Homology modelling with Chimera/Modeller
Hi: I am trying to do homology modelling with Chimera/Modeler for a Fc fusion protein, which contains three domains, one is Fc, one is receptor and the 3rd is ligand. Fc has many PBD structures in PDB database and the receptor has couple of 3D structures with the ligand as well. I used the fusion protein sequence to do blast in Chimera and it gave matched sequence files to Fc domain only, no sequence files for the receptor-ligand complex, even it already has couple of solved 3D crystal structure files in PDB database. Is there any suggestion about this issue? Can I do separately, use Fc domain alone as search sequence for its template and use receptor-ligand sequences as search sequence for its template? If it is ok, there are two template files. How to make them into one template file for modelling late? Thanks very much for your suggestion. Sincerely TW Sent from Mail for Windows 10
Hi TW, The Chimera interface to Modeler is simplified so you cannot necessarily do any type of modeling that might be possible if you used Modeller directly. I'm not completely sure either of the following would work, but possible things to try: (A) open all the separate template structures and if they don't associate automatically, use the Multalign Viewer (sequence viewer window) associations dialog to manually associate all of the structures to your single long fusion sequence. Then you can choose all of them as templates. However, the modeling may not pay attention to the current relative positions of these domains in the structures. They might be modeled in different orientations not interacting with each other. (B) If the PDB structures are already the correct sequences and all you are trying to do is connect them with linkers without moving them relative to each other, a different approach to try would be to first combine all the parts you want in your fusion into a single chain in a single model (e.g. see Model Panel function copy/combine). Then associate that single chain (which will have missing segments, the linkers) with your long fusion sequence. Then use the "missing loops" option of the Chimera Modeller interface to try to fill them without moving the existing parts relative to each other. If I misunderstood you and you are actually trying to model a complex of more than one chain (not just one single fusion chain), you can't use the Chimera interface for Modeller for that. The interface only models single chains. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 13, 2021, at 2:38 PM, StaidsonBio <yong.yin@staidsonbio.com> wrote:
Hi:
I am trying to do homology modelling with Chimera/Modeler for a Fc fusion protein, which contains three domains, one is Fc, one is receptor and the 3rd is ligand. Fc has many PBD structures in PDB database and the receptor has couple of 3D structures with the ligand as well. I used the fusion protein sequence to do blast in Chimera and it gave matched sequence files to Fc domain only, no sequence files for the receptor-ligand complex, even it already has couple of solved 3D crystal structure files in PDB database. Is there any suggestion about this issue? Can I do separately, use Fc domain alone as search sequence for its template and use receptor-ligand sequences as search sequence for its template? If it is ok, there are two template files. How to make them into one template file for modelling late?
Thanks very much for your suggestion.
Sincerely
TW
Hi Elaine: Thanks very much for your explanation. Indeed, I am trying to model a Fc fusion protein with two chains. Besides Fc having 3D structures, the other receptor and ligand have their 3D complex structures. In such a case, can the Modeller (eg. Modeller 9.24 version) alone do the modeling job? I highly appreciate your help. Best regards TW On Tue, Feb 16, 2021 at 9:31 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi TW, The Chimera interface to Modeler is simplified so you cannot necessarily do any type of modeling that might be possible if you used Modeller directly. I'm not completely sure either of the following would work, but possible things to try:
(A) open all the separate template structures and if they don't associate automatically, use the Multalign Viewer (sequence viewer window) associations dialog to manually associate all of the structures to your single long fusion sequence. Then you can choose all of them as templates.
However, the modeling may not pay attention to the current relative positions of these domains in the structures. They might be modeled in different orientations not interacting with each other.
(B) If the PDB structures are already the correct sequences and all you are trying to do is connect them with linkers without moving them relative to each other, a different approach to try would be to first combine all the parts you want in your fusion into a single chain in a single model (e.g. see Model Panel function copy/combine). Then associate that single chain (which will have missing segments, the linkers) with your long fusion sequence. Then use the "missing loops" option of the Chimera Modeller interface to try to fill them without moving the existing parts relative to each other.
