Twist and shear in beta-sheets and beta-ribbons

Journal of Molecular Biology
Bosco K Ho, Paul M G Curmi

Abstract

The structures of the beta-sheets and the beta-ribbons have been analysed using high-resolution protein structure data. Systematic asymmetries measured in both parallel and antiparallel beta-structures include the sheet twist and the strand shear. In order to determine the origin of these asymmetries, numerous interactions and correlations were examined. The strongest correlations are observed for residues in antiparallel beta-sheets and beta-ribbons that form non-H-bonded pairs. For these residues, the sheet twist is correlated to the backbone phi angle but not to the psi angle. Our analysis supports the existence of an inter-strand C(alpha)H(alpha)...O weak H-bond, which, together with the CO...HN H-bond, constitutes a bifurcated H-bond that links neighbouring beta-strands. Residues of beta-sheets and beta-ribbons in high-resolution protein structures form a distinct region of the Ramachandran plot, which is determined by the formation of the bifurcated H-bond, the formation of an intra-strand O...H(alpha) non-bonded polar interaction, and an intra-strand O...C(beta) steric clash. Using beta-strands parameterised by phi-psi values from the allowed beta-sheet region of the Ramachandran plot, the shear and the right-hand twist ...Continue Reading

Citations

Dec 14, 2011·Journal of the American Chemical Society·Hammad NaveedJie Liang
Jul 23, 2009·Proceedings of the National Academy of Sciences of the United States of America·Hammad NaveedJie Liang
Nov 17, 2005·Bioinformatics·Eunhee KohHyun-Soo Cho
Aug 4, 2012·BMC Structural Biology·Kazuo FujiwaraMasamichi Ikeguchi
Feb 16, 2005·BMC Structural Biology·Jordi Bella, Martin J Humphries
Dec 6, 2008·PLoS Computational Biology·Da-Wei LiShuanghong Huo
Sep 11, 2003·Proceedings of the National Academy of Sciences of the United States of America·David Eisenberg
Sep 20, 2005·Proceedings of the National Academy of Sciences of the United States of America·Steven L KazmirskiJohn Kuriyan
Feb 11, 2016·Journal of the American Chemical Society·Meishan LinJie Liang
Jun 4, 2015·Proceedings of the National Academy of Sciences of the United States of America·András MicsonaiJózsef Kardos
Jul 25, 2012·The Biochemical Journal·Audrey Agopian, Zhefeng Guo
Nov 5, 2016·Proceedings of the National Academy of Sciences of the United States of America·Craig O MackenzieGevorg Grigoryan
Aug 22, 2014·PLoS Computational Biology·Cyril F ReboulMichelle A Dunstone
Apr 5, 2017·European Biophysics Journal : EBJ·Robert W Janes
Oct 24, 2003·Protein Science : a Publication of the Protein Society·Bosco K HoRobert Brasseur
May 27, 2004·Proteins·Annick ThomasRobert Brasseur
Jun 12, 2014·Nature Communications·R Bryn FenwickXavier Salvatella
Apr 13, 2010·The Journal of Biological Chemistry·Brent Wathen, Zongchao Jia
Jan 10, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Tunazzina IslamJing He
Jun 17, 2008·Protein Science : a Publication of the Protein Society·Zhefeng Guo, David Eisenberg
Apr 28, 2006·Protein Science : a Publication of the Protein Society·Jemima HoskinsTom L Blundell
Aug 2, 2013·Protein Science : a Publication of the Protein Society·Pierrick CraveurAlexandre G de Brevern
Nov 2, 2018·Protein Science : a Publication of the Protein Society·Naomi L HaworthMerridee A Wouters
Jul 18, 2002·The Journal of Biological Chemistry·Lin Jiang, Luhua Lai
Aug 21, 2007·Proteins·Vikas Nanda, Ann Schmiedekamp
Nov 8, 2008·Angewandte Chemie·Ishu SaraogiAndrew D Hamilton
Oct 15, 2009·Journal of Computational Chemistry·Hao WuShuanghong Huo
Sep 27, 2005·Proteins·Marc Parisien, François Major
Feb 18, 2006·The Journal of Biological Chemistry·Adela Garcia-MartinPaula Braun
Oct 27, 2015·BMC Structural Biology·Kazuo FujiwaraMasamichi Ikeguchi
Apr 14, 2011·Proteins·Yifan SongDavid Baker
Jan 28, 2014·Proteins·Kazuo FujiwaraMasamichi Ikeguchi
May 10, 2019·APL Bioengineering·Brock SchumanChristopher M Yip
Mar 30, 2012·Journal of Computational Chemistry·David J Huggins
Nov 1, 2015·Biochemical Society Transactions·Erin E CuttsGeorgios N Hatzopoulos
Jan 31, 2018·Proceedings of the National Academy of Sciences of the United States of America·Wei TianHammad Naveed
Nov 22, 2011·Acta Crystallographica. Section D, Biological Crystallography·T D Fenn, M J Schnieders
Jul 19, 2018·Proteins·Nobuaki KikuchiMasamichi Ikeguchi
Jul 17, 2007·Progress in Biophysics and Molecular Biology·Pinak Chakrabarti, Rajasri Bhattacharyya
Oct 24, 2020·The Journal of Chemical Physics·Carmen Giovana Granados-Ramírez, Mauricio D Carbajal-Tinoco
Jun 1, 2010·The Journal of Physical Chemistry. B·Aleksandra Fulara, Wojciech Dzwolak

❮ 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

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Ronald Jackups, Jie Liang
Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Ronald Jackups, Jie Liang
Conference Proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society
David Jimenez-MoralesJie Liang
© 2022 Meta ULC. All rights reserved