Molecular biopolymers

A possible explanation of the hysteresis could be the non-equilibrium of the DNA hydration. In that case the value of hysteresis has to depend on the size of the experimental sample. However, such a dependence is not observed in the wide range of DNA film thicknesses (0.05-0.2 fmi) [14], [12]. Thus, hysteresis cannot be a macroscopic phenomenon and does reflect the molecular interaction of water and the biopolymer. 

D. Beglov and B. Roux. Dominant solvations effects from the primary shell of hydration Approximation for molecular dynamics simulations. Biopolymers, 35 171-178, 1994. 

In biological systems molecular assemblies connected by non-covalent interactions are as common as biopolymers. Examples arc protein and DNA helices, enzyme-substrate and multienzyme complexes, bilayer lipid membranes (BLMs), and aggregates of biopolymers forming various aqueous gels, e.g, the eye lens. About 50% of the organic substances in humans are accounted for by the membrane structures of cells, which constitute the medium for the vast majority of biochemical reactions. Evidently organic synthesis should also develop tools to mimic the Structure and propertiesof biopolymer, biomembrane, and gel structures in aqueous media. 

At first glance, the contents of Chap. 9 read like a catchall for unrelated topics. In it we examine the intrinsic viscosity of polymer solutions, the diffusion coefficient, the sedimentation coefficient, sedimentation equilibrium, and gel permeation chromatography. While all of these techniques can be related in one way or another to the molecular weight of the polymer, the more fundamental unifying principle which connects these topics is their common dependence on the spatial extension of the molecules. The radius of gyration is the parameter of interest in this context, and the intrinsic viscosity in particular can be interpreted to give a value for this important quantity. The experimental techniques discussed in Chap. 9 have been used extensively in the study of biopolymers. 

RE Bruccoleri, M Karplus. Conformational sampling using high-temperature molecular dynamics. Biopolymers 29 1847-1862, 1990. 

Molecular mechanisms of penicillins binding with biopolymers and membranes 98ZOR655. 

Owing to the weak hydrophobicity of the PEO stationary phases and reversibility of the protein adsorption, some advantages of these columns could be expected for the isolation of labile and high-molecular weight biopolymers. Miller et al. [61] found that labile mitochondrial matrix enzymes — ornitine trans-carbomoylase and carbomoyl phosphate synthetase (M = 165 kDa) could be efficiently isolated by means of hydrophobic interaction chromatography from the crude extract. 

The green chemistry approach, and the surge of biopolymers as candidates for substituting synthetic ones in several applications require detailed understanding of the following aspects, at the molecular level ... 

With the LC-MS interfaces now available, a wide range of analytes, from low-molecular-weight drugs and metabolites (<1000 Da) to high-molecular-weight biopolymers (>100000 Da), may be studied. 

Note that for the determination of molecular weight, the charge-state distribution is not of great importance as it does not affect the m/z value of the ion involved and thus the calculated molecular weight. If the conformational state of the biopolymer is of interest, however, the distribution of charged states is a fundamental consideration and any parameter likely to change this distribution must be carefully controlled. 

The application areas for LC-MS, as will be illustrated later, are diverse, encompassing both qualitative and quantitative determinations of both high-and low-molecular-weight materials, including synthetic polymers, biopolymers, environmental pollutants, pharmaceutical compounds (drugs and their metabolites) and natural products. In essence, it is used for any compounds which are found in complex matrices for which HPLC is the separation method of choice and where the mass spectrometer provides the necessary selectivity and sensitivity to provide quantitative information and/or it provides structural information that cannot be obtained by using other detectors. 

The polarity and thermal instability of biopolymers, together with the almost exclusive formation of singly charged ions renders APCl an inappropriate ionization technique for their study. Much of the early work involving electrospray ionization, on the other hand, was connected with the analysis of this type of molecule, in particular determining the molecular weight of proteins for which it is particularly effective. 

This is a task for which electrospray ionization is well suited although, as discussed earlier in Section 4.7, this is a soft ionization technique that yields almost exclusively molecular ions with little fragmentation and consequently, in the case of biopolymers, little sequence information directly. 

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