Molecular modelling of biomolecules

Published FF parameters for MM (Jalaie and Lipkowitz, 2000 Osawa and Lip-kowitz, 1995) and software for molecular modeling (Boyd, 1995) have been compiled. Some of the MM programs applicable to molecular modeling of biomolecules are listed in Table 14.1. 

Optimized potentials for liquid simulation (OPES) was designed for modeling bulk liquids. It has also seen significant use in modeling the molecular dynamics of biomolecules. OPLS uses five valence terms, one of which is an electrostatic term, but no cross terms. 

For example, the chapter-opening photograph shows a molecular model of atorvastatin, better known as Lipitor . In the body, Lipitor inhibits the action of a key enzyme, called HMG-CoA reductase (we will discuss enzymes in Section 14.7). HMG-CoA reductase is a large complex biomolecule that is critical in the biochemical sequence that synthesizes cholesterol in the liver, and inhibition of its action leads to reduced cholesterol production. The molecules of Lipitor have two properties that lead to their pharmaceutical effectiveness ... 

B. Krebs and G. Henkel, Transition metal thiolates — from molecular fragments of sulfidic solids to models of active centers in biomolecules. Angew. Chem. Int. Ed. 30 (1991) 769. 

Lamoureux G, Harder E, Vorobyov IV, Roux B, MacKerell AD (2006) A polarizable model of water for molecular dynamics simulations of biomolecules. Chem Phys Lett 418(l-3) 245-249... 

Recent solid state NMR studies of liquid crystalline materials are surveyed. The review deals first with some background information in order to facilitate discussions on various NMR (13C, ll, 21 , I9F etc.) works to be followed. This includes the following spin Hamiltonians, spin relaxation theory, and a survey of recent solid state NMR methods (mainly 13C) for liquid crystals on the one hand, while on the other hand molecular ordering of mesogens and motional models for liquid crystals. NMR studies done since 1997 on both solutes and solvent molecules are discussed. For the latter, thermotropic and lyotropic liquid crystals are included with an emphasis on newly discovered liquid crystalline materials. For the solute studies, both small molecules and weakly ordered biomolecules are briefly surveyed. 

Combining 2D-NOESY and 2D-ROESY NMR experiments with molecular modelling protocols, Kuhn and Kunz32 have been able to study the saccharide-induced peptide conformational behaviour of the recognition region of Ll-Cadherin. The detailed conformational analysis of this key biomolecule not only proves that the saccharide side chain exerts a marked influence on the conformation of the peptide chain, but also that the size and type of the saccharide indeed strongly affects the conformation of the main chain. 

Regarding the mechanism of biomolecules functionalized CNTs entering into cells, endocytosis mechanism may be responsible for the phenomena, a theory model is also suggested (Gao et al., 2005) the optimal size of particles entering into cells is between 20 nm and 700 nm or so, too small nanopaiticles are very difficult to enter into cells because of cellular surface tension force and adhesion. The further mechanism of effects of CNTs on human healthcare and environment is being investigated from the following four scales such as molecular, cellular, animals, and environment levels. 

Inner slip, between the solid wall and an adsorbed film, will also influence the surface-liquid boundary conditions and have important effects on stress propagation from the liquid to the solid substrate. Linked to this concept, especially on a biomolecular level, is the concept of stochastic coupling. At the molecular level, small fluctuations about the ensemble average could affect the interfacial dynamics and lead to large shifts in the detectable boundary condition. One of our main interests in this area is to study the relaxation time of interfacial bonds using slip models. Stochastic boundary conditions could also prove to be all but necessary in modeling the behavior and interactions of biomolecules at surfaces, especially with the proliferation of microfluidic chemical devices and the importance of studying small scales. 

---