Protein Structure - Revision history

Carol: /* Visualization & PyMOL */

2026-09-29T10:38:25Z

Visualization & PyMOL

← Older revision		Revision as of 11:38, 29 September 2026
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	⇒ Now select the best complex and load it into PyMOL using the ''fetch'' command.		⇒ Now select the best complex and load it into PyMOL using the ''fetch'' command.

	(If you cannot solve question 1 use this alternate ~~code~~ to continue the exercise: ''fetch'' 7SBG)		(If you cannot solve question 1 use this '''alternate''' structure to continue the exercise: ''fetch'' 7SBG)

	You can toggle the object on and off by clicking on its name. Try this. To the right of the object name, there are five buttons: A(ction), S(how), H(ide), L(abel) and C(olor).		You can toggle the object on and off by clicking on its name. Try this. To the right of the object name, there are five buttons: A(ction), S(how), H(ide), L(abel) and C(olor).

Carol: /* Getting started */

2026-09-28T18:03:52Z

Getting started

← Older revision		Revision as of 19:03, 28 September 2026
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	We know that protein function is closely related to 3D structure. Therefore, to understand what differs between plant and mammalian profilins, we are going to examine experimentally determined protein structures from plants and mammals.		We know that protein function is closely related to 3D structure. Therefore, to understand what differs between plant and mammalian profilins, we are going to examine experimentally determined protein structures from plants and mammals.


	⇒ First go to the Protein Data Bank (PDB) https://www.rcsb.org/		⇒ First go to the Protein Data Bank (PDB) https://www.rcsb.org/


	[[Image:PDB.png\|thumb\|center\|border\|400px\|'''Figure 2.''' The Protein Data Bank.]]		[[Image:PDB.png\|thumb\|center\|border\|400px\|'''Figure 2.''' The Protein Data Bank.]]

			We are looking for an antibody of the IgE class (the antibody class associated with allergic responses) in complex with a plant allergen. In this case, we will use Hev b 8, a profilin allergen from ''Hevea brasiliensis'', the rubber tree.

	~~We are looking for and antibody of the class E (those are related to allergy) in complex with a plant allergen (in this case we will use Hevea brasiliensis, the rubber tree).~~		⇒ Search for ''IgE'' AND ''Hev b 8''.

	⇒ ~~And search~~ for ''IgE'' AND ''Hev b 8''

	~~We are looking for a protein structure complex, so dismiss all the search results that do not contain a protein complex including both the '''IgE''' AND '''Hev b 8'~~''.

			We are interested in a protein complex, so exclude any search results that do not contain a complex including both '''IgE''' and '''Hev b 8'''.

	'''Question 1.''' Look at the ~~method~~ X-~~RAY~~ diffraction ~~(Å)~~. Which of the ~~complexes is of better~~ quality and ~~why~~?		'''Question 1.''' Look carefully inside the entries determined by X-ray diffraction. Which complex has the best quality?, and which '''parameters''' have you compared from the different complexes to make your choice?

	== Visualization & PyMOL ==		== Visualization & PyMOL ==

Carol: /* Getting started */

2026-09-28T17:57:08Z

Getting started

← Older revision		Revision as of 18:57, 28 September 2026
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	== Getting started ==		== Getting started ==

	We know that protein ~~functions are~~ closely ~~correlated~~ to ~~their~~ 3D structure, ~~so in order~~ to understand what ~~is different in Profilin proteins from plants~~ and ~~mammals~~ we are going to ~~gather some~~ experimentally determined protein structures from ~~plant~~ and ~~mammal proteins~~.		We know that protein function is closely related to 3D structure. Therefore, to understand what differs between plant and mammalian profilins, we are going to examine experimentally determined protein structures from plants and mammals.


	⇒ First go to the Protein Data Bank (PDB) https://www.rcsb.org/		⇒ First go to the Protein Data Bank (PDB) https://www.rcsb.org/
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	'''Question 1.''' Look at the method X-RAY diffraction (Å). Which of the complexes is of better quality and why?		'''Question 1.''' Look at the method X-RAY diffraction (Å). Which of the complexes is of better quality and why?


