Bcell Epitope prediction ans - Revision history

Carol: /* Q3. Which residues form the epitopes? Are they linear? Do they have a linear core? */

2026-10-28T10:58:16Z

Q3. Which residues form the epitopes? Are they linear? Do they have a linear core?

← Older revision		Revision as of 11:58, 28 October 2026
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	=== Q3. Which residues form the epitopes? Are they linear? Do they have a linear core? ===		=== Q3. Which residues form the epitopes? Are they linear? Do they have a linear core? ===

	'''4FQI (23 contacts):'''		'''4FQI (18 contacts):'''
	* HA1, '''A''': ~~38, 40, 41, 42,~~ 291, 292, 293, 318.		* HA1, '''A''': 291, 292, 293, 318.
	* HA2, '''B''': 18, 19, 20, 21, 36, 37, 38, 41, 42, 45, 46, 48, 49, 52, 56.		* HA2, '''B''': 18, 19, 20, 21, 36, 37, 38, 41, 42, 45, 46, 48, 49, 52, 56.

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	'''Interpretation:''' Both are predominantly '''conformational (discontinuous) epitopes''', because the contacting residues occur in sequence-distant regions that come together in three dimensions. They contain short contiguous stretches or potential ''linear cores'', for example 4FQI B:18–21 and B:36–38, and 7K39 A:90–93 and A:269–273. These patches do not make the overall epitopes linear or show that the corresponding isolated peptides would bind the antibody.		'''Interpretation:''' Both are predominantly '''conformational (discontinuous) epitopes''', because the contacting residues occur in sequence-distant regions that come together in three dimensions. They contain short contiguous stretches or potential ''linear cores'', for example 4FQI B:18–21 and B:36–38, and 7K39 A:90–93 and A:269–273. These patches do not make the overall epitopes linear or show that the corresponding isolated peptides would bind the antibody.

	The complexes do '''not''' target the same region: CR9114 binds the '''stem''' (involving HA1 and HA2), while the 7K39 antibody binds primarily the '''head''' (mostly HA1). HA1=head and HA2=stem are useful teaching approximations, but HA1 also contributes to the structural stem.		The antibody complexes do '''not''' target the same region: CR9114(4FQI) binds the '''stem''' (involving HA1 and HA2), while the 7K39 antibody binds primarily the '''head''' (mostly HA1). HA1=head and HA2=stem are useful teaching approximations, but HA1 also contributes to the structural stem.

	== Part B. Sequence-based prediction: BepiPred-2.0 and BepiPred-3.0 ==		== Part B. Sequence-based prediction: BepiPred-2.0 and BepiPred-3.0 ==

Carol: /* Q2. Show the epitopes, count residues, and describe secondary structure */

2026-10-28T10:56:45Z

Q2. Show the epitopes, count residues, and describe secondary structure

← Older revision		Revision as of 11:56, 28 October 2026
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	=== Q2. Show the epitopes, count residues, and describe secondary structure ===		=== Q2. Show the epitopes, count residues, and describe secondary structure ===

	Using the experimental ~~CIF~~ coordinates, excluding waters, and applying the 5 Å ~~protein-heavy-atom~~ cutoff:		Using the experimental PDB coordinates, excluding waters, and applying the 5 Å cutoff

	{\| class="wikitable"		{\| class="wikitable"
	! Complex !! HA1 (A) contact residues !! HA2 (B) contact residues !! Total !! Qualitative structural location		! Complex !! HA1 (A) contact residues !! HA2 (B) contact residues !! Total !! Qualitative structural location
	\|-		\|-
	\| '''4FQI, stem-binding CR9114''' \|\| 8 \|\| 15 \|\| '''23''' \|\| Mainly at the HA stem, including an HA2 helical region and adjacent loops/turns.		\| '''4FQI, stem-binding CR9114''' \|\| 4 \|\| 14 \|\| '''18''' \|\| Mainly at the HA stem, including an HA2 helical region and adjacent loops/turns.
	\|-		\|-
	\| '''7K39, head-binding Fab''' \|\| 14 \|\| 1 \|\| '''15''' \|\| Mainly on HA1 in the head, distributed among accessible loops and neighboring structural elements.		\| '''7K39, head-binding Fab''' \|\| 14 \|\| 1 \|\| '''15''' \|\| Mainly on HA1 in the head, distributed among accessible loops and neighboring structural elements.
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	-->		-->

	'''Why the previous 4FQI counts differed:''' The earlier PyMOL screenshot highlighted 18 residues (4 in A and 14 in B). A complete calculation with both antibody protein chains identifies another five within 5 Å: '''A:38, A:40, A:41, A:42 and B:52''', producing 23. An earlier estimate of 25 mistakenly allowed water atoms from the antibody-chain records to contribute contacts, adding A:18 and B:53. The protein-only, solvent-excluded result is '''23'''.

