Protein hydrogen bond patterns

Fig. 1. The two principal elements of secondary stmcture in proteins, (a) The a-helix stabilized by hydrogen bonds between the backbone of residue i and i + 4. There are 3.6 residues per turn of helix and an axial translation of 150 pm per residue. represents the carbon connected to the amino acid side chain, R. (b) The P sheet showing the hydrogen bonding pattern between neighboring extended -strands. Successive residues along the chain point...

Figure 2.5 Schematic illustrations of antiparallel (3 sheets. Beta sheets are the second major element of secondary structure in proteins. The (3 strands are either all antiparallel as in this figure or all parallel or mixed as illustrated in following figures, (a) The extended conformation of a (3 strand. Side chains are shown as purple circles. The orientation of the (3 strand is at right angles to those of (b) and (c). A p strand is schematically illustrated as an arrow, from N to C terminus, (bj Schematic illustration of the hydrogen bond pattern in an antiparallel p sheet. Main-chain NH and O atoms within a p sheet are hydrogen bonded to each other.

An important step is to validate the structure, that is, to compare features of the structure to features in known protein structures. This includes localized fit to density, hydrogen bonding patterns, divergence from standard geometry, and much more [12]. Such calculations can highlight where the model requires further improvement. 

Instead, including the protein environment in a QM MM description gives a correct and stable hydrogen-bond pattern at a low computational cost. 

Figure 3 Decision scheme for the prediction of the conformation of a mutated residue. This scheme is based on two observations (1) A point mutation seldom leads to large alterations in the overall structure of the protein. The mutated residue adapts to the structure of the rest of the protein rather than the other way around. (2) Most residues sit lit the statistically preferred conformation, and when exceptions occur, they can normally be explaimi on the basis of hydrogen-bonding patterns. (Adapted from Ref. 37.)...

In the following, the geometrical data obtained from a number of protein crystal structures determined at high resolution are analyzed in terms of hydrogen-bonding patterns, and then the data are compared metrically. This procedure and the data analysis are taken mainly from a review of Baker and Hubbard [596], who considered in detail the protein structures listed in Thble 19.1. 

Another similar approach is to use the known three-dimensional structures to create look-up tables which contain the most favorable environmental parameters of each amino acid. The parameter sets are created in terms of secondary structure, hydrogen bonding pattern, solvent accessibility, and local presence of polar atoms [30,32], In this manner the three-dimensional information is encoded into a one-dimensional string. A comparison is then made of the test protein sequence with this one-dimensional string. If the test sequence is similar, a model fold can be created for further analysis. 

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