Protein Dynamics- Protein Regulation and Post-Translational Modification PDF

Protein Dynamics- Protein Regulation and Post-Translational Modification by Matthew K. Pelletier, PhD Professor of Human Genetics Director of Assessment and Outcomes Reading Resource Please note that while my source material comes from this text, you sho...

Protein Dynamics- Protein Regulation and Post-Translational Modification by Matthew K. Pelletier, PhD Professor of Human Genetics Director of Assessment and Outcomes Reading Resource Please note that while my source material comes from this text, you should be able to learn and apply the level of detail needed from my PowerPoint slides for this topic. If you want to learn more details because you are curious or you want to look something up in the book to supplement your understanding, then I recommend focusing on the following sections of this textbook (there are a few physical copies at the LUCOM library): Section 3.2 Protein Folding Section 3.4 Regulating Protein Function Figures 14.1 and 14.2 Section 14.5 Receptor-Mediated Endocytosis Section 14.6 Directing Membrane Proteins and Cytosolic Materials to the Lysosomes for Degradation Lecture Overview Post- Receptor- Factors Translatio Protein Protein Mediated Affecting nal Protein Folding Degradati Endocytos Protein Modificati Targeting Overview on is and Activity on of Disease Proteins  Learning Objectives Explain how proteins fold into a native state and give examples of how misfolding can lead to disease. Outline the factors that determine the activity level for a particular protein in a cell at any given time. Outline the processes that regulate protein degradation.  Learning Objectives Compare the secretory pathway to the pathways targeting proteins to mitochondria, nuclei, and peroxisomes. Outline the purpose and process of receptor-mediated endocytosis and give examples of how of how defects in this process can lead to disease. Outline the functions and mechanisms involved in the post-translational modification of proteins. Predict how a mutation that impacts the amino acid sequence of a protein might impact the phosphorylation or glycosylation of that protein.  How do proteins reach their native conformation? Primary AA Sequences Non-Covalent Forces Clustering of Hydrophobic AA LO: Explain how proteins fold into a native state and give examples of how misfolding can lead to disease.  A Silly yet Informative Animation on Protein Folding LO: Outline the factors that determine the activity level for a particular protein in a cell at any given time.  Proteins help proteins fold! AB40 Misfolding and Disease APP AB42 (forms Alzheimer’s Disease plaques) APP processing is complex Prions cause Creutzfeldt-Jakob Disease Infectious proteins LO: Outline the factors that determine the activity level for a particular protein in a cell at any given time.  What Number of Copies and determines Functional Activity per the activity Copy level of a Copies Activity given protein function in a cell? Synthesis Post- translational Modifications Degradation Interactions LO: Outline the factors that determine the activity level for a particular protein in a cell at any given time.  What Number of Copies and determines Functional Activity per the activity Copy level of a Copies Activity given protein function in a cell? Synthesis Post- translational Modifications Degradation Interactions LO: Outline the factors that determine the activity level for a particular protein in a cell at any given time. Overview of Protein Degradation Why do proteins need to be degraded? they have a temporal function. they are misfolded. our digestive system breaks them down to individual amino acids. Proteases are proteins that may function to “degrade” target proteins or they may make specific ‘cuts’ in a target protein to activate or de-activate the target Diverse (>500 genes in humans) Many are synthesized as zymogens (inactive precursors) The activity of proteases must be tightly regulated both in time and cellular location, and there are many mechanisms by which this is accomplished. LO: Outline the processes that regulate Protein Degradation and Cell Location Cytosol and Nucleus (Degradation Largely by Proteasomes) Lysosomes (pH 5-many enzymes to break down proteins and nucleic acids) Extracellular Spaces (~300 different proteases) LO: Outline the processes that regulate Degradation of Cytosolic and Nuclear Proteins  Proteasomes (large molecular machines with ~50 polypeptides)  Ubiquitin “Tags”  Ubiquitin-Activating and Conjugating Enzymes  Ubiquitin Ligase  How are target proteins recognized to be “tagged”? LO: Outline the processes that regulate Post-Translational Modifications  Simple (often reversible) vs. Complex  How is post-translational modification of proteins useful to the organism?  