1. Protein Purification

2. Compartmentalization provides an opportunity for a purification step e Protein profile for compartments of gram-negative prokaryotes

3. Cell Disruption  Chemical: alkali, organic solvents, detergents  Enzymatic: lysozyme, glucanases, chitinase  Physical: osmotic shock, freeze/thaw  Mechanical: sonication, homogenization, wet milling, French press

4. Chemical Disruption Detergents such as Trition X-100 or NP40 can permeabilize cells by solubilizing membranes. Detergents can be expensive, denature proteins, and must be removed after disruption

5. French Press Cells are placed in a stainless steel container. A tight fitting piston is inserted and high pressures are applied to force cells through a small hole.

6. Homogenization Cells are placed in a closed vessel (usually glass). A tight fitting plunger is inserted and rotated with a downward force. Cells are disrupted as they pass between the plunger and vessel wall. Also, shaking with glass beads works, BUT: Friction = Heat

7. Sonication A sonicator can be immersed directly into a cell suspension. The sonicator is vibrated and high frequency sound waves disrupt cells.

8. Differential centrifugation

9. Inclusion bodies provide a rapid purification step Inclusion bodies provide storage space for protein, carbohydrate and lipid material in prokaryotes However, proteins exist as aggregates in inclusion bodies thus special precautions must be taken during purification

10. 10% Glycerol 40% Glycerol Even proteins can be separated by their sedimentation properties Function of both size and shape

11. Proteins have unique properties resulting from their amino acid composition  Localization  Charge  Hydrophobicity  Size  Affinity for ligands Arbitrary protein

12. The charge on a protein is dependent upon pH  The content of amino acids with ionizable side chains determines the overall charge of a protein  Thus, a protein containing a majority of basic residues (ie. R and K) will be positively charged and will bind to a cation-exchange support Ion exchange column Supports (examples)

13. Separation based on surface charge

14. Cation exchange chromatography Protein -- -- -- - - -- - - - - -- - - - - Na + Cl -  Protein samples are applied to this column at low ionic strength, and positively charged proteins bind to the column support  Proteins are eluted using a gradient of increasing ionic strength, where counterions displace bound protein, changing pH will also elute protein  Choice of functional groups on distinct column supports allow a range of affinities

15.  Conversely, at a pH two orders of magnitude above their pKa, acidic amino acids will be negatively charged, thus proteins with a majority of acidic amino acids (D and E) will be negatively charged at physiological pH  Negatively charged proteins can be separated using anion exchange chromatography

16. Na + Cl - Protein  Protein samples are applied to this column at low ionic strength, and negatively charged proteins bind to the column support  Proteins are eluted using a gradient of increasing ionic strength, where counterions displace bound protein, changing pH will also elute protein  Choice of functional groups on distinct column supports allow a range of affinities  Bead size affects resolution in both anion and cation exchange Anion exchange chromatography + + ++ + ++ + ++ + + + + + + + ++ +

17. Hydrophobic Interaction Chromatography  Although most hydrophobic amino acids are buried in the interior of proteins, many proteins have hydrophobic surfaces or patches which can be used for separation  A protein’s hydrophobic character is typically enhanced by addition of high salt concentrations  Proteins are eluted from HIC columns via a gradient of high salt to low salt concentrations

18. For any protein, there is a characteristic pH at which the protein has no net charge (isoelectric point). At the isoelectric pH, the protein will not migrate in an electric field. Isoelectric Focusing

19. Isoelectric focusing

20. Protein Precipitation  Precipitation is caused by changes that disrupt the solvating properties of water  Changes in pH, ionic strength, temperature, and the addition of solvents can cause precipitation (loss of solubility)  Most proteins have a unique set of conditions that result in precipitation

21. Precipitation with Salt  In practice, most procedures use the salt ammonium sulfate (NH 4 ) 2 SO 4 to precipitate proteins  The amount of salt required is directly related to the number and distribution of charged and nonionic polar amino acids exposed on the surface of the protein

22. At low ionic strengths, the charges on the surface of a protein attract counter ions, decreasing electrostatic free energy and increasing solubility. Addition of low concentrations of salt, then, increase solubility of proteins ("salting in"). At high salt concentrations, however, protein solubility decreases ("salting out"). This is due to electrostatic repulsion between the surface ions and the hydrophobic interior of the protein and to the avid interaction of salts with water. This disrupts the ordered water in the hydration layer. Salts vary in their ability to salt out proteins and generally follow the Hofmeister series: Cations: NH4+ > K+ > Na+ > Mg++ > Ca++ > guanidium Anions: SO4-- > HPO4-- > acetate > citrate > tartrate > Cl- > NO3- Salt effects on protein solubility

