The Structure of Proteins

To some extent, the properties of the protein are mainly determined by its primary structure (i.e., the amino acid sequence). The two kinds of structural protein, fibroin and spidroin have a distinct and highly repetitive primary structure, which results in specific secondary and tertiary 

Repeating motifs GAGAGS, GAGAGY GPGGX/GPGQQ, 

The tertiary structure of fibroin is stabilized by a combination of hydrogen bonds, a high level of crystallinity, and hydrophobic interactions. Such a 

C- and N-terminal regions of spidroin are highly conserved among the spider silk proteins and play an important role in the assembly of spidroin (Huemmerich et al., 2004 Motriuk-Smith et al., 2005). 

In addition, one hypothesis for the secondary structure in spidroin suggests that there are amorphous phases, highly oriented crystals, and oriented noncrystalline phases coexisting (Grubb et al., 1997). This structure model has been used to explain the super-contraction of dragline (Liu et al., 2005b). 

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The visuahzation of hundreds or thousands of connected atoms, which are found in biological macromolecules, is no longer reasonable with the molecular models described above because too much detail would be shown. First of aU the models become vague if there are more than a few himdied atoms. This problem can be solved with some simplified models, which serve primarily to represent the secondary structure of the protein or nucleic acid backbone [201]. (Compare the balls and sticks model (Figure 2-124a) and the backbone representation (Figure 2-124b) of lysozyme.)... 

The input to a minimisation program consists of a set of initial coordinates for the system. The initial coordinates may come from a variety of sources. They may be obtained from an experimental technique, such as X-ray crystallography or NMR. In other cases a theoretical method is employed, such as a conformational search algorithm. A combination of experimenfal and theoretical approaches may also be used. For example, to study the behaviour of a protein in water one may take an X-ray structure of the protein and immerse it in a solvent bath, where the coordinates of the solvent molecules have been obtained from a Monte Carlo or molecular dynamics simulation. 

The amount of sample required is quite small as little as 10 mole is typical So many peptides and proteins have been sequenced now that it is impossible to give an accurate count What was Nobel Prize winning work m 1958 is routine today Nor has the story ended Sequencing of nucleic acids has advanced so dramatically that it is possible to clone the gene that codes for a particular protein sequence its DNA and deduce the structure of the protein from the nucleotide sequence of the DNA We 11 have more to say about DNA sequencing m the next chapter... 

Rather than existing as a single polypeptide chain some proteins are assemblies of two or more chains The manner m which these subunits are organized is called the quater nary structure of the protein... 

Ellenberger, T.E., et al. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted a helices crystal structure of the protein-DNA complex. Cell 71 1223-1237, 1992. 

Deisenhofer, J., et al. Structure of the protein subunits in the photosynthetic reaction center of Rhodopseudomonas viridis at 3 A resolution. Nature 318 618-624, 1985. 

Since there are so few direct packing interactions between protein molecules in a crystal, small changes in, for example, the pH of the solution can cause the molecules to pack in different ways to produce different crystal forms. The structures of some protein molecules such as lysozyme and myoglobin have been determined in different crystal forms and found to be essentially similar, except for a few side chains involved in packing interactions. Because they are so few, these interactions between protein molecules in a crystal do not change the overall structure of the protein. However,... 

Figure 18.17 Two-dimensional NMR spectnim of the C-terminal domain of a cellulase. The peaks along the diagonal correspond to the spectrum shown in Figure 18.16b. The off-diagonal peaks in this NOE spectrum represent interactions between hydrogen atoms that are closer than 5 A to each other in space. From such a spectrum one can obtain information on both the secondary and tertiary structures of the protein. (Courtesy of Per Kraulis, Uppsala.)...

In NMR the magnetic-spin properties of atomic nuclei within a molecule are used to obtain a list of distance constraints between those atoms in the molecule, from which a three-dimensional structure of the protein molecule can be obtained. The method does not require protein crystals and can be used on protein molecules in concentrated solutions. It is, however, restricted in its use to small protein molecules. 

Remember that, by convention, the NH2 group of each amino acid is written at the left the COOH group is at the right Other reagents split the chain at different points. By correlating the results of different hydrolysis experiments, it is possible to deduce the primary structure of the protein (or polypeptide). Example 23.10 shows how this is done in a particularly simple case. 

Protein chains (Figure 23.8) can align themselves so that certain patterns are repeated. These repeating patterns establish what we call the secondary structure of the protein. The nature of the pattern is determined in large part by hydrogen bonding. Oxygen atoms on C=0... 

Determination of a three-dimensional structure of the protein with both ligands. 

In nature, there are 20 amino acids available for incorporation into the protein chain. They are arranged in a specific and characteristic sequence along the molecule. This sequence is generally referred to as the primary structure of the protein. Also part of the primary structure is the relative molar mass of the macromolecule. 

The tertiary structure - the spatial arrangement of all of the amino acids in a single protein chain, i.e. the three-dimensional structure of the protein. 

As the availability of crystal structures increased in the early 1990s, a number of experimental and computational methods were developed to use the structure of the protein target as a route to discover novel hit compounds. The methods include de novo design, virtual screening, and fragment-based discovery. These developments are covered in more detail in the later chapters of this book, but their main features can be summarized as follows. 

This approach can be generalized to all possible types of experimental data that may be generated. All chemical structures available in public databases or internal to a company typically feature at least the in vitro binding assay data and additionally, the three-dimensional structure of the protein and/or bound ligand. A chemical compound C will therefore be ... 

A primary structure represents a polypeptide as a simple linear string of amino acids. Actually, within long polypeptides, certain sections fold into sheets or twist into coils. These regions with specific structural characteristics constitute the secondary structure of the protein. Figures 13-37 and 13-38 show the two most common secondary structures. 

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