20 Primary Amino Acids (~100 after simple chemical modification)  Alter Structure  Activity  Cellular Location  Interactions LO: Outline the functions and mechanisms involved in the post-translational modification of proteins.  Cell Res. 2014 Feb; Overview of Post-Translational Modifications 24(2): 143–160. Figure 1 Target proteins to proteasome Commonly on O-linked (on serine lysine and or threonine) or N- arginine. linked (on asparagine) Irreversible Serine, Can activate or Threonine, or deactivate a target Tyrosine protein Often a Molecular LO: Outline the functions and mechanisms involved in the post-translational Switch modification of proteins.  Protein Dynamics- Protein Targeting and Receptor-Mediated Endocytosis by Matthew K. Pelletier, Ph.D Professor of Human Genetics Director of Assessment and Outcomes  Since you will not be treating any plants, you can ignore the chloroplast part.  Translation Begins in Cytoplasm Non-Secretory Targeting Pathway Protein May Remain in Protein released from Cytoplasm ribosome in cytoplasm and then is “targeted” “Secretory” to nucleus, Pathway mitochondria, or Ribosome peroxisomes. “docks” at ER and protein is Lysosom “targeted” to ER es membrane or lumen ER Golgi Plasma Membran e The Secretory Pathway Integral Membrane Proteins LO: Compare the secretory pathway to the pathways targeting proteins to mitochondria, nuclei, and peroxisomes.  The Secretory Pathway Targeting Signals Signal Peptide How do proteins get from ER to the golgi, lysosomes, or the cell surface? various types of vesicles ‘pinch off’ a donor membrane and then “walk” along microtubule tracks to fuse with a target membrane. Chemical/Structural modifications occur in various compartments of the secretory pathway. From Trans-Golgi, proteins may move to lysosomes or to the plasma membrane. LO: Compare the secretory pathway to the pathways targeting proteins to mitochondria, nuclei, and peroxisomes. Protein Targeting for Non-Secretory Proteins Post-Translational Bidirectional for Nucleus Targeting Signals Glycosylation LO: Compare the secretory pathway to the pathways targeting proteins to Top Hat x mitochondria, nuclei, and peroxisomes. 3 Receptor-Mediated Endocytosis Purpose Receptors and Clathrin-Coated Pits General Process LO: Outline the purpose and process of receptor-mediated endocytosis and give examples of how of how defects in this  Receptor-Mediated Endocytosis of LDL LO: LO#1Outline the purpose and process of receptor-mediated endocytosis and give examples 0 of how of how defects in this process can lead to disease. Familial Hypercholesterolemia  Familial hypercholesterolemia High Serum LDL 170-200mg/dL in children 220mg/dL in adults Many Mutations LO#1 LO: Outline the purpose and process of receptor-mediated endocytosis and give examples of how of how 0 defects in this process can lead to disease. Lecture Summary Proteins inside of cells fold quite quickly into their unique three- dimensional shapes, largely dictated by the primary amino acid sequence, and with the aid of chaperone proteins. The activity level of a given protein within a cell is dictated by both the number of copies of that protein, along with the activity level of each copy. Protein degradation is a crucial and highly regulated process that ensures damaged or superfluous proteins are degraded and plays a role in regulating the activity of many proteins. Post-translational modification of proteins is very common in human cells, and is often crucial for the proper structure/function of the protein.  Lecture Summary (continued) All proteins that function in places other than the cytoplasm are actively targeted to the appropriate cellular locations. The secretory pathway includes both soluble and membrane-bound proteins destined for the rough ER, Golgi apparatus, lysosomes, the plasma membrane, or secretion from the cell. Many different types of post-translational modifications occur as proteins move through the secretory pathway. Proteins targeted to the nucleus, mitochondria, and peroxisomes have different targeting mechanisms as compared to the secretory pathway. Receptor-mediated endocytosis provides a mechanism for cells to take in important nutrients that may not be soluble in the blood stream, and genetic defects in these processes may lead to diseases such as familial hypercholesterolemia.