Chameleon sequences-Structural effects

Abstract

The predisposition of amino acids towards accepting the appropriate secondary structure form is ambiguous. The identified sequences (6-12 aa in length - ChSeq data base) of the chameleon type (the same sequence accepting different secondary structures) constitute a puzzle that makes it difficult to indicate the initial conformation in a chain with a given amino acid sequence. The analysis of proteins presented in this paper uses the hydrophobicity distribution in protein body as the criterion for comaparable analysis of the status of helica/Beta-structural chameleon fragments in pairs of proteins. The sub-base is the object of analysis containg the proteins representing the organisation of hydrophobicity in one protein of the pair as ordered according to micelle-like organisation (hydrophobic core with polar surface) and the second one in pair with disordered hydrophobicity organisation. The status of chameleon sections appears to represent local organisation of hydrophobicity highly accordant in both proteins in chameleon pair independently on the status of the structural unit they belong to. The fuzzy oil drop model (FOD) in its modified form (FOD-M) is applied for analysis. This work aims to verify the hypothesis assuming the subordination of the form of secondary structure to the superior goal of obtaining a hydrophobicity distribution suitable for the given biological activity of the protein, ensuring biological functionality. Secondary structure is not an aim by itself. It is shown, that the main goal is to reach the structure representing specific activity. Secondary structure is a means to achieve this goal.

Fig 1. Visualisation of the model used.

A – example of T, O and R distribution – form reduced to 1D. B – determined value of parameter RD =  0.725, suggesting micelle-like status. C – method of determining the value of the K parameter – the value corresponds to the minimum D_KL value for the (O | M) relationship. D – summary of T, O and M distributions for the K value determined as per C.

Fig 2. The summary of the influence of the specific environment on the structuring of a polypeptide chain with a hydrophobicity (red O)/polarity (blue X) distribution of amino acids – aa sequences with varied hydrophobicity – top line with a highlighted different secondary structure for chameleon sections (boxes).

A – the effect of environment with varying polarity on the structuring of the sequence listed as 1. B – the effect of environment with varying polarity on the structuring of the sequence listed as 2. HHH… denotes a helical fragment; BBB… denotes a beta-structural fragment.

Fig 3. The characteristics of the sub-base of ChSeq base restricted to proteins showing a varied status: one protein in a pair with RD >  0.5; the other protein in a pair with RD <  0.5.

A – scatter diagram for the system: X-axis – RD values higher in the pair, Y-axis – RD values lower in the analysed pair. Red points – the status of structural units containing chameleon sections, blue points – the status of chameleon sections (RD(FR)). B – the identification of outliers (red points) – representatives with the highest degree of divergence from the equal status are discussed in detail later in the paper. For each point, the status is expressed by RD(FR). C – the identification of pairs of proteins represented in the detailed analysis. Here, the points with the highest divergence from a linear relationship and dots representing pairs with extreme statuses for maximal RD (examples 1,2) and minimal RD (example 7) were selected. Red dots – as in A, blue dots – as in A. Green lines link the status of of chameleon fragments (blue dots – RD(FR)) with the status of structural units (red dots - RD).

Fig 4. Pair characterisation (example 1 in

Fig 3.C) – the pair discussed is on the position 617 in ChSeq data base. A – T, O and M distribution for the K value (given in the legend) describing the status of oxidoreductase (3N2S). B – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – 3N2S, C – T, O and M distribution for the K value (given in the legend) describing the status of transferase (2Q80). D – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – 2Q80. Additionally, the positions of the catalytic residues are highlighted in pink. E – T and O distribution for the chameleon section in oxidoreductase (3N2S). F – set of T and O distributions for the chameleon section in transferase (2Q80). The blue dots on X-axis in A and C – chameleon fragment.

Fig 5. Pair characterisation (2 in

Fig 3.C) - – the pair discussed is on the position 243 in ChSeq data base. A – T, O and M distribution for the K value (given in the legend) describing the status of hydrolase (2YGL). B – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – (2YGL). C – T, O and M distribution for the K value (given in the legend) describing the status of transferase (2PZI). D – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – 2PZI. E – T and O distribution for the chameleon section in hydrolase (2YGL). F – set of T and O distributions for the chameleon section in transferase (2PZI) The blue dots on X-axis in A and C – chameleon fragment.

Fig 6. Pair characterisation (3 in

Fig 3.C) - – the pair discussed is on the position 458 in ChSeq data base. A – T, O and M distribution for the K value (given in the legend) describing the status of cell adhesion (2J6R). B – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – (2J6R). C – T, O and M distribution for the K value (given in the legend) describing the status of DNA-binding protein (4JW3). D – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – 4JW3. E – T and O distribution for the chameleon section in cell adhesion (2J6R). F – set of T and O distributions for the chameleon section in DNA-binding protein (4JW3). The blue dots on X-axis in A and C – chameleon fragment.

Fig 7. Pair characterisation (4 in

Fig 3.C) - – the pair discussed is on the position 583 in ChSeq data base. A – T, O and M distribution for the K value (given in the legend), describing the status of transferase (2P8U). B – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – (2P8U). C – T, O and M distribution for the K. value (given in the legend), describing the status of hydrolase (3LXU). D – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – 3LXU. E – T and O distribution for the chameleon section in transferase (2P8U). F –T and O distributions for the chameleon section in hydrolase (3LXU). The blue dots on X-axis in A and C – chameleon fragment.

Fig 8. Pair characterisation (5 in

Fig 3.C) - – the pair discussed is on the position 683 in ChSeq data base. A – T, O and M distribution for the K value (given in the legend), describing the status of ribosomal protein (3U5E). B – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – (3U5E). C – T, O and M distribution for the K value (given in the legend), describing the status of cytokine (1EER). D – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – 1EER. E – T and O distribution for the chameleon section in ribosomal protein (3U5E). F – T and O distributions for the chameleon section in cytokine (1EER). The blue dots on X-axis in A and C – chameleon fragment.

Fig 9. Pair characterisation (6 in

Fig 3.C) - – the pair discussed is on the position 408 in ChSeq data base. A – T, O and M distribution for the K value (given in the legend), describing the status of transferase (1WXX). B – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – (1WXX). C – T, O and M distribution for the K value (given in the legend), describing the status of lyase (1SZQ). D – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – 1SZQ. E – T and O distribution for the chameleon section in transferase (1WXX). F – T and O distributions for the chameleon section in lyase (1SZQ). The blue dots on X-axis in A and C – chameleon fragment.

Fig 10. Pair characterisation (7 in

Fig 3.C) - – the pair discussed is on the position 237 in ChSeq data base. A – T, O and M distribution for the K value (given in the legend), describing the status of transferase (4C5I). B – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – (4C5I). C – T, O and M distribution for the K value (given in the legend), describing the status of lyase (3UNF-H). D – 3D representation of the structural unit for which the parameters have been determined with the chameleon section (red) highlighted – 3UNF-H. E – T and O distribution for the chameleon section in transferase (4C5I). F – T and O distributions for the chameleon section in lyase (3UNF-H). The blue dots on X-axis in A and C – chameleon fragment.