Proteins are three-dimensional objects

Under physiological conditions, nearly all proteins have at least one well-defined three-dimensional structure and the biological activity of that protein depends on that structure. 

Chemists are not quite as odd as they are frequently depicted. Given that dedicating a professional life to moving around molecules one way or another may seem a bit wide of the mark to most people, chemists do have a life outside the laboratory. In my experience, chemists have more than the usual affinity for the arts music and painting in particular. 

In the last chapter we established that the primary stracture for all members of a particular protein—say ribonuclease A or insulin—in a single species is identical. We owe that key insight to Fred Sanger. This concept translates to higher dimensions the primary stmcture of a protein is basically one-dimensional, a chain of symbols. 

This chain can wrap itself up in space in innumerable ways. Here we learn that, for example, all ribonuclease A molecules from a particular species wrap themselves up in exactly the same way an amazing and amazingly important fact. 

Proteins have unique three-dimensional structures 

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The chemical organization (i.e., the primary amino acid sequence) and the folded structure (i.e., the secondary, tertiary, and quaternary structure), including the generation of a surface topography as a discrete three-dimensional object, are the essential features of a polypeptide and protein around which a high-performance separation can be designed. Two sets of factors must come into play for these separation skills to be developed. The first set... 

Reaction centers of purple bacteria. The exact composition varies, but the properties of reaction centers from several genera of purple bacteria are similar. In Rhodopseudomonas viridis there are three peptide chains designated H, M, and L (for heavy, medium and light) with molecular masses of 33,28, and 24 kDa, respectively. Together with a 38-kDa tetraheme cytochrome (which is absent from isolated reaction centers of other species) they form a 1 1 1 1 complex. This constitutes reaction center P870. The three-dimensional structure of this entire complex has been determined to 0.23-nm resolution288 319 323 (Fig. 23-31). In addition to the 1182 amino acid residues there are four molecules of bacteriochlorophyll (BChl), two of bacteriopheophytin (BPh), a molecule of menaquinone-9, an atom of nonheme iron, and four molecules of heme in the c type cytochrome. In 1984, when the structure was determined by Deisenhofer and Michel, this was the largest and most complex object whose atomic structure had been described. It was also one of the first known structures for a membrane protein. The accomplishment spurred an enormous rush of new photosynthesis research, only a tiny fraction of which can be mentioned here. 

Biological systems provide numerous examples of self-assembled objects. Owing to the relatively weak interactions involved, a self-assembled structure is much more sensitive and responsive to its environment than a more rigid structure held together by covalent bonds. Unlike processes involving simple surfactants, polymers, and nanoparticles, self-assembly processes in biological systems are usually directional and functional and often lead to the formation of extremely complex structures. For example, the three-dimensional structure adopted by a protein in solution is critical to the protein s function, and this structure is determined by both strong (covalent) and weak... 

Structure comparison methods are a way to compare three-dimensional structures. They are important for at least two reasons. First, they allow for inferring a similarity or distance measure to be used for the construction of structural classifications of proteins. Second, they can be used to assess the success of prediction procedures by measuring the deviation from a given standard-of-truth, usually given via the experimentally determined native protein structure. Formally, the problem of structure superposition is given as two sets of points in 3D space each connected as a linear chain. The objective is to provide a maximum number of point pairs, one from each of the two sets such that an optimal translation and rotation of one of the point sets (structural superposition) minimizes the rms (root mean square deviation) between the matched points. Obviously, there are two contrary criteria to be optimized the rms to be minimized and the number of matched residues to be maximized. Clearly, a smaller number of residue pairs can be superposed with a smaller rms and, clearly, a larger number of equivalent residues with a certain rms is more indicative of significant overall structural similarity. 

These LDG( T, m . Am) objects are usually complicated three-dimensional bodies with intricate shape features which seem to be well suited for a topological sh analysis. Most LDG( T, a . Am) objects obtained from a globular protein are multiply connected, as a consequence of the gradual mergers of electron density clouds due to nonbonded interactions, as the density threshold a is gradually lowered. 

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