Modeling the Effects of Microgravity On Oxidation in Results - PowerPoint PPT Presentation

Abstract Introduction Methods Modeling the Effects of Microgravity On Oxidation in Results Mitochondria: A Protein Damage Assessment Across a Conclusions Diverse Set of Life Forms References Thanks To Oliver Bonham-Carter, Jay Pedersen, Lotfollah Najjar, Dhundy Bastola College of Information Science & Technology, University of Nebraska 1110 South 67 Street, Omaha, NE 68182 USA Email: { obonhamcarter, jaypedersen, lnajjar, dkbastola } @unomaha.edu December 2013 1 / 23

Overview Abstract Motivation: Introduction Methods Protein degradation (leading to muscular atrophy, for Results example) appears to be exacerbated by exposure to Conclusions microgravity. References Thanks To Study Objective: To determine some of the general trends of motifs which attract oxidative carbonylation across a wide set of organismal protein sequence data. Conclusions: We show that there are less motifs attracting carbonylation in mitochondrial protein than in non-mitochondrial sequence data. 1 / 23

Houston, We have a Problem! Abstract Rats in Space: Major Findings (corroborated by the literature) Introduction Oxidative High degrees of oxidative protein stresses Damage Methods Evidence of damage: cell & mitochondrial (Mt) proteins Results Rats acquired degraded and irregular-shaped Mt Conclusions Muscle protein: Reduced Mt function References Generalized myofibrillar edema (tissue swelling ) Thanks To Onset of muscular atrophy Cell death and on-set of heart failures 2 / 23

This is Houston: We Also Have the Same Problem!! Abstract Introduction Approximately 10% of the proteome is more prone to Oxidative Damage carbonylation during ageing, starvation or disease. Methods Results Ageing causes oxidative stress to protein on Earth. Conclusions References Accumulation of oxygen radicals causes irreversible protein Thanks To damage. 3 / 23

Damage By Carbonylation Abstract Introduction Oxidative Damage Methods Carbonylation refers to the oxidation of protein side chains. Results Conclusions References Oxidative Stress Condition: Irreversible, non-enzymatic Thanks To protein modification Oxidative damage may lead to loss of protein function. Considered a widespread indicator of severe oxidative damage 4 / 23

Carbonylation: Some Causes Abstract Protein Carbonyl Groups Introduction Protein degradation may come from free radicals generated Oxidative Damage in making energy. Methods Reactive Oxygen Species (ROS) Results ROS: peptide bond cleavage Conclusions Proteins are major targets for ROS and secondary References by-products of oxidative stress. Thanks To Direct oxidation of protein side chains: Lysine (K), Arginine (R), Proline (P), and Threonine (T) 5 / 23

Carbonylation With Microgravity Simulated Weightlessness Abstract Type of oxidative stresses could be explored and studied by Introduction Oxidative simulation: Damage Methods Prescribed immobility - Coma and bed rest patients Results Suspension - Unused muscle tissue Conclusions Common ailments: References Muscular atrophy; negative impact on heart function Thanks To Insulin resistance Inhibited function of brain tissues 6 / 23

Damage to Mitochondrial Function In both Gravity and Microgravity Environments Abstract The build-up of mutations and deletions in mtDNA may Introduction Oxidative impair respiratory chain function (energy production). Damage Methods Mt function impairment and cell death Results Conclusions May impact other Mt functions References Ageing: Protein degradation Thanks To Links to diseases: Parkinson’s, Alzheimer’s and Huntington’s 7 / 23

Recovery After Exposure to Carbonylation Source Abstract Introduction Healthy protein regrowth is not always certain Oxidative Damage Methods Possible healing may be possible after a short-term Results exposure to microgravity Conclusions References Therapy is often necessary Thanks To 8 / 23

Research Question Abstract Is it likely that Mt have fewer oxidative accidents due to Introduction protein composition? Oxidative Damage Methods Since Mt perform oxidative processes to produce energy, Results does it appear that Mt protein has evolved some form of Conclusions protection from the side effects of oxidation? References Does is appear that non-Mt protein also have this Thanks To protection? 9 / 23

Avoidance of Dangerous Words In Sequence Data Abstract ISBRA 2012 – Dallas, TX Introduction Methods Motifs Data Results Conclusions References Thanks To There are dangerous words in biological sequence data. These words may be found in low abundance: Below expected rates. Words may be influenced evolutionary pressures. 10 / 23

