Introduction to protein structure - Revision history

Ann Taylor at 01:11, 30 January 2025

2025-01-30T01:11:09Z

Ann Taylor at 02:43, 6 February 2020

2020-02-06T02:43:53Z

← Older revision		Revision as of 02:43, 6 February 2020
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	<StructureSection load='1a3n_au' size='350' side='right' caption='Structure of Hemoglobin (PDB entry [[1a3n]])' scene='' pspeed='8'>		<StructureSection load='1a3n_au' size='350' side='right' caption='Structure of Hemoglobin (PDB entry [[1a3n]])' scene='' pspeed='8'>
	This tutorial illustrates some basic properties of protein structure and useful commands in Jmol and Proteopedia. Clicking the green links changes the view in the structure box to illustrate the principle described by the text. To identify a particular atom, toggle off any rotation and hold the mouse button over the atom of interest. This indicates the amino acid residue, the position in the chain, which chain, what atom it is (CA means the alpha carbon), and the overall number of the atom.		''This tutorial illustrates some basic properties of protein structure and useful commands in Jmol and Proteopedia. It assumes familiarity with concepts from college level Chemistry courses, including polarity, dihedral angles, and functional groups. For a simpler presentation, please go to [[Basics of Protein Structure]]. Clicking the green links changes the view in the structure box to illustrate the principle described by the text. To identify a particular atom, toggle off any rotation and hold the mouse button over the atom of interest. This indicates the amino acid residue, the position in the chain, which chain, what atom it is (CA means the alpha carbon), and the overall number of the atom.''

	== Levels of Protein Structure ==		== Levels of Protein Structure ==

Ann Taylor at 03:14, 4 February 2020

2020-02-04T03:14:18Z

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 *[[Introduction to molecular visualization]] explains common renditions and color schemes.
 *[[Four levels of protein structure]] -- [[Four levels of protein structure (Spanish)|Los cuatro niveles estructurales de las proteínas]]
 =='''Content Donators'''==
 Created with content from [[Structural Templates]] written by [[User:Alexander Berchansky|Alexander Berchansky]], [[User:James D Watson|James D Watson]], [[User:Eran Hodis|Eran Hodis]]

Eric Martz at 19:22, 4 August 2019

2019-08-04T19:22:47Z

← Older revision		Revision as of 19:22, 4 August 2019
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	==See Also==		==See Also==
			*[[Introduction to molecular visualization]] explains common renditions and color schemes.
	*[[Four levels of protein structure]] -- [[Four levels of protein structure (Spanish)\|Los cuatro niveles estructurales de las proteínas]]		*[[Four levels of protein structure]] -- [[Four levels of protein structure (Spanish)\|Los cuatro niveles estructurales de las proteínas]]

	=='''Content Donators'''==		=='''Content Donators'''==
	Created with content from [[Structural Templates]] written by [[User:Alexander Berchansky\|Alexander Berchansky]], [[User:James D Watson\|James D Watson]], [[User:Eran Hodis\|Eran Hodis]]		Created with content from [[Structural Templates]] written by [[User:Alexander Berchansky\|Alexander Berchansky]], [[User:James D Watson\|James D Watson]], [[User:Eran Hodis\|Eran Hodis]]

Jaime Prilusky at 05:14, 31 January 2019

2019-01-31T05:14:50Z

← Older revision		Revision as of 05:14, 31 January 2019
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	<StructureSection load='1a3n_au' size='350' side='right' caption='Structure of Hemoglobin (PDB entry [[1a3n]])' scene='' pspeed='8'>		<StructureSection load='1a3n_au' size='350' side='right' caption='Structure of Hemoglobin (PDB entry [[1a3n]])' scene='' pspeed='8'>
	This tutorial illustrates some basic properties of protein structure and useful commands in Jmol and Proteopedia. Clicking the green links changes the view in the structure box to illustrate the principle described by the text. ~~If the structure box has a puzzle piece in it, please make sure you have the latest version of [[Java]] installed and follow the directions to allow Proteopedia to run.~~ To identify a particular atom, toggle off any rotation and hold the mouse button over the atom of interest. This indicates the amino acid residue, the position in the chain, which chain, what atom it is (CA means the alpha carbon), and the overall number of the atom.		This tutorial illustrates some basic properties of protein structure and useful commands in Jmol and Proteopedia. Clicking the green links changes the view in the structure box to illustrate the principle described by the text. To identify a particular atom, toggle off any rotation and hold the mouse button over the atom of interest. This indicates the amino acid residue, the position in the chain, which chain, what atom it is (CA means the alpha carbon), and the overall number of the atom.

