Wenxiang 3.0: Evolutionary Visualization of α,π,and 3/10 Helices

Introduction

Wenxiang diagrams ¹ illustrate protein helices as spirals on a plane (Figure 1) and thus have the advantage over helical wheels ² of being planar graphs. Wenxiang 3.0 extends the original version by adding 3 major features: (1) individual amino acid residues can be colored according to their evolu-tionary conservation in comparative multiple sequence alignments using CONSURF ³ encoding (Figure 1a and b); (2) α, π, and 3/10 helices can be illustrated by overlaying arcs representative of the pitches of these helices ((Figure 1b and c); and, (3) the physicochemical properties of amino acids residues in the protein sequence can be represented by colored geometric shapes (Figure 1c).

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Figure 1.

(a) Wenxiang 3.0 interface wherein the sequence of a 3/10 helix from 1GPB (glycogen phosphorylase B from rabbit (Oryctolagus cuniculus)) and its notation of evolutionary conservation using the key from CONSURF applied to a correlated multiple sequence alignment. (b) Arcs representing hydrogen bonding interactions for an alpha helix in 1GPB (glycogen phosphorylase B) with sequential residue numbers on each amino acid residue in the peptide and again with evolutionary conservation coloring. (c) Arcs representing hydrogen bonding interactions for a Pi helix in 1GPB (glycogen phosphorylase B) with coloring of physicochemical properties (acidic, basic, hydrophobic, polar) and geometry of size (triangular = small, rhombic = medium, pentagonal = large, and hexagonal = very large).

Besides helical wheels, 3 additional planar visualization tools of alpha helices in protein secondary structure include helixvis, ⁴ HELIQUEST, ⁵ : and helical net-diagrams. ⁶ We examined all 4 approaches to develop 5 different design criteria that we felt would be particularly helpful in featuring different aspects of the structure, function, and evolution of helices in proteins. In order to find relevant α, π, and 3/10 helical regions in protein sequences, we used STRIDE. ⁷

Software Features

Our 5 different reasons for developing Wenxiang 3.0 are: First, π and 3/10 helices are not currently represented in any helix planar visualization tool of protein secondary structure that we are could find. Kumar and Bansal ⁸ review the importance of π helices and Cooley et al ⁹ and Khrustalev et al ¹⁰ review the importance of 3/10 helices. Ren et al ¹¹ stress that large winding and unwinding of helices occur in membrane proteins such as rhodopsin and these result in transformations among these 3 configurations. Thus, a tool for analyzing potential helical interactions of a single amino acid sequence can provide helpful insights. As educators, we have extensively used origami models of α, π, and 3/10 helices ¹² and 3D printed models of helices (Herman et al ¹³ and Davenport et al ¹⁴ ). Yet our students still struggled with understanding the differences between these 3 types of helices and the importance of using evolutionary conservation to comprehend which residues or residue types were important to sustaining structure and function of proteins.

Second, in order to understand the different pitches of α, π, and 3/10 helices we wanted to overlay arcs representative of whether hydrogen bonding was occurring between either every third, fourth, or fifth residue in the pitches of these helices. These are in close correspondence to the various pitches which are usually reported to be pitches of 3 residues per turn for 3/10 helices ²⁰ , 3.6 for α helices, and 4.4 for π helices. While there is not a one-to-one correspondence between our integer values with measured values fractional values around these 3 integers, we believe our visualization of arcs representing different helical pitches has heuristic value in inferring vertical interactions between different amino acid residues involved in helical structures that contribute to their stability. We are particularly interested in identifying weak non-covalent potential interactions including hydrophobic interactions, salt bridges, van der Waals forces, etc. that have been evolutionarily conserved.

Third, residue size (small, medium, large, very large) was based upon the Voronoi polyhedral volumes (in cubic Angstroms) of amino acid residues which were divided into these bins based upon breaks in properties.

Fourth, chemical properties residues (acidic, basic, polar, hydrophobic) could be represented by different geometries and colors.

Fifth, and finally, we adopted a numerical identification of successive residues in the helical region of the amino acid sequence.