CAPITULO III: El camino a la liberación
3.1. La dimensión estética
3.1.1. El arte en la industria cultural
When assessing whether a contact is conserved between two alignment positions, it is necessary to take into account gaps th a t have been included in the multiple structure alignment. A conserved contact is the percentage of all the contacts ob served between two alignment positions. However, it is not possible to assess the contact statu s between residues corresponding to gaps in the alignment. Therefore, a residue-residue comparison for a given structure is considered void if either one of
Chapter 2. Inter-Residue Contacts for Structural Comparison 63
th e residues equates to a gap in the alignm ent. The degree of contact conservation (CC) for a given alignm ent position (i, j) can therefore be defined in equation 2.1.
_ Number of structures with residues in contact
Number of structures w ith residues present in both alignment positions
However, if this measure is to be employed as an assessment of contact con servation, it is also necessary to take into account th e num ber of stru ctu res used for th e calculation. Otherwise, if only one stru ctu re had residues present in both alignm ent positions (i, j) then a single contact in this stru ctu re would be considered as 100% conserved despite only being derived from a single structure. Therefore an additional measure of alignm ent conservation (AC) was also calculated for each alignm ent position (i, j) (see equation 2.2).
_ Number of structures with residues present in both alignm ent positions Number of structures in alignm ent
Since contact m aps are sym m etrical ab o u t the diagonal axis, th e two halves of the plots could be used to display a different statistical analysis of the contacts observed in the same m ultiple stru ctu re alignm ent. In the case of the conserved contact m ap, the degree of plot intensity reflects the contact conservation in the top-right half and alignm ent conservation in the bottom -left half. An example of the plot generated by C O C O P L O T is shown in figure 2.4. This is derived from the C O RA m ultiple stru ctu re alignm ent of three representative stru ctu res in the oxidoreductase superfam ily found in the a jd-roll architecture of CATH (classification code 3.10.30.70).
Chapter 2. Inter-Residue Contacts for Structural Comparison 64
F ig u r e 2.4: A consensus contact map (COCOPLOT, I. Sillitoe) for a multiple structure alignment from the oxidoreductase superfamily in the a^-roll architecture (3.10.30.70). The top-right half of the plot indicates the degree of conservation of contacts with plot intensity increasing for a higher proportion of contacts between positions in the alignment. The bottom-left half indicates the degree of conserva tion between the alignment positions regardless of inter-residue distance. The plot intensity increases with a higher proportion of structures included in those alignment positions, thus gaps in the alignment are shown as pale bands and intersecting gaps as white blocks.
Chapter 2. Inter-Residue Contacts for Structural Comparison 65
A v e ra g e D is ta n c e a n d S t a n d a r d D e v ia tio n
In addition to generating plots solely based on contacts, C O C O P L O T was also w ritten to generate distance plots, where all inter-residue distances are calculated and the m agnitude of the distance is indicated by th e plot intensity. In th e case of the consensus plots from the m ultiple stru c tu ra l alignm ents, th e distance was taken to be the average inter-residue distance between the two positions in the alignm ent. Again this distance was only calculated for stru ctu res w ith residues present in bo th alignm ent positions (i, j) being considered.
To com plem ent the m easure of average distance, the stan d ard deviation for these values was also calculated and displayed in th e opposing half of th e plot. An exam ple of this plot is illu strated in figure 2.5 using the same m ultiple stru ctu re align ment from figure 2.4. The stan d ard deviation also provides a useful m easure of the conservation of inter-residue distances between alignm ent positions, regardless of the distance itself. Thus, insights can be gained into the conservation of sections of stru ctu re th a t may not necessarily be in contact. As expected, a correlation between low average distance and low stan d ard deviation is observed in m ost cases, which is especially noticeable between secondary stru ctu re interactions. This presents more evidence for the use of contacts as a m easure of stru ctu ral homology since th e most conserved regions of stru ctu re are usually found close in 3D space.
Interestingly, there are examples where the distances between regions of the m ultiple stru ctu re alignm ent are well conserved (low stan d ard deviation) despite being spatially d istan t (high average distance). Since th e representative proteins used in this alignm ent all display less th a n 35% sequence identity, conserved features are likely to be th e result of genuine stru c tu ra l or functional constraints ra th e r th an lack of evolutionary distance. This type of highly conserved long-range constraint is unusual w ithin such evolutionarily d istan t proteins and could therefore be of use when assessing a new stru ctu re for evolutionary relationships. However, due to th e small num ber of stru ctu ral relatives in m any superfam ilies, th e m ajority of these m ultiple stru c tu ra l alignm ents only contain between two and four structures (see section 2.7). This relatively low num ber of stru ctu res negates th e use of the stan d ard deviation m easure for anything other th a n a qualitative investigative tool.
Chapter 2. Inter-Residue Contacts for Structural Comparison 66 13 •-1 ’ I '■ 26 37 ■ ■ ' ■ 1 ■ ■ ■ ' T " - 49 61 ... 73 85 , . . . . 97 ...... 109 121 A L IG N M E N T M A T R IX CATH 3.10.30.70 MINSEODIS 8 LENGTH 121 AV_LOWER 8.0 ■ 0.0 0.0 STRUCTURES 4 AV.U PPER 20.0 ■ 2.0 0.3 CONTACTS 100 156 SD_LOWER 0.5
■
4.0 0.6 CONTACTS all 265 SD .U P PE R 3.0 ■ 6.0 0.9 STRUCTURES 1a2vA2 ___ 8 .0 1.2 1av402 _ 1 0.0 1.5 1 oacA4 12.0 1.8 1kslA2 1 4.0 2.1 _ 16.0 2 .4 1 8.0 __2 .7 2 0 .0 __3.01 Av. DIst. S id D ev. |
F ig u r e 2.5; A consensus distance plot (I. Sillitoe, COCOPLOT) for the oxidoreduc tase superfainily in the a /?-roll architecture of CATH (classification code 3.10.30.70). The top-right half of the plot illustrates the average distance between alignment po sitions with plot intensity increasing with shorter distances. The bottom -left half of the plot illustrates the standard deviation for these alignment positions a.s the plot intensity increases where the structural variability decreases.
Chapter 2. Inter-Residue Contacts for Structural Comparison 67