Coarse-grained molecular simulations of large biomolecules

Recently, we saw a dramatic increase in the number of researches that rely on coarse-grained (CG) simulations for large biomolecules. Here, first, we briefly describe recently developed and used CG models for proteins and nucleic acids. Balance between structure-based and physico-chemical terms is a key issue. We also discuss the multiscale algorithms used to derive CG parameters. Next, we comment on the dynamics used in CG simulations with an emphasis on the importance of hydrodynamic interactions. We then discuss the pros and cons of CG simulations. Finally, we overview recent exciting applications of CG simulations. Publicly available tools and software for CG simulations are also summarized.     

Fast relaxation processes and structural changes in immunoactive biomolecules

Based upon an analysis of the absorption spectra, the fluorescence and fluorescence excitation spectra, and the lifetime of the excited states of aqueous solutions (pH 7.4) of 2,3-dimethoxy-8-azagona-1,3,5(10),13-tetraene-12,17-dione, it is established that two centers of different type exist: one emits long-wave (L-centers) and the other short-wave (S-centers) fluorescence. Irradiation of solutions increases the number of L-centers and greatly decreases that of S-centers. Examination of the picosecond transient absorption spectra and their kinetics revealed that the initial photochemical stage is defined as the ionization of a considered molecule and the subsequent one, as the formation, most probably, of the dehydroderivative of a parent molecule.     

Polarized infrared spectra of crystalline glycosaminoglycans

Polarized infrared spectra have been recorded for oriented, crystalline specimens of hyaluronates, chondroitin 4-sulfate and 6-sulfate, dermatan sulfate, and a cartilage proteoglycan, having different known chain conformations as determined by X-ray diffraction. The dichroism data for the vibrational modes of the amide and carboxyl groups have been interpreted with respect to the particular molecular structures.     

A factorization method for the classification of infrared spectra

Background  

Bioinformatics data analysis often deals with additive mixtures of signals for which only class labels are known. Then, the overall goal is to estimate class related signals for data mining purposes. A convenient application is metabolic monitoring of patients using infrared spectroscopy. Within an infrared spectrum each single compound contributes quantitatively to the measurement.     

A systematic methodology for defining coarse-grained sites in large biomolecules

Coarse-grained (CG) models of biomolecules have recently attracted considerable interest because they enable the simulation of complex biological systems on length-scales and timescales that are inaccessible for atomistic molecular dynamics simulation. A CG model is defined by a map that transforms an atomically detailed configuration into a CG configuration. For CG models of relatively small biomolecules or in cases that the CG and all-atom models have similar resolution, the construction of this map is relatively straightforward and can be guided by chemical intuition. However, it is more challenging to construct a CG map when large and complex domains of biomolecules have to be represented by relatively few CG sites. This work introduces a new and systematic methodology called essential dynamics coarse-graining (ED-CG). This approach constructs a CG map of the primary sequence at a chosen resolution for an arbitrarily complex biomolecule. In particular, the resulting ED-CG method variationally determines the CG sites that reflect the essential dynamics characterized by principal component analysis of an atomistic molecular dynamics trajectory. Numerical calculations illustrate this approach for the HIV-1 CA protein dimer and ATP-bound G-actin. Importantly, since the CG sites are constructed from the primary sequence of the biomolecule, the resulting ED-CG model may be better suited to appropriately explore protein conformational space than those from other CG methods at the same degree of resolution.     

Cluster analysis of protein fourier transform infrared spectra

Cluster analysis techniques were used to examine a set of Fourier transform infrared (FT-IR) spectra of bovine serum albumin (BSA) in the adsorbed and nonadsorbed states. The region from 1480 to 1600 cm^?1, comprising the amide II band, was used. Spectra were preprocessed to compensate for linear baseline variation, and the single linkage method of cluster analysis was applied. As expected, the spectra of adsorbed and nonadsorbed BSA fell into two distinct clusters. However, no further clustering was observed among the adsorbed BSA spectra on the basis of surface type, suggesting that surface specificity of the spectral changes induced in BSA by adsorption is not detectable above experimental variation. This work illustrates the value of using cluster analysis in the FT-IR study of proteins as a complement to other data analysis methods.     

Second-derivative Fourier transform infrared spectra of seaweed galactans

The Fourier transform infrared spectra of agar, agarose, -, -, and -carrageenan, and ofChondrus canaliculatus, Iridaea ciliata, I. membranacea, I. laminarioides andGracilaria chilensis polysaccharides were recorded in the 4000–400 cm^-1 region. The bands in the second derivative mode are sharper and more bands are resolved than in the normal spectra.Agar, agarose andG. chilensis phycocolloids exhibit diagnostic bands at 790 and 713 cm^-1. -, - and -carrageenans, and native carrageenan-type polysaccharides fromC. canaliculatus andIridaea species exhibit bands at around 1160, 1140, 1100, 1070, 1040, 1008, 610, and 580 cm^-1. Therefore, FT-IR spectroscopy in the second-derivative mode may be applied to differentiate between agar- and carrageenan-types seaweed galactans.     

A correction to the calculation of the Gibbs free energy of adsorption for biomolecules in ion-exchange systems

We wish to propose a correction to the methodology introduced by Gerstner et al. [J.A. Gerstner, J.A. Bell, S.M. Cramer, Biophys. Chem. 52 (1994) 97-106] for the calculation of Gibbs free energies of adsorption of biomolecules to ion-exchange systems. Our approach is based on the requirement that the mobile phase and stationary phase concentrations be expressed in exactly the same units and the equilibrium constant be strictly dimensionless. The Gibbs free energies of ion-exchange calculated based on this correction appear to be more negative than those originally calculated by Gertner et al.     

Fourier transform infrared spectra of cells treated with the drug adriamycin

Fourier Transform Infrared Spectroscopy (FT-IR) is used to study the interaction of adriamycin molecule with DNA and/or cells. For the drug-DNA complexes, the data show that adriamycin interacts not only with the bases pair but also with the sugar-phosphate of DNA within intercalating process. In the case of treated tumor cells, spectra suggest that adriamycin could be interacting also with the proteins of the membrane. The obtained results show that FT-IR is a powerful technique in the study of biological system, say cells.