University of Madras
 

Protein misfolding and aggregation have attracted much research interest not only due to their roles in conformational diseases such as Alzheimer’s, Parkinson’s diseases and other amyloid neuropathies, but also because well ordered aggregates can lead to design of novel nanomaterials with desired characteristics. Aggregation is also a major hurdle in commercial manufacturing of biotechnology products such as enzymes and biopharmaceuticals. Hence, it is essential to develop methods for identifying amyloid forming peptides to address these issues.

We have developed a method for discriminating amyloid forming peptides and amorphous peptides using a dataset of 139 amyloids and 168 amorphous peptides. The method was tested with an additional dataset of 40 hexapeptides, 15 hexapeptides from Protein Data Bank and 310 peptides of different lengths.Our method showed an accuracy of more than 90% in all the datasets. Datsets used in this work are available here.

 

GAP identifies the amyloid forming peptides and discriminates amorphous peptides.

For discrimination enter your sequence in a single letter code in the following box in fasta format. Gap also accepts multiple sequences.



Example Peptides

Amyloid Fibril forming peptides

RVFNIM
HYFNIF
GTFNII
HLVYIM
SQFYIT
HGWLIM


Amorphous Beta Aggregate

RMFNII
KMFFIQ
WYFYIQ
FMFFII
HAFLII

Datasets used in this work are available here


Reference

A. Mary Thangakani, Sandeep Kumar, R. Nagarajan, D.Velmurugan and M. Michael Gromiha (2014) GAP: Towards almost hundred percent prediction of β-strand mediated aggregating peptides with distinct morphologies. Bioinformatics, 30(14), 1983-1990

A.M. Thangakani, S. Kumar, D. Velmurugan and M.M. Gromiha (2012) How do thermophilic proteins resist aggregation? PROTEINS: Structure, Function and Bioinformatics, 80:1003-15.

M.Michael Gromiha, A.M. Thangakani, S. Kumar and D. Velmurugan (2012) Sequence analysis and discrimination of amyloid and non-amyloid peptides. Comm. Comp. Inf. Sci. 304, 447-452.

A.M. Thangakani, S. Kumar, D. Velmurugan and M. Michael Gromiha (2013) Distinct position-specific sequence features of hexa-peptides that form amyloid-fibrils: application to discriminate between amyloid fibril and amorphous β- aggregate forming peptide sequences. BMC Bioinformatics 2013;14 Suppl 8:S6. doi: 10.1186/1471-2105-14-S8-S6. Epub 2013 May 9.

A.M. Thangakani, S. Kumar, R. Nagarajan, D. Velmurugan and M. Michael Gromiha (2014) GAP: towards almost 100 percent prediction for β-strand-mediated aggregating peptides with distinct morphologies. Bioinformatics, btu167. doi: 10.1093/bioinformatics/btu167.


Contributors

A. Mary Thangakani, University of Madras

Dr. Sandeep Kumar, Pfizer

Dr. D. Velmurugan, University of Madras

Dr. M. Michael Gromiha, IIT Madras