If I misunderstood you and you are actually trying to model a complex of more than one chain (not just one single fusion chain), you can't use the Chimera interface for Modeller for that. The interface only models single chains.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 13, 2021, at 2:38 PM, StaidsonBio <yong.yin@staidsonbio.com> wrote:
Hi:
I am trying to do homology modelling with Chimera/Modeler for a Fc fusion protein, which contains three domains, one is Fc, one is receptor and the 3rd is ligand. Fc has many PBD structures in PDB database and the receptor has couple of 3D structures with the ligand as well. I used the fusion protein sequence to do blast in Chimera and it gave matched sequence files to Fc domain only, no sequence files for the receptor-ligand complex, even it already has couple of solved 3D crystal structure files in PDB database. Is there any suggestion about this issue? Can I do separately, use Fc domain alone as search sequence for its template and use receptor-ligand sequences as search sequence for its template? If it is ok, there are two template files. How to make them into one template file for modelling late?
Thanks very much for your suggestion.
Sincerely
TW
Hi TW, If you have a template for the whole multichain complex (all the template chains together in a single structure in the desired locations relative to each other), you may be able to do it with the Modeller interface in ChimeraX instead of Chimera. However, if you don't have a template that includes the Fc in the proper spatial relationship to the other receptor and ligand, Modeller is not going to make it up for you. Instead you would need to predict that using some kind of protein-protein docking method, or just place them by hand if you have a good enough idea of how they are supposed to interact. Chimera and ChimeraX do not have protein-protein docking tools, other than hand placement. For multichain modeling, you would also need a sequence opened in ChimeraX for each unique chain, with the template structure for that chain associated with that sequence. For multichain Modeller with ChimeraX, see: <https://www.rbvi.ucsf.edu/chimerax/features.html#multichain-modeller> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 16, 2021, at 10:22 AM, Y Y <yong.yin@staidsonbio.com> wrote:
Hi Elaine:
Thanks very much for your explanation.
Indeed, I am trying to model a Fc fusion protein with two chains. Besides Fc having 3D structures, the other receptor and ligand have their 3D complex structures. In such a case, can the Modeller (eg. Modeller 9.24 version) alone do the modeling job?
I highly appreciate your help.
Best regards
TW
On Tue, Feb 16, 2021 at 9:31 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi TW, The Chimera interface to Modeler is simplified so you cannot necessarily do any type of modeling that might be possible if you used Modeller directly. I'm not completely sure either of the following would work, but possible things to try:
(A) open all the separate template structures and if they don't associate automatically, use the Multalign Viewer (sequence viewer window) associations dialog to manually associate all of the structures to your single long fusion sequence. Then you can choose all of them as templates.
However, the modeling may not pay attention to the current relative positions of these domains in the structures. They might be modeled in different orientations not interacting with each other.
(B) If the PDB structures are already the correct sequences and all you are trying to do is connect them with linkers without moving them relative to each other, a different approach to try would be to first combine all the parts you want in your fusion into a single chain in a single model (e.g. see Model Panel function copy/combine). Then associate that single chain (which will have missing segments, the linkers) with your long fusion sequence. Then use the "missing loops" option of the Chimera Modeller interface to try to fill them without moving the existing parts relative to each other.
If I misunderstood you and you are actually trying to model a complex of more than one chain (not just one single fusion chain), you can't use the Chimera interface for Modeller for that. The interface only models single chains.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 13, 2021, at 2:38 PM, StaidsonBio <yong.yin@staidsonbio.com> wrote:
Hi:
I am trying to do homology modelling with Chimera/Modeler for a Fc fusion protein, which contains three domains, one is Fc, one is receptor and the 3rd is ligand. Fc has many PBD structures in PDB database and the receptor has couple of 3D structures with the ligand as well. I used the fusion protein sequence to do blast in Chimera and it gave matched sequence files to Fc domain only, no sequence files for the receptor-ligand complex, even it already has couple of solved 3D crystal structure files in PDB database. Is there any suggestion about this issue? Can I do separately, use Fc domain alone as search sequence for its template and use receptor-ligand sequences as search sequence for its template? If it is ok, there are two template files. How to make them into one template file for modelling late?
