Evolution of oligomeric state through geometric coupling of protein interfaces.

Proceedings of the National Academy of Sciences of the United States of America
Tina PericaSarah A Teichmann

Abstract

Oligomerization plays an important role in the function of many proteins. Thus, understanding, predicting, and, ultimately, engineering oligomerization presents a long-standing interest. From the perspective of structural biology, protein-protein interactions have mainly been analyzed in terms of the biophysical nature and evolution of protein interfaces. Here, our aim is to quantify the importance of the larger structural context of protein interfaces in protein interaction evolution. Specifically, we ask to what extent intersubunit geometry affects oligomerization state. We define a set of structural parameters describing the overall geometry and relative positions of interfaces of homomeric complexes with different oligomeric states. This allows us to quantify the contribution of direct sequence changes in interfaces versus indirect changes outside the interface that affect intersubunit geometry. We find that such indirect, or allosteric mutations affecting intersubunit geometry via indirect mechanisms are as important as interface sequence changes for evolution of oligomeric states.

References

Aug 28, 1975·Nature·C Chothia, J Janin
Jan 20, 1995·Science·T Clackson, J A Wells
Mar 29, 1996·Journal of Molecular Biology·V MainfroidK Goraj
Jul 7, 1998·Journal of Molecular Biology·A A Bogan, K S Thorn
Feb 2, 1999·Journal of Molecular Biology·L Lo ConteJ Janin
Jan 25, 2002·Annual Review of Pharmacology and Toxicology·Elias J Fernandez, Elias Lolis
Apr 12, 2002·Proteins·Pinak Chakrabarti, Joël Janin
Apr 27, 2002·Science·Hunter B FraserMarcus W Feldman
Nov 26, 2002·Journal of Molecular Biology·Sarah A Teichmann
May 6, 2003·Proceedings of the National Academy of Sciences of the United States of America·Buyong MaRuth Nussinov
Jul 11, 2003·The EMBO Journal·Irene M A Nooren, Janet M Thornton
Sep 23, 2003·Journal of Molecular Biology·Patrick AloyRobert B Russell
Jul 23, 2004·Proceedings of the National Academy of Sciences of the United States of America·Deepa RajamaniCarlos J Camacho
Mar 26, 2005·Protein Engineering, Design & Selection : PEDS·Ozlem Keskin, Ruth Nussinov
Jul 27, 2005·Proceedings of the National Academy of Sciences of the United States of America·Julian Mintseris, Zhiping Weng
May 16, 2006·Structure·Jung-Hoon HanSarah A Teichmann
Jul 11, 2006·Proceedings of the National Academy of Sciences of the United States of America·Robert B BestMichele Vendruscolo
Oct 3, 2006·PLoS Computational Biology·Wan Kyu KimMichael Schroeder
Nov 23, 2006·PLoS Computational Biology·Emmanuel D LevySarah A Teichmann
Jan 12, 2008·Science·Dirk GrueningerGeorg E Schulz
Jan 15, 2008·Biochemistry·Sertan Cansu, Pemra Doruker
Jun 7, 2008·Microbiology and Molecular Biology Reviews : MMBR·Charles L Turnbough, Robert L Switzer
Jun 20, 2008·Nature·Emmanuel D LevySarah A Teichmann
Sep 2, 2008·Proceedings of the National Academy of Sciences of the United States of America·Eyal AkivaHanah Margalit
Sep 25, 2008·Quarterly Reviews of Biophysics·Joël JaninPinak Chakrabarti
Jul 8, 2009·The Journal of Biological Chemistry·Jeanne A Hardy, James A Wells
Nov 3, 2009·Journal of Molecular Biology·Judith E DayhoffAnna R Panchenko
Dec 8, 2009·Science·Sebastian KühnerAnne-Claude Gavin
May 12, 2010·Current Opinion in Structural Biology·Tina Perica, Cyrus Chothia
Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Qiangfeng Cliff ZhangBarry H Honig
Nov 5, 2010·Proceedings of the National Academy of Sciences of the United States of America·Kosuke Hashimoto, Anna R Panchenko
Nov 11, 2010·Nucleic Acids Research·David A de Lima MoraisJulian Gough
Apr 5, 2011·Molecular Cell·John KaranicolasDavid Baker

❮ Previous
Next ❯

Citations

Dec 14, 2012·Journal of the Royal Society, Interface·Panagiotis L Kastritis, Alexandre M J J Bonvin
May 29, 2014·PLoS Biology·Joseph A Marsh, Sarah A Teichmann
Aug 29, 2014·Journal of the Royal Society, Interface·Tobias Sikosek, Hue Sun Chan
Sep 17, 2015·Journal of Molecular Biology·Shanshan Cheng, Charles L Brooks
Jul 1, 2015·Proceedings of the National Academy of Sciences of the United States of America·Tatjana BraunEdward H Egelman
Sep 3, 2013·Protein Science : a Publication of the Protein Society·Petras J KundrotasJoël Janin
Nov 26, 2013·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Joseph A Marsh, Sarah A Teichmann
Aug 1, 2014·Progress in Biophysics and Molecular Biology·Govindarajan SudhaNarayanaswamy Srinivasan
Jul 25, 2015·Journal of Molecular Structure·Martin K SafoJ Eric Russell
Jul 31, 2013·Current Opinion in Structural Biology·Xiuwei ZhangSarah A Teichmann
Dec 11, 2014·Annual Review of Biochemistry·Joseph A Marsh, Sarah A Teichmann
Sep 5, 2014·Structure·Andreas C JoergerAntonina Andreeva
Aug 22, 2014·PLoS Computational Biology·Cyril F ReboulMichelle A Dunstone
Mar 17, 2017·Annual Review of Biophysics·Georg K A Hochberg, Joseph W Thornton
Aug 23, 2018·Angewandte Chemie·Hector Garcia-SeisdedosEmmanuel D Levy
Jun 4, 2019·PLoS Computational Biology·Alexander S Leonard, Sebastian E Ahnert
Nov 26, 2013·The Journal of Biological Chemistry·Virginia P RonchiArthur L Haas
May 2, 2019·Structural Dynamics·Kyle M StiersLesa J Beamer

❮ 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.

Related Papers

Journal of Molecular Biology
Judith E DayhoffAnna R Panchenko
Proceedings of the National Academy of Sciences of the United States of America
Michael Lynch
© 2021 Meta ULC. All rights reserved