On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences

The Journal of Physical Chemistry. B
Pablo Turjanski, Diego U Ferreiro

Abstract

All known terrestrial proteins are coded as continuous strings of ≈20 amino acids. The patterns formed by the repetitions of elements in groups of finite sequences describes the natural architectures of protein families. We present a method to search for patterns and groupings of patterns in protein sequences using a mathematically precise definition for "repetition", an efficient algorithmic implementation and a robust scoring system with no adjustable parameters. We show that the sequence patterns can be well-separated into disjoint classes according to their recurrence in nested structures. The statistics of the occurrences of patterns indicate that short repetitions are sufficient to account for the differences between natural families and randomized groups of sequences by more than 10 standard deviations, while contiguous sequence patterns shorter than 5 residues are effectively random in their occurrences. A small subset of patterns is sufficient to account for a robust "familiarity" definition between arbitrary sets of sequences.

References

Nov 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·J D Bryngelson, P G Wolynes
Dec 6, 1985·Science·M Lewis, D C Rees
Sep 15, 1999·Proceedings of the National Academy of Sciences of the United States of America·E Bornberg-Bauer, H S Chan
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·V Muñoz, W A Eaton
Jan 27, 2000·Cell·M KirschnerT Mitchison
Sep 16, 2000·Journal of Theoretical Biology·O WeissH Herzel
Apr 23, 2008·Journal of the Royal Society, Interface·David T F DrydenJohn H White
Jul 11, 2009·The Journal of Physical Chemistry. a·Praveen D Chowdary, Martin Gruebele
Dec 2, 2009·Bioinformatics·Daniel T Lavelle, William R Pearson
Jul 20, 2010·Proceedings of the National Academy of Sciences of the United States of America·Shlomi ReuveniJoseph Klafter
Jul 21, 2010·Journal of Molecular Biology·Asa K BjörklundArne Elofsson
Aug 6, 2010·PLoS Computational Biology·Russell F Doolittle
Dec 29, 2010·Methods in Enzymology·Andrew Leaver-FayPhilip Bradley
Nov 23, 2011·Proceedings of the National Academy of Sciences of the United States of America·Faruck MorcosMartin Weigt
Nov 1, 2012·Proceedings of the National Academy of Sciences of the United States of America·Peter G WolynesAlan R Fersht
Jun 14, 2013·The Journal of Physical Chemistry. B·R Gonzalo ParraDiego U Ferreiro
Oct 8, 2013·Briefings in Bioinformatics·Isabel Schwende, Tuan D Pham
Dec 7, 2013·Nucleic Acids Research·Tomás Di DomenicoSilvio C E Tosatto
Jan 29, 2014·Journal of Bioinformatics and Computational Biology·Eddy Taillefer, Jonathan Miller
Aug 3, 2014·Molecular Biology and Evolution·Teresa KrickIgnacio E Sánchez
Aug 13, 2014·Proceedings of the National Academy of Sciences of the United States of America·Faruck MorcosPeter G Wolynes
Sep 17, 2014·Quarterly Reviews of Biophysics·Diego U FerreiroPeter G Wolynes
Oct 14, 2014·Israel Journal of Chemistry·N P SchaferP G Wolynes
Nov 1, 2015·Biochemical Society Transactions·Rocío EspadaDiego U Ferreiro
Feb 26, 2016·Biophysical Journal·Morten Beck TrelleElizabeth A Komives
Apr 6, 2016·Scientific Reports·Pablo TurjanskiDiego U Ferreiro
Nov 1, 2017·Proceedings of the National Academy of Sciences of the United States of America·William A Eaton, Peter G Wolynes
Nov 5, 2017·Current Opinion in Structural Biology·Diego U FerreiroPeter G Wolynes
Apr 22, 2018·Biochemical Society Transactions·Alexandr P Kornev
May 8, 2018·Proceedings of the National Academy of Sciences of the United States of America·Paul RobustelliDavid E Shaw

❮ 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.