Copy - BASIC DARK PRESENTATION

Protein Structure Secondary Structure

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Bonds Between Amino Acid Chains

Hydrogen bonds between different amino acids in the chain are responsible for secondary structure. Hydrogen bonds form between the R groups of amino acids. Hydrogen bonding between the variable "R" groups of amino acid side-chains causes coiling alpha helices or folding beta sheets

Beta Sheet Structure

Beta sheets are a type of secondary protein.They are characterised by extended zig-zag-like chains of amino acids connected by hydrogen bonds.

The stability of beta sheets relies on hydrogen bonds formed between the amide groups of the petide bonds in the amino acid chains

Beta Sheet - Hydrogen Bonds

In a parallel beta sheet, adjacent strands run in the same direction while in antiparallel beta sheets, adjacent strands run in opposite directions

Types of Beta Sheets

1.Parallel

2.Antiparallel

Alpha Helix

These are tightly coiled structures which are formed by hydrogen bonds (the C=O have small + and - charges which are able to attract and therefore a hydrogen bond is formed between the amino acids) between the carbonyl oxygen group of one of the amino acid, leading to the helical shape.

Alpha Helix: Major Groove and DNA

The structure of an alpha helix matches the width of a DNA major groove (this is the big space between the two twisting strands of the double helix) which is 1.2 x 10^-2.This allows them to fit together tightly.

Alpha Helices in Transmembrane Protein

This particular structure causes the extension of amino acid side chains. When several of alpha helices are closely packed together, their side chains clash with one another. Also, the high amount of energy between them (steric constrains) may cause the formation of linking channels. However, the amino acid pointed outwards must be hydrophobic to interact with fatty acid chain of the lipid bilayers. (This is about 3mm thick)Transmembrane proteins are identified by the presence of hydrophobic part.

A peptide bond is a link of amide that is formed between carboxylic acid group of one amino acid and amine group of another amino acid.Polypeptide chains form by a condensation reaction and the peptide bonds are broekn by hydrolysis.Two amino acids form a dipeptide and more than two amino acids form a polypeptide.

A polyeptide is a molecule made of amino acids joined together by peptide bonds.

Polyeptide Chain

Super Secondary Protein Structure

The supersecondary structure, also called the structural motif, is a combination of elements of secondary structures. The structural motif reflects the arrangment of atoms in space.Supersecondary structures act as nucleatins in the process of protein folding. Supersecondary structures or motifs are characteristic combinations of a secondary structure. There are 10-40 residues in length that reoccurs in different proteins.

Motifs

Motifs can have a specific ligand binding function that can contribute to the structure of a domain:- The four alpha helix bundel motif provides a cavity for enzymes to bind prthetic groups or co-factors- Motifs can also be a mixture of both Alpha and Beta conformations. The same motif can perform similar function in different proteins. They bridge the gap between less specific regularaties of a secondary structure.Can be used to predict the tertiary structure since predicting only with amino acids may not be sufficient.

G = 3-turn helix (310 helix). Min length 3 residues. H = 4-turn helix (α helix). Minimum length 4 residues. I = 5-turn helix (π helix). Minimum length 5 residues. T = hydrogen bonded turn (3, 4 or 5 turn) E = extended strand in parallel and/or antiparallel β-sheet conformation. Min length 2 residues. B = residue in isolated β-bridge (single pair β-sheet hydrogen bond formation) S = bend (the only non-hydrogen-bond based assignment). C = coil (residues which are not in any of the above conformations).

History of the Secondary Protein Structure

The concept of secondary struture was first introduced by Kaj Ulrik Linderstorm-Lang at Stanford 1952.Our initial classification of thr secondary structure was made of three states;HELIX, (H) strand, (S) and coil (C)

Initially to determine a secondary structure between the first 3 states we would use the Chou-Fasman Method, the basis of this method was to look at the relative frequencies of each amino acid in alpha helices, beta sheets, and turns based on known protein structures which were found out through x ray crystallography. However while at the time we thought this to be a success with an accuracy of 60% updated studies show that it was much lower than that After this we made significant progress using Multiple sequence alignment which boosted the accuracy of prediction from >60% to almost 80% In modern day as evaluated by the Critical Assessment of protein Structure Prediction experiments we now know the most accurate prediction method, just short of 90% accurate, to be PSIPRED which uses artificial learning in order to make distinctions between the proteins of the DSSP

History of the Secondary Protein Structure Prediction

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