Zinc Finger Prediction - Protein

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					Zinc Finger Prediction



 An overview of goals and
        progress
  Classifying Amino Acids
• Interaction with H2O:
  – Hydrophilic
  – Hydrophobic
• pH
  – Acidic
  – Basic
Hydrophobic:            pH:
  Folds to the middle     Acidic
  of the protein
Hydrophilic:              Basic
  Folds to outer edge
  of protein
          Amino Acid Characteristics
•   Alanine       Ala- A- hydrophobic
•   Arginine      Arg- R- free amino group makes it basic and hydrophilic
•   Asparagine Asn- N- carbohydrate can be covalently linked ("N-linked) to its -NH
•   Aspartic acid Asp- D- free carboxyl group makes it acidic and hydrophilic
•   Cysteine      Cys- C- oxidation of their sulfhydryl (-SH) groups link 2 Cys (S-S)
•   Glutamic acid Glu- E- free carboxyl group makes it acidic and hydrophilic
•   Glutamine     Gln- Q- moderately hydrophilic
•   Glycine       Gly- G- so small it is amphiphilic (can exist in any surroundings)
•   Histidine     His- H- basic and hydrophilic
•   Isoleucine    Ile - I- hydrophobic
•   Leucine       Leu- L- hydrophobic
•   Lysine        Lys- K- strongly basic and hydrophilic
•   Methionine    Met- M- hydrophobic
•   Phenylalanine Phe- F- very hydrophobic
•   Proline       Pro- P- causes kinks in the chain
•   Serine        Ser- S- carbohydrate can be covalently linked ("O-linked") to its -OH
•   Threonine     Thr- T- carbohydrate can be covalently linked ("O-linked") to its -OH
•   Tryptophan    Trp- W- scarce in most plant proteins
•   Tyrosine       Tyr- Y- phosphate or sulfate group can covalently attach to its -OH
•   Valine        Val- V- hydrophobic
        DNA binding Proteins
• Amphipathic helix
   – -leucine zipper
   – -helix-loop-helix
• Helix-turn-helix
   – homeodomain
   – POU domain
• Zinc finger
   – C2H2
   – C2C2
               Amphipathic Helix
• Hydrophobic
  residues
  (Val, Leu, Ile, Met, Phe)

• Hydrophilic residues
  (Asn, Glu, Gln, Asp, His, Lys, Arg)

• form dimers
                Helix-turn-Helix
• bind as dimers
• their binding sites are palindromic.
   – estrogen receptor: GGTCAnnnTGACC
   – glucocorticoid receptor: GAACAnnnTGTTC
   – thyroid response element: GGTCATGACC
• They contain 3 a helical regions separated
  by short turns.
• One protein helix (helix 3) in each subunit of
  the dimer occupies the major groove of two
  successive turns of the DNA helix.
             Zinc Fingers
                     Our “baby”
• Zinc required for protein activity.
• cysteine and histidine the most important amino acids
  for binding zinc
• zinc is bound between pairs of cysteines and
  histidines – hence zinc finger.
• Phenylalanine or tyrosine residues which occur at
  invariant positions required for DNA binding. Similar
  sequences have been found in a range of other DNA
  binding proteins.
• 2 cysteines and 2 histidines is called a C2H2 zinc
  finger.
• 4 cysteines is called a C2C2 zinc finger.
             Cys2His2
• conserved beta beta alpha structure,
  and amino acids on the surface of the
  alpha-helix contact bases in the major
  groove
• every 3.6 residues make one turn,
• the distance between two turns is 0.54
  nm,
• the C=O (or N-H) of one turn is
  hydrogen bonded to N-H (or C=O) of
  the neighboring turn.
  Helix Makers and Breakers
Prefers:               Disrupt:
• Alanine, Leucine,    • Glycine, Proline,
  Methionine,            Aspartic Acid,
  Phenylalanine,         Asparagine, Serine
  Glutamic Acid,
  Glutamine,
  Histidine, Lysine,
  Arginine



       Glycine                  Proline
             Beta Sheet
• Bifurcatedhydrogen bond
  – O atom shared with two H-bonds
     C=O...H-N & CaHa...O,
  – sheet is sheared to accomodate
     birfuracted hydrogen bonds.
  – Once the bifurcated hydrogen bonds
     are considered, the hydrogen
     bonding patterns between the
     antiparallel and parallel β-sheets
     look very similar.
Parallel & Antiparallel Beta
          Sheets
  Beta Sheet Makers

            Prefers:
Tyrosine, Trytophan, (Phe, Met),
 Isoleucine, Valine, Threonine,
             Cystine
                      Goals
1. Predict Protein’s DNA binding domain
  •   Use Secondary structure and probable
      Tertiary structure
      •   Position of Amino Acids (especially on Alpha
          Helix) determine Domain
2. Predict Protein’s Tertiary Structure
  •   Predict Zinc Fingers
      •   Predict Alpha Helices
      •   Predict Beta Sheets
                 Zn Finger Prediction
1. Cys2His2          CX2-4C…HX2-4H
  Example: Transcription Factor SP1



2. Cys4      CX2CS13CX2CX14-15-CX5CX9CX2C
  Example: Estrogen Receptor



3. Cys6      CX2CX6CX5-6CX2CX6C
  Example: Regulatory Protein GAL4
               Acknowledgements

• http://bssv01.lancs.ac.uk/ADS/BIOS336/336L7.html
• http://www.web-books.com/MoBio/Free/Ch2C4.htm
• http://boscoh.com/protein/structural-features-of-the-beta-sheet
• http://tonga.usip.edu/gmoyna/biochem341/lecture14.html
•   http://://ekhidna.biocenter.helsinki.fi/downloads/teaching/spring2
    006/proteiinianalyysi/Proteiinianalyysi-06-VI-AppendixA.htm
•   http://www.imb-jena.de/image_library/GENERAL/alpha_r_helix_1.gif
• http://web-books.com/MoBio/free/ch4f2.htm

				
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