Studying Lactoferrin N-Glycosylation.

Lactoferrin is a multifunctional glycoprotein found in the milk of most mammals. In addition to its well-known role of binding iron, lactoferrin carries many important biological functions, including the promotion of cell proliferation and differentiation, and as an anti-bacterial, anti-viral, and anti-parasitic protein. These functions differ among lactoferrin homologs in mammals. Although considerable attention has been given to the many functions of lactoferrin, its primary nutritional contribution is presumed to be related to its iron-binding characteristics, whereas the role of glycosylation has been neglected. Given the critical role of glycan binding in many biological processes, the glycan moieties in lactoferrin are likely to contribute significantly to the biological roles of lactoferrin. Despite the high amino acid sequence homology in different lactoferrins (up to 99%), each exhibits a unique glycosylation pattern that may be responsible for heterogeneity of the biological properties of lactoferrins. An important task for the production of biotherapeutics and medical foods containing bioactive glycoproteins is the assessment of the contributions of individual glycans to the observed bioactivities. This review examines how the study of lactoferrin glycosylation patterns can increase our understanding of lactoferrin functionality

Force-induced misfolding in RNA

RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of its importance in modern biophysics, the current understanding of RNA folding kinetics is limited by the complex interplay between the weak base-pair interactions that stabilize the native structure and the disordering effect of thermal forces. The possibility of mechanically pulling individual molecules offers a new perspective to understand the folding of nucleic acids. Here we investigate the folding and misfolding mechanism in RNA secondary structures pulled by mechanical forces. We introduce a model based on the identification of the minimal set of structures that reproduce the patterns of force-extension curves obtained in single molecule experiments. The model requires only two fitting parameters: the attempt frequency at the level of individual base pairs and a parameter associated to a free energy correction that accounts for the configurational entropy of an exponentially large number of neglected secondary structures. We apply the model to interpret results recently obtained in pulling experiments in the three-helix junction S15 RNA molecule (RNAS15). We show that RNAS15 undergoes force-induced misfolding where force favors the formation of a stable non-native hairpin. The model reproduces the pattern of unfolding and refolding force-extension curves, the distribution of breakage forces and the misfolding probability obtained in the experiments.Comment: 28 pages, 11 figure

Symmetry Breaking of Relativistic Multiconfiguration Methods in the Nonrelativistic Limit

The multiconfiguration Dirac-Fock method allows to calculate the state of relativistic electrons in atoms or molecules. This method has been known for a long time to provide certain wrong predictions in the nonrelativistic limit. We study in full mathematical details the nonlinear model obtained in the nonrelativistic limit for Be-like atoms. We show that the method with sp+pd configurations in the J=1 sector leads to a symmetry breaking phenomenon in the sense that the ground state is never an eigenvector of L^2 or S^2. We thereby complement and clarify some previous studies.Comment: Final version, to appear in Nonlinearity. Nonlinearity (2010) in pres

First-principles study of high conductance DNA sequencing with carbon nanotube electrodes

Rapid and cost-effective DNA sequencing at the single nucleotide level might be achieved by measuring a transverse electronic current as single-stranded DNA is pulled through a nano-sized pore. In order to enhance the electronic coupling between the nucleotides and the electrodes and hence the current signals, we employ a pair of single-walled close-ended (6,6) carbon nanotubes (CNTs) as electrodes. We then investigate the electron transport properties of nucleotides sandwiched between such electrodes by using first-principles quantum transport theory. In particular we consider the extreme case where the separation between the electrodes is the smallest possible that still allows the DNA translocation. The benzene-like ring at the end cap of the CNT can strongly couple with the nucleobases and therefore both reduce conformational fluctuations and significantly improve the conductance. The optimal molecular configurations, at which the nucleotides strongly couple to the CNTs, and which yield the largest transmission, are first identified. Then the electronic structures and the electron transport of these optimal configurations are analyzed. The typical tunneling currents are of the order of 50 nA for voltages up to 1 V. At higher bias, where resonant transport through the molecular states is possible, the current is of the order of several $\mu$A. Below 1 V the currents associated to the different nucleotides are consistently distinguishable, with adenine having the largest current, guanine the second-largest, cytosine the third and finally thymine the smallest. We further calculate the transmission coefficient profiles as the nucleotides are dragged along the DNA translocation path and investigate the effects of configurational variations. Based on these results we propose a DNA sequencing protocol combining three possible data analysis strategies.Comment: 12 pages, 17 figures, 3 table

Simulation studies for surfaces and materials strength

A realistic potential energy function comprising angle dependent terms was employed to describe the potential surface of the N+O2 system. The potential energy parameters were obtained from high level ab-initio results using a nonlinear fitting procedure. It was shown that the potential function is able to reproduce a large number of points on the potential surface with a small rms deviation. A literature survey was conducted to analyze exclusively the status of current small cluster research. This survey turned out to be quite useful in understanding and finding out the existing relationship between theoretical as well as experimental investigative techniques employed by different researchers. Additionally, the importance of the role played by computer simulation in small cluster research, was documented

Computational characterization and prediction of metal-organic framework properties

In this introductory review, we give an overview of the computational chemistry methods commonly used in the field of metal-organic frameworks (MOFs), to describe or predict the structures themselves and characterize their various properties, either at the quantum chemical level or through classical molecular simulation. We discuss the methods for the prediction of crystal structures, geometrical properties and large-scale screening of hypothetical MOFs, as well as their thermal and mechanical properties. A separate section deals with the simulation of adsorption of fluids and fluid mixtures in MOFs

High Conductance Ratio in Molecular Optical Switching of Functionalized Nanoparticle Self-Assembled Nanodevices

Self-assembled functionalized nano particles are at the focus of a number of potential applications, in particular for molecular scale electronics devices. Here we perform experiments of self-assembly of 10 nm Au nano particles (NPs), functionalized by a dense layer of azobenzene-bithiophene (AzBT) molecules, with the aim of building a light-switchable device with memristive properties. We fabricate planar nanodevices consisting of NP self-assembled network (NPSANs) contacted by nanoelectrodes separated by interelectrode gaps ranging from 30 to 100 nm. We demonstrate the light-induced reversible switching of the electrical conductance in these AzBT NPSANs with a record on/off conductance ratio up to 620, an average value of ca. 30 and with 85% of the devices having a ratio above 10. Molecular dynamics simulation of the structure and dynamics of the interface between molecular monolayers chemisorbed on the nano particle surface are performed and compared to the experimental findings. The properties of the contact interface are shown to be strongly correlated to the molecular conformation which in the case of AzBT molecules, can reversibly switched between a cis and a trans form by means of light irradiations of well-defined wavelength. Molecular dynamics simulations provide a microscopic explanation for the experimental observation of the reduction of the on/off current ratio between the two isomers, compared to experiments performed on flat self-assembled monolayers contacted by a conducting cAFM tip.Comment: pdf files : publication and supporting informatio