in a diluted water solution. The studies were carried out as a total ensemble of 1.2 nanosecond condensed phase molecular dynamics trajectories. In this study the focus is on a 500 ps trajectory starting with the solute in the crystalline conformation. The presence of water was found to significantly alter the accessible conformational space of the solute. All potential intra-molecular hydrogen bonds were found to be exchanged to surrounding water molecules and the simulations suggest that the sucrose conformation is stabilized by the dynamic presence of two interring bridging water molecules: O-2g...Ow...O-3f and O-2g...Ow...O-lf. The overall shift in conformation of the solute induced by the presence of water was found to improve the theoretical models of experimental traits. It is demonstrated that the hydration structure and the internal and overall motions of sucrose compare extremely well with NMR data such as glycosidic heteronuclear coupling constants and the molecular tumbling time, with X-ray data of two partially hydrated sucrose structures in a protein complex and with translational diffusion coefficients and hydration numbers established from experimental studies.

Carbohydrate Conformation↗

PubMed1996

A molecular builder for carbohydrates: application to polysaccharides and complex carbohydrates.

A new procedure (POLYS) for producing three-dimensional structures of polysaccharides and complex carbohydrates is described. This employs a builder concept combining a database of monosaccharide structures with a database containing information on populations of independent neighboring glycosidic linkages in disaccharide fragments. The computer program is written in C, and it can cope with both the complexity and the diversity of carbohydrates and the unique topological features arising from multiple branching. A simple ASCII syntax was developed for describing the primary structures in accordance with IUPAC nomenclature. The translation of the primary structure is made through the combined use of a lexical analyzer and a command interpreter. In this way the program can be considered as a compiler of primary structures of carbohydrates. However, it also generates secondary and tertiary structures in the form of Cartesian coordinates in formats used by most molecular mechanics programs and packages. In our laboratory POLYS was exhaustively tested on standard homopolysaccharide systems such as cellulose and mannan and found to work very well. We now report the ease of use and the efficiency of the molecular builder in applications to more complex carbohydrate systems. These include the structural exploration of a pentaantennary oligosaccharide having 135 residues, the complex family of pectic polysaccharides including the organization and distribution of side chains (arabinan, arabinogalactan, and galactan) on the rhamnogalacturonan backbone.

Algorithms↗

PubMed1996

Modeling polysaccharides: present status and challenges.

The most recent tools that have been developed for modeling the three-dimensional features of polysaccharides and carbohydrate polymers are presented. The presentation starts with a description of the conformations of the monosaccharides, and of the flexible rings such as in the case of five-membered rings, and a thorough description of the conformational space that is available for a disaccharide unit, either in vacuo or in an aqueous phase. The extension to the modeling of the parent polysaccharides is addressed, based on the assumption that owing to the size and relative rigidity of the intervening monosaccharides units, the rotations at a particular linkage can be, under some conditions, considered as independent of nearest neighbor interactions. Appropriate modeling techniques are described that can provide insights into the dimensions of the chain in a solution which is best described as a random coil accompanied by the occurrence of local "helical" regions. With the help of such descriptors such as helical parameters, the ordered state of polysaccharide strands can be readily characterized. The generation of double or triple helices can be then attempted in order to explore the occurrence of such multi-stranded arrangements that may be energetically stable. The final step in the determination of the structure of polysaccharides in the ordered state, is the investigation of the interactions of different helices. This may lead to either the best arrangement(s) between two polymeric chains, or to the prediction of the dimensions, and the symmetry of a three-dimensional lattice. Some of the tools which have been developed should allow automatic scarches for meaningful correlations between structures and functions, through exploratory data analysis. Structure-function or structure-property correlation could be then used to model changes arising from structural alterations. This would open the field of polysaccharide engineering.

Carbohydrate Conformation↗

PubMed1995

Travelling on the potential energy surfaces of carbohydrates: comparative application of an exhaustive systematic conformational search with an heuristic search.

The calculated ensembles found by a heuristic conformational search algorithm, CICADA, for three small carbohydrates, ethyl beta-lactoside, methyl alpha-D-galactoside, and methyl beta-D-galactoside, are evaluated in terms of their ability to reproduce time-averaged optical rotation and NMR data. A unique dynamic model for methyl beta-D-galactoside has been obtained by fitting experimental NOESY volumes to the theoretical ones elaborated from the CICADA ensemble internuclear distances with the model-free formalism. In the case of ethyl beta-lactoside, the CICADA ensemble is compared to that of an exhaustive systematic grid-search method. The CICADA algorithm proved to be a very efficient method to find most of the important minima on even very complex potential energy surfaces, and the spectral quality of the CICADA ensemble was found to be of equal quality, if not superior, to that of the exhaustive systematic grid-search method. The CICADA algorithm has several advantages over other conformational search algorithms: (1) It has polynomial dependence of dimensions on computer time in contrast to the grid search, which has exponential dependence, (2) the conformations found are free of artificial harmonic constraint potentials, (3) it passes all barriers amongst families of conformations on conformational hypersurface but spends almost all its time in the essential highly populated areas, (4) the inherent properties of the algorithm make rigorous minimization criteria superfluous and provide good convergence behavior, and (5) as an important spin-off, it provides low-energy interconversion pathways that can, amongst others, be used for estimating adiabatic rotational barriers.

Algorithms↗

PubMed1993

Conformations of disaccharides by empirical force field calculations. Part V: Conformational maps of beta-gentiobiose in an optimized consistent force field.

A recently optimized set of potential energy functions is used to investigate the conformational flexibility of the beta-(1-->6) glycosidic linkage in beta-gentiobiose. Relaxed Ramachandran maps in vacuo are presented in the torsional angles phi and omega, with torsional angle psi allowed to relax freely, as are all other internal degrees of freedom. The study reveals two almost iso-energetic low energy domains in (phi, psi, omega) space, and cross-sections in the low-energy domains at omega = -60 degrees and omega = 60 degrees show that more than 60% and 70% respectively of the area of the conformational maps are accessible within 40 kJ mol-1. The molecular structure in the crystal, including the exoanomeric effect, is well reproduced. The structure belongs to the potential energy well which includes the global potential energy minimum in vacuo. The most profound structural difference between the crystal structure and the calculated global minimum in vacuo is the 20 degrees deviation of the psi torsional angle (24 degrees from perfect trans). It occurs in the most flexible glucosidic degree of freedom, psi, and is caused by optimization of the hydrogen bonding network and not by the exoanomeric effect.

Carbohydrate Conformation↗