Identification of reaction organization patterns that naturally cluster enzymatic transformations

BMC Systems Biology
Carlos Vazquez-HernandezRosa-Maria Gutierrez-Rios

Abstract

Metabolic reactions are chemical transformations commonly catalyzed by enzymes. In recent years, the explosion of genomic data and individual experimental characterizations have contributed to the construction of databases and methodologies for the analysis of metabolic networks. Some methodologies based on graph theory organize compound networks into metabolic functional categories without preserving biochemical pathways. Other methods based on chemical group exchange and atom flow trace the conversion of substrates into products in detail, which is useful for inferring metabolic pathways. Here, we present a novel rule-based approach incorporating both methods that decomposes each reaction into architectures of compound pairs and loner compounds that can be organized into tree structures. We compared the tree structure-compound pairs to those reported in the KEGG-RPAIR dataset and obtained a match precision of 81%. The generated tree structures naturally clustered all reactions into general reaction patterns of compounds with similar chemical transformations. The match precision of each cluster was calculated and used to suggest reactant-pairs for which manual curation can be avoided because this is the main goal of the method...Continue Reading

References

Oct 18, 2000·Nature·H JeongA L Barabási
Nov 4, 2000·Nature Biotechnology·D A Fell, A Wagner
Dec 26, 2001·Nucleic Acids Research·Minoru KanehisaAkihiro Nakaya
Aug 31, 2002·Science·E RavaszA L Barabási
Feb 6, 2004·Proceedings of the National Academy of Sciences of the United States of America·Masanori Arita
Dec 17, 2004·Journal of the American Chemical Society·Masaaki KoteraMinoru Kanehisa
May 23, 2007·Journal of Chemical Information and Modeling·Mina OhMinoru Kanehisa
Feb 15, 2008·Journal of the American Chemical Society·Jeremiah W HanesTadhg P Begley
Nov 11, 2008·Nucleic Acids Research·R M KuhnW J Kent
Mar 14, 2009·Journal of Molecular Biology·Karoline FaustJacques van Helden
Dec 22, 2009·Molecular BioSystems·Gipsi Lima-Mendez, Jacques van Helden
Mar 20, 2010·Annual Review of Biochemistry·Olga Khersonsky, Dan S Tawfik
Jan 8, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Markus HeinonenJuho Rousu
Jun 8, 2011·Bio Systems·Karoline FaustJacques van Helden
Sep 12, 2012·Journal of Chemical Information and Modeling·Mario LatendressePeter D Karp
Feb 7, 2013·Journal of Chemical Information and Modeling·Ai MutoMinoru Kanehisa
Jan 15, 2014·Nature Methods·Syed Asad RahmanJanet M Thornton

❮ Previous
Next ❯

Citations

Aug 26, 2018·BMC Research Notes·Carlos Vazquez-HernandezRosa-Maria Gutierrez-Rios

❮ Previous
Next ❯

Methods Mentioned

BETA
phosphotransferases
RCLASS

Software Mentioned

GNU
Inkscape
RCLASS
Octave
COMPOUND
RPAIR
RPairs
R scripts
Perl scripts
RStudio

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

Related Papers

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Tatsuya Akutsu
Bioprocess and Biosystems Engineering
Mate BaranyFerenc Friedler
Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics
Jin YangWilliam S Hlavacek
Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Markus HeinonenJuho Rousu
© 2022 Meta ULC. All rights reserved