23. Salting out provides a purification step

24. Proteins can be separated on the basis of size  Gradient centrifugation  Gel filtration

25. Gel Filtration provides a molecular sieve Figures from Scopes, Protein Purification on Reserve

26. Gel Filtration Chromatography Proteins that enter porous beads will migrate slower than proteins that are excluded from the pores. Separation is a function of relative size and shape

27. Size exclusion can be used to determine oligomeric state V o = Void volume (the excluded volume surrounding the beads) V e = Intermediate volume (partially excluded) Construct a standard curve using known proteins of known sizes

28. Gel Filtration Chromatography Log Mol Wt V e - V o

29. A protein’s substrate preference can be used in a very specific purification step Intrinsic If a protein binds ATP, put over a column support that has ATP crosslinked on it, thus selecting for ATP-binding proteins (can be done or a wide range of substrates such as sugars, Proteins, etc.) Added Specific protein domains can be fused to proteins of interest at the gene level to facilitate purification (ie. Fuse a maltose binding protein domain to any random protein, then it will bind specifically to a maltose containing column)

30. Metal chelation is a popular affinity purification method Various “expression vectors” create fusions to poly-Histidine tags, which allow the protein to bind to columns containing chelated metal supports (ie. Ni +2 ) Figures from Qiagen Product literature

31. Examining your purified protein

32. Use of SDS-PAGE vs. Native gel electrophoresis

33. Two dimensional gel electrophoresis

34. Assessing your purification procedure

35. Total vs. specific activity

36. We can “control” protein expression With the notable exception of proteins such as those that compose the ribosome, many proteins are found only in low abundance (particularly Proteins involved in regulatory processes) Thus, we need to find ways to grow cells that allow ample expression of proteins that would be interesting for biochemical characterization.

37. Find conditions for cell growth that enhance a protein’s expression For example, cytochrome c 2 is utilized by R.sphaeroides for both respiratory and photosynthetic growth; a slight increase in levels of this protein is observed under photosynthetic growth conditions. However, Light-Harvesting complexes are only synthesized under photosynthetic growth conditions; obviously if you want to purify this protein you need to grow cells under photosynthetic conditions

38. Molecular Biology allows us to manipulate genes  Understanding the basic mechanisms of gene expression has allowed investigators to exploit various systems for protein expression  Prokaryotic expression systems  Eukaryotic expression systems Yeast Mammalian  Viral expression systems Baculovirus and Insects

39. What do we need to produce a protein? lamB A gene lamB Promoter Transcriptional unit Terminator lamB Ribosome binding site Translational unit

40. Molecular Biology presents an opportunity for useful genetic constructs lamB Promoter Terminator bla Plasmid ori Antibiotic resistance gene Origin of Replication Can fuse gene to other sequences conferring affinity

41. Choice of promoter allows control over transcription levels  Intrinsic promoters can be sufficient for overexpression in multi-copy plasmids  Constitutive promoters with high activity (ie. promoters for ribosomal genes) can be useful for producing non-toxic proteins  Inducible promoters allow control of expression, one can “titrate” the promoter activity using exogenous agents

42. An expression system utilizing lactose and T7 RNA polymerase is a popular choice in prokaryotes lamB bla ori Plasmid T7 polymerase dependent promoter T7 pol Lactose-inducible promoter Genome

43. Inclusion bodies provide a rapid purification step Proteins exist as aggregates in inclusion bodies thus special precautions must be taken during purification. Typically, inclusion bodies can be readily isolated via cell fractionation. following isolation the proteins must be denatured and renatured to retrieve active protein.

44. Additional concerns regarding protein expression Modifications Inclusion bodies Codon usage

45. Cells exhibit nonrandom usage of codons This provides a mechanism for regulation; however, genes cloned for purposes of heterologous protein expression may contain “rare” codons that are not normally utilized by cells such as E. coli. Thus, this could limit protein production. Codon usage has been used for determination of highly expressed proteins.

