Missing residues

Here we encountered a typical situation in the de novo sequencing—there is a part of the sequence that is not covered by any ion series. Not all bonds between amino acids are of equal strength, and some of them might be particularly resistant to collisions, which in turn results in the missing mass-shifts (and missing residues). 

The crystal structure of human HO-1 complexed with heme has been determined to 2.07 A (163). In order to obtain crystals for high-resolution studies 164), it was necessary to use an E. coli expressed version of HO-1 consisting of residues 1-233 (missing residues 234-288, which includes the C-terminal membrane anchor). This shorter version of HO-1 is soluble and retains about 50% wild-type activity (165). As shown in Fig. 16, HO-1 is formed exclusively by helices and connecting segments of random coil. Although the rich helical content is similar to that of... 

Here, the molar ellipticities are calculated per residue, which is the usual practice in peptide and protein work, and kn is the number of missing residues. For a peptide without blocking groups, the number of amides is one less than the number of residues, r=n — 1, and kr=kn — 1. If one terminus is blocked to form an additional amide, e.g. N-acylation or C-carboxyamidation, r and n are equal and so are kr and kn. If both termini are converted into amides, r=n +1 and kr=kn +1. 

Figure 4.10. PDB file (partial) for 3D structure of hen s egg-white lysozyme (ILYZ.pdb). The abbreviated file shows partial atomic coordinates for residues 34-36. Informational lines such as AUTHOR (contributing authors of the 3D structure), REVDAT, JRNL (primary bibliographic citation), REMARK (other references, corrections, refinements, resolution and missing residues in the structure), SEQRES (amino acid sequence), FTNOTE (list of possible hydrogen bonds), HELIX (initial and final residues of a-helices), SHEET (initial and final residues of / -sheets), TURN (initial and final residues of turns, types of turns), and SSBOND (disulfide linkages) are deleted here for brevity. Atomic coordinates for amino acid residues are listed sequentially on ATOM lines. The following HETATM lines list atomic coordinates of water and/or ligand molecules.

If you are faced with a choice of deciding which structure(s) to work with, one consideration should be whether the mutations or missing residues are in areas that are relevant to the question to be solved using the structure. A mutation in the binding site, for example, would certainly affect any information to be gained about ligands binding at that site. 

Fig. 3. Molecular dynamics simulations of peptide fragments corresponding to the predicted secondary structure in Fig. 2. H2.5 was discovered while trying to model the missing residues from the PrP prediction. All simulations began with the peptide in the a-helical conformation, and the average percentage of helix over the 2 ns simulation is given.

Figure 4.6 Remark records taken from PDB ID 2cdz showing information regarding missing atoms and missing residues.

Figure 5.3. Testing a three-dimensional viewer for sequence numbering artifacts with the structure 3TS1 (Brick et al., 1989). WebMol, a Java applet, correctly indicates both the explicit and implicit sequences of the structure. Note the off-by-two difference in the numbering in the two columns of numbers in the inset window on the lower right. The actual sequence embedded in the PDB file is 419 residues long, but the COOH-terminal portion of the protein is lacking coordinates it also has two missing residues. (See color plate.)...

The missing 96 residues at the amino termini of the three chains, in the vicinity of the central domain, preclude definition of the hydrophobic domains that pair with the Ea and Eb sites, but one predicts the capacity of these missing residues to arrange in formation of hydrophobic domains with which to pair with the total of four Ea and Eb sites. 

Add missing residues. Many residues are often missing from a published crystallographic study. Especially at either the C- or N-terminus of the protein, there may be no or very low electron density as a result of the high... 

Table 8.3. C-terminal regions of hemoglobin a- and 3-chains indicating missing residues in the digestion products of carboxypeptidase A (CPA) and carboxypeptidase B (CPB) [468]...

The reason for the inability to bind tRNA could be that the fourteen missing residues are involved in the binding, but it could also be that removing this part of the domain connection prevents the domains from adopting the proper relative orientation. 

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