Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship

Abstract

BackgroundSecondary structures are elements of great importance in structural biology, biochemistry and bioinformatics. They are broadly composed of two repetitive structures namely α-helices and β-sheets, apart from turns, and the rest is associated to coil. These repetitive secondary structures have specific and conserved biophysical and geometric properties. PolyProline II (PPII) helix is yet another interesting repetitive structure which is less frequent and not usually associated with stabilizing interactions. Recent studies have shown that PPII frequency is higher than expected, and they could have an important role in protein – protein interactions.Methodology/Principal FindingsA major factor that limits the study of PPII is that its assignment cannot be carried out with the most commonly used secondary structure assignment methods (SSAMs). The purpose of this work is to propose a PPII assignment methodology that can be defined in the frame of DSSP secondary structure assignment. Considering the ambiguity in PPII assignments by different methods, a consensus assignment strategy was utilized. To define the most consensual rule of PPII assignment, three SSAMs that can assign PPII, were compared and analyzed. The assignment rule was defined to have a maximum coverage of all assignments made by these SSAMs. Not many constraints were added to the assignment and only PPII helices of at least 2 residues length are defined.Conclusions/SignificanceThe simple rules designed in this study for characterizing PPII conformation, lead to the assignment of 5% of all amino as PPII. Sequence – structure relationships associated with PPII, defined by the different SSAMs, underline few striking differences. A specific study of amino acid preferences in their N and C-cap regions was carried out as their solvent accessibility and contact patterns. Thus the assignment of PPII can be coupled with DSSP and thus opens a simple way for further analysis in this field.

Switching from blue to yellow: altering the spectral properties of a high redox potential laccase by directed evolution

“…(Sreeram & Woody 1994). Usually, polyproline helixes are short (only 3-6 amino acids) and they are classified as an unordered structure (Mansiaux et al 2011). Moreover, the specific ellipticity of polyproline helixes varies from 45000 up to 100 000 degr .cm 2 dmol -1 (Sreeram & Woody 1994).…”

Proline: The Distribution, Frequency, Positioning, and Common Functional Roles of Proline and Polyproline Sequences in the Human Proteome

“…Tri-proline sequences may fold into right-handed or left-handed helices, referred to as polyproline I (PPI) or polyproline II (PPII), respectively [6]–[8]. The left-handed version is far more common.…”

“…In addition to their role in molecular conformation, polyproline II helices are important in protein-protein interactions, mediating signal transduction, as with adjacent SH3, EVH1, and WW motifs [9]–[20]. Other amino acids, referred to as “guests”, such as glycine, asparagine, alanine, glutamine, valine, aspartic acid, histidine and lysine, may participate in PPII helical conformations [8], [21], [22].…”

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

“…b-Turns account for about 25% of the residues in proteins [146]. Other favourable local structures involve PolyProline II helices [147], hairpin loops, corner motifs, b-bulges, etc. [148].…”