Characteristic features of amino acid residues in coiled-coil protein structures

Biophysical Chemistry
M Michael Gromiha, David A D Parry

Abstract

Detailed analyses of protein structures provide an opportunity to understand conformation and function in terms of amino acid sequence and composition. In this work, we have systematically analyzed the characteristic features of the amino acid residues found in alpha-helical coiled-coils and, in so doing, have developed indices for their properties, conformational parameters, surrounding hydrophobicity and flexibility. As expected, there is preference for hydrophobic (Ala, Leu), positive (Lys, Arg) and negatively (Glu) charged residues in coiled-coil domains. However, the surrounding hydrophobicity of residues in coiled-coil domains is significantly less than that for residues in other regions of coiled-coil proteins. The analysis of temperature factors in coiled-coil proteins shows that the residues in these domains are more stable than those in other regions. Further, we have delineated the medium- and long-range contacts in coiled-coil domains and compared the results with those obtained for other (non-coiled-coil) parts of the same proteins and non-coiled-coil helical segments of globular proteins. The residues in coiled-coil domains are largely influenced by medium-range contacts, whereas long-range interactions play a dom...Continue Reading

References

Dec 1, 1977·Archives of Biochemistry and Biophysics·P Manavalan, P K Ponnuswamy
Oct 19, 1978·Nature·P Manavalan, P K Ponnuswamy
Nov 16, 1976·Biochemistry·F R Maxfield, H A Scheraga
Nov 5, 1976·Journal of Molecular Biology·B Robson, E Suzuki
Feb 1, 1991·International Journal of Biological Macromolecules·J F Conway, D A Parry
May 24, 1991·Science·A LupasJ Stock
Oct 1, 1990·International Journal of Biological Macromolecules·J F Conway, D A Parry
Aug 20, 1988·Journal of Molecular Biology·N Qian, T J Sejnowski
Jun 5, 1988·Journal of Molecular Biology·D J Barlow, J M Thornton
Jan 1, 1986·Methods in Enzymology·D Ringe, G A Petsko
Oct 1, 1980·Biophysical Journal·H Frauenfelder, G A Petsko
Jun 1, 1980·Biopolymers·Y IsogaiH A Scheraga
Jun 26, 1980·Biochimica Et Biophysica Acta·P K PonnuswamyP Manavalan
Sep 1, 1980·Biopolymers·M I Kanehisa, T Y Tsong
Aug 29, 1995·Proceedings of the National Academy of Sciences of the United States of America·B BergerP S Kim
Mar 1, 1995·International Journal of Peptide and Protein Research·M M Gromiha, P K Ponnuswamy
Oct 1, 1993·International Journal of Peptide and Protein Research·P K Ponnuswamy, M M Gromiha
Jan 1, 1993·Progress in Biophysics and Molecular Biology·P K Ponnuswamy
Jun 11, 1993·Science·M BlaberB W Matthews
Jun 1, 1997·Protein Science : a Publication of the Protein Society·E WolfB Berger
Jun 1, 1997·Current Opinion in Structural Biology·A Lupas
May 1, 1997·Protein Engineering·M M GromihaP K Ponnuswamy
Jan 7, 1998·Protein Science : a Publication of the Protein Society·S Parthasarathy, M R Murthy
Apr 20, 1999·Biophysical Chemistry·M M Gromiha, S Selvaraj
Aug 18, 1999·Proceedings of the National Academy of Sciences of the United States of America·J P Gallivan, D A Dougherty
Oct 27, 1999·Proceedings of the National Academy of Sciences of the United States of America·P Koehl, M Levitt
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Dec 11, 1999·Nucleic Acids Research·S Kawashima, M Kanehisa
Dec 28, 1999·Journal of Molecular Biology·D A Debe, W A Goddard
Dec 26, 2001·Proceedings of the National Academy of Sciences of the United States of America·A E KeatingP S Kim
Mar 27, 2002·Journal of Computational Chemistry·Marek OrzechowskiLucjan Piela
Jun 11, 2002·Journal of Molecular Biology·Jie LiuMin Lu
Nov 29, 2002·Preparative Biochemistry & Biotechnology·M Michael GromihaC Santhosh
Jan 10, 2003·Nucleic Acids Research·Brigitte BoeckmannMichel Schneider

❮ Previous
Next ❯

Citations

Nov 14, 2012·Chemical Reviews·A Subha Mahadevi, G Narahari Sastry
Oct 12, 2005·Proceedings of the National Academy of Sciences of the United States of America·Harald BärHarald Herrmann
Apr 6, 2005·Proceedings of the National Academy of Sciences of the United States of America·Eric L DeszoEric R Vimr
Jun 7, 2006·Proceedings of the National Academy of Sciences of the United States of America·Jody M MasonKatja M Arndt
Jul 8, 2015·Proceedings of the National Academy of Sciences of the United States of America·Keenan C TaylorIvan Rayment
Nov 6, 2007·DNA Repair·Miroslav Chovanec, Thomas E Wilson
May 10, 2008·Journal of Peptide Science : an Official Publication of the European Peptide Society·Eva M JouauxKatja M Arndt
Jul 17, 2015·Briefings in Bioinformatics·Chen LiAshley M Buckle
Jun 5, 2015·Proceedings. Biological Sciences·Andrew A WalkerTara D Sutherland
Mar 19, 2014·Journal of Structural Biology·Tim KükenshönerKatja M Arndt
Jan 1, 2013·Proteomics Insights·Amutha Selvaraj Maheshwari, Govindaraju Archunan
Dec 22, 2009·The Journal of Eukaryotic Microbiology·Guillermo Paz-Y-Miño C, Avelina Espinosa

❮ 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.