A structural explanation for the twilight zone of protein sequence homology

Structure
S Y Chung, S Subbiah

Abstract

Homology modeling of protein structures as a function of sequence breaks down at the twilight zone limit of sequence identity between the template and target proteins. Our results suggest that protein sequences that have diverged from a common ancestor beyond the twilight zone may adopt side-chain interactions that are very different from those endowed by the ancestral sequence.

References

Mar 27, 1975·Nature·C Chothia
Jun 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·V Daggett, M Levitt
Jun 1, 1991·Journal of Biomolecular Structure & Dynamics·P TufferyR Lavery
Jan 20, 1991·Journal of Molecular Biology·C Lee, S Subbiah
Nov 1, 1994·Protein Science : a Publication of the Protein Society·D V LaurentsM Levitt
Dec 1, 1994·Protein Science : a Publication of the Protein Society·R TanimuraH Nakamura
Nov 1, 1993·Protein Science : a Publication of the Protein Society·T P FloresJ M Thornton
Mar 20, 1993·Journal of Molecular Biology·R L Dunbrack, M Karplus
Jun 5, 1993·Journal of Molecular Biology·F EisenmengerR Abagyan
Nov 1, 1995·Protein Science : a Publication of the Protein Society·S Y Chung, S Subbiah

❮ Previous
Next ❯

Citations

May 6, 1998·Protein Science : a Publication of the Protein Society·L J BeamerD Eisenberg
Nov 29, 2007·Journal of Molecular Evolution·Seán J CostelloePaul A Dalby
Sep 23, 2003·Journal of Molecular Biology·Patrick AloyRobert B Russell
Jun 8, 2002·Journal of Molecular Biology·Burkhard Rost
Oct 17, 2002·Journal of Molecular Biology·Patrice Koehl, Michael Levitt
Apr 1, 1997·Current Opinion in Structural Biology·R Sánchez, A Sali
May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·S E BrennerT J Hubbard
Oct 17, 1998·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·W N Grundy
Dec 7, 2010·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Xin Liu, Ya-Pu Zhao
Oct 1, 2011·Database : the Journal of Biological Databases and Curation·Khader ShameerRamanathan Sowdhamini
Sep 6, 2000·Genes & Development·B S CobbS T Smale
Oct 25, 2000·Protein Science : a Publication of the Protein Society·A FiserA Sali
Feb 29, 2008·Annual Review of Biochemistry·Christina KielLuis Serrano
Feb 27, 2010·PloS One·Venkataramanan SoundararajanRam Sasisekharan
Feb 26, 2016·Frontiers in Plant Science·Chunyang WangGuan-Zhu Han
Sep 12, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Lina YangHuiwu Luo
Feb 22, 2003·Journal of Molecular Biology·Per Källblad, Philip M Dean
Aug 22, 2003·Protein Science : a Publication of the Protein Society·Sharon Goldsmith-Fischman, Barry Honig
Apr 21, 2005·Protein Science : a Publication of the Protein Society·Dennis R Livesay, David La
Aug 3, 2007·Proteins·Alejandro Sánchez-FloresLorenzo Segovia
Feb 26, 2015·Proteins·Ivan AnishchenkoIlya A Vakser
Jul 30, 2015·Journal of Chemical Information and Modeling·Matthew P Baumgartner, Carlos J Camacho
May 13, 2015·Nucleic Acids Research·Sayoni DasChristine A Orengo
Aug 7, 2004·Structure·Suvobrata Chakravarty, Roberto Sanchez
Aug 15, 2000·Annual Review of Biophysics and Biomolecular Structure·M A Martí-RenomA Sali
Oct 25, 2014·PloS One·Giacomo BastianelliJean-Christophe Barale
Nov 10, 2001·Annual Review of Biomedical Engineering·C ZhuN Wang
Feb 5, 1999·Journal of Molecular Biology·K Fukami-KobayashiK Nishikawa
Jul 9, 1999·Journal of Molecular Biology·R ThieleT Lengauer
Oct 8, 2009·Experimental Mechanics·G Bao
Mar 28, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Strahinja StevanovićTom Solmajer
Apr 9, 1999·Protein Engineering·B Rost
Aug 2, 2005·Journal of Peptide Science : an Official Publication of the European Peptide Society·Bernard BusettaGilles Précigoux
Nov 1, 2003·Nature Materials·G Bao, S Suresh
Jan 1, 1997·Annual Review of Biochemistry·M LevittJ Tsai

❮ 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.