Words Susceptible To Oxidative Damage Abstract Introduction Methods Literature: Motifs (words) that may attract oxidation: Motifs Data RKPT : Contains a combination of Proline (P), Arginine Results (R), Lysine (K), Threonine (T) Conclusions RKPT-enriched motifs were often found at carbonylation References sites in protein samples. Thanks To Mass spectrometry: Carbonylation sites may contain RKPT motifs (Maisonneuve et al. ). PEST : A combination of Proline (P), Glutamic Acid (E), Serine (S) and Threonine (T) Involved in proteolytic signaling for rapid protein degradation by cellular regulation Dealing with stress: the up-regulation of genes for stress responses in plants 11 / 23

Motif Set Populations in Protein Sequence Data Compositions Abstract Introduction Methods Motifs Motifs: RKPT and PEST sets Data Results Protein Sequences: Conclusions References One long sequence: All proteins from an organism are placed end to end with delimiters. Thanks To Obtained from Uniprot Protein Knowledgebase Documented Protein Sequence Data: Mitochondrial and non-Mitochondrial Enzymatic and non-Enzymatic Diverse organisms 12 / 23

Diverse Organismal Data Abstract Introduction Common Name Scientific Name Methods 1 Xenopus laevis African Clawed Frog Motifs Data 2 Amoeba Acanthamoeba castellanii Results 3 Arabidopsis thaliana Mustard Plant Conclusions 4 Aspergillus fumigata Aspergillus References 5 Saccharomyces cerevisiae Bakers Yeast Thanks To 6 Canis familiaris Domestic Dog 7 Fruit Fly Sophophora melanogaster 8 House Mouse Mus musculus 9 Human Homo sapiens 10 Maize Zea mays 11 Norway rat Rattus norvegicus 12 European Rabbit Oryctolagus cuniculus 13 Nematode Worm Caenorhabditis elegans 14 Zebrafish Danio rerio 13 / 23

Number of Studied Proteins By Organism Abstract Introduction Organism Mt Non-Mt Methods 1 African Clawed Frog 169 3202 Motifs Data 2 Amoeba 32 17 Results 3 Mustard Plant 707 11517 Conclusions 4 Aspergillus fumigata 87 794 References 5 Bakers Yeast 1056 6744 Thanks To 6 Dog 60 743 7 Fruit Fly 204 2994 8 House Mouse 973 15652 9 Human 1027 19240 10 Maize 38 680 11 Norway Rat 571 7287 12 European Rabbit 46 843 13 Nematode Worm 199 3232 14 Zebrafish 202 2696 14 / 23

Proportions Find the Coverage of Each Motif in Each Protein Sequence Abstract Introduction Methods Motifs Data Results Conclusions References Thanks To 15 / 23

Generaly Less Oxidation-Attracting Motif Content in Mt Protein Abstract Introduction Methods Results Conclusions References Thanks To 16 / 23

Motifs Coverage in Protein Sequences Typical Examples of motif coverage Abstract The absence of motif content in the large blank spaces in Mt proteins Introduction Fruit Fly mitochondrial Proteins Methods Results Conclusions References Thanks To Human mitochondrial Proteins Yellow = Mt,Enzyme; Red = MT,nonEnzyme; Purple = nonMt, Enzyme; Green = nonMt, nonEnzyme 17 / 23

Conclusions Mitochondrial Protein Data is Has Fewer Oxidation Motifs Abstract Introduction Methods Results Conclusions References Thanks To The average amount of RKPT and PEST motif content was least in mitochondrial proteins. 18 / 23

Average Proportions of RKPT and PEST across organismal proteins Abstract Introduction Methods Results Conclusions References Thanks To The average amount of RKPT and PEST motif content was least in mitochondrial proteins. ME = Mt, Enzymatic, MN = Mt, Non-Enzymatic, NE = Non-Mt, Enzymatic, NN = Non-Mt, Non-Enzymatic 19 / 23

Average Proportions of RKPT and PEST Abstract Introduction Methods Results Conclusions References Thanks To Rankings of R , K , T , P , E and S residues across the protein classes of all organisms. Note how the enzymatic protein content had closer groupings of individual amino acid residues. 20 / 23

Future Works Abstract If there are motifs in Mt which attract oxidation: Introduction Methods How are these motifs distributed? Results Conclusions Do these motifs help form the same kinds of protein secondary structures (e.g., coils, sheets, helices?) References Thanks To Do structures appear to be necessary (e.g., exist in small amounts to add some structure)? 21 / 23