Regions of minimal structural variation among members of protein domain superfamilies: application to remote homology detection and modelling using distant relationships

FEBS Letters
Saikat Chakrabarti, Ramanathan Sowdhamini

Abstract

Structurally conserved regions or structural templates have been identified and examined for features such as amino acid content, solvent accessibility, secondary structures, non-polar interaction, residue packing and extent of structural deviations in 179 aligned members of superfamilies involving 1208 pairs of protein domains. An analysis of these structural features shows that the retention of secondary structural conservation and similar hydrogen bonding pattern within the templates is 2.5 and 1.8 times higher, respectively, than full-length alignments suggesting that they form the minimum structural requirement of a superfamily. The identification and availability of structural templates find value in different areas of protein structure prediction and modelling such as in sensitive sequence searches, accurate sequence alignment and three-dimensional modelling on the basis of distant relationships.

References

Nov 1, 1977·European Journal of Biochemistry·F C BernsteinM Tasumi
Apr 1, 1992·Protein Engineering·D L OllisJ Schrag
Nov 5, 1992·Journal of Molecular Biology·G ChelvanayagamP Argos
Jun 1, 1990·Trends in Biochemical Sciences·G K Farber, G A Petsko
Mar 20, 1990·Journal of Molecular Biology·G J Barton, M J Sternberg
Feb 14, 1971·Journal of Molecular Biology·B Lee, F M Richards
Sep 15, 1982·Journal of Molecular Biology·A M Lesk, C Chothia
Sep 1, 1993·Protein Engineering·M B Swindells, J M Thornton
Nov 1, 1993·Protein Science : a Publication of the Protein Society·T P FloresJ M Thornton
Oct 20, 1993·Journal of Molecular Biology·M S Johnson, J P Overington
Jun 5, 1993·Journal of Molecular Biology·M S JohnsonT L Blundell
Jan 1, 1997·Annual Review of Biophysics and Biomolecular Structure·C ChothiaA Murzin
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Aug 15, 1997·Structure·C A OrengoJ M Thornton
Aug 15, 1998·Nucleic Acids Research·Z ZhangS F Altschul
Sep 9, 1998·Bioinformatics·K MizuguchiJ P Overington
Oct 1, 1998·Structure·R SowdhaminiT L Blundell
Jun 22, 1999·Nucleic Acids Research·J D ThompsonO Poch
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Nov 25, 2003·Protein Engineering·Saikat ChakrabartiR Sowdhamini

❮ Previous
Next ❯

Citations

Apr 14, 2006·Journal of Molecular Evolution·Lorraine Marsh
Nov 22, 2011·Computers in Biology and Medicine·Shih-Yen Ku, Yuh-Jyh Hu
Oct 13, 2005·Journal of Biomolecular Structure & Dynamics·S SandhyaN Srinivasan
Oct 6, 2010·Journal of Biomolecular Structure & Dynamics·Ganesan PugalenthiPrasanna R Kolatkar
Jan 24, 2007·Bioinformatics·Ganesan PugalenthiSaikat Chakrabarti
Jun 28, 2005·Nucleic Acids Research·Saikat ChakrabartiR Sowdhamini
Oct 16, 2007·Nucleic Acids Research·Ganesan PugalenthiSaikat Chakrabarti
Nov 5, 2005·Journal of Molecular Biology·J Bradley Holmes, Jerry Tsai
Sep 24, 2014·Journal of Biomolecular Structure & Dynamics·Aparajita NayakRaja Mazumder
Apr 21, 2018·Proteins·Prachi MehrotraNarayanaswamy Srinivasan
Mar 2, 2019·Database : the Journal of Biological Databases and Curation·Pritha GhoshRamanathan Sowdhamini
Jun 9, 2006·Acta Biochimica Et Biophysica Sinica·Li-Xia LiuLin Jiang

❮ 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.