title: The conservation profile of a protein bears the imprint of the molecule that is evolutionarily coupled to the protein.
abstract: The conservation profile of a protein is a curve of the conservation levels of amino acids along the sequence. Biologists are usually more interested in individual points on the curve (namely, the conserved amino acids) than the overall shape of the curve. Here, we show that the conservation curves of proteins bear the imprints of molecules that are evolutionarily coupled to the proteins. Our method is based on recent studies that a sequence conservation profile is quantitatively linked to its structural packing profile. We find that the conservation profiles of nucleic acid (NA) binding proteins are better correlated with the packing profiles of the protein-NA complexes than those of the proteins alone. This indicates that a nucleic acid binding protein evolves to accommodate the nucleic acid in such a way that the residues involved in binding have their conservation levels closely coupled with the specific nucleotides.
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, 30050, Taiwan, Republic of China.
authors.forename: Yu-Wen
authors.initials: YW
authors.lastname: Huang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, 30050, Taiwan, Republic of China.
authors.forename: Chih-Min
authors.initials: CM
authors.lastname: Chang
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, 30050, Taiwan, Republic of China.
authors.forename: Chi-Wen
authors.initials: CW
authors.lastname: Lee
authors.affiliation: Institute of Bioinformatics and Systems Biology, National Chiao Tung University, HsinChu, 30050, Taiwan, Republic of China.|Department of Bioinformatics and Medical Engineering, Asia University, Taichung City, 41354, Taiwan, Republic of China.
authors.forename: Jenn-Kang
authors.initials: JK
authors.lastname: Hwang
mesh_terms: D000595:Amino Acid Sequence; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D030562:Databases, Protein; D019143:Evolution, Molecular; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA
keywords: nucleic acid binding protein; protein structure; sequence conservation; structural packing; weighted contact number