Protein Structure & Function 2022-2023 PDF

Protein Structure & Function Foundation - I Module Johar Iqbal Faculty of Medicine 2022-2023  Objectives Levels of protein structure: Primary, secondary, tertiary and quater...

Protein Structure & Function Foundation - I Module Johar Iqbal Faculty of Medicine 2022-2023  Objectives Levels of protein structure: Primary, secondary, tertiary and quaternary Various types of bonds and forces that stabilizes these structures Protein denaturation Prion and Prion related diseases Conjugated proteins Globular and fibrous proteins Functions of proteins  Levels of Protein Structure Types of bonds in protein structure Covalent bonds Non-covalent bond (Interactions) Peptide Hydrophobic Interactions Disulphide Ionic Interactions Hydrogen bonds All bonds shown together  Primary structure of proteins Primary Structure: What are the amino acids that make up the protein and how are they arranged in the chain? (The amino acid sequence) ala arg asn asp cys gln glu gly his ile leu lys met phe pro ser thr trp tyr val  Peptide Bond In a protein, Amino Acids are joined covalently by peptide bonds Characteristics of peptide bond – It is a partial double-bond. – It is shorter than a single bond – Rigid & planar, no rotation – Trans in configurations – Uncharged but polar  Physiologically important peptides Glutathione 3 Angiotensin II 8 Enkephalin 5 Oxytocin 9 GnRH 10 Vasopressin 9 Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly Oxytocin Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly Vasopressin  Glutathione Tripeptide Pseudopeptide Function of Glutathione (GSH) Detoxification Antioxidant Glucose-6-phosphate dehydrogenase deficiency  Secondary Structure of Proteins α-Helix – Most common β-sheets β-Bends & Loops  Secondary structure: the a helix It is the most common conformation. It is a spiral structure. Tightly packed coiled polypeptide backbone, with extending side chains. The formation of the α-helix is spontaneous. It is stabilized by H-bonding e.g. – Keratin - entirely α-helical – Myoglobin - 80% helical. *Proline and glycine break helices  An amino acid that disrupts an α helix - – Glycine and proline, – bulky amino acids (tryptophan, valine), – charged amino acids (glutamate, histidine) The disruption of the helix is important as it introduces additional folding of the polypeptide backbone to allow the formation of globular proteins.  Secondary structure: the b sheets β-sheets are either parallel or antiparallel. Makes up the core of many proteins – Parallel chain: two peptide strands running in the same direction held together by hydrogen bonds – Anti-parallel chain: two peptide strands running in opposite directions held together by hydrogen bonds  β-Sheets β-sheets is stabilized by Hydrogen-bonding. Unlike the compact backbone of the α helix, the peptide backbone of the β sheet is highly extended.  β-Bends & Loops Roughly half of the residues in a “typical” globular protein reside in α helices and β sheets while the rest in loops, turns, bends, and other extended conformational features. β-Bends are generally composed of four amino acids, one of which may be proline. Glycine, the smallest amino acid is also frequently found in β-bends. β-Bends are stabilized by the formation of hydrogen and ionic bonds.  Components of Tertiary Structure Fold – used differently in different contexts – most broadly a reproducible and recognizable 3-dimensional arrangement Domain – a compact and self folding component of the protein that usually represents a discreet structural and functional unit Motif (super-secondary structure) a recognizable subcomponent of the fold – several motifs usually comprise a domain  Tertiary Structure of Globular proteins Tertiary structure refers to the complete three-dimensional structure of the polypeptide units of a given protein. It is stabilized by following interactions – Hydrogen bonds – Disulfide bonds – Hydrophobic interaction – Ionic interactions  Protein Folding Protein folding takes place in Endoplasmic Reticulum Some proteins fold spontaneously Some proteins require help to fold correctly – Molecular chaperones Proteins that interact with partially folded or improperly folded proteins and provide a microenvironment in which folding can occur Details of the mechanism of action remain unknown  Chaperones Two classes of molecular chaperones – Chaperonins – Heat shock proteins (example: Hsp70) Heat shock proteins are expressed in large quantities after cells experience high temperatures Recognize denatured proteins by binding to hydrophobic patches  Protein Denaturation The normal three-dimensional conformation (i.e., normally folded) of proteins which is primarily maintained due to intracellular physiological conditions can be disturbed when exposed to extreme conditions not typically found inside a cell, e.g., heat, pH or organic solvents, etc., which may result into partial or complete loss of tertiary structure is called denaturation. Factors causing denaturation – Temperature – Organic solvents e.g., Urea – pH – Shear force  Prion Prions are misfolded proteins. Prions cause diseases, but they aren't viruses or bacteria or fungi or parasites. They are proteins. When they encounter normally folded proteins of our body, they can change their conformation and make them misfolded (abnormal).  Prion related diseases Bovine spongiform encephalopathy (BSE or mad cow disease) is seen in cattle and livestock and Creutzfeldt-Jakob disease (CJD) is seen in humans. ‘Mad cow’ epidemic that hit England in 1986 Scrapie in sheep and goats has the same basis. Kuru, a transmissible spongiform encephalopathy, is found in the people of a tribe in New Guinea due to their practice of cannibalism.  Quaternary structure Quaternary structure only exist in proteins containing two or more than two polypeptide. e.g., Myoglobin – One Polypeptide – No Quaternary Structure, whereas hemoglobin carrying four polypeptides and does have the quaternary structure. It is stabilized by hydrogen, ionic bonds and hydrophobic interactions. o Hemoglobin – Four Polypeptide o Lactate Dehydrogenase – Four Polypeptide o Creatine Kinase – Two Polypeptide Hemoglobin and Myoglobin structure MYOGLOBIN  Protein Classification Monomeric proteins - One polypeptide chain Multimeric proteins - More than one polypeptide chains – Homomultimer – all one kind of chain e.g., Lactate Dehydrogenase (H4) – Heteromultimer - two or more different chains For example, hemoglobin is made up of 2𝛼 and 2𝛽 chains, therefore, it is a heterotetramer.  Protein Classification Fibrous Protein – – Polypeptides arranged in long strands or sheets – Water insoluble – made up of lots of hydrophobic amino acids – Strong but flexible – They perform mainly Structural functions e.g., keratin, collagen Globular Protein (Soluble Protein)– – Polypeptide chains folded into a spherical or globular form – Water soluble – Contain several types of secondary structure – They perform a variety of functions inside a cell e.g., enzymes, immunoglobulins, regulatory proteins, etc.  Conjugated PROTEIN Simple – composed only of amino acid residues Conjugated – contain prosthetic groups (metal ions, co-factors, lipids, carbohydrates) Example: Hemoglobin – Heme Phosphoprotein Nucleoprotein Glycoprotein Lipoprotein e.g. Mucin Casein (Milk Protein) LDL Telomerase  Protein Function – Enzymes (Amylase, Hexokinase, Urokinase) – Structural (Collagen, Laminin) – Transport (Albumin) – Motor (Actin) – Storage (Ferritin) – Signaling (Integrins and Cadherin) – Receptors (GPCRs - G-protein coupled receptors) – Gene regulation (transcription factors e.g., HIF-1) Q1-Which of the following bonds stabilizes the secondary structures of proteins? A. Ionic interactions B. Hydrophobic interactions C. Disulfide linkage D. Peptide bonds Q2-Which of the following proteins is more likely to have a quaternary structure? A. Lactate dehydrogenase B. Oxytocin C. Glucagon D. Vasopressin  Q3-Which of the following diseases is caused by prion proteins? A. Scrub typhus B. Scabies C. Scrapie D. Scleroderma  Q4-Ferritin is an example of which of the following categories of proteins? A. Structural B. Transport C. Storage D. Signaling  Thank you Faculty of Medicine 2022-2023