Chemistry, protein structure levels

One of the most fertile areas of chemistry is the interface between chemistry and biology, It is there that chemists, armed with modern tools for separation and spectroscopic analysis, bring to light the structural and mechanistic workings of nature at the molecular level. This basic knowledge drives further investigations in diverse areas such as chemical synthesis, protein structure and function, and cell biology, and ultimately leads to advances in the treatment of diseases of humans, animals, and plants, all of which impact upon the quality of our lives. 

Linus Pauling, an American chemist, was the first to take a closer look at the electrical difference of bonds. He tested the differences in energies of covalent bonds. In 1939, he published The Nature of the Chemical Bond which discussed the energy levels of molecules. Pauling was recognized for his work with protein structures. His electrochemical valency theory won the Nobel Prize for Chemistry in 1954. 

Besides the classical techniques for structural determination of proteins, namely X-ray diffraction or nuclear magnetic resonance, molecular modelling has become a complementary approach, providing refined structural details [4—7]. This view on the atomic scale paves the way to a comprehensive smdy of the correlations between protein structure and function, but a realistic description relies strongly on the performance of the theoretical tools. Nowadays, a full size protein is treated by force fields models [7-10], and smaller motifs, such as an active site of an enzyme, by multiscale approaches involving both quantum chemistry methods for local description, and molecular mechanics for its environment [11]. However, none of these methods are ab initio force fields require a parameterisation based on experimental data of model systems DPT quantum methods need to be assessed by comparison against high level ab initio calculations on small systems. 

The sequence of oxidation steps which converts the mussel adhesive protein to underwater glue was investigated using model peptides. The three-dimensional structure of the protein was derived from the decapeptide sequence with the help of computer modeling studies. The oxidation chemistries were then applied to the three-dimensional protein structure to develop a mechanistic picture, at the molecular level, showing how the mussel attaches itself to solid surfaces. 

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