Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB)

Nur Syatila Ab Ghani, Mohd Firdaus Mohd Raih

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The three-dimensional structure of a protein can provide insights regarding its function. Functional relationship between proteins can be inferred from fold and sequence similarities. In certain cases, sequence or fold comparison fails to conclude homology between proteins with similar mechanism. Since the structure is more conserved than the sequence, a constellation of functional residues can be similarly arranged among proteins of similar mechanism. Local structural similarity searches are able to detect such constellation of amino acids among distinct proteins, which can be useful to annotate proteins of unknown function. Detection of such patterns of amino acids on a large scale can increase the repertoire of important 3D motifs since available known 3D motifs currently, could not compensate the ever-increasing numbers of uncharacterized proteins to be annotated. Here, a computational platform for an automated detection of 3D motifs is described. A fuzzy-pattern searching algorithm derived from IMagine an Amino Acid 3D Arrangement search EnGINE (IMAAAGINE) was implemented to develop an automated method for searching of hypothetical patterns of amino acid side chains in Protein Data Bank (PDB), without the need for prior knowledge on related sequence or structure of pattern of interest. We present an example of the searches, which is the detection of a hypothetical pattern derived from known structural motif of C2H2 structural pattern from zinc fingers. The conservation of particular patterns of amino acid side chains in unrelated proteins is highlighted. This approach can act as a complementary method for available structure-and sequence-based platforms and may contribute in improving functional association between proteins.

Original languageEnglish
Title of host publication2017 UKM FST Postgraduate Colloquium
Subtitle of host publicationProceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium
PublisherAmerican Institute of Physics Inc.
Volume1940
ISBN (Electronic)9780735416321
DOIs
Publication statusPublished - 4 Apr 2018
Event2017 UKM FST Postgraduate Colloquium - Selangor, Malaysia
Duration: 12 Jul 201713 Jul 2017

Other

Other2017 UKM FST Postgraduate Colloquium
CountryMalaysia
CitySelangor
Period12/7/1713/7/17

Fingerprint

amino acids
proteins
constellations
platforms
homology
conservation
zinc

ASJC Scopus subject areas

  • Physics and Astronomy(all)

Cite this

Ghani, N. S. A., & Mohd Raih, M. F. (2018). Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB). In 2017 UKM FST Postgraduate Colloquium: Proceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium (Vol. 1940). [020079] American Institute of Physics Inc.. https://doi.org/10.1063/1.5027994

Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB). / Ghani, Nur Syatila Ab; Mohd Raih, Mohd Firdaus.

2017 UKM FST Postgraduate Colloquium: Proceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium. Vol. 1940 American Institute of Physics Inc., 2018. 020079.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Ghani, NSA & Mohd Raih, MF 2018, Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB). in 2017 UKM FST Postgraduate Colloquium: Proceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium. vol. 1940, 020079, American Institute of Physics Inc., 2017 UKM FST Postgraduate Colloquium, Selangor, Malaysia, 12/7/17. https://doi.org/10.1063/1.5027994
Ghani NSA, Mohd Raih MF. Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB). In 2017 UKM FST Postgraduate Colloquium: Proceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium. Vol. 1940. American Institute of Physics Inc. 2018. 020079 https://doi.org/10.1063/1.5027994
Ghani, Nur Syatila Ab ; Mohd Raih, Mohd Firdaus. / Computational mining for hypothetical patterns of amino acid side chains in protein data bank (PDB). 2017 UKM FST Postgraduate Colloquium: Proceedings of the University Kebangsaan Malaysia, Faculty of Science and Technology 2017 Postgraduate Colloquium. Vol. 1940 American Institute of Physics Inc., 2018.
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