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

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==Secondary structure elements==
==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/>
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 along with a number of small turns in the chain and random coil (folds that do not fit into a classification) are known as secondary structures. <br/>


α-helices
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)
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
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.  
A single beta-strand can be described as a flat helix with 2 residues per turn although this may not be initially obvious. When two or more beta strands lie next to each other, forming hydrogen bonds between them, this is what is termed a β-sheet. As the backbones need to come close together to interact and form a sheet, the sidechains are oriented away from the plane of the sheet. As the polypeptide chain is synthesised from the amino terminus to the carboxyl terminus it has a directionality (represented in cartoon form as an arrowhead on beta strands). β-sheets therefore occur in two varieties:<OL>
 
<LI>Anti-parallel - here the beta strands aligned next to each other run in opposite directions. As the interacting carbonyls and amides align well, the hydrogen bonds appear to be straight.
There are two ways the strands can orient themselves to form &beta sheets: parallel and anti-parallel.
<LI>Parallel - here the interacting strands run alongside each other and point in the same direction. In this conformation the carbonyl oxygen and the amides tend to be more staggered than in an anti-parallel sheet, therefore the hydrogen bonds tend to be angled.
 
</OL>
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.


Turns and loops
Select | All
There are a number of small hydrogen bonded motifs and patterns which are observed regularly. These are described below:<UL>
Color | Cartoon | By Scheme | Secondary Structure
<LI>Beta Turns - originally defined by the one hydrogen bond common to all (an i, i+3 hydrogen bond) but some modern descriptions do not require a hydrogen bond.
<LI>Beta Bulge Loops - often associated with beta sheets and result from an additional residue being found in one strand. This interrupts the regular hydrogen bonding and causes a distinctive bulge.
<LI>Alpha turns - the simplest of all motifs and is characterised by one (i, i+4) hydrogen bond. It is found as part of the hydrogen bonding network of alpha helices as well as occurring on its own.
<LI>Paperclip/Schellman Motifs - a common motif found at the C-termini of alpha helices which is essentially a reverse turn that breaks the alpha helix out of its cycle. It is characterised by the presence of a left handed residue and two hydrogen bonds: an i, i+3 bond and an i, i+5 bond.
<LI>Gamma Turns - these rarer type of turns are characterised by an (i, i+2) hydrogen bond, which is rather weak because of the bent geometry involved.
</UL>


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




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QUESTIONS
QUESTIONS
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