User:James D Watson/Structural Templates: Difference between revisions

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==Secondary structure elements==

Proteins are formed from linear chains of amino acids joined together by peptide bonds. These chains then fold up to form the three dimensional shape. However, the relative rigidity of the peptide bond combined with the presence of amino acid sidechains, means that not all conformations are acceptable and there are many cases where the various atoms in the chain start to collide with one another. Two of the most stable (and therefore most commonly observed) conformations are the '''α-helix''' and the '''β-pleated sheet'''. These are known as secondary structures. <br/>

α-helices

The α-helix is formed when the amino acid backbone forms a right handed spiral with 3.6 amino acids per turn. The sidechains point outward, away from the centre of the helix, where athey can interact with solvent, other protein, small molecules or macromolecules. The structure is stabilised by regular hydrogen bonds that form between the backbone carbonyl oxygens and amide hydrogens. The bonding pattern for the α-helix is characterised by the carbonyl group of residue i hydrogen interacting with the amide group of residue i+4, this is known as an (i, i+4) interaction. The alpha-helix can take other less common forms including π-helices, 3<sub>10</sub>-helices and their left handed forms (see table 1 for the helix parameters)

β-sheets occur in two varieties: parallel and anti-parallel. Different kinds of turns in the chain are also classified as secondary structures. A fourth and final type of secondary structure, known as random coil, refers to folds of the protein that do not fit into a classification. About 50% of all protein structure comes under this category.

Peptide Bonds

Peptide bonds are formed as a protein is synthesized, between the carboxylic acid group of one amino acid and the amimo group of the next. Peptide bonds are rigid, planar bonds due to a degree of resonance that gives them a partial double bond character. There is no rotation around a peptide bond, so it confers some limitations to the folding of a protein chain.

β-sheets

β sheets are compact and stable structures. They are formed when two or more lengths of a protein chain lie next to each other so as to form hydrogen bonds between their respective backbones. In order for the backbones to be close enough for hydrogen bonds to form, the sidechains must not come between the backbones. Each length that participates in a β sheet is called a β strand.

There are two ways the strands can orient themselves to form &beta sheets: parallel and anti-parallel.

Anti-parallel β Sheets

Protein chains are synthesized starting at the amino terminus and ending at the carboxyl terminus. Thus a protein chain has a directionality. In an anti-parallel β sheet, the beta strands are aligned next to each other, running in opposite directions.

Hydrogen bonding

The backbone hydrogen bonding partners are the carbonyl oxygens and amide hydrogens. They are lined up nearly directly across from each other when the strands of a sheet are anti-parallel. They form fairly straight hydrogen bonds.

Sidechain conformation

The sidechains project out of the plane of the sheet, each consecutive sidechain emerging from the opposite side of the sheet.

Parallel β sheets

When β strands are in the parallel orientation, i.e., they run alongside each other in the same direction, the carbonyl oxygen and the amide protons are staggered, and the hydrogen bonds are on an angle across to the opposite strand.

As with the α-helix, the sidechains of the β sheet are free to interact with the environment, and the tertiary structure of the protein will be influenced by the sidechains projecting out of the β-sheet.

Secondary structure and the Jmol Menu

The secondary structure of a protein can be quickly seen using menu commands. First click View Animation to reset the display.

Select | All

Color | Cartoon | By Scheme | Secondary Structure

The α-helices are magenta, β sheets are yellow, and random coil is white.

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QUESTIONS

The following interactive question(s) require you to interact with the structure to arrive at the correct answer. You may use any of the visualization controls or the dropdown menus to help you to answer the questions - direct manipulation of the structure may be required.

Question 1- Load structure

The α heilix and β sheets we've been looking at are parts of the ribosomal protein L9. It is composed of two globular domains with a very long α-helix between them. Given this image of L9 in spacefill, colored by element, use the Jmol menu to change the display to so that you can clearly see both (1) the pattern of the protein chain and (2) the default colors for secondary structure.

View Answer

Question 2 - Load structure

Explore the Jmol menu to find commands relating to hydrogen bonds. Given this display of the backbone of ribosomal L9, display the hydrogen bonds that stabilize secondary structres.

