Protein structure basic elements

Disulfide bridges are, of course, true covalent bonds (between the sulfurs of two cysteine side chains) and are thus considered part of the primary structure of a protein by most definitions. Experimentally they also belong there, since they can be determined as part of, or an extension of, an amino acid sequence determination. However, proteins normally can fold up correctly without or before disulfide formation, and those SS links appear to influence the structure more in the manner of secondary-structural elements, by providing local specificity and stabilization. Therefore, it seems appropriate to consider them here along with the other basic elements making up three-dimensional protein structure. 

All of the simulation approaches, other than harmonic dynamics, include the basic elements that we have outlined. They differ in the equations of motion that are solved (Newton s equations, Langevin equations, etc.), the specific treatment of the solvent, and/or the procedures used to take account of the time scale associated with a particular process of interest (molecular dynamics, activated dynamics, etc.). For example, the first application of molecular dynamics to proteins considered the molecule in vacuum.15 These calculations, while ignoring solvent effects, provided key insights into the important role of flexibility in biological function. Many of the results described in Chapts. VI-VIII were obtained from such vacuum simulations. Because of the importance of the solvent to the structure and other properties of biomolecules, much effort is now concentrated on systems in which the macromolecule is surrounded by solvent or other many-body environments, such as a crystal. 

Since atomic fluctuations are the basic elements of the dynamics of proteins (see Chapt. VI.A), it is important to have experimental tests of the accuracy of the simulation results. For the magnitudes of the motions, the most detailed data are provided, in principle, by an analysis of Debye-Waller or temperature factors obtained in crystallographic refinements of X-ray structure. 

Before we draw attention to new functions of elements we must ask if there has been any basic developments of proteins, particularly those associated with metal ions. In Section 4.11, we described their very basic fold structures while in Sections 5.5 and 7.10, we referred to the features including the folds of metal-bound... 

An important element in the three-dimensional structure of a protein is the secondary structure. The secondary structure results from the formation of hydrogen bonds between the—N—H groups and the carbonyl (C O) groups of the peptide bonds —N—H 0=C. There are two basic ways to do this. We can form a helix or we can form a sheet. The great American chemist Linus Pauling won the Nobel Prize in Chemistry in 1954 for the elucidation of these structures. 

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