scale-free behaviour of amino acid pair interactions in folded proteins无标度行为折叠蛋白质的氨基酸对交互.pdfVIP

Scale-Free Behaviour of Amino Acid Pair Interactions in Folded Proteins Steffen B. Petersen1,2,3*, Maria Teresa Neves-Petersen1,4*, Svend B. Henriksen5., Rasmus J. Mortensen5,6., Henrik M. Geertz-Hansen7. 1 Int Iberian Nanotechnol Laboratory INL, Braga, Portugal, 2 Department of Health Science and Technology, Aalborg University, Aalborg, Denmark, 3 The Institute for Lasers, University at Buffalo, The State University of New York at Buffalo, Photonics and Biophotonics, Buffalo, New York, United States of America, 4 Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University, Aalborg, Denmark, 5 Department of Physics and Nanotechnology, Aalborg University, Aalborg, Denmark, 6 Department of Infectious Disease Immunology, Statens Serum Institute, Copenhagen, Denmark, 7 Technical University of Denmark, Novo Nordisk Foundation Center for Biosustainability Fremtidsvej, Hørsholm, Copenhagen, Denmark Abstract 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 i