Scale-free behaviour of amino acid pair interactions in folded proteins.

The protein structure is a cumulative result of interactions between amino acid residues interacting with each other through space and/or chemical bonds. Despite the large number of high resolution protein structures, the "protein structure code" has not been fully identified. Our manuscri...

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Autores principales:	Steffen B Petersen, Maria Teresa Neves-Petersen, Svend B Henriksen, Rasmus J Mortensen, Henrik M Geertz-Hansen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/d90041243276450b918b37a70ac23c89
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spelling	oai:doaj.org-article:d90041243276450b918b37a70ac23c892021-11-18T07:10:53ZScale-free behaviour of amino acid pair interactions in folded proteins.1932-620310.1371/journal.pone.0041322https://doaj.org/article/d90041243276450b918b37a70ac23c892012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22848462/?tool=EBIhttps://doaj.org/toc/1932-6203The protein structure is a cumulative result of interactions between amino acid residues interacting with each other through space and/or chemical bonds. Despite the large number of high resolution protein structures, the "protein structure code" has not been fully identified. Our manuscript presents a novel approach to protein structure analysis in order to identify rules for spatial packing of amino acid pairs in proteins. We have investigated 8706 high resolution non-redundant protein chains and quantified amino acid pair interactions in terms of solvent accessibility, spatial and sequence distance, secondary structure, and sequence length. The number of pairs found in a particular environment is stored in a cell in an 8 dimensional data tensor. When plotting the cell population against the number of cells that have the same population size, a scale free organization is found. When analyzing which amino acid paired residues contributed to the cells with a population above 50, pairs of Ala, Ile, Leu and Val dominate the results. This result is statistically highly significant. We postulate that such pairs form "structural stability points" in the protein structure. Our data shows that they are in buried α-helices or β-strands, in a spatial distance of 3.8-4.3Å and in a sequence distance >4 residues. We speculate that the scale free organization of the amino acid pair interactions in the 8D protein structure combined with the clear dominance of pairs of Ala, Ile, Leu and Val is important for understanding the very nature of the protein structure formation. Our observations suggest that protein structures should be considered as having a higher dimensional organization.Steffen B PetersenMaria Teresa Neves-PetersenSvend B HenriksenRasmus J MortensenHenrik M Geertz-HansenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 7, p e41322 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Steffen B Petersen Maria Teresa Neves-Petersen Svend B Henriksen Rasmus J Mortensen Henrik M Geertz-Hansen Scale-free behaviour of amino acid pair interactions in folded proteins.
description	The protein structure is a cumulative result of interactions between amino acid residues interacting with each other through space and/or chemical bonds. Despite the large number of high resolution protein structures, the "protein structure code" has not been fully identified. Our manuscript presents a novel approach to protein structure analysis in order to identify rules for spatial packing of amino acid pairs in proteins. We have investigated 8706 high resolution non-redundant protein chains and quantified amino acid pair interactions in terms of solvent accessibility, spatial and sequence distance, secondary structure, and sequence length. The number of pairs found in a particular environment is stored in a cell in an 8 dimensional data tensor. When plotting the cell population against the number of cells that have the same population size, a scale free organization is found. When analyzing which amino acid paired residues contributed to the cells with a population above 50, pairs of Ala, Ile, Leu and Val dominate the results. This result is statistically highly significant. We postulate that such pairs form "structural stability points" in the protein structure. Our data shows that they are in buried α-helices or β-strands, in a spatial distance of 3.8-4.3Å and in a sequence distance >4 residues. We speculate that the scale free organization of the amino acid pair interactions in the 8D protein structure combined with the clear dominance of pairs of Ala, Ile, Leu and Val is important for understanding the very nature of the protein structure formation. Our observations suggest that protein structures should be considered as having a higher dimensional organization.
format	article
author	Steffen B Petersen Maria Teresa Neves-Petersen Svend B Henriksen Rasmus J Mortensen Henrik M Geertz-Hansen
author_facet	Steffen B Petersen Maria Teresa Neves-Petersen Svend B Henriksen Rasmus J Mortensen Henrik M Geertz-Hansen
author_sort	Steffen B Petersen
title	Scale-free behaviour of amino acid pair interactions in folded proteins.
title_short	Scale-free behaviour of amino acid pair interactions in folded proteins.
title_full	Scale-free behaviour of amino acid pair interactions in folded proteins.
title_fullStr	Scale-free behaviour of amino acid pair interactions in folded proteins.
title_full_unstemmed	Scale-free behaviour of amino acid pair interactions in folded proteins.
title_sort	scale-free behaviour of amino acid pair interactions in folded proteins.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/d90041243276450b918b37a70ac23c89
work_keys_str_mv	AT steffenbpetersen scalefreebehaviourofaminoacidpairinteractionsinfoldedproteins AT mariateresanevespetersen scalefreebehaviourofaminoacidpairinteractionsinfoldedproteins AT svendbhenriksen scalefreebehaviourofaminoacidpairinteractionsinfoldedproteins AT rasmusjmortensen scalefreebehaviourofaminoacidpairinteractionsinfoldedproteins AT henrikmgeertzhansen scalefreebehaviourofaminoacidpairinteractionsinfoldedproteins
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Scale-free behaviour of amino acid pair interactions in folded proteins.

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