The Study Of Interactions Between Several Typical Biopolymers And Water On The Single Molecule Level

Water, one of the most important substances on the Earth, is also an important resource for all lives, and one of the most important component of organisms. For the biopolymers, the aqueous solution provides an appropriate environment, in which they can possess their native structure and express the relevant functions. In recent years, scientists have been attracted by the intermolecular interactions between water and macromolecules. However, these researches are all based on aqueous environment, in which it is difficult to discern the effects of water molecules to the structure of macromolecules. Therefore, if the water environment is displaced by the pure organic solvents as the micro-environment, the effects of water to the structure of macromolecules can be studied alone.In this thesis, by using SMFS, Quantum Mechanics (QM) based theoretical models, and molecular dynamics (MD) simulations, the single-chain stretching behaviors of several macromolecules in non-aqueous media have been studied. By studying the single-chain stretching behaviors of these macromolecules in water and non-aqueous media respectively, the effects of water environment to the stability of macromolecular structure are shown in details at the single molecule level.In Chapter 2, the effects of non-aqueous environments on the stability of dsDNA has been studied. By using UV-Vis spectroscopy, it is found that, when dsDNA is disolved in 99% alcohols, the structure will be unstable on different levels due to the absence of the hydrophobic interactions. Specifically, the stability of dsDNA will be lowered with the decrease of the polarity of solvents, because the solvophobic effects become weaker. By using SMFS, the single-chain mechanical behaviors of dsDNA in pure methanol and methanol/water mixed solvents can be shown as follows:when it is in water, the structure of dsDNA is in a stable duplex state under the protection of water environment. With the increase of methanol contents to 50% (v/v), the methanol molecules can form H-bonds with bound water molecules of dsDNA. This will distabilize dsDNA, which can be reflected by the shortened "B-S" transition plateau in the force curves. As the content of methanol is incresed to 70%, most of bound water molecules around dsDNA are "occupied" by methanol molecules, and then the duplex structure of dsDNA disstablized further. In this case, there are two states of DNA coexisting in the mixed solvents, consisting of native dsDNA and unwound dsDNA. When the content rises up to 90%-100%, the dsDNA have been completely denatured into ssDNA.In Chapter 3, the effects of non-aqueous environments on the stability of protein has been studied. By SMFS, it is find that when protein is pulled from water to nonpolar solvents, it will be unfolded into an unstructured polypeptide spontaneously, due to the broken of the salvation layer of water. This finding is corroborated by MD simulations where 1278 is dragged from water into a nonpolar solvent, revealing details of the unfolding process at the water/nonpolar solvent interface. Based on these experimental results, a new QM-WLC model is proposed and used to fit these curves. The fitting results reveal that the single-chain elastic behavior of protein can be described by the model successfully, when the persistence length lp is equal to the length of one amino acid unit of protein,0.38 nm. Then the hydrophobicity of the micro-environment in a typical protease motor protein C1pX is analyzed. It is shown that the denaturation mechanism may be employed in protein machines in vivo. There is a polar/nonpolar interface existing in the entry of protease, which may lead to the unfolding of protein under a tiny stretching force generated by molecular motor. Moreover, the interactions between water and polypeptide are studied by SMFS. On the basis of the results, it is proposed that water may play a vital role in the prebiotic chemical evolution of protein.In Chapter 4, the effects of non-aqueous environments on the single-chain mechanics of two kinds of poly(lactic acid) (PLA) has been studied. In octylbenzene, the inherent single-chain stretching elasticity of PLLA is same to that of PDLLA. The comparison between the force curves of PLLA obtained in water and octylbenzene (both are poor solvent for PLA) shows that there are no specific interactions between the PLLA chain and water. Then a new QM-FRC model is proposed and used to fit these force curves. The fitting results indicate that the inherent stretching elasticity of PLA can be described well by the model, when the length of rotating unit lb is equal to the length of one repeating unit of PLA,0.36 nm. In good solvents, the PLLA chain exists in an a helical state because of its highly regularity, while the PDLLA chain exists in a random coil state because of the random distribution of L- and D- units in the PDLLA chain.In general, when protein/DNA is pulled across the water/nonpolar interface, the supramolecular structure can be unfolded/unwound under a tiny force. When the denatured structures are returned to the water environment, the previous folded/duplex structure can be reformed. This denaturation method is not only available to DNA but also to protein, and is reversible with the change of micro-environment. This denaturation is an easy performing, environmental friendly and controllable process. Thus, this study may cast a new light on the design of novel molecular denaturation devices in the future.