Protein secondary structure assignment revisited: a detailed analysis of different assignment methods

Abstract

BackgroundA number of methods are now available to perform automatic assignment of periodic secondary structures from atomic coordinates, based on different characteristics of the secondary structures. In general these methods exhibit a broad consensus as to the location of most helix and strand core segments in protein structures. However the termini of the segments are often ill-defined and it is difficult to decide unambiguously which residues at the edge of the segments have to be included. In addition, there is a "twilight zone" where secondary structure segments depart significantly from the idealized models of Pauling and Corey. For these segments, one has to decide whether the observed structural variations are merely distorsions or whether they constitute a break in the secondary structure.MethodsTo address these problems, we have developed a method for secondary structure assignment, called KAKSI. Assignments made by KAKSI are compared with assignments given by DSSP, STRIDE, XTLSSTR, PSEA and SECSTR, as well as secondary structures found in PDB files, on 4 datasets (X-ray structures with different resolution range, NMR structures).ResultsA detailed comparison of KAKSI assignments with those of STRIDE and PSEA reveals that KAKSI assigns slightly longer helices and strands than STRIDE in case of one-to-one correspondence between the segments. However, KAKSI tends also to favor the assignment of several short helices when STRIDE and PSEA assign longer, kinked, helices. Helices assigned by KAKSI have geometrical characteristics close to those described in the PDB. They are more linear than helices assigned by other methods. The same tendency to split long segments is observed for strands, although less systematically. We present a number of cases of secondary structure assignments that illustrate this behavior.ConclusionOur method provides valuable assignments which favor the regularity of secondary structure segments.

Protein beta-turn assignments

“…[9,13,14] Here, we have added the assignment of β-turns and compared their corresponding distribution. A high quality non-redundant set of 887 protein structures was selected from the PDB database according to the following criteria: X-ray structures with 1.6 Å or better resolution, and, no more than 20% pair wise sequence identity.…”

“…[8] KAKSI is a recent approach based on distance between Cα atoms and dihedral angles. [9] SEGNO uses also the φ and ψ dihedral angles coupled with other angles to assign the secondary structures. [10] Nonetheless, only half of the residues are concerned with α-helices and β-strands.…”

“…[12] A serious issue raised by the variety of SSAMs is that they often yield diverging results about the extents of repetitive secondary structures. [9 ,13,14]. Numerous analyses and prediction methods have been performed on the β-turns, but none comparison of β-turns assignment has been performed.…”

Dihedral angle and secondary structure database of short amino acid fragments

“…The non-redundant dataset (cullpdb_pc90_res2.0_R0.25) was obtained from the PISCES protein sequence culling server for removing redundancy. [8] Even though there are many protein secondary structure assignment programs as described elsewhere [7], we chose the most widely used STRIDE for this analysis [ 7] and it is shown to perform better than DSSP. [ 6] …”

From local structure to a global framework: recognition of protein folds

“…There are several methods available for assigning secondary structures, based on local backbone dihedral angles or hydrogen bonds. It is interesting to note that the assignments made by different methods do not agree to a significant extent [124][125][126]. Figure 3 presents the comparison of secondary structure assigned based on the three-dimensional structure of methyglyoxal synthase [127] with that of predictions made by different methods.…”