Genome-wide computational determination of the human metalloproteome

Proteins
Ariel AziaVladimir Sobolev

Abstract

Accurate prediction of protein function in humans is important for understanding biological processes at the molecular level in biomedicine and drug design. Over a third of proteins are commonly held to bind metal, and ∼10% of human proteins, to bind zinc. Therefore, an initial step in protein function prediction frequently involves predicting metal ion binding. In recent years, methods have been developed to predict a set of residues in 3D space forming the metal-ion binding site, often with a high degree of accuracy. Here, using extensions of these methods, we provide an extensive list of human proteins and their putative metal ion binding site residues, using translated gene sequences derived from the complete, resolved human genome. Under conditions of ∼90% selectivity, over 900 new human putative metal ion binding proteins are identified. A statistical analysis of resolved metal ion binding sites in the human metalloproteome is furnished and the importance of remote homology analysis is demonstrated. As an example, a novel metal-ion binding site involving a complex of a botulinum substrate with its inhibitor is presented. On the basis of the location of the predicted site and the interactions of the contacting residues at ...Continue Reading

References

May 25, 1977·Journal of Molecular Biology·F C BernsteinM Tasumi
Nov 1, 1996·Nature Structural Biology·C A Kim, J M Berg
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
May 13, 1999·Bioinformatics·V SobolevM Edelman
Feb 3, 2000·Nature Structural Biology·K ScheffzekP Gierschik
Jan 16, 2003·Nucleic Acids Research·S Sri KrishnaNick V Grishin
Aug 13, 2003·Bioinformatics·Guoli Wang, Roland L Dunbrack
Feb 24, 2004·Protein Science : a Publication of the Protein Society·Michael L Sierk, William R Pearson
Feb 24, 2004·Journal of Computational Chemistry·Eran EyalVladimir Sobolev
Jul 29, 2004·Cell Cycle·Rainer K Brachmann
Aug 18, 2004·Journal of Molecular Biology·Jaspreet Singh SodhiDavid T Jones
Feb 24, 2005·Proteins·Mariana BaborVladimir Sobolev
Oct 11, 2005·Annual Review of Cell and Developmental Biology·Aron B Jaffe, Alan Hall
Jan 7, 2006·Journal of Proteome Research·Claudia AndreiniAntonio Rosato
Sep 12, 2006·Journal of Molecular Biology·David J SegalNancy C Horton
Dec 5, 2006·PLoS Computational Biology·Andrew B Goryachev, Alexandra V Pokhilko
Apr 25, 2007·Acta Crystallographica. Section D, Biological Crystallography·Gerd Prehna, C Erec Stebbins
Jul 28, 2007·Proteins·Mariana BaborMarvin Edelman
Nov 29, 2007·Protein Science : a Publication of the Protein Society·Jessica C Ebert, Russ B Altman
Jan 11, 2008·Structure·John Moult
Jul 8, 2008·Journal of Biological Inorganic Chemistry : JBIC : a Publication of the Society of Biological Inorganic Chemistry·Claudia AndreiniJanet M Thornton
Jan 10, 2009·Nature Protocols·Da Wei HuangRichard A Lempicki
Feb 20, 2009·Genome Biology·Yaniv LoewensteinAnna Tramontano
Aug 12, 2009·The Journal of Biological Chemistry·Laura SturlaElena Zocchi
Aug 29, 2012·Computational Biology and Chemistry·Marcelo BoaretoVitor B P Leite
Jan 29, 2013·Nature Methods·Predrag RadivojacIddo Friedberg
Mar 22, 2013·Biochemical Society Transactions·Alexander E Kister, Vladimir Potapov
May 22, 2013·Proceedings of the National Academy of Sciences of the United States of America·Jeffrey Skolnick, Mu Gao
Nov 21, 2013·Nucleic Acids Research·UNKNOWN UniProt Consortium
Jan 5, 2014·PloS One·Sarah MeinhardtLiskin Swint-Kruse

❮ Previous
Next ❯

Citations

Jul 1, 2016·Protein Engineering, Design & Selection : PEDS·Sharon L GuffyBrian Kuhlman
Aug 7, 2016·Frontiers in Chemistry·Marvin Edelman, Monica Colt
Sep 28, 2018·Chembiochem : a European Journal of Chemical Biology·Jana AupičRoman Jerala
Apr 26, 2019·Metallomics : Integrated Biometal Science·Yan ZhangYinzhen Xu
Dec 1, 2015·Proteomes·Peter-Leon Hagedoorn
Jul 30, 2020·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Yan Zhang, Junge Zheng
Mar 10, 2021·Protein Science : a Publication of the Protein Society·Israel SilmanLev Weiner

❮ Previous
Next ❯

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.