Abnormal Proteins and Protein Aggregation BMS 532 Lecture Notes PDF

Abnormal Proteins and Protein Aggregation BMS 532 BLOCK 4 LECTURE 3 Objectives 1. Define: molecular chaperone, protein aggregation, prion, and post-translational modification 2. Summarize the types of post-translational modification and assess the consequences for changes in post-translati...

Abnormal Proteins and Protein Aggregation BMS 532 BLOCK 4 LECTURE 3 Objectives 1. Define: molecular chaperone, protein aggregation, prion, and post-translational modification 2. Summarize the types of post-translational modification and assess the consequences for changes in post-translational modifications (Link amino acid to specific changes and correlated consequences) 3. Summarize the components of protein folding and the features required for proper folding 4. Summarize the steps of protein folding via molecular chaperones and the process of protein aggregation 5. Explain the consequence of protein aggregation in terms of cell function and human disease 6. Explain the role of post-translational modification in regulation of cellular processes LO1, LO2 Post-translational Modifications Any change or addition to a protein made after translation can technically be classified as a post- translational modification The most common form of post-translational modifications involves the addition of key functional groups necessary to regulate or alter protein function Proteins that exhibit altered folding or structure frequently lose the expected pattern or capability in modifications ◦ Example: loss of key amino acids needed for phosphorylation events or trapping those sites in inaccessible areas of the misfolded protein These processes are CRITICAL to signaling and regulation of cellular division LO1, LO2 Post Translational Modifications Phosphorylation ◦ Balance between kinase activity and phosphatase activity ◦ Can turn the protein activity ON or shut it OFF ◦ Types of Kinases: Serine/Threonine kinases, Tyrosine kinases, and dual specificity kinases ATP ADP KINASE P P OFF ON P P PHOSPHOTASE ON OFF P 4 LO1, LO2 Post Translational Modifications Hydroxylation ◦ Addition of hydroxyl groups via Hydroxylase Sulfation ◦ Addition of sulfur groups via enzymatic activity such as sulfotransferases Disulfide Bonds ◦ Can play an important role in protein folding S S S S S S S S 5 LO1, LO2 Post Translational Modifications The Addition of Hydrophobic molecules ◦ Prenylation (addition of isoprenoid lipids) ◦ Acyl Lipidation Acetylation ◦ The addition of acetyl groups via acetyl transferases 6 LO1, LO2 Post Translational Modifications Methylation ◦ The addition of methyl groups via methyl transferases Glycosylation ◦ Addition of sugar moieties Ubiquitylation ◦ Addition of ubiqutin Proteolysis ◦ Partial or complete degradation of protein/protein structures 7 LO3 Protein Structure and Folding Review Proteins must follow a careful balance of synthesis, folding, transport and degradation in order to maintain homeostasis Tertiary structure = protein folding Confers or enables critical function for the protein Availability of domains and binding elements are part of the tertiary structure and are essential to quaternary structure and molecular function Involves non-covalent interactions of both the polypeptide backbone and amino acid side chains ◦ Hydrophobic effects play a key role in driving this process Simulations of the molecular dynamics of protein folding have demonstrated that protein folding is frequently spontaneous and relatively consistent ◦ Protein folding was found to follow a single dominant route lending the final functional product its critical shapes or domains Lindorff-Larsen et al 2011 LO3, LO4 Molecular Chaperones Complex or large proteins often have intermediates in the folding process These intermediates form as a result of kinetic barriers in the process ◦ Intermediates have the potential to form aberrant, non-native interactions Such proteins require the use of assistance to achieve native folds = molecular chaperones Chaperones can be ATP-independent or require energy to complete their function Disfunction in chaperones is correlated with protein misfolding and disease (i.e. ALS) LO4, LO5 Misfolding and Protein Aggregation Protein intermediates that fail to achieve native confirmations or mutated genes that encode for products that can never achieve native conformations are typically referred to as misfolded Misfolded proteins have the potential to gather together = protein aggregation Protein aggregate accumulation correlates with aging and pathological consequences in many eukaryotes ◦ In prokaryotes, protein aggregation is associated with altered growth rates, stress resistance, and virulence ◦ Understanding of the role of protein aggregation in fitness remains of clinical import ◦ Neurodegenerative diseases Schramm et al 2020 LO4, LO5 Aggregation Summary in Bacteria Schramm et al 2020 LO1, LO5 Unique Class of Misfolded Proteins: Prions and Disease Prions = small infectious protein particles resistant to modification and degradation ◦ Transmissible Spongiform Encephalopathies Although prions are their own class of misfolded proteins, some misfolded proteins do take on prion-like behavior with infectious properties and aggregation that causes significant disease ◦ ALS has been shown to contain proteins with prion-like behavior for superoxide dismutase ◦ Amyloid plaques in Alzheimer's have been shown to have prion-like infectivity Hara and Sakaguchi 2021 LO5 Prion Disease: Spongiform encephalopathy Disease forms can be: ◦ sporadic (80-95% of cases; mean survival of 6 months), ◦ Genetic (10-15%) (often familial), or ◦ Acquired (~1%) ~1.2 cases per million people each year Prion protein (PRPN) gene mutations LO2, LO6 Combinations of Modifications and Shape = DIVERSITY Prenylation + Proteolysis + Methylation = active molecule 14 LO2, LO6 Combinations of the Modifications = Linking Modifications to Activities 15 Question Time… A protein that does not spontaneously fold and is no longer capable of interacting with folding machinery would not be capable of what level(s) of protein structure? (LO1 and LO3) A structurally abnormal protein that is capable of inducing altered structure of normal protein variants would be classified as what and would most likely cause what? (LO1, LO4, and LO5) The genetic sequence of a protein whose active site is made available via conformational changes induced via phosphorylation is altered turning all serine sites to threonine. What is the potential consequence of this change? (LO6)