When designing fusion proteins, you usually want to preserve the structure of the individual domains. You therefore, whenever possible, start from the structures or good models of the individual domains, move these into the desired relative orientation using a graphical modelling tool, e.g. DeepView, Chimera or even just PyMOL, then decide on the optimal linker. For flexible linkers, I prefer Gly/Ser linkers. As a rule of thumb, I use about half as many amino acids as the distance in Å (this would be sufficient to bridge the distance of the ends to be connected in a semicircle, assuming a beta-sheet conformation). For a rigid linker based on a continuous helix, I start from an ideal alpha helix and superimpose the two domains onto this helix in different rasters, select those that do not lead to clashes to get models with different relative orientation, then optimise the sequence of the linker region using rosetta fixBB.

for more information, see

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In other cases, the linkage may be flexible, but a minimal length of the linker is crucial:

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Mohammad Moein Sadeghi

The Swiss model server predicts the 3D structure of a protein from sequence information

Mohammad Moein Sadeghi

The accuracy of the structure prediction depending on the level of sequence similarity between target and template sequences.

Seyyed Mohammad Amin Kashani

Thanks for your helpful comment.

I think your suggestions are useful in docking.

s. Thamotharan

Thanks for your constructive replying.

It helped me.

Dear Mohammad Moein Sadeghi ,

It depends (of course) a bit on what you do know about your peptides and proteins.

As a starting point you can consider I-Tasser which is one of the best performing 3D prediction programs available. Just use the so-called FASTA form for every mutation you want to check.

https://zhanglab.ccmb.med.umich.edu/I-TASSER/

Again depending on what you (already) know about your peptide/protein you can obtain additional info using Heliquest to investigate matters like overall hydrophobicity, hydrophobic moment and net charge of particular regions:

http://heliquest.ipmc.cnrs.fr/

In addition you could check/verify the 3D prediction by using one of the many secondary structure prediction programs. Such like SOPMA (but there are many more!):

https://npsa-prabi.ibcp.fr/cgi-bin/npsa_automat.pl?page=/NPSA/npsa_sopma.html

Best regards and good luck.

PS. If you want a quick look at how to use I-Tasser, Heliquest and secondary prediction programs you can see for example:

Article The role and significance of potential lipid-binding regions...

Dear Rob Keller

Sincerely thanks for your exhaustive guidance. I will follow your explanations.

Actually I'm looking for possible 3D structure of a new fusion protein that is formed by linking some functional domains. At first preserving secondary structures of that domains in new fusion protein and then possible ultimate 3D structure of the protein is important to me.

Respectfully

When designing fusion proteins, you usually want to preserve the structure of the individual domains. You therefore, whenever possible, start from the structures or good models of the individual domains, move these into the desired relative orientation using a graphical modelling tool, e.g. DeepView, Chimera or even just PyMOL, then decide on the optimal linker. For flexible linkers, I prefer Gly/Ser linkers. As a rule of thumb, I use about half as many amino acids as the distance in Å (this would be sufficient to bridge the distance of the ends to be connected in a semicircle, assuming a beta-sheet conformation). For a rigid linker based on a continuous helix, I start from an ideal alpha helix and superimpose the two domains onto this helix in different rasters, select those that do not lead to clashes to get models with different relative orientation, then optimise the sequence of the linker region using rosetta fixBB.

for more information, see

Article DARPin-Based Crystallization Chaperones Exploit Molecular Ge...

Article Rigidly connected multispecific artificial binders with adju...

Article Structural Basis for the Selective Inhibition of c-Jun N-Ter...

Article Rigid fusions of designed helical repeat binding proteins ef...

In other cases, the linkage may be flexible, but a minimal length of the linker is crucial:

Article Development of a generic adenovirus delivery system based on...

Article Structural Basis for Eliciting a Cytotoxic Effect in HER2-Ov...

Dear Annemarie Honegger

Thank you for sharing your wisdom with me.

I wholeheartedly appreciate time you spent to reply my question.

Gratefully

Hi

I used combination of software for protein structure prediction and helped me a lot. You can use phyre 2 which will provide you maximum of the information by comparing with the online database. Later you can import the protein structure in Schroedinger software for detail analysis and comparing two protein structures.

Thank You

Dear SAMEE ULLAH

Thanks for helping me.

Regards

Dear Yashika Raheja

Thanks for your comment.

Wishes

ITasser and pyre.

Hello Mohammad Moein Sadeghi

As many others have recorded their responses, supporting the usage of Phyre2 & iTASSER for designing new proteins like enzymes and receptors as you have asked, i would also suggest you the same. In addition, i would also like to add another tool to this lineup, trRosetta, a server that models your proteins based on CASP13 structure prediction. Besides, the 3D models from this server do come energy-minimized and refined by default.

The link for the server is given below:

https://yanglab.nankai.edu.cn/trRosetta/

Hope it helps.

Dear Johnson Samuel

Thanks for your helpful recommendation.

Regards.

Hi Mohammad Moein Sadeghi ,

Swiss model is quite straightforward and simple to use online tool. it uses homology modeling technique to model your 3D protein structure. Chimera modeler is another one stand alone tool you can use to model 3D structure of protein, this tool is widely used and highly confident.