An example of a β-sheet, with the stabilizing hydrogen bonds between adjacent strands (shown as dotted lines), is shown in the image below: β-sheets consist of several β-strands, stretched segments of the polypeptide chain kept together by a network of hydrogen bonds between adjacent strands. The second major secondary structure element in proteins is the β-sheet. We should also note that in addition to the “simple” helical structures mentioned here, there is a number of so-called coiled-coil structures, in which two or more α-helices together build higher-order helical structures. The first detailed analysis of the occurrence of the π-helix in proteins, based on the analysis of entries in the Protein Data Bank (PDB), was published by Fodje & Al-Karadaghi, 2002. The 3_10 helix has a smaller radius, compared to the α-helix, while the π-helix has a larger radius. Other helical structures include the 3_10 helix, which is stabilized by hydrogen bonds of the type (i, i+3) and the π-helix, which is stabilized by hydrogen bonds of the type (i, i+5). The α-helix is not the only helical structure in proteins. The hydrogen bonds are shown on the figure as dashed lines. Together these groups form a hydrogen bond, one of the main forces in the stabilization of secondary structure in proteins. When looking at the helix in the figure below, notice how the carbonyl (C=O) oxygen atoms (shown in red) point in one direction, towards the amide NH groups 4 residues away (i, i+4). The repeating structural pattern in helices is a result of repeating (similar) φ and ψ values, which is reflected in the clustering of the torsion angles within the helical region of the Ramachandran plot. Each residue is translated 1.5 Å along the helix axis, which gives a vertical distance of 5.4 Å between structurally equivalent atoms in a turn (pitch of a turn). There are 3.6 residues/turn in an α-helix, which means that there is one residue every 100 degrees of rotation (360/3.6). To get a better impression of how a helix looks like, only the main chain of the polypeptide is shown, no side chains. This type of representation of a protein structure is called “sticks representation”. An example of an α-helix is shown on the image below. The prediction was confirmed when the first three-dimensional structure of a protein, myoglobin (by Max Perutz and John Kendrew) was determined by X-ray crystallography. Linus Pauling was the first to predict the existence of α-helices. The most common type of secondary structure in proteins is the α-helix. Many of the features discussed here are essential for practical applications − for example in sequence alignment and analysis, homology modelling and analysis of model quality, in planning mutations or when analyzing protein-ligand interactions. Angewandte Chemie International Edition Wiley In the following we will focus on the general aspects of protein secondary structure. We speculate that many RING domains may share a similar mechanism of substrate recognition and molten‐globule‐like character. This study reveals novel insights into the folding mechanism and recruitment of binding partners by the Ste5 RING‐H2 domain. Binding of the Ste5 RING‐H2 domain to the physiological Gβ/γ (Ste4/Ste18) ligand is accompanied by a conformational transition into a better folded, more globular structure. Furthermore, it exhibits high thermal stability in native conditions. With structural and biophysical studies, we show that the Ste5 RING‐H2 domain exists as a molten globule under native buffer conditions, in yeast extracts, and even in denaturing conditions containing urea (7 M). Upon pheromone stimulation, Ste5 (through its RING‐H2 domain) interacts with the β and γ subunits of an activated heterodimeric G protein and promotes activation of the MAP‐kinase cascade. Ste5 is a scaffold protein that controls the pheromone response of the MAP‐kinase cascade in yeast cells. Samatanga, Brighton van Drogen, Frank Peter, Matthias Jelesarov, Ilian Wider, Gerhard The RING Domain of the Scaffold Protein Ste5 Adopts a Molten Globular Character with High Thermal and Chemical Stability The RING Domain of the Scaffold Protein Ste5 Adopts a Molten Globular Character with High Thermal.

Secondary structure protein scaffold