	== Visualization & PyMOL ==		== Visualization & PyMOL ==

Carol at 17:55, 28 September 2026

2026-09-28T17:55:44Z

← Older revision		Revision as of 18:55, 28 September 2026
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	⇒ Today, we will investigate the following question: Why do plant profilins trigger an allergenic response despite their high conservation across species?		⇒ Today, we will investigate the following question: Why do plant profilins trigger an allergenic response despite their high conservation across species?

			[[Image:Allergen-response.jpg\|thumb\|center\|border\|300px\|'''Figure 1.''' The allergen response.]]

	~~[[Image.jpg\|thumb\|center\|border\|300px\|'''Figure 1.''' The allergen response.]]~~

	== Getting started ==		== Getting started ==

Carol: /* A bit of background */

2026-09-28T17:54:40Z

A bit of background

← Older revision		Revision as of 18:54, 28 September 2026
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	⇒ Today, we will investigate the following question: Why do plant profilins trigger an allergenic response despite their high conservation across species?		⇒ Today, we will investigate the following question: Why do plant profilins trigger an allergenic response despite their high conservation across species?


	[[Image.jpg\|thumb\|center\|border\|300px\|'''Figure 1.''' The allergen response.]]		[[Image.jpg\|thumb\|center\|border\|300px\|'''Figure 1.''' The allergen response.]]

Carol: /* A bit of background */

2026-09-28T17:54:00Z

A bit of background

← Older revision		Revision as of 18:54, 28 September 2026
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	== A bit of background ==		== A bit of background ==

	~~The question of today’s~~ exercise ~~is about~~ allergens.		Today’s exercise focuses on allergens.

	Allergens are fascinating because they ~~aren’t~~ random proteins; they cluster into certain protein families that repeatedly trigger allergic sensitization in humans.		Allergens are fascinating because they are not random proteins; instead, they tend to cluster into certain protein families that repeatedly trigger allergic sensitization in humans.

	~~However, one very~~ interesting allergen protein family is the profilins. Here’s why:		One particularly interesting allergen protein family is the profilins. Here’s why:

	They are highly conserved across species.		They are highly conserved across species.

	Profilins are small actin-binding proteins found in almost all eukaryotic cells (plants, animals, fungi).		Profilins are small actin-binding proteins found in almost all eukaryotic cells, including those of plants, animals, and fungi.

	Despite their ubiquity and structural conservation, humans typically ~~only~~ become allergic to plant profilins ~~(e.g.~~, from birch pollen, grass pollen, the rubber tree, or certain fruits/vegetables).		Despite their ubiquity and structural conservation, humans typically become allergic to plant profilins, such as those from birch pollen, grass pollen, the rubber tree, or certain fruits and vegetables.

	⇒ Today we ~~would seek to understand~~: Why ~~only~~ plant profilins ~~are giving~~ an allergenic response despite their high conservation across species?		⇒ Today, we will investigate the following question: Why do plant profilins trigger an allergenic response despite their high conservation across species?

	[[Image~~:Allergen-response~~.jpg\|thumb\|center\|border\|300px\|'''Figure 1.''' The allergen response.]]		[[Image.jpg\|thumb\|center\|border\|300px\|'''Figure 1.''' The allergen response.]]

	== Getting started ==		== Getting started ==

Carol at 17:52, 28 September 2026

2026-09-28T17:52:52Z

← Older revision		Revision as of 18:52, 28 September 2026
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	== Overview ==		== Overview ==

	In this exercise you will learn how to		In this exercise, you will learn how to:
	* Search diferent protein databases to obtain protein structures.
	* Critically choose the best structure, when more than one is available.
	* Visualize a protein structure using PyMOL
	* Highlight features of interest and perform a basic alignment.

