A protein contact map represents the distance between all possible amino acid residue pairs of a three-dimensional protein structure using a binary two-dimensional matrix. For two residues i {\displaystyle i} and j {\displaystyle j} , the i j {\displaystyle ij} element of the matrix is 1 if the two residues are closer than a predetermined threshold, and 0 otherwise. Various contact definitions have been proposed: The distance between the Cα-Cα atom with threshold 6-12 Å; distance between Cβ-Cβ atoms with threshold 6-12 Å (Cα is used for Glycine); and distance between the side-chain centers of mass.
Overview Contact maps provide a more reduced representation of a protein structure than its full 3D atomic coordinates. The advantage is that contact maps are invariant to rotations and translations. They are more easily predicted by machine learning methods. It has also been shown that under certain circumstances (e.g. low content of erroneously predicted contacts) it is possible to reconstruct the 3D coordinates of a protein using its contact map. Contact maps are also used for protein superimposition and to describe similarity between protein structures. They are either predicted from protein sequence or calculated from a given structure.
Contact map prediction With the availability of high numbers of genomic sequences it becomes feasible to analyze such sequences for coevolving residues. The effectiveness of this approach results from the fact that a mutation in position i of a protein is more likely to be associated with a mutation in position j than with a back-mutation in i if both positions are functionally coupled (e.g. by taking part in an enzymatic domain, or by being adjacent in a folded protein, or even by being adjacent in an oligomer of that protein). Several statistical methods exist to extract from a multiple sequence alignment such coupled residue pairs: observed versus expected frequencies of residue pairs (OMES); the McLachlan Based Substitution correlation (McBASC); statistical coupling analysis; Mutual Information (MI) based methods; and recently direct coupling analysis (DCA). Machine learning algorithms have been able to enhance MSA analysis methods, especially for non-homologous proteins (ie. shallow MSA's). Predicted contact maps have been used in the prediction of membrane proteins where helix-helix interactions are targeted.
HB Plot Knowledge of the relationship between a protein's structure and its dynamic behavior is essential for understanding protein function. The description of a protein three dimensional structure as a network of hydrogen bonding interactions (HB plot) was introduced as a tool for exploring protein structure and function. By analyzing the network of tertiary interactions, the possible spread of information within a protein can be investigated. HB plot offers a simple way of analyzing protein secondary structure and tertiary structure. Hydrogen bonds stabilizing secondary structural elements (secondary hydrogen bonds) and those formed between distant amino acid residues - defined as tertiary hydrogen bonds - can be easily distinguished in HB plot, thus, amino acid residues involved in stabilizing protein structure and function can be identified.
Features The plot distinguishes between main chain-main chain, main chain-side chain and side chain-side chain hydrogen bonding interactions. Bifurcated hydrogen bonds and multiple hydrogen bonds between amino acid residues; and intra- and interchain hydrogen bonds are also indicated on the plots. Three classes of hydrogen bondings are distinguished by color-coding; short (distance smaller than 2.5 Å between donor and acceptor), intermediate (between 2.5 Å and 3.2 Å) and long hydrogen bonds (greater than 3.2 Å).
Secondary structure elements in HB plot
In representations of the HB plot, characteristic patterns of secondary structure elements can be recognised easily, as follows:
Helices can be identified as strips directly adjacent to the diagonal. Antiparallel beta sheets appear in HB plot as cross-diagonal. Parallel beta sheets appears in the HB plot as parallel to the diagonal. Loops appear as breaks in the diagonal between the cross-diagonal beta-sheet motifs.
Examples of usage
Cytochrome P450s The cytochrome P450s (P450s) are xenobiotic-metabolizing membrane-bound heme-containing enzymes that use molecular oxygen and electrons from NADPH cytochrome P450 reductase to oxidize their substrates. CYP2B4, a member of the cytochrome P450 family is the only protein within this family, whose X-ray structure in both open 11 and closed form 12 is published. The comparison of the open and closed structures of CYP2B4 structures reveals large-scale conformational rearrangement between the two states, with the greatest conformational change around the residues 215-225, which is widely open in ligand-free state and shut after ligand binding; and the region around loop C near the heme.
Examining the HB plot of the closed and open state of CYP2B4 revealed that the rearrangement of tertiary hydrogen bonds was in excellent agreement with the current knowledge of the cytochrome P450 catalytic cycle. The first step in P450 catalytic cycle is identified as substrate binding. Preliminary binding of a ligand near to the entrance breaks hydrogen bonds S212-E474, S207-H172 in the open form of CYP2B4 and hydrogen bonds E218-A102, Q215-L51 are formed that fix the entrance in the closed form as the HB plot reveals. The second step is the transfer of the first electron from NADPH via an electron transfer chain. For the electron transfer a conformational change occurs that triggers interaction of the P450 with the NADPH cytochrome P450 reductase. Breaking of hydrogen bonds between S128-N287, S128-T291, L124-N287 and forming S96-R434, A116-R434, R125-I435, D82-R400 at the NADPH cytochrome P450 reductase binding site—as seen in HB plot—transform CYP2B4 to a conformation state, where binding of NADPH cytochrome P450 reductase occurs. In the third step, oxygen enters CYP2B4 in the closed state - the state where newly formed hydrogen bonds S176-T300, H172-S304, N167-R308 open a tunnel which is exactly the size and shape of an oxygen molecule.
Lipocalin family
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