	To reproduce the selection in PyMOL, for 4FQI:		To reproduce the selection in PyMOL, for 4FQI:

Carol: /* Q1. List chain IDs for antigen versus antibody in each complex */

2026-10-28T10:53:44Z

Q1. List chain IDs for antigen versus antibody in each complex

← Older revision		Revision as of 11:53, 28 October 2026
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	\|}		\|}

	For the 7K39 calculations below use '''A/B''' as the antigen and '''G/H''' as a single Fab (G is light, H is heavy)~~. The other equivalent antigen/Fab combinations are C/D with I/J, and E/F with K/L.~~		For the 7K39 calculations below use '''A/B''' as the antigen and '''G/H''' as a single Fab (G is light, H is heavy).

	~~'''Note:''' The AlphaFold 3 ZIP files use their own chain labels. Do not transfer the experimental PDB chain mapping to the predicted complexes without checking their sequences~~.

	=== Q2. Show the epitopes, count residues, and describe secondary structure ===		=== Q2. Show the epitopes, count residues, and describe secondary structure ===

Carol: /* Q2. Show the epitopes, count residues, and describe secondary structure */

2026-10-28T10:52:03Z

Q2. Show the epitopes, count residues, and describe secondary structure

← Older revision		Revision as of 11:52, 28 October 2026
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	color red, epitope		color red, epitope
	</pre>		</pre>
	For 7K39, replace the Fab selection with ~~<code>(~~chain G+H~~) and polymer.protein</code> and keep A/B as the chosen antigen protomer.~~		For 7K39, replace the Fab selection with chain G+H

	=== Q3. Which residues form the epitopes? Are they linear? Do they have a linear core? ===		=== Q3. Which residues form the epitopes? Are they linear? Do they have a linear core? ===

Carol: /* Q2. Show the epitopes, count residues, and describe secondary structure */

2026-10-28T10:51:34Z

Q2. Show the epitopes, count residues, and describe secondary structure

← Older revision		Revision as of 11:51, 28 October 2026
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	fetch 4fqi		fetch 4fqi
	remove solvent		remove solvent
	select ag, (chain A+B) ~~and polymer.protein~~		select Ag, (chain A+B)
	select ab, (chain H+L) ~~and polymer.protein~~		select Fab, (chain H+L)
	select epitope, byres (~~ag within~~ 5 ~~of ab~~)		select epitope, byres (Fab around 5)
	color red, epitope		color red, epitope
	</pre>		</pre>

Carol: /* B-cell epitope prediction — Instructor answer key */

2026-10-28T10:50:10Z

B-cell epitope prediction — Instructor answer key

← Older revision		Revision as of 11:50, 28 October 2026
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	= B-cell epitope prediction ~~— Instructor answer key~~ =		= B-cell epitope prediction =

	''Worked solution to the [https://teaching.healthtech.dtu.dk/22145/index.php/Bcell_Epitope_prediction DTU 22145 exercise]. The experimental structures are [https://www.rcsb.org/structure/4FQI 4FQI] (H5N1 influenza HA with stem-binding antibody CR9114) and [https://www.rcsb.org/structure/7K39 7K39] (H3N2 HA with a head-binding antibody). Numbers refer to the supplied structural and prediction files.''		== Analysis Tips and conventions ==

	== Analysis conventions ==

	* '''Experimental epitope definition:''' An HA amino-acid residue belongs to the antibody-binding footprint if any of its non-hydrogen protein atoms is strictly less than 5.0 Å from a non-hydrogen protein atom of the selected antibody. Exclude waters and other non-protein molecules. Count a residue only once, even if several of its atoms contact the antibody.		* '''Experimental epitope definition:''' An HA amino-acid residue belongs to the antibody-binding footprint if any of its non-hydrogen protein atoms is strictly less than 5.0 Å from a non-hydrogen protein atom of the selected antibody. Exclude waters and other non-protein molecules. Count a residue only once, even if several of its atoms contact the antibody.

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