Secondary structure

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[[Hydrogen bond|Hydrogen bond]] formation causes the protein secondary structure to be stabilised.There are two main forms of protein secondary structure, the [[Alpha-helix|alpha helix ]] and the [[Beta sheet|beta sheet]], however, other forms such as the [[Beta-turn|beta-turn]] and the omega loop are known to exist <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.  
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[[Hydrogen bond|Hydrogen bond]] formation causes the protein secondary structure to be stabilised.There are two main forms of protein secondary structure, the [[Alpha-helix|alpha helix ]]and the [[Beta sheet|beta sheet]], however, other forms such as the [[Beta-turn|beta-turn]] and the omega loop are known to exist <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.  
  
 
== Alpha helix  ==
 
== Alpha helix  ==
  
The structure of the alpha helix, first predicted by [[Linus Pauling|Pauling]] and Corey in 1951 <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>, consists of a coiled helical structure held together by [[Hydrogen bonds|hydrogen bonds]] <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The helix can be left or right handed, coiling in an anticlockwise or clockwise direction respectively; however the right-handed configuration is more energetically favourable due the fact that the side chains of the peptide backbone do not interfere with each other as much <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds that stabilise the structure are formed between the [[carbonyl oxygen|carbonyl oxygen]] (CO group) of the nth residue and the [[amide hydrogen|amide hydrogen]] (NH group) of the n+4th residue <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. A turn of the helix consists of 3.6 amino acid residues and the rise from one residue to the next is approximately 1.5 A<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.  
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The structure of the alpha helix, first predicted by [[Linus Pauling|Pauling]] and Corey in 1951 <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>, consists of a coiled helical structure held together by [[Hydrogen bonds|hydrogen bonds]] <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The helix can be left or right handed, coiling in an anticlockwise or clockwise direction respectively; however the right-handed configuration is more energetically favourable due the fact that the side chains of the peptide backbone do not interfere with each other as much <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds that stabilise the structure are formed between the [[Carbonyl oxygen|carbonyl oxygen]] (CO group) of the nth residue and the [[Amide hydrogen|amide hydrogen]] (NH group) of the n+4th residue <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. A turn of the helix consists of 3.6 amino acid residues and the rise from one residue to the next is approximately 1.5 A<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.  
  
When it was discovered, the alpha helix was found in the protein [[α-keratin|α-keratin]], which is abundant in skin and its derivatives- hair, nails and horns. Short regions of alpha helix are mainly present in proteins that are embedded in cell membranes such as transport proteins and receptors<ref> Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roff M., Roberts K., Walter P. (2013), Essentials Cell Biology, 4th edition, New York: Garland Science. page 132 </ref>.  
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When it was discovered, the alpha helix was found in the protein [[Α-keratin|α-keratin]], which is abundant in skin and its derivatives- hair, nails and horns. Short regions of alpha helix are mainly present in proteins that are embedded in cell membranes such as transport proteins and receptors<ref> Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roff M., Roberts K., Walter P. (2013), Essentials Cell Biology, 4th edition, New York: Garland Science. page 132 </ref>.  
  
 
Sometimes two or three alpha helices will wrap around one another to form a particularly stable structure known as a coiled-coil. This structure forms when the alpha helices have most of their nonpolar side chains on one side so that they can twist around each other with these side chains facing inward- minimizing their contact with the aqueous cytosol. Long, rodlike coiled-coils form the structural framework for many elongated proteins. Examples include α-keratin, which forms the intracellular fibres that reinforce the outer layer of the skin, and [[Myosin]], the motor protein responsible for muscle contraction<ref>Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roff M., Roberts K., Walter P. (2013), Essentials Cell Biology, 4th edition, New York: Garland Science. page 133-134 </ref>.  
 
Sometimes two or three alpha helices will wrap around one another to form a particularly stable structure known as a coiled-coil. This structure forms when the alpha helices have most of their nonpolar side chains on one side so that they can twist around each other with these side chains facing inward- minimizing their contact with the aqueous cytosol. Long, rodlike coiled-coils form the structural framework for many elongated proteins. Examples include α-keratin, which forms the intracellular fibres that reinforce the outer layer of the skin, and [[Myosin]], the motor protein responsible for muscle contraction<ref>Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roff M., Roberts K., Walter P. (2013), Essentials Cell Biology, 4th edition, New York: Garland Science. page 133-134 </ref>.  
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== Beta sheet  ==
 
== Beta sheet  ==
  
The beta sheet is the other main secondary structure of proteins, beta sheets are made up of two or more peptide chains called beta strands <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. Hydrogen bonds are formed between two adjacent beta strands <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The side chains of the amino acid residues point out perpendicularly in opposite directions (up and down) to the plain of the peptide backbone of the beta strands<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.  
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The beta sheet is the other main [[Secondary_structure|secondary structure]] of proteins, beta sheets are made up of two or more peptide chains called beta strands <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. Hydrogen bonds are formed between two adjacent beta strands <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The side chains of the amino acid residues point out perpendicularly in opposite directions (up and down) to the plain of the peptide backbone of the beta strands<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.  
  
 
There are two types of beta sheets, anti-parallel and parallel. Anti-parallel beta sheets are formed from adjacent beta strands running in an alternating configurations, if beta strand n runs from the N terminus to the C terminus the beta strand n+1 runs from the C terminus to the N terminus and the strands of the beta sheet alternate in that manner <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds are formed between the amide hydrogen (NH group) and the carbonyl oxygen (CO group) of one beta strand and the carbonyl oxygen (CO group) and the amide hydrogen (NH group) of the adjacent strand respectively <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds in an anti-parallel beta sheet are short and straight making them strong <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.The parallel beta sheets are formed from adjacent beta strands running in the same configuration, if beta strand n runs from the N terminus to the C terminus then beta strand n+1 also runs from the N terminus to the C terminus <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds are formed between the amide hydrogen (NH group) of an amino acid residue on beta strand n and the carbonyl oxygen (CO group) of the adjacent strand beta strand, n+1 <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The carbonyl oxygen (CO group) of beta strand n forms hydrogen bonds with the amide hydrogen (NH group) of the amino acid residue two residues further down on the adjacent strand<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds in parallel beta strands are long and angled making them weaker than those found in anti-parallel beta sheet <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.  
 
