From_sequence_to_model

1.- Get the initial model looking for homologous proteins

Basics in homology modeling: We need look for a template to provide the structure to borrow and build a MSA to stablish the best sequence correlation between template and target.

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Modeling workflow to get the first model of the alpha subunit of the human haemoglobin using a sequence homologous template (upper part of the alpha subunit modeling workflow):

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Auxiliary information

Specimen	PDB	UniProt	EMDB
HEMOBLOGIN	1PBX	P69905	3488

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1. Step 1b: Import human haemoglobin alpha subunit sequence (details in modeling tutorial and protocol appendix)

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2. Step 5a: Import atomic structure to be used as model template (details in modeling tutorial and protocol appendix)

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3. Steps 5b, 5c, 5d and 5e: Import additional sequences to prepare your sequence alignment (details in modeling tutorial and protocol appendix)

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4. Step 6a: ChimeraX model_from_template protocol to get the first approximation to the atomic structure of the human Hgb alpha subunit (details in modeling tutorial and protocol appendix)

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Once ChimeraX GUI is opened:

Go to Tools -> Sequence -> Modeller Comparative

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5. Modeller menu to retrieve human Hgb alpha subunit models based on sequence homology (details in modeling tutorial and protocol appendix)

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At this point wait for a while until the retrieved models appear.

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Once you have the retrieved models, select one of them, for instance #3.2. Complete the model with the HEME group from the atomic structure used as template, and save it in Scipion with the next command lines:

1.- Rename model #3.2 as #4.

• rename #3.2 id #4

Does model #4 have HEM group?

If YES:

2.- Save chain A with HEM group:

• scipionwrite #4 prefix Hgb_alpha_

If NOT:

2.- Save chain A of the renamed model in tmp folder.

• save /tmp/chainA.cif format mmcif models #4

3.- Open saved chain A as model #4; hide the rest of the models and observe that HEME group is still missing.

• open /tmp/chainA.cif

4.- Borrow HEME group from template model #2. First select it.

• select #2/A:144

5.- Then save it in tmp folder.

• save /tmp/HEME.cif format mmcif models #2 selectedOnly true

5.- Open HEME group as model #5.

• open /tmp/HEME.cif

6.- Combine chain A and its respective HEME group (models #4 and #5 to generate model #6).

• scipioncombine #4,5

7.- Save this new model #6 as the alpha subunit of the human Haemoglobin.

• scipionwrite #6 prefix Hgb_alpha_

ALTERNATIVE TO COMMANDS 1-7:

• rename #3.2 id #4

• select #4

• select add #2/A:144

• delete ~ sel

• combine #2,4 modelid 10

• scipionwrite #10 prefix Hgb_alpha_

QUIZ: Is the result identical to the previous one? Answer this question after running the next step of the workflow (6c).

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6. Step 6c: Recovering of previous ChimeraX session (details in modeling tutorial and protocol appendix)

NOTE: homologous sequences can be obtained using BLAST