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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. © 2018 American Chemical Society.

Registro:

Documento: Artículo
Título:On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences
Autor:Turjanski, P.; Ferreiro, D.U.
Filiación:KAPOW, Departamento de Computación, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-ICC, Buenos Aires, Argentina
Protein Physiology Lab, Departamento de Química Biológica, Facultad de Ciencias Exactas y Naturales, UBA-CONICET-IQUIBICEN, Buenos Aires, Argentina
Palabras clave:Amino acids; Bioinformatics; Structure (composition); Adjustable parameters; Amino acid patterns; Natural architecture; Natural structures; Precise definition; Protein sequences; Sequence patterns; Standard deviation; Proteins
Año:2018
Volumen:122
Número:49
Página de inicio:11295
Página de fin:11301
DOI: http://dx.doi.org/10.1021/acs.jpcb.8b07206
Título revista:Journal of Physical Chemistry B
Título revista abreviado:J Phys Chem B
ISSN:15206106
CODEN:JPCBF
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_15206106_v122_n49_p11295_Turjanski

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Citas:

---------- APA ----------
Turjanski, P. & Ferreiro, D.U. (2018) . On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences. Journal of Physical Chemistry B, 122(49), 11295-11301.
http://dx.doi.org/10.1021/acs.jpcb.8b07206
---------- CHICAGO ----------
Turjanski, P., Ferreiro, D.U. "On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences" . Journal of Physical Chemistry B 122, no. 49 (2018) : 11295-11301.
http://dx.doi.org/10.1021/acs.jpcb.8b07206
---------- MLA ----------
Turjanski, P., Ferreiro, D.U. "On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences" . Journal of Physical Chemistry B, vol. 122, no. 49, 2018, pp. 11295-11301.
http://dx.doi.org/10.1021/acs.jpcb.8b07206
---------- VANCOUVER ----------
Turjanski, P., Ferreiro, D.U. On the Natural Structure of Amino Acid Patterns in Families of Protein Sequences. J Phys Chem B. 2018;122(49):11295-11301.
http://dx.doi.org/10.1021/acs.jpcb.8b07206