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

Publication: Research - peer-reviewJournal article – Annual report year: 2012

Standard

Scale-free behaviour of amino acid pair interactions in folded proteins. / Petersen, Steffen B. ; Neves-Petersen, Maria Teresa; Mortensen, Rasmus J. ; Henriksen, Svend B. ; Geertz-Hansen, Henrik Marcus.

In: P L o S One, Vol. 7, No. 7, 2012, p. e41322-e41322.

Publication: Research - peer-reviewJournal article – Annual report year: 2012

Harvard

Petersen, SB, Neves-Petersen, MT, Mortensen, RJ, Henriksen, SB & Geertz-Hansen, HM 2012, 'Scale-free behaviour of amino acid pair interactions in folded proteins' P L o S One, vol 7, no. 7, pp. e41322-e41322.

APA

Petersen, S. B., Neves-Petersen, M. T., Mortensen, R. J., Henriksen, S. B., & Geertz-Hansen, H. M. (2012). Scale-free behaviour of amino acid pair interactions in folded proteins. P L o S One, 7(7), e41322-e41322.

CBE

Petersen SB, Neves-Petersen MT, Mortensen RJ, Henriksen SB, Geertz-Hansen HM. 2012. Scale-free behaviour of amino acid pair interactions in folded proteins. P L o S One. 7(7):e41322-e41322.

MLA

Petersen, Steffen B. et al."Scale-free behaviour of amino acid pair interactions in folded proteins". P L o S One. 2012, 7(7). e41322-e41322.

Vancouver

Petersen SB, Neves-Petersen MT, Mortensen RJ, Henriksen SB, Geertz-Hansen HM. Scale-free behaviour of amino acid pair interactions in folded proteins. P L o S One. 2012;7(7):e41322-e41322.

Author

Petersen, Steffen B. ; Neves-Petersen, Maria Teresa; Mortensen, Rasmus J. ; Henriksen, Svend B. ; Geertz-Hansen, Henrik Marcus / Scale-free behaviour of amino acid pair interactions in folded proteins.

In: P L o S One, Vol. 7, No. 7, 2012, p. e41322-e41322.

Publication: Research - peer-reviewJournal article – Annual report year: 2012

Bibtex

@article{9017e987b343492a8b2336bded6ded45,
title = "Scale-free behaviour of amino acid pair interactions in folded proteins",
publisher = "Public Library of Science",
author = "Petersen, {Steffen B.} and Neves-Petersen, {Maria Teresa} and Mortensen, {Rasmus J.} and Henriksen, {Svend B.} and Geertz-Hansen, {Henrik Marcus}",
year = "2012",
volume = "7",
number = "7",
pages = "e41322--e41322",
journal = "P L o S One",
issn = "1932-6203",

}

RIS

TY - JOUR

T1 - Scale-free behaviour of amino acid pair interactions in folded proteins

A1 - Petersen,Steffen B.

A1 - Neves-Petersen,Maria Teresa

A1 - Mortensen,Rasmus J.

A1 - Henriksen,Svend B.

A1 - Geertz-Hansen,Henrik Marcus

AU - Petersen,Steffen B.

AU - Neves-Petersen,Maria Teresa

AU - Mortensen,Rasmus J.

AU - Henriksen,Svend B.

AU - Geertz-Hansen,Henrik Marcus

PB - Public Library of Science

PY - 2012

Y1 - 2012

N2 - 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<br/>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 a-helices or b-strands, in a<br/>spatial distance of 3.8–4.3A° 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.

AB - 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<br/>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 a-helices or b-strands, in a<br/>spatial distance of 3.8–4.3A° 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.

JO - P L o S One

JF - P L o S One

SN - 1932-6203

IS - 7

VL - 7

SP - e41322-e41322

ER -