There are two types of beta sheets, anti-parallel and parallel. Anti-parallel beta sheets are formed from adjacent beta strands running in an alternating configurations, if beta strand n runs from the N terminus to the C terminus the beta strand n+1 runs from the C terminus to the N terminus and the strands of the beta sheet alternate in that manner <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds are formed between the amide hydrogen (NH group) and the carbonyl oxygen (CO group) of one beta strand and the carbonyl oxygen (CO group) and the amide hydrogen (NH group) of the adjacent strand respectively <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds in an anti-parallel beta sheet are short and straight making them strong <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.The parallel beta sheets are formed from adjacent beta strands running in the same configuration, if beta strand n runs from the N terminus to the C terminus then beta strand n+1 also runs from the N terminus to the C terminus <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds are formed between the amide hydrogen (NH group) of an amino acid residue on beta strand n and the carbonyl oxygen (CO group) of the adjacent strand beta strand, n+1 <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The carbonyl oxygen (CO group) of beta strand n forms hydrogen bonds with the amide hydrogen (NH group) of the amino acid residue two residues further down on the adjacent strand<ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>. The hydrogen bonds in parallel beta strands are long and angled making them weaker than those found in anti-parallel beta sheet <ref>Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42</ref>.  

Revision as of 11:11, 1 December 2017

Hydrogen bond formation causes the protein secondary structure to be stabilised.There are two main forms of protein secondary structure, the alpha helix and the beta sheet, however, other forms such as the beta-turn and the omega loop are known to exist [1].

Alpha helix

The structure of the alpha helix, first predicted by Pauling and Corey in 1951 [2], consists of a coiled helical structure held together by hydrogen bonds [3]. The helix can be left or right handed, coiling in an anticlockwise or clockwise direction respectively; however the right-handed configuration is more energetically favourable due the fact that the side chains of the peptide backbone do not interfere with each other as much [4]. The hydrogen bonds that stabilise the structure are formed between the carbonyl oxygen (CO group) of the nth residue and the amide hydrogen (NH group) of the n+4th residue [5]. A turn of the helix consists of 3.6 amino acid residues and the rise from one residue to the next is approximately 1.5 A[6].

When it was discovered, the alpha helix was found in the protein α-keratin, which is abundant in skin and its derivatives- hair, nails and horns. Short regions of alpha helix are mainly present in proteins that are embedded in cell membranes such as transport proteins and receptors[7].

Sometimes two or three alpha helices will wrap around one another to form a particularly stable structure known as a coiled-coil. This structure forms when the alpha helices have most of their nonpolar side chains on one side so that they can twist around each other with these side chains facing inward- minimizing their contact with the aqueous cytosol. Long, rodlike coiled-coils form the structural framework for many elongated proteins. Examples include α-keratin, which forms the intracellular fibres that reinforce the outer layer of the skin, and Myosin, the motor protein responsible for muscle contraction[8].

Beta sheet

The beta sheet is the other main secondary structure of proteins, beta sheets are made up of two or more peptide chains called beta strands [9]. Hydrogen bonds are formed between two adjacent beta strands [10]. The side chains of the amino acid residues point out perpendicularly in opposite directions (up and down) to the plain of the peptide backbone of the beta strands[11].

There are two types of beta sheets, anti-parallel and parallel. Anti-parallel beta sheets are formed from adjacent beta strands running in an alternating configurations, if beta strand n runs from the N terminus to the C terminus the beta strand n+1 runs from the C terminus to the N terminus and the strands of the beta sheet alternate in that manner [12]. The hydrogen bonds are formed between the amide hydrogen (NH group) and the carbonyl oxygen (CO group) of one beta strand and the carbonyl oxygen (CO group) and the amide hydrogen (NH group) of the adjacent strand respectively [13]. The hydrogen bonds in an anti-parallel beta sheet are short and straight making them strong [14].The parallel beta sheets are formed from adjacent beta strands running in the same configuration, if beta strand n runs from the N terminus to the C terminus then beta strand n+1 also runs from the N terminus to the C terminus [15]. The hydrogen bonds are formed between the amide hydrogen (NH group) of an amino acid residue on beta strand n and the carbonyl oxygen (CO group) of the adjacent strand beta strand, n+1 [16]. The carbonyl oxygen (CO group) of beta strand n forms hydrogen bonds with the amide hydrogen (NH group) of the amino acid residue two residues further down on the adjacent strand[17]. The hydrogen bonds in parallel beta strands are long and angled making them weaker than those found in anti-parallel beta sheet [18].

References

  1. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  2. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  3. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  4. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  5. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  6. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  7. Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roff M., Roberts K., Walter P. (2013), Essentials Cell Biology, 4th edition, New York: Garland Science. page 132
  8. Alberts B., Bray D., Hopkin K., Johnson A., Lewis J., Roff M., Roberts K., Walter P. (2013), Essentials Cell Biology, 4th edition, New York: Garland Science. page 133-134
  9. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  10. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  11. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  12. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  13. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  14. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  15. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  16. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  17. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
  18. Berg J., Tymoczko J and Stryer L. (2007) Biochemistry, 6th edition, New York: WH Freeman. page 40-42
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