	== Levels of Protein Structure ==		== Levels of Protein Structure ==

Joel L. Sussman at 22:05, 30 July 2018

2018-07-30T22:05:05Z

← Older revision		Revision as of 22:05, 30 July 2018
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	<StructureSection load='~~1a3n~~' size='350' side='right' caption='Structure of Hemoglobin (PDB entry [[1a3n]])' scene='' pspeed='8'>		<StructureSection load='1a3n_au' size='350' side='right' caption='Structure of Hemoglobin (PDB entry [[1a3n]])' scene='' pspeed='8'>
	This tutorial illustrates some basic properties of protein structure and useful commands in Jmol and Proteopedia. Clicking the green links changes the view in the structure box to illustrate the principle described by the text. If the structure box has a puzzle piece in it, please make sure you have the latest version of [[Java]] installed and follow the directions to allow Proteopedia to run. To identify a particular atom, toggle off any rotation and hold the mouse button over the atom of interest. This indicates the amino acid residue, the position in the chain, which chain, what atom it is (CA means the alpha carbon), and the overall number of the atom.		This tutorial illustrates some basic properties of protein structure and useful commands in Jmol and Proteopedia. Clicking the green links changes the view in the structure box to illustrate the principle described by the text. If the structure box has a puzzle piece in it, please make sure you have the latest version of [[Java]] installed and follow the directions to allow Proteopedia to run. To identify a particular atom, toggle off any rotation and hold the mouse button over the atom of interest. This indicates the amino acid residue, the position in the chain, which chain, what atom it is (CA means the alpha carbon), and the overall number of the atom.

Ann Taylor at 16:08, 19 January 2018

2018-01-19T16:08:54Z

← Older revision		Revision as of 16:08, 19 January 2018
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	== Levels of Protein Structure ==		== Levels of Protein Structure ==
	Proteins are condensation polymers of amino acids. The <scene name='57/575866/Primary_sequence/2'>primary structure</scene> is the amino acid sequence, from the N terminus to the C terminus of the protein. The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/3'>hydrogen bonds</scene> along the <scene name='57/575866/Backbone/2'>backbone</scene>. These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>. Some proteins, such as the displayed hemoglobin molecule, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.		Proteins are condensation polymers of amino acids. The <scene name='57/575866/Primary_sequence/3'>primary structure</scene> is the amino acid sequence, from the N terminus to the C terminus of the protein. The <scene name='57/575866/Secondary_sequence/1'>secondary structure</scene> is the local structure over short distances. This level of structure is stabilized by <scene name='57/575866/H_bond_a_helix/3'>hydrogen bonds</scene> along the <scene name='57/575866/Backbone/2'>backbone</scene>. These secondary structures <scene name='57/575866/Global_secondary_structures/1'>pack together</scene> to form the overall form of the entire peptide chain, called the <scene name='57/575866/Tertiary/1'>tertiary structure</scene>. Some proteins, such as the displayed hemoglobin molecule, have more than one polypeptide chain that associate to form the functional unit of the protein; this is called <scene name='57/575866/Tertiary/2'>quaternary structure</scene>.
	'''Questions based upon these scenes:'''		'''Questions based upon these scenes:'''

Eric Martz at 20:31, 9 March 2017

2017-03-09T20:31:27Z

← Older revision		Revision as of 20:31, 9 March 2017
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	</StructureSection>		</StructureSection>

			==See Also==
			*[[Four levels of protein structure]] -- [[Four levels of protein structure (Spanish)\|Los cuatro niveles estructurales de las proteínas]]

