Chapter 3. Protein Structure and Function

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1 Chapter 3 Protein Structure and Function

2 Broad functional classes So Proteins have structure and function... Fine! -Why do we care to know more???? Understanding functional architechture gives us POWER to: Diagnose and find reasons for diseases Create modifying drugs Engineer our own designerproteins

3 Protein structure determines function DNA (mrna) Translation: Translation into 3D structure: Modifications: Chemical modification of aminoacids Interaction with other molecules Proteolytic cleavage (Location) 3D structure determines function: New 3D structure New function Proteins are single, unbranched chains of amino acid monomers There are 20 different amino acids The amino acid sidechains in a peptide can become modified, extending the functional repetoire of aminoacids to more than hundred different amino acids. A protein s amino acid sequence determines its three-dimensional structure (conformation) In turn, a protein s structure determines the function of that protein Conformation (=function) is dynamically regulated in several different ways

4 All amino acids have the same general structure but the side chain (R group) of each is different Cα R: Hydrophilic: Basic Acidic Non-charged Hydrophobic Special

5 Hydrophilic amino acids

6 Hydrophobic and special amino acids

7 Peptide bonds connect amino acids into linear chains Backbone Side-chains

8 Side chain modifications change the chemical (functional) properties of proteins Acetylation Phosphorylation Hydroxylation Methylation Carboxylation => Expanding the repetoire of existing amino acid side-chains to > 100 variations! Glycosylation Ubiquitylation

9 Four levels of structure determine the shape of proteins Primary: the linear sequence of amino acids peptide bonds Secondary: the localized organization of parts of a polypeptide chain (e.g., the α helix or β sheet) backbone hydrogen bonds Tertiary: the overall, threedimensional arrangement of the polypeptide chain hydrophobic interactions, hydrogen bonds (non-covalent bonds in general) and sulfur-bridges Quaternary: the association of two or more polypeptides into a multisubunit complex

10 Primary and secondary structure (example: hemagglutinin) β-strand α-helix

11 Secondary structure α Helix β Sheet β (U)-turn

12 Tertiary structure Motifs are regular combinations of secondary structures. Motifs form domains! Three examples of Motifs from different types of DNA-binding proteins

13 Tertiary structure Structural, functional or topological domains are modules of secondary and tertiary structure Each of these proteins contain the EGF globular domain. - But each of these proteins have a different function Globular domain Tertiary structure

14 Different graphical representations of the same protein (tertiary structure)

15 Quaternary structure

16 Multiprotein complexes: molecular machines

17 Sequence homology suggests functional and evolutionary relationships between proteins When the stucture of a newly discovered protein is known, comparison to other proteins across species can help predict function

18 Folding, modification, and degradation of proteins The life of a protein can briefly be described as: synthesis, folding, modification, function, degradation. A newly synthesized polypeptide chain must undergo folding and often chemical modification to generate the final protein All molecules of any protein species adopt a single conformation (the native state), which is the most stably folded form of the molecule Most proteins have a limited lifespan before they are degraded (turn-over time)

19 Aberrantly folded proteins are implicated in slowly developing diseases An amyloid plaque in Alzheimer s disease is a tangle of protein filaments

20 The information for protein folding is encoded in the sequence

21 Folding of proteins in vivo is promoted by chaperones Large proteins with a lot of secondary structure may require assisted folding to avoid aggregation of unfolded protein - Molecular chaperones and chaperonins prevent aggregation of unfolded protein

22 Folding of proteins in vivo is promoted by chaperones Large proteins with a lot of secondary structure may require assisted folding to avoid aggregation of unfolded protein - Chaperones and chaperonins prevent aggregation of unfolded protein

23 Functional design of proteins Protein function often involves conformational changes Proteins are designed to bind a range of molecules (ligands) Binding is characterized by two properties: affinity and specificity Antibodies and enzymes exhibit precise ligand/substratebinding specificity But can have variable affinities Enzymes are highly efficient and specific catalysts An enzyme s active site binds substrates(ligands) and carries out catalysis

