https://digitalcommons.imsa.edu/protein_folding/1002/thumbnail.jp

Chung, Esther, \u2716

Dovgin, Sarah, \u2716

Qian, Michael, \u2716

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Illinois Mathematics and Science Academy: DigitalCommons@IMSA

Secondary Structure Michael Qian, Sarah Dovgin, and Esther Chung Figure 3. Secondary structures can be separated into two common groups: Alpha Helix2	-  phi and psi bonds are both around -60 degrees which cause ideal hydrogen bonds to form between the  C,O and H,N.  Beta Pleated Sheet2	-  phi bonds are around -120 and psi bonds are around +135 Figure 2. Image of a Ramachandran plot. This plot identifies the most ideal torsion angles throughout the secondary structure (shown by the darkest areas on the graph). Steric hindrance plays a factor in restricting the angles, meaning different amino acid R-groups can affect the torsion angles. The most ideal angles are denoted on the graph by the the darkest areas. Certain degrees of rotation form different types of secondary structures1.  What Causes Secondary Structure? Secondary structures are composed of torsion angles which aid in the formation of helices and sheets. Turns, and hydrophobicity additionally affect the secondary structure of a protein resulting in alternative protein structures. Figure 1. Depiction of phi (ϕ), psi (Ψ), and omega (ω) angles between 2 amino acids. The phi and psi bonds are the torsion bonds connecting the amine and the carboxylic acid groups to the alpha carbon in the center of the amino acid. Phi angles are bond between N and Cα. Psi angles are bond between Cα	and C. Omega angles are flat 180 degree angles and occur between peptide bonds. Only phi and psi angles can rotate, and their rotation depends on the steric hindrance caused by the R-group of the amino acid1.   Types of Secondary Structure Beta Pleated Sheets Figure 4. Additional substructures exist within the group of helices ●  Alpha helices (3.613): 100° turn in helix3	●  3.10 helices: 120° turn in helix4	●  pi helices: 87° turn in helix5	The various degree turns in the helices additionally affect how tightly the helix is coiled.  Types of Helices Hydrophobicity Types Turns Figure 5. Additional substructures exist within the group of beta pleated sheets2	●  parallel beta pleated sheet ●  anti-parallel beta pleated sheet   Figure 6. Common turns that are used at in beta pleated sheets. Each turn uses 4 amino acids. Prolines are common when phi is negative, and glycines are common when phi is positive.7	Figure 8. Adjacent side chains of a β pleated sheet can be oriented so that one side of the sheet is hydrophobic while the other side is hydrophilic. This aids in creating a boundary between water and oily environments.8	Figure 7. The alpha helix is amphiphatic. The figure depicts the orientation of hydrophilic and hydrophobic amino acids from a top view of the helix. The numbers indicate the position of each of the amino acids, in their optimal positions according to hydrophobicity, from the first amino acid to the last.7	Bibliography 1. Karadaghi, S.A., (2015) “Torsion Angles and the Ramachandran Plot” Basics of Protein Structure. Retrieved from http://www.proteinstructures.com/Structure/Structure/Ramachandran-plot.html 2. Jakubowski, H., “Protein Conformation” UCDavis Biowiki. Retrieved from http://biowiki.ucdavis.edu/Biochemistry/Proteins/Protein_Conformation 3. Karadaghi, S.A., (2015) “Protein Secondary Structure: a-helices and B-sheets” Basics of Protein Structure. Retrieved from http://www.proteinstructures.com/Structure/Structure/secondary-sructure.html 4. 3.10 Helix. (2 October 2015) Wikipedia. Retreived from https://en.wikipedia.org/wiki/310_helix 5. Pi Helix. (1 September 2015) Wikipedia. Retreived from https://en.wikipedia.org/wiki/Pi_helix 6. Turn (Biochemistry). (28 October 2015) Wikipedia. Retreived from https://en.wikipedia.org/wiki/Turn_(biochemistry) 7. “a-Helix”, Protein Structure: a-helix, B-sheet and turns. Retrieved from http://www.whatislife.com/reader/protein/protein.html 8. Protein structure. (12 February 2010) Wikipedia. Retreived from http://en.citizendium.org/wiki/Protein_structure  Campbell, Neil A., and Jane B. Reece. Biology. 7. San Francisco: Pearson: Benjamin Cummings, 2005.  Berndt, K.D., (31 May 1996) “3.1 Helices.” Types of Secondary Structure. Retrieved from http://www.cryst.bbk.ac.uk/PPS2/course/section8/ss-960531_5.html Turn (Biochemistry). (28 October 2015) Wikipedia. Retreived from https://en.wikipedia.org/wiki/Turn_(biochemistry) “a-Helix”, Protein Structure: a-helix, B-sheet and turns. Retrieved from http://www.whatislife.com/reader/protein/protein.html Beta Sheet. (18 October 2015) Wikipedia. Retreived from https://en.wikipedia.org/wiki/Beta_sheet Nigro, A. The Three-Dimensional Structure of Proteins. [PDF document] Retrieved from Western Connecticut State University Web site: http://people.wcsu.edu/nigroa/CHE%20421/Lectures/CHP%204%20Three%20Dimensional%20Structure%20of%20Proteins.pdf Protein structure. (12 February 2010) Wikipedia. Retreived from http://en.citizendium.org/wiki/Protein_structure 

Poster 3: Secondary Structure

https://digitalcommons.imsa.edu/cgi/viewcontent.cgi?article=1002&amp;context=protein_folding

Poster 3: Secondary Structure

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