Residue interaction dynamics in Vaucheria aureochrome1 light-oxygen-voltage: Bridging theory and experiments.

Proteins
Anwesha DebDevrani Mitra

Abstract

Allosteric communication is the basis of signaling and information transfer. Collective interactions between amino acid residues, which are spatially distributed in the three dimensional structure of a protein molecule, form the basis of allosteric network. While the construction of residue interaction graphs (RIG) is based on static crystal structures of proteins, it is important to extract information on protein dynamics to understand allostery. Therefore, quantitative analysis of RIG based on the framework of differential network (DN), is immensely helpful in identifying key amino acid residue interactions within such communication pathways. While the simultaneous availability of protein structures from two different states is essential for DN, there are additional challenges. Crystallographic artifacts like nonbiological dimeric arrangements within the crystal lattice automatically influence the construction and eventually the interpretation of RIG. Therefore, experimental validation of predictions from the analyses of RIG is naturally scarce in the literature. Herein, we study the photo sensor domain of the signaling photoreceptor transcription factor, aureochrome1, to understand light-driven signaling. We perform direct e...Continue Reading

References

Aug 22, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M VendruscoloM Karplus
Dec 17, 2002·Nature Structural Biology·Gürol M SüelRama Ranganathan
Dec 22, 2004·Biochemistry·Shannon M HarperKevin H Gardner
Sep 10, 2005·Biophysical Journal·K V Brinda, Saraswathi Vishveshwara
Aug 29, 2006·Biophysical Journal·Peter L FreddolinoKlaus Schulten
May 19, 2007·Science·Brian D ZoltowskiBrian R Crane
Sep 26, 2007·PLoS Computational Biology·Chakra Chennubhotla, Ivet Bahar
Nov 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Fumio TakahashiHironao Kataoka
Oct 24, 2008·Biochemistry·Rebecca A Ayers, Keith Moffat
Feb 21, 2009·PLoS Computational Biology·Michael D Daily, Jeffrey J Gray
Aug 26, 2009·Cell·Najeeb HalabiRama Ranganathan
Sep 1, 2009·Nature Chemical Biology·Brian D ZoltowskiBrian R Crane
Sep 10, 2010·The Journal of Biological Chemistry·Masahiro KasaharaKengo Tainaka
Mar 18, 2011·Journal of the American Chemical Society·Sarah RaffelbergAba Losi
Nov 29, 2012·Chemical Reviews·L Di PaolaA Giuliani
Jan 30, 2014·PloS One·Josiah P Zayner, Tobin R Sosnick
Mar 15, 2015·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Soumya Jyoti BanerjeeSoumen Roy
Jul 26, 2015·Bioinformatics·Rajdeep Kaur GrewalSoumen Roy
Jul 29, 2015·Protein and Peptide Letters·Rajdeep K Grewal, Soumen Roy
Dec 3, 2015·Scientific Reports·Soumya Jyoti BanerjeeSoumen Roy
Feb 19, 2016·Chemical Reviews·Elena PapaleoRuth Nussinov
Feb 20, 2016·Chemical Reviews·Nikolay V Dokholyan
Mar 2, 2016·Proceedings of the National Academy of Sciences of the United States of America·Spencer T GlantzBrian Y Chow
Jul 10, 2018·Chemical Reviews·Aba LosiAndreas Möglich
May 11, 2019·Methods in Enzymology·Estella F YeeBrian R Crane
Nov 9, 2019·Trends in Plant Science·Sudakshina Banerjee, Devrani Mitra

❮ Previous
Next ❯

Citations

Jan 9, 2021·Bioinformatics·Saptarshi SinhaSoumen Roy
Aug 17, 2021·Journal of the Indian Institute of Science·Saptarshi SinhaSoumen Roy

❮ 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

Nihon rinsho. Japanese journal of clinical medicine
K ShigaH Okamoto
Occupational Health & Safety
Cory Houston
Eye, Ear, Nose & Throat Monthly
K M Illig
Molecular Reproduction and Development
K D Taylor, L Pikó
Proceedings of the National Academy of Sciences of the United States of America
Chad A EllisGeoffrey J Clark
© 2021 Meta ULC. All rights reserved