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Leveraging family-specific signatures for AMP discovery and high-throughput annotation.

Waghu FH, Barai RS, Idicula-Thomas S - Sci Rep (2016)

Bottom Line: As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance.The webserver is available online at www.campsign.bicnirrh.res.in.In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India.

ABSTRACT
Antimicrobial peptides (AMPs) are diverse, biologically active, essential components of the innate immune system. As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance. They are widely researched for their therapeutic potential, especially against multi-drug resistant pathogens. AMPs are known to have family-specific sequence composition, which can be mined for their discovery and rational design. Here, we present a detailed family-based study on AMP families. The study involved the use of sequence signatures represented by patterns and hidden Markov models (HMMs) present in experimentally studied AMPs to identify novel AMPs. Along with AMPs, peptides hitherto lacking antimicrobial annotation were also retrieved and wet-lab studies on randomly selected sequences proved their antimicrobial activity against Escherichia coli. CAMPSign, a webserver has been created for researchers to effortlessly exploit the use of AMP family signatures for identification of AMPs. The webserver is available online at www.campsign.bicnirrh.res.in. In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.

No MeSH data available.


Related in: MedlinePlus

Flowchart of the protocol adopted for generation and use of signatures for AMP discovery.
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f3: Flowchart of the protocol adopted for generation and use of signatures for AMP discovery.

Mentions: Pattern-restricted sequence alignment: To identify/refine the probable AMP region within the retrieved sequence, multiple sequence viewer of Schrödinger Suite Release 2014-2 (Schrödinger Release 2014-2: Prime, version 3.6, Schrödinger, LLC, New York, NY, 2014) was used to perform multiple sequence alignment of the experimentally validated AMPs belonging to a particular AMP family along with the retrieved sequence. This tool has an option to restrict the alignment based on a user-defined pattern. Pattern and the experimentally validated AMPs represent a particular AMP family, while the retrieved sequence is predicted to be a member of this family based on the pattern. Flowchart of the work implemented in this study can be viewed in Fig. 3.


Leveraging family-specific signatures for AMP discovery and high-throughput annotation.

Waghu FH, Barai RS, Idicula-Thomas S - Sci Rep (2016)

Flowchart of the protocol adopted for generation and use of signatures for AMP discovery.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4836297&req=5

f3: Flowchart of the protocol adopted for generation and use of signatures for AMP discovery.
Mentions: Pattern-restricted sequence alignment: To identify/refine the probable AMP region within the retrieved sequence, multiple sequence viewer of Schrödinger Suite Release 2014-2 (Schrödinger Release 2014-2: Prime, version 3.6, Schrödinger, LLC, New York, NY, 2014) was used to perform multiple sequence alignment of the experimentally validated AMPs belonging to a particular AMP family along with the retrieved sequence. This tool has an option to restrict the alignment based on a user-defined pattern. Pattern and the experimentally validated AMPs represent a particular AMP family, while the retrieved sequence is predicted to be a member of this family based on the pattern. Flowchart of the work implemented in this study can be viewed in Fig. 3.

Bottom Line: As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance.The webserver is available online at www.campsign.bicnirrh.res.in.In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.

View Article: PubMed Central - PubMed

Affiliation: Biomedical Informatics Centre of Indian Council of Medical Research, National Institute for Research in Reproductive Health, Mumbai-400012, India.

ABSTRACT
Antimicrobial peptides (AMPs) are diverse, biologically active, essential components of the innate immune system. As compared to conventional antibiotics, AMPs exhibit broad spectrum antimicrobial activity, reduced toxicity and reduced microbial resistance. They are widely researched for their therapeutic potential, especially against multi-drug resistant pathogens. AMPs are known to have family-specific sequence composition, which can be mined for their discovery and rational design. Here, we present a detailed family-based study on AMP families. The study involved the use of sequence signatures represented by patterns and hidden Markov models (HMMs) present in experimentally studied AMPs to identify novel AMPs. Along with AMPs, peptides hitherto lacking antimicrobial annotation were also retrieved and wet-lab studies on randomly selected sequences proved their antimicrobial activity against Escherichia coli. CAMPSign, a webserver has been created for researchers to effortlessly exploit the use of AMP family signatures for identification of AMPs. The webserver is available online at www.campsign.bicnirrh.res.in. In this work, we demonstrate an optimised and experimentally validated protocol along with a freely available webserver that uses family-based sequence signatures for accelerated discovery of novel AMPs.

No MeSH data available.


Related in: MedlinePlus