	~~This exercise is written a bit~~ different~~. Instead of the step wise exercise we are going~~ to try a different method called inquiry-based learning, where students explore real-world problems and questions, taking ownership of their learning by asking questions, conducting research, and developing their own solutions and understandings.		* Search different protein databases to obtain protein structures.

	~~Therefore today we are going to start with a biological question we want to answer:~~		* Critically evaluate and choose the most appropriate structure when more than one is available.

	'''Why ~~only~~ plant profilins ~~are giving an~~ allergic ~~response~~ despite ~~their~~ high conservation across species? Why are we not allergic to ~~mammal~~ profilins~~, for example~~?'''		* Visualize a protein structure using PyMOL.

			*Highlight features of interest and perform a basic structural alignment.

			This exercise is organized differently from the previous step-by-step exercises. Instead, we are going to use an inquiry-based learning approach, in which students explore real-world problems and questions and take ownership of their learning by asking questions, conducting research, and developing their own explanations and conclusions.

			Therefore, today we are going to start with a biological question that we want to answer:

			'''Why do plant profilins trigger allergic responses despite the high conservation of profilins across species? Why, for example, are we generally not allergic to mammalian profilins?'''

	== A bit of background ==		== A bit of background ==

Carol: /* Visualization & PyMOL */

2026-09-28T17:39:24Z

Visualization & PyMOL

← Older revision		Revision as of 18:39, 28 September 2026
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	⇒ Now we want to colour which specific residues of the allergen are in close contact with the antibody (exactly at a distance of 4Å). We will call this object the “epitope”. To define the distance, we can use the command ''around''.		⇒ Now we want to colour which specific residues of the allergen are in close contact with the antibody (exactly at a distance of 4Å). We will call this object the “epitope”. To define the distance, we can use the command ''around''.

	In order to select the full residues and not just the atoms of the allergen that are in direct contact we have to do a trick and select by residue using the command ''br.''.		In order to select the full residues and not just the atoms of the allergen that are in direct contact we have to do a trick and select by residue using the command ''br.'' or ''byres''.

	'''Hint:''' ''select'' ZZ, ''br''.(XX ''around'' 6) With this command we can select all residues in a distance of 6Å to XX, and name this new ~~objext~~ ZZ		'''Hint:''' ''select'' ZZ, ''br''.(XX ''around'' 6) With this command we can select all residues in a distance of 6Å to XX, and we will name this new object "ZZ"

Carol: /* Visualization & PyMOL */

2026-09-28T17:01:31Z

Visualization & PyMOL

← Older revision		Revision as of 18:01, 28 September 2026
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	If you show the sequence, you will notice that each of the chains have a name; H and L for the antibody (heavy and light chain), and C for the allergen.		If you show the sequence, you will notice that each of the chains have a name; H and L for the antibody (heavy and light chain), and C for the allergen.

	⇒ Colour the different chains of the antibody (IgE) in yellow and blue and the allergen (Hev b 8) in green.		⇒ Colour the different chains of the antibody (IgE) in yellow and blue, and the allergen (Hev b 8) in green.

Carol: /* Visualization & PyMOL */

2026-09-28T17:00:57Z

Visualization & PyMOL

← Older revision		Revision as of 18:00, 28 September 2026
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	⇒ Remove the water molecules and cofactors (''hetatm'') used for making the crystal using the command ''remove'' (these are not part of the of the protein complex).		⇒ Remove the water molecules and cofactors (''hetatm'') used for making the crystal using the command ''remove'' (these are not part of the of the protein complex).
	If you show the sequence, you will notice that each of the chains have a name H and L for the antibody (heavy and light chain) and C for the allergen.		If you show the sequence, you will notice that each of the chains have a name; H and L for the antibody (heavy and light chain), and C for the allergen.

	⇒ Colour the different chains of the antibody (IgE) in yellow and blue and the allergen (Hev b 8) in green.		⇒ Colour the different chains of the antibody (IgE) in yellow and blue and the allergen (Hev b 8) in green.