Proteins single-force molecular interaction

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

Many experiments have been carried out by using this setup the stretching of single DNA molecules, the unfolding of RNA molecules or proteins, and the translocation of molecular motors (Fig. 2). Here we focus our attention on force experiments where mechanical work can be exerted on the molecule and nonequilibrium fluctuations are measured. The most successful studies along this line of research are the stretching of small domain molecules such as RNA [83] or protein motifs [84]. Small RNA domains consist of a few tens of nucleotides folded into a secondary structure that is further stabilized by tertiary interactions. Because an RNA molecule is too small to be manipulated with micron-sized beads, it has to be inserted between molecular handles. These act as polymer spacers that avoid nonspecific interactions between the bead and the molecule as well as the contact between the two beads. 

Fat absorption of protein additives has been studied less extensively than water absorption and consequently the available data are meager. Although the mechanism of fat absorption has not been explained, fat absorption is attributed mainly to the physical entrapment of oil (7). Factors affecting the protein-lipid interaction include protein conformation, protein-protein interactions, and the spatial arrangement of the lipid phase resulting from the lipid-lipid interaction. Non-covalent bonds, such as hydrophobic, electrostatic, and hydrogen, are the forces involved in protein-lipid interactions no single molecular force can be attributed to protein-lipid interactions ( ). 

---