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Information about 4D STRUCTURE OF PROTEINS

Published on February 22, 2014

Author: drmustansar



PowerPoint Presentation: Protein 3-D structure: 3 o and 4 o structure and protein folding. 3o Structure: 3 o Structure third level of protein organization folding of polypeptide chain causes 2 o structures to interact formation of motifs and domains Proteins with similar 1o structure also have similar 3o structure: Proteins with similar 1 o structure also have similar 3 o structure tuna 1 G DVA KG K K T F VQ KCAQCHTVE N GG K HKVGPNL W GLFGR KT GQAEGYSYTDANK S K G I VWN yeast 1 G SA KKG AT L FKT R C L QCHTVEKGG P HKVGPNL H G I FGR H SGQAEGYSYTDAN IK K N V W D E rice 1 G NP K A G E K I FKTKCAQCHTV D KG A G HK Q GPNL N GLFGR Q SG TTP GYSY S T ANK MAV IW E E tuna 61 E TL M EYL E NPKKYIPGTKM I F A G I KK KG ER Q DL V A YLK S ATS yeast 61 N N M S EYL T NPKKYIPGTKM A F G GLKK EK D R N DLI T YLK K A CE rice 61 NTL Y D YL L NPKKYIPGTKM V F P GLKK PQ ER A DLI S YLK E ATS PowerPoint Presentation: Common Motifs PowerPoint Presentation: Parallel twisted sheet Alpha/beta barrel Domains are independent folding units in a 3o structure of a protein Individual domains have specific function Hydrophobic interactions are the major driving force in folding domains Motifs Combine to form Domains Protein family members share common domain structures: lactate dehydrogenase malate dehydrogenase C O O - C H 2 C O C O O - C O O - C H H O C H 2 C O O - 3 C O O - C H C H H O C O O - C C H 3 O + NADH + NAD + + NADH + NAD + Protein family members share common domain structures 4o Structure: 4 o Structure Quaternary structure describes the organization of subunits in a protein with multiple subunits (oligomeric protein) Can have homo-multimers or hetero-multimers PowerPoint Presentation: a2b2 a2bg 4o Structure: 4 o Structure Determine molecular weight of native protein by gel permeation chromatography Determine molecular weight of individual subunits by SDS-PAGE Can use the information to determine subunit composition PowerPoint Presentation: If……. Native protein – 160,000 daltons and a-Subunit – 50,000 daltons b-Subunit – 30,000 daltons Then…… Protein can have a2b2 structure 4o Structure: 4 o Structure Subunits held together by non-covalent interactions Oligomeric protein is more stable than disassociated subunits Active site often made up of AA residues from different subunits 4 o and 3 o structure is often affected by ligand (substrate or inhibitor) binding. Important in enzyme regulation Protein denaturation: Protein denaturation Denaturation – disruption of native conformation Heat commonly used to denature proteins Tm = temperature where 50% folded/50% unfolded. Typical Tm = 40-60 o C Tm for thermophiles >100 o C (Taq DNA polymerase) Chemical denaturants Chaotrophic agents = Urea, KCN detergents = SDS Protein Folding: Protein Folding Ribonuclease A (RNase A) will refold to native structure spontaneously (1 minute) >10 50 possible conformations If 10 -13 sec per conformation would take 10 30 years to sample enough to determine structure How do proteins fold so quickly? Factors driving protein folding: Factors driving protein folding Conformational entropy A+B  C decreases entropy (unfavorable) Non-covalent interactions give favorable enthalpy value Hydrophobic effect increases entropy by freeing water (favorable) PowerPoint Presentation: + - DG = DH - TDS Protein Folding: Protein Folding Structures of globular proteins are not static Proteins “breathing” between different conformations Proteins fold towards lowest energy conformation Multiple paths to lowest energy form PowerPoint Presentation: All folding paths funnel towards lowest energy form Local low energy minimum can slow progress towards lowest energy form Pathway of Protein Folding: Pathway of Protein Folding 1) Nucleation of folding - Rapid and reversible formation of local 2 o structures form PowerPoint Presentation: 2) Formation of domains (Molten Globular intermediates) through aggregation of local 2o structures 3) Domain conformations adjust to form native protein Chaperonins : Chaperonins Protein complexes that promote protein folding Chaperonins don’t determine native structure Prevent misfolding and aggregation of protein Sequesters unfolded protein from other proteins PowerPoint Presentation: Require ATP for protein binding, after ATP hydrolysis native protein released Thought to bind unfolded regions of protein Disulfides Bonds: Disulfides Bonds Stabilize native structure Formed after native conformation achieved Abundant in secreted proteins but not in intracellular proteins Protein disulfide isomerase catalyzes reduction of incorrect disulfide linkages

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