Thanks very much for your suggestion.
Sincerely
TW
Hi Elaine: Thanks a lot. I'll give it a try. Best Regards TW On Tue, Feb 16, 2021 at 11:40 AM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hi TW, If you have a template for the whole multichain complex (all the template chains together in a single structure in the desired locations relative to each other), you may be able to do it with the Modeller interface in ChimeraX instead of Chimera. However, if you don't have a template that includes the Fc in the proper spatial relationship to the other receptor and ligand, Modeller is not going to make it up for you. Instead you would need to predict that using some kind of protein-protein docking method, or just place them by hand if you have a good enough idea of how they are supposed to interact. Chimera and ChimeraX do not have protein-protein docking tools, other than hand placement.
For multichain modeling, you would also need a sequence opened in ChimeraX for each unique chain, with the template structure for that chain associated with that sequence.
For multichain Modeller with ChimeraX, see: <https://www.rbvi.ucsf.edu/chimerax/features.html#multichain-modeller> <https://www.rbvi.ucsf.edu/chimerax/docs/user/tools/modeller.html>
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 16, 2021, at 10:22 AM, Y Y <yong.yin@staidsonbio.com> wrote:
Hi Elaine:
Thanks very much for your explanation.
Indeed, I am trying to model a Fc fusion protein with two chains. Besides Fc having 3D structures, the other receptor and ligand have their 3D complex structures. In such a case, can the Modeller (eg. Modeller 9.24 version) alone do the modeling job?
I highly appreciate your help.
Best regards
TW
On Tue, Feb 16, 2021 at 9:31 AM Elaine Meng <meng@cgl.ucsf.edu> wrote: Hi TW, The Chimera interface to Modeler is simplified so you cannot necessarily do any type of modeling that might be possible if you used Modeller directly. I'm not completely sure either of the following would work, but possible things to try:
(A) open all the separate template structures and if they don't associate automatically, use the Multalign Viewer (sequence viewer window) associations dialog to manually associate all of the structures to your single long fusion sequence. Then you can choose all of them as templates.
However, the modeling may not pay attention to the current relative positions of these domains in the structures. They might be modeled in different orientations not interacting with each other.
(B) If the PDB structures are already the correct sequences and all you are trying to do is connect them with linkers without moving them relative to each other, a different approach to try would be to first combine all the parts you want in your fusion into a single chain in a single model (e.g. see Model Panel function copy/combine). Then associate that single chain (which will have missing segments, the linkers) with your long fusion sequence. Then use the "missing loops" option of the Chimera Modeller interface to try to fill them without moving the existing parts relative to each other.
If I misunderstood you and you are actually trying to model a complex of more than one chain (not just one single fusion chain), you can't use the Chimera interface for Modeller for that. The interface only models single chains.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Feb 13, 2021, at 2:38 PM, StaidsonBio <yong.yin@staidsonbio.com> wrote:
Hi:
I am trying to do homology modelling with Chimera/Modeler for a Fc fusion protein, which contains three domains, one is Fc, one is receptor and the 3rd is ligand. Fc has many PBD structures in PDB database and the receptor has couple of 3D structures with the ligand as well. I used the fusion protein sequence to do blast in Chimera and it gave matched sequence files to Fc domain only, no sequence files for the receptor-ligand complex, even it already has couple of solved 3D crystal structure files in PDB database. Is there any suggestion about this issue? Can I do separately, use Fc domain alone as search sequence for its template and use receptor-ligand sequences as search sequence for its template? If it is ok, there are two template files. How to make them into one template file for modelling late?
Thanks very much for your suggestion.
Sincerely
TW
participants (3)
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Elaine Meng -
StaidsonBio -
Y Y