Protein Processing & Function

Protein Shape Determines Function Protein Structure A protein’s specific function depends • Post-translation modification on its shape and distribution of – polypeptide Æ functional protein functional groups. • Specific 3-D shape • Shape is critical to function

• Denaturation = loss of shape Ë loss of function DNA polymerase: its active site fits DNA lysozyme

Levels of Protein Structure Primary structure of protein: ÿPrimary the amino acid sequence ÿPolypeptide sequence

ÿSecondary ÿFolding coils & pleats

ÿTertiary ÿComplete 3-D shape Primary structure is due to strong ÿQuarternary covalent peptide bonds joining amino ÿCombining polypeptides acids together. lysozyme

Primary Structure & Protein Trafficking Modification of primary structure Leading sequence of amino acids in a polypeptide being synthesized determines its fate: cytosolic, membrane-bound, nuclear, or secreted.

1 Polypeptide 2 An SRP binds 3 The SRP binds to a 4 The SRP leaves, and 5 The signal- 6 The rest of synthesis begins to the signal receptor protein in the ER the polypeptide resumes cleaving the completed on a free peptide, halting membrane. This receptor growing, meanwhile enzyme polypeptide leaves ribosome in synthesis is part of a protein complex translocating across the cuts off the the ribosome and the cytosol. momentarily. (a translocation complex) membrane. (The signal signal peptide. folds into its final • Chemical alteration of amino acid side groups that has a membrane pore peptide stays attached conformation. and a signal-cleaving enzyme. to the membrane.) – Methylation; hydroxylation; etc. Ribosome – E.g.: • N-terminal methyl-methionine fi protects peptide from mRNA Signal amino-peptidases. peptide ER membrane Signal Signal- peptide • Collagen contains many hydroxy-prolines & hydroxy- recognition Protein removed particle lysines fi allows condensation with oligosaccharides (SRP) SRP receptor CYTOSOL protein

Translocation complex Figure 17.21

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Modification of primary structure Secondary structure: group of amino acids • Cleavage of polypeptide chain folded repetitively to – Zymogens: • inactive pre-enzyme minus fragment Æ active enzyme make a discrete shape. – Isolation of fragments within a protein: • Insulin polypeptide folds over to be cross-linked with itself, and is then cleaved into two polypeptides due to hydrogen – Multiple products: • Pro-opiomelanocortin (POMC) — translated bonds between polypeptide cleaved into fragments: amino acids’ 1. Endorphin (opioid) 2. Melanocyte stimulating hormone backbones. 3. Corticotropin stimulating hormone

Tertiary structure: Tertiary structure involves several kinds of bonds between side the overall 3-d groups of amino conformation of acids at various a polypeptide. (Salt bridge) locations along the polypeptide backbone. Covalent disulfide bonds between cystine lysozyme residues are the strongest and most stable.

Tertiary Structure Quaternary Structure Most proteins are hydrophilic outside, hydrophobic inside. Multiple Tertiary structure is polypeptides maintained by amino joined to make a acids interacting single protein. with other amino (May be the same acids and with or products of water. separate genes)

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Quaternary Structure Hemoglobin Genes and Gene Products 2 b-chain polypeptides

2 a-chain polypeptides collagen hemoglobin http://www.mun.ca/biology/desmid/brian/BIOL3530/DB_Ch09/fig9_24.jpg

Hemoglobin Gene Product Production Prosthetic groups Yolk sac Liver Spleen Bone marrow Non-amino acid groups added to a polypeptide. • Carbohydrate fi glycoprotein

HbF: 2α and • Lipid fi lipoprotein 2γ HbA1: 2α and 2β

HbE: 2ζ and HbA2: 2α and • Nucleic acid fi nucleoprotein 2 2ε δ • Phosphate fi phosphoprotein • “activated” protein • Metal ion fi metalloprotein • Heme (organic porphyrin ring with an iron

Mehta, A. B., and A. V. Hoffbrand. 2000. Haematology at a glance, Blackwell Science, Malden, Mass. core) fi hemoprotein

Cytochrome C Hemoglobin Molecule An electron carrier

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How Proteins Fold Protein Shape Determines Function

v A protein’s function depends on • How do proteins get its folding. folded into the required conformation?

DNA polymerase: its active site fits DNA

DNA polymerase: its active site fits DNA

HbA – ß chain HbS – ß chain glu val Hemoglobin Electrophoresis hydrophobic

Homozygous HbS Heterozygous HbS

Sickle Cell Normal Hemoglobin: adult Normal folding neonate depends on HbSC primary

structure http://themedicalbiochemistrypage.org/hemoglobin-myoglobin.html

How Proteins Fold Protein folding: Is it all downhill?

v A protein’s function depends on its folding. Ribonuclease v There may be more than 1 way can renature for a big polypeptide to fold. itself. This makes it an unusually tough protein.

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Structure of an artificial protein Designing a protein to fold predicted observed

—hydrophobic amino acid residues

Understanding protein structure is How Proteins Fold important v A protein’s function depends on Nutlin, a tumor- its folding. suppressing drug that v There may be more than 1 way mimics the for a big polypeptide to fold. shape of protein p53 v Some proteins can fold on their (transcription own, but many require help. factor). v Chaperonins are proteins that help fold other proteins.

A Chaperonin unfolded folded Unfolded or incompletely folded proteins may be destroyed.

Provides a “safe folding environment” — Probably binds to polypeptide, to induce the correct folding conformation

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Proteins v Incorrectly folded proteins don’t work, the Molecular Machines and they clump together (they become insoluble). v If not refolded or destroyed, they can accumulate and cause problems. ß Eg., excess accumulated misfolded proteins (plaques) in neural tissue Æ ßParkinson disease ßAlzheimers disease ßMad cow disease

Prion Basics

v Prions are an unusual kind of Prions misfolded protein.

infectious protein agents v Prions can cause CNS diseases like mad cow, scrapie, kuru, and Creutzfeldt-Jakob disease. v Prions can be transmitted from one individual to another.

Prion Basics Prion Basics vEverybody has prion proteins (PrP). vEverybody has prion proteins (PrP). vPrP comes in 2 forms: good and bad.

normal & prion versions of PrP Prion protein structure is conserved.

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Prion Basics vEverybody has prion proteins (PrP). vPrP comes in 2 forms: good and bad. vBad PrP catalyzes the misfolding of good PrP, changing good PrP to bad.

Prion Original prion Misfolded bad

Many prions PrP catalyzes

Normal New the misfolding protein prion of good PrP. Figure 18.13

Prion Basics Prion Disease: Open Questions vEverybody has prion proteins (PrP). vWhat does good PrP normally do? vPrP comes in 2 forms: good and bad. vHow specifically does bad PrP convert good PrP? vBad PrP catalyzes the misfolding of good PrP, changing good PrP to bad. vCan conversion be blocked? vConsuming bad PrP can turn all vWhy isn’t PrP digested/destroyed your good PrP bad (chain reaction). when eaten? • Transmitted by food, transfusions, vHow does bad PrP get to the brain? transplants, brain extracts. vHow does bad PrP cause disease?

Other Protein Folding Research Accumulations of misfolded proteins v Alzheimer’s disease is completely v Prion disease: misfolded protein different from prion diseases. catalyzes more misfolding. v However, both are caused by v Alzheimer’s: cause of misfolding accumulations of misfolded unknown, but failure of “unfolded protein response” pathway is key. proteins.

Alzheimer’s Creutzfeldt-Jakob Alzheimer’s Creutzfeldt-Jakob

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