Problems and advices related protein modelling and Protein protein interaction

[R A J Rajkishore]

Hello Everyone , 

I have a protein named LOXL1 (Human). This protein has no so called structures in PDB,neither any other databases.It just contains a structure with less identity in ProteinModel DB.

I am modelling this protein. As far I have investigated this , this protein contains 57% of disordered region ,30% structural identity and query coverage of 10%.I have collected all the 

details of the protein and identified that it causes pseudoexfoliation disease with binding another protein named FIBULIN 5.This protein has also same affairs like LOXL1.Also I have 

check the mutation region of this two proteins which is around 50% with each other.

Now Please be kind to suggest me my doubts , 

1. Need I must refer for Protein protein Interaction between this two protein?

2. How can I model LOXL1 , I have generated the model in servers like I-tassar , Swiss Model , Phyre2 and Rosetta.

So from all this structures which is the best one .. how can I recommend and also I have the model structured by Modeller.

How can I do model of this protein ..??

Please suggest me .. !!

Regards , 

Raj Kishore Mohapatra

Lab of Computational Biology

Center For DNA Fingerprinting and Diagnostics (CDFD)

​ 

DBT Lab.​

Hyderabad - 500001

Mobile :  +91 9030912109

                 +91 9861233393

[Ravi Kant Pathak]

Dear Raj,

As the query coverage is very less I would suggest not to go for homology modeling. Rather fold recognition and ab initio method would be more helpful. Once you get the structure from these methods, go for structure optimization, side chain refinement and loop modeling using PROCHECK, Modeller, SCWRL3 etc. This is not all, you must go for structure validation using structure quality assurance servers and further the molecular dynamics software to check whether the structure is stable or it is unfolding with some force applied to it.

Hope this will solve your query of structure prediction.

Thanks and Regards

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Ravi Kant Pathak

MS By Research (Bioinformatics)

Asst. Prof
Domain of Genetics and Molecular Biology

School of Biotechnology and Biosciences

Lovely Professional University

Punjab-144402

India
+91-9501424486

[Bojja, Ravi Shankar]

did you purify this protein first to understand its structure or just started de nevo modeling without any biophysical properties ?

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From: predictprot...@googlegroups.com [predictprot...@googlegroups.com] on behalf of R A J Rajkishore [rajkisho...@gmail.com]
Sent: Saturday, April 19, 2014 6:11 AM
To: predictprot...@googlegroups.com
Subject: [predictprotein-science:643] Problems and advices related protein modelling and Protein protein interaction

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[R A J Rajkishore]

Dear Sir,

Thanks for your honest response.

The field you have suggested , I have gone through it.

Please be kind to share your mail id or contact info.

With lots of thanks , 

Rajkishore

LCB , 

CDFD.

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