title: A content and structural assessment of oxidative motifs across a diverse set of life forms.
abstract: Exposure to weightlessness (microgravity) or other protein stresses are detrimental to animal and human protein tissue health. Protein damage has been associated with stress and is linked to aging and the onset of diseases such as Alzheimer׳s, Parkinson׳s, sepsis, and others. Protein stresses may cause alterations to physical protein structure, altering its functional identity. Alterations from stresses such as microgravity may be responsible for forms of muscle atrophy (as noted in returning astronauts), however, protein stresses come from other sources as well. Oxidative carbonylation is a protein stress which is a driving force behind protein decay and is attracted to protein segments enriched in R, K, P, T, E and S residues. Since mitochondria apply oxidative processes to produce ATP, their proteins may be placed in the same danger as those that are exposed to stresses. However, they do not appear to be impacted in the same way. Across 14 diverse organisms, we evaluate the coverage of motifs which are high in the amino acids thought to be affected by protein stresses such as oxidation. For this study, we study RKPT and PEST motifs which are both responsible for attracting forms of oxidation across mitochondrial and non-mitochondrial proteins. We show that mitochondrial proteins have fewer of these oxidative sites compared to non-mitochondrial proteins. Additionally, we analyze the oxidative regions to determine that their motifs preferentially tend to make up the connection points between the four kinds of structures of folded proteins (helices, turns, sheets, and coils).
authors.affiliation: College of Information Science & Technology, School of Interdisciplinary Informatics, University of Nebraska, 1110 South 67 Street, Omaha, NE 68182, USA. Electronic address: obonhamcarter@unomaha.edu.
authors.forename: Oliver
authors.initials: O
authors.lastname: Bonham-Carter
authors.affiliation: College of Information Science & Technology, School of Interdisciplinary Informatics, University of Nebraska, 1110 South 67 Street, Omaha, NE 68182, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Pedersen
authors.affiliation: College of Information Science & Technology, School of Interdisciplinary Informatics, University of Nebraska, 1110 South 67 Street, Omaha, NE 68182, USA.
authors.forename: Dhundy
authors.initials: D
authors.lastname: Bastola
mesh_terms: D020816:Amino Acid Motifs / Q000502:physiology*; D000818:Animals; D016000:Cluster Analysis; D015233:Models, Statistical; D010084:Oxidation-Reduction; D010944:Plants; D050050:Protein Carbonylation / Q000502:physiology*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D011506:Proteins
keywords: Carbonylation; Composition; Mitochondrial protein; Oxidative damage; Sequence comparison