24 Antibody/antigen interaction: an example for ligand-binding with high affinity and specificity

25 Enzymes have high substrate affinity sites and catalytic sites

26 Kinetics of an enzymatic reaction are described by V max and K m

27 Kinetics of an enzymatic reaction are described by V max and K m

28 Enzymes in one pathway can be physically associated

29 Mechanisms that regulate protein activity Altering protein synthesis rate and proteasomal degradation Allosteric transitions Release of catalytic subunits, active inactive states, cooperative binding of ligands Chemical modification: Phosphorylation, acetylation etc. dephosphorylation, deacetylation etc. Proteolytic activation Compartmentalization

30 Protein degradation via the ubiquitin-mediated pathway ATP Cells contain several other pathways for protein degradation in addition to this pathway

31 Allosteric transitions: Cooperative binding of ligands Sigmoidal curve indicates cooperative binding (of ligands, substrates, ca ions) in contrast to standard Michaelis-Menten Kinetics

32 Conformational changes induced by Ca 2+ binding to calmodulin Cooperative binding of calcium: binding of one calcium enhances the affinity for the next calcium When 4 calcium are bound a major allosteric conformational change occurs Calmodulin is a switch protein because this effect in turn regulates other proteins bound by the compact calmodulin

33 Another class of switch proteins: GTPases

34 Chemical modification Example: Phosphorylation dephosphorylation

35 Proteolytic cleavage of proinsulin to produce active insulin

36 Compartmentalization Example:Membrane proteins Each cell membrane has a set of specific membrane proteins that allows the membrane to carry out its activities Membrane proteins are either integral or peripheral Integral transmembrane proteins contain one or more transmembrane α helices Peripheral proteins are associated with membranes through interactions with integral proteins

37 Schematic of membrane proteins in a lipid bilayer

38 Mechanisms that regulate protein activity Altering protein synthesis rate and proteasomal degradation Allosteric transitions Release of catalytic subunits, active inactive states, cooperative binding of ligands Chemical modification: Phosphorylation, acetylation etc. dephosphorylation, deacetylation etc. Proteolytic activation Compartmentalization

39 Example containing all levels of regulatin of protein activity GFP-tagged GLUT4

40 Now that you KNOW the basic principles of protein structure and function you can UNDERSTAND: Protein and Proteome Analytical techniques

41 Purifying, detecting, and characterizing proteins A protein must be purified to determine its structure and mechanism of action Detecting known proteins can be usefull for diagnostic purposes Molecules, including proteins, can be separated from other molecules based on differences in physical and chemical properties (size, mass, density, polarity, affinity...) Elementary toolbox includes: centrifugation, electrophoresis, liquid chromatography (LC), spectrometry, ionization/radiation. -applied in various advanced forms and combinations.

42 Centrifugation can separate molecules that differ in mass or density

43 Electrophoresis separates molecules according to their charge:mass ratio SDS-polyacrylamide gel electrophoresis Even coating of proteins allows even charge distribution -> larger mass = higher total charge

44 Two-dimensional electrophoresis separates molecules according to their charge and their mass

45 Highly specific enzymes and antibody assays can detect individual proteins Immunoblot (= Western Blot) based on affinity

46 Liquid chromotography (LC): Separation of proteins by size: gel filtration chromatography Add mobile phase: buffer Stationary phase:

47 Separation of proteins by charge: ion exchange chromatography Also: Reversed-phase LC: separation by hydrophobicity Stationary phase: non-polar, Mobile phase: moderately polar

48 Separation of proteins by specific binding to another molecule: affinity chromatography

49 Proteomics, the analysis of complex protein mixtures Genome databases allow prediction of genes -> protein primary structure Each protein can be fragmented into peptides which are composed of aa s. Each aa has a unique mass to charge ratio at a given ph Each protein therefore has a unique peptide-fingerprint Technique: proteins->peptides->mass/charge ratio measurement -> compare against whole proteome (genome based) database -> identify proteins

50 Time-of-flight mass spectrometry measures the mass of proteins and peptides Matrix-Assisted-Laser-Desorption/Ionization Time-offlight mass spectrometry (MALDI-TOF MS)

51 MS spectrum

52 Example of a proteome analysis workflow Cell/tissue of interest Isolate organelles (fractionation) Confirm organelle-specific proteins Subfractionate, detect peptides, identify corresponding proteins

53 X-ray crystallography is used to determine protein structure Other techniques such as cryoelectron microscopy and NMR spectroscopy may be used to solve the structures of certain types of proteins

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