Correlated mutations: advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families

Proteins
Inbal HalperinRuth Nussinov

Abstract

Correlated mutations have been repeatedly exploited for intramolecular contact map prediction. Over the last decade these efforts yielded several methods for measuring correlated mutations. Nevertheless, the application of correlated mutations for the prediction of intermolecular interactions has not yet been explored. This gap is due to several obstacles, such as 3D complexes availability, paralog discrimination, and the availability of sequence pairs that are required for inter- but not intramolecular analyses. Here we selected for analysis fusion protein families that bypass some of these obstacles. We find that several correlated mutation measurements yield reasonable accuracy for intramolecular contact map prediction on the fusion dataset. However, the accuracy level drops sharply in intermolecular contacts prediction. This drop in accuracy does not occur always. In the Cohesin-Dockerin family, reasonable accuracy is achieved in the prediction of both intra- and intermolecular contacts. The Cohesin-Dockerin family is well suited for correlated mutation analysis. Because, however, this family constitutes a special case (it has radical mutations, has domain repeats, within each species each Dockerin domain interacts with eac...Continue Reading

References

Mar 15, 1979·Journal of Molecular Evolution·T MiyataT Yasunaga
Mar 1, 1991·Immunology Today·G F Mitchell
Mar 21, 1986·Journal of Theoretical Biology·W R Taylor
Oct 28, 1971·Journal of Molecular Biology·A D McLachlan
Mar 17, 1994·Nature·W R MoyleX Wang
Mar 1, 1994·Protein Engineering·W R Taylor, K Hatrick
Apr 1, 1994·Proteins·U GöbelA Valencia
Jan 4, 1994·Proceedings of the National Academy of Sciences of the United States of America·E Neher
Nov 1, 1995·Protein Science : a Publication of the Protein Society·N D Clarke
Mar 29, 1996·Journal of Molecular Biology·O LichtargeF E Cohen
Feb 16, 1996·The Journal of Biological Chemistry·R E van KesterenW P Geraerts
Mar 19, 1996·Proceedings of the National Academy of Sciences of the United States of America·M Jucovic, R W Hartley
Jul 19, 1996·Molecular & General Genetics : MGG·J Ninio
Aug 29, 1997·Journal of Molecular Biology·F PazosA Valencia
Dec 24, 1997·Journal of Molecular Biology·G A TavaresP M Alzari
Jan 15, 1999·Immunogenetics·A L Hughes, M Yeager
Mar 5, 1999·Protein Engineering·P Fariselli, R Casadio
Mar 13, 1999·Journal of Molecular Biology·D D PollockN Goldman
Nov 5, 1999·Journal of Molecular Biology·O OlmeaA Valencia
Dec 10, 1999·Protein Engineering·B A GalitskyA E Kister
Feb 10, 2000·Molecular Biology and Evolution·W R AtchleyA W Dress
May 3, 2000·Genes & Genetic Systems·Y ChenW Stephan
Dec 9, 2000·Molecular Biology and Evolution·K K KoretkeJ R Brown
May 2, 2001·Nature Reviews. Genetics·T D Petes
Dec 14, 2001·Protein Engineering·P FariselliR Casadio
Feb 7, 2002·Journal of Molecular Biology·Srinivasan MadabushiOlivier Lichtarge
Apr 27, 2002·Science·Hunter B FraserMarcus W Feldman
Jun 5, 2002·Annual Review of Biochemistry·Myron F Goodman
Jun 11, 2002·Journal of Molecular Biology·K Fukami-KobayashiS A Benner
Jul 12, 2002·Proteins·William S J Valdar

❮ Previous
Next ❯

Citations

Sep 25, 2008·Quarterly Reviews of Biophysics·Joël JaninPinak Chakrabarti
May 31, 2008·Proceedings of the National Academy of Sciences of the United States of America·Hocine Madaoui, Raphaël Guerois
Jul 19, 2012·Journal of Biomolecular Structure & Dynamics·Gitanjali YadavDebasisa Mohanty
Sep 24, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Mert KarakaşJens Meiler
Dec 11, 2007·Bioinformatics·Angelika FuchsDmitrij Frishman
May 8, 2009·Nucleic Acids Research·Allison N TeggeJianlin Cheng
Nov 26, 2010·Nucleic Acids Research·Qibin LuoDmitrij Frishman
Jan 14, 2010·Protein Engineering, Design & Selection : PEDS·Haim Ashkenazy, Yossef Kliger
Oct 19, 2012·Protein Engineering, Design & Selection : PEDS·Chan-Seok Jeong, Dongsup Kim
Feb 29, 2008·Annual Review of Biochemistry·Christina KielLuis Serrano
Nov 16, 2011·BMC Bioinformatics·Janardanan SreekumarAalt D J van Dijk
Jan 12, 2012·BMC Bioinformatics·Bin Li, Daisuke Kihara
Apr 5, 2007·BMC Bioinformatics·Jianlin Cheng, Pierre Baldi
Jul 13, 2007·BMC Bioinformatics·Milana Frenkel-MorgensternShmuel Pietrokovski
Oct 29, 2010·BMC Genomics·Aalt D J van Dijk, Roeland C H J van Ham
Aug 13, 2008·BMC Structural Biology·Dorota Latek, Andrzej Kolinski
Apr 17, 2009·BMC Structural Biology·Sergey A SamsonovM Teresa Pisabarro
May 8, 2009·BMC Structural Biology·Xin GaoMing Li
Dec 19, 2012·BMC Research Notes·Mireille GomesCharlotte M Deane
Nov 22, 2008·PLoS Computational Biology·Jonathan M CarlsonDavid Heckerman
Sep 7, 2012·PLoS Computational Biology·Jessica AndreaniRaphaël Guerois
Dec 17, 2011·PloS One·Svend B HenriksenSteffen B Petersen
Feb 21, 2013·Advances in Bioinformatics·Ning ZhangTao Zhang
Feb 20, 2008·FEBS Letters·David JuanAlfonso Valencia
Jan 29, 2013·Journal of Theoretical Biology·Motoshi IchinoseMasasuke Takefu
Apr 26, 2011·Current Opinion in Biotechnology·Jürgen Pleiss
Apr 19, 2011·Current Opinion in Structural Biology·Mark N WassMichael J E Sternberg
Jul 29, 2008·Theoretical Population Biology·Motoshi IchinoseMasasuke Takefu
Apr 24, 2015·Computational and Structural Biotechnology Journal·Thomas SciorEduardo M Salinas-Stefanon

❮ 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.