46. Molecular Biology allows us to manipulate genes  Understanding the basic mechanisms of gene expression has allowed investigators to exploit various systems for protein expression  Prokaryotic expression systems  Eukaryotic expression systems Yeast Mammalian  Viral expression systems Baculovirus and Insects

47. Non-prokaryotic expression systems have emerged due to increasing simplicity and the need for proper modifications. Although you can express a eukaryotic cDNA in a prokaryote is the protein you purify, what the eukaryotic cell uses? Invitrogen : www.invitrogen.comwww.invitrogen.com Gateway vectors Novagen: www.novagen.comwww.novagen.com

48. Several hyperthermophilic archaeal species have also been shown to be dependent on tungsten (W), also Cd important in diatoms

49. Fe is most abundant, followed by Zn

50. Metals in Biology Enzyme co-factors Redox active centers in many enzymes Fe: Electron transport, SOD, Cytochrome P450 Zn: SOD Mg, Mn: Photosynthesis Cu: Electron transport Ca: Cell signaling Ca, Na, etc: Substrates in ion pumps Structural components of enzymes Fe: Hemoglobin, Cell structure Zn: Zn fingers in transcription factors Ca: Bone structure, Cell structure

51. Metals and their biological effects Block essential function of biomolecules e.g. Ion pumps: Divalent metals inhibit Ca pumps Displace essential metal co-factors e.g. Cd can replace Cu in electron transport enzymes Modify configuration of biomolecules: Zn can be replaced Cd in Zn fingers

52. Metals and reactive oxygen species Redox potential of O 2 ~ + 1 V; Extremely oxidizing If there is a source of electrons: O 2 + e -  O 2  - + e - + 2 H +  H 2 O 2 + e -   OH + OH - + e - + 2 H +  H 2 O All but water are reactive oxygen species (ROS) and are biologically damaging In above order: superoxide, hydrogen peroxide, hydroxyl radical Biomolecules are a good source of reducing power: i.e. electrons Redox active metals can catalyze electron transfer from biomolecules to O 2

53. Metals, cannot be metabolized Sequestered and/or excreted Metallothioneins: Cu, Zn, Cd, Ni binding Small sulphur containing proteins – free Cys residues Bind to metals sequestering them SH + Cd ++ S-S- S-S- + 2 H + Cd ++ ~ 4 metal ions per protein Binding region similar to Zn fingers Expression induced by metal transcription factors (MTFs)

54. Metals in Enzymes All ribozymes are metalloenzymes, divalent cations are required for chemistry, and often aid in structural stabilization. Protein enzymes are divided into six classes by the Enzyme Commision: 1.Oxidoreductase 2.Transferase 3.Hydrolase 4.Lyase 5.Isomerase 6.Ligase Zn is the only element found in all of these classes of enzymes.

55. Proteins bind metals based on size, charge, and chemical nature Each metal has unique properties regarding ionic charge ionic radii, and ionization potential Typically, metals are classified as “hard” or “soft” in correlation with their ionic radii, electrostatics, and polarization Hard metals prefer hard ligands, soft prefer soft, Borderline metals can go either way.

56. Properties of metal ions determine their biological utility

57. Soft Hard

58. Metals favor distinct coordination in proteins M L L L L M L L L L M L LL L L L M L L L L L Tetrahedral Square Planar Trigonal bipyramidal Octahedral M = Metal L = Ligand

59. Unsaturated coordination spheres usually have water as additional ligands to meet the favored 4 or 6 coordination

60. Protein sequence analyses have revealed certain metal binding motifs Structural Zn are generally bound by 4 cysteines Catalytic Zn bound by three residues (H, D, E, or C) and one water Coordination in primary sequence of alcohol dehydrogenase Catalytic L 1 -few aa-L 2 -several aa-L 3 Structural L 1 -3-L 2 -3-L 3 -8-L 4 L = Ligand

62. Biological roles of transition metals  Coordination Structure (protein and protein-substrate)  Electrophilic catalysis Positive charge attracts electrons, polarize potential reactant, increase reactivity  General Acid – Base catalysis  Redox reactions  Metalloorganic chemistry Free radicals (not just limited to proteins*)

63. Carbonic Anhydrase catalytic mechanism

64. Molybdenum?? http://www.dl.ac.uk/SRS/PX/bsl/scycle.html

65. Tetrapyrroles (heme, chlorophyll) make proteins “visible” along with certain metals

66. Spectroscopy is a study of the interaction of electromagnetic radiation with matter A =  cl Absorbance = extinction coefficient x concentration x path length Beer-Lambert Law The amount of light absorbed is proportional to the number of molecules of the chromophore, through which the light passes Units: None = M -1 cm -1 M cm

67. c-type cytochromes have a characteristic absorbance spectrum

68. Purification of GFP overview  Protein stability  Protein precipitation  Hydrophobic Interaction chromatography  Gel electrophoresis  Optical spectroscopy

69. Lab reports Introduction – Rationale for why these experiments are important (not simply from a course work perspective) Materials & Methods – Concise, but detailed description of how experiments were performed Results – Summary of data (Simply report data, ie. purifica- tion table, etc.) Discussion – Implications of results All lab reports must be type-written (please)

70. Keeping a purification table