	=='''Content Donators'''==		=='''Content Donators'''==
	Created with content from [[Structural Templates]] written by [[User:Alexander Berchansky\|Alexander Berchansky]], [[User:James D Watson\|James D Watson]], [[User:Eran Hodis\|Eran Hodis]]		Created with content from [[Structural Templates]] written by [[User:Alexander Berchansky\|Alexander Berchansky]], [[User:James D Watson\|James D Watson]], [[User:Eran Hodis\|Eran Hodis]]

Alexander Berchansky at 09:40, 5 March 2017

2017-03-05T09:40:16Z

← Older revision		Revision as of 09:40, 5 March 2017
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	'''Cys''' - X<sub>(2-4)</sub> - '''Cys''' - X<sub>(3)</sub> - Phe - X<sub>(5)</sub> - Leu - X<sub>(2)</sub> - '''His''' - X<sub>(3)</sub> - '''His'''		'''Cys''' - X<sub>(2-4)</sub> - '''Cys''' - X<sub>(3)</sub> - Phe - X<sub>(5)</sub> - Leu - X<sub>(2)</sub> - '''His''' - X<sub>(3)</sub> - '''His'''

	The example structure shown is that of Zif268 protein-DNA complex from Mus musculus (PDB entry 1AAY). In this example (a C2H2 class zinc finger) the conserved <scene name='~~User:James_D_Watson~~/~~Structural_Templates~~/Zinc_finger_cysteine/1'>cysteine</scene> and <scene name='~~User:James_D_Watson~~/~~Structural_Templates~~/Zinc_finger_histidine/2'>histidine</scene> residues form ligands to a <scene name='~~User:James_D_Watson~~/~~Structural_Templates~~/Zinc_finger_zn/1'>zinc ion</scene> whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the <scene name='~~User:James_D_Watson~~/~~Structural_Templates~~/Zinc_finger_recognition/1'>recognition helices</scene> to bind to the <scene name='~~User:James_D_Watson~~/~~Structural_Templates~~/Zinc_finger_major_groove/1'>major groove of the DNA</scene>.		The example structure shown is that of Zif268 protein-DNA complex from Mus musculus (PDB entry 1AAY). In this example (a C2H2 class zinc finger) the conserved <scene name='57/575866/Zinc_finger_cysteine/1'>cysteine</scene> and <scene name='57/575866/Zinc_finger_histidine/1'>histidine</scene> residues form ligands to a <scene name='57/575866/Zinc_finger_zn/1'>zinc ion</scene> whose coordination is essential to stabilise the tertiary fold of the protein. The fold is important because it helps orientate the <scene name='57/575866/Zinc_finger_recognition/1'>recognition helices</scene> to bind to the <scene name='57/575866/Zinc_finger_major_groove/1'>major groove of the DNA</scene>.
	{{Clear}}		{{Clear}}

Alexander Berchansky at 09:28, 5 March 2017

2017-03-05T09:28:45Z

← Older revision		Revision as of 09:28, 5 March 2017
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	One of the most common and widely distributed motifs is the [[Rossmann fold]] that appears in dinucleotide binding proteins.		One of the most common and widely distributed motifs is the [[Rossmann fold]] that appears in dinucleotide binding proteins.

	Another example is the <scene name='~~User:James_D_Watson~~/~~Structural_Templates~~/Zinc_finger_highlight/1'>zinc finger motif</scene> that is readily identified by the following consensus sequence pattern (where "X" represents ''any'' amino acid):<br/>		Another example is the <scene name='57/575866/Zinc_finger_highlight/1'>zinc finger motif</scene> that is readily identified by the following consensus sequence pattern (where "X" represents ''any'' amino acid):<br/>

	'''Cys''' - X<sub>(2-4)</sub> - '''Cys''' - X<sub>(3)</sub> - Phe - X<sub>(5)</sub> - Leu - X<sub>(2)</sub> - '''His''' - X<sub>(3)</sub> - '''His'''		'''Cys''' - X<sub>(2-4)</sub> - '''Cys''' - X<sub>(3)</sub> - Phe - X<sub>(5)</sub> - Leu - X<sub>(2)</sub> - '''His''' - X<sub>(3)</sub> - '''His'''