View Answer

@@ Line 19: / Line 19: @@
 ==Secondary structure elements==
+Proteins are formed from linear chains of amino acids joined together by peptide bonds. These chains then fold up to form the three dimensional shape. However, the relative rigidity of the peptide bond combined with the presence of amino acid sidechains, means that not all conformations are acceptable and there are many cases where the various atoms in the chain start to collide with one another. Two of the most stable (and therefore most commonly observed) conformations are the '''α-helix''' and the '''β-pleated sheet'''. These are known as secondary structures. <br/>
+α-helices
+The α-helix is formed when the amino acid backbone forms a right handed spiral with 3.6 amino acids per turn. The sidechains point outward, away from the centre of the helix, where athey can interact with solvent, other protein, small molecules or macromolecules. The structure is stabilised by regular hydrogen bonds that form between the backbone carbonyl oxygens and amide hydrogens. The bonding pattern for the α-helix is characterised by the carbonyl group of residue i hydrogen interacting with the amide group of residue i+4, this is known as an (i, i+4) interaction. The alpha-helix can take other less common forms including π-helices, 3<sub>10</sub>-helices and their left handed forms (see table 1 for the helix parameters)
+β-sheets occur in two varieties: parallel and anti-parallel. Different kinds of turns in the chain are also classified as secondary structures. A fourth and final type of secondary structure, known as random coil, refers to folds of the protein that do not fit into a classification. About 50% of all protein structure comes under this category.
+Peptide Bonds
+Peptide bonds are formed as a protein is synthesized, between the carboxylic acid group of one amino acid and the amimo group of the next. Peptide bonds are rigid, planar bonds due to a degree of resonance that gives them a partial double bond character. There is no rotation around a peptide bond, so it confers some limitations to the folding of a protein chain.
+β-sheets
+β sheets are compact and stable structures. They are formed when two or more lengths of a protein chain lie next to each other so as to form hydrogen bonds between their respective backbones. In order for the backbones to be close enough for hydrogen bonds to form, the sidechains must not come between the backbones. Each length that participates in a β sheet is called a β strand.
+There are two ways the strands can orient themselves to form &beta sheets: parallel and anti-parallel.
+Anti-parallel β Sheets
+Protein chains are synthesized starting at the amino terminus and ending at the carboxyl terminus. Thus a protein chain has a directionality. In an anti-parallel β sheet, the beta strands are aligned next to each other, running in opposite directions.
+Hydrogen bonding
+The backbone hydrogen bonding partners are the carbonyl oxygens and amide hydrogens. They are lined up nearly directly across from each other when the strands of a sheet are anti-parallel. They form fairly straight hydrogen bonds.
+Sidechain conformation
+The sidechains project out of the plane of the sheet, each consecutive sidechain emerging from the opposite side of the sheet.
+Parallel β sheets
+When β strands are in the parallel orientation, i.e., they run alongside each other in the same direction, the carbonyl oxygen and the amide protons are staggered, and the hydrogen bonds are on an angle across to the opposite strand.
+As with the α-helix, the sidechains of the β sheet are free to interact with the environment, and the tertiary structure of the protein will be influenced by the sidechains projecting out of the β-sheet.
+Secondary structure and the Jmol Menu
+The secondary structure of a protein can be quickly seen using menu commands. First click View Animation to reset the display.
+Select | All
+Color | Cartoon | By Scheme | Secondary Structure
+The α-helices are magenta, β sheets are yellow, and random coil is white.
+--------------------------------------------------------------------------------
+QUESTIONS
+The following interactive question(s) require you to interact with the structure to arrive at the correct answer. You may use any of the visualization controls or the dropdown menus to help you to answer the questions - direct manipulation of the structure may be required.
+Question 1- Load structure
+The α heilix and β sheets we've been looking at are parts of the ribosomal protein L9. It is composed of two globular domains with a very long α-helix between them. Given this image of L9 in spacefill, colored by element, use the Jmol menu to change the display to so that you can clearly see both (1) the pattern of the protein chain and (2) the default colors for secondary structure.
+View Answer
+Question 2 - Load structure
+Explore the Jmol menu to find commands relating to hydrogen bonds. Given this display of the backbone of ribosomal L9, display the hydrogen bonds that stabilize secondary structres.
+View Answer
 <applet load='5p21' size='350' frame='true' align='left' script='James_D_Watson/Proteins_Intro/Superposition_ras_structures/1' />
 <applet load='5p21' size='350' frame='true' align='right' script='James_D_Watson/Proteins_Intro/Superposition_ras_ploops/2' />