Dictionary of Protein Secondary Structure Pattern Recognition of - PowerPoint by izy20048

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									Dictionary of Protein Secondary Structure
 Pattern Recognition of Hydrogen-Bonded and
            Geometrical Features
                Wolfgang Kabsch, Christian Sander
                    Biopolymers Vol.22 (1983)

     Proseminar Bioinformatik SS2003

                            Anna Dehof




                                        http://pga.lbl.gov/images/header/helix.gif

Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                  1
                                The Paper
     Dictionary of Protein Secondary Structure:
      Pattern Recognition of
      Hydrogen-Bonded       and   Geometrical
      Features


                            Pattern recognition
                                 algorithm
                                                                       Dictionary
Xray-                                                                  of Proteins
coordinates
      Focus on secondary structure prediction
 Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                 2
                    Outline of the talk
    Motivation (for Structure Prediction)
    Introduction (Basics of Protein Structure)
    Algorithm
         energy
         hbond pattern
         geometrical structure
    Example
    Conclusion and Outlook

Secondary Structure Prediction by Hydrogen Bond Pattern Recognition   3
               Motivation for Structure
                     Prediction
   Sequence ) Structure ) Function
   Medicine - Understanding biological functions.
   Finding "targets" for docking drugs.
   Agriculture - Genetic engineering of better and
    richer crops.
   Industry - Synthesis of enzymes (e.g.
    detergents).
   Potential Nobel Prize ;-)

    Secondary Structure Prediction by Hydrogen Bond Pattern Recognition   4
            Basics: Secondary Structure
   Hierarchy in Protein Structure:
      Primary                 Secondary

    Quarternary                   Tertiary


   The primary structure of a
    protein is its linear sequence of
    amino acids and the location of
                                                         http://users.rcn.com/jkimball.ma.ultranet/Biolo
    any disulfide (-S-S-) bridges.                       gyPages/P/PrimaryStructure.html




       Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                             5
              Basics: Secondary Structure
   Most proteins contain one or
    more stretches of amino acids
    that take on a characteristic
    structure in 3-D space.
                             http://star.tau.ac.il/~caspi/fold_lect/SMCT_lect/alpha2b.gif
   The most common of these
    are the alpha helix and the
    beta conformation.
   Discovered in 1951 by Linus
    Pauling and Robert Corey

                                      http://www.enzim.hu/~gaspar/caspase/imageMA1.JPG

         Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                6
                   Basics: Tertiary and
                  Quarternary Structure
   Tertiary structure refers
    to the three-dimensional
    structure of the entire
    polypeptide chain.
   Quarternary Structure:
    Complexes of 2 or more
    polypeptide chains held
    together by noncovalent
    forces but in precise
    ratios and with a precise                    http://pymol.sourceforge.net/pmimag/800/1tii.jpg
    3-D configuration.

    Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                     7
          How to find a secondary structure
                      element?
 Ramachandran-Plot:                            H-Bond characteristic:




  http://tonga.usip.edu/gmoyna/biochem341/ra   http://intro.chem.okstate.edu/1515SP01/L
  machandran.jpg                               ecture/Chapter12/Water4.GIF



Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                       8
      Pattern recognition: Energy
   Electrostatic: Coulomb potential




                                    f dimensional factor 332

           Hbond(i,j) := E < -0.5kcal/mol

Secondary Structure Prediction by Hydrogen Bond Pattern Recognition   9
                  HBondPattern: n-turn

 Hbond from CO(i) to NH(i+n):

                                  NH(i+n)
                                                    i+n

n-turn(i) := Hbond(i,i+n) n=3,4,5

                                                            i
  n=0 and n=1 are sterically
  disallowed, n=2 demands                       CO(i)
    specific conformation
                                                http://www.bmsc.washington.edu/people/verlinde/helix.gif

     Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                            10
   Cooperative Hbond patterns:
       (1) Minimal Helices
 3-helix(i,i+2) := [3-turn(i-1) and 3-turn(i)]

                   Minimal length: 3 residues!


                                                   i+1
                                 i-1
                                                     i+2
                                        i


           http://www.imb-jena.de/image_library/GENERAL/helix_3_10_weblab_1.gif


Secondary Structure Prediction by Hydrogen Bond Pattern Recognition               11
   Cooperative Hbond patterns:
       (1) Minimal Helices
 4-helix(i,i+3) := [4-turn(i-1) and 4-turn(i)]

                    Minimal length: 4 residues!


                                  i                    i+3
                         i-1                     i+2




              http://www.imb-jena.de/image_library/GENERAL/alpha_l_helix_weblab_1.gif
Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                     12
   Cooperative Hbond patterns:
       (1) Minimal Helices
 5-helix(i,i+4) := [5-turn(i-1) and 5-turn(i)]

                  Minimal length: 5 residues!

                                                   i+3
                                                            i+4
                                     i-1

                                           i



                 http://www.imb-jena.de/image_library/GENERAL/pi_helix_weblab_1.gif
Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                   13
   Cooperative Hbond patterns:
           (2) Helices
  a-helix, 3,10-helix, and p-helix as overlap of minimal
                          helices!




                  http://www.hhmi.princeton.edu/sw/2002/psidelsk/alpha_helix.gif
Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                14
    Cooperative Hbond patterns:
        (2) Minimal Helices




                                http://www.chembio.uoguelph.ca/educmat/chm730/gif/helices.gif


2-helix looking similar to ß-strand
 Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                            15
  HBondPattern: parallel bridge
     Parallel Bridge (i,j) :=
                                                                                i-1
Hbond(i-1,j) and Hbond(j,i+1)
                                                             j
                                                                                 i

                                                                               i+1




                              http://www.agsci.ubc.ca/courses/fnh/301/protein/proprin8.gif

Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                     16
  HBondPattern: parallel bridge
     Parallel Bridge (i,j) :=
                                                                                 i-1
Hbond(i-1,j) and Hbond(j,i+1)
                                                             j
                                                                                  i

                                                                                i+1




                          http://www.agsci.ubc.ca/courses/fnh/301/protein/proprin8.gif

Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                      17
  HBondPattern: parallel bridge
     Parallel Bridge (i,j) :=
                                                                                 i-1
Hbond(i-1,j) and Hbond(j,i+1)
                                                             j
                                                                                  i

                                                                                i+1




                          http://www.agsci.ubc.ca/courses/fnh/301/protein/proprin8.gif

Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                      18
          HBondPattern: antiparallel
                  bridge
     Antiparallel Bridge (i,j) :=
                                                           i-1
    [Hbond(i,j) and Hbond(j,i)]
                                                            i
                        or                                                     j
                                                           i+1
[Hbond(i-1,j+1) and Hbond(j-1,i+1)]




                             http://www.agsci.ubc.ca/courses/fnh/301/protein/proprin8.gif

   Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                      19
          HBondPattern: antiparallel
                  bridge
     Antiparallel Bridge (i,j) :=
                                                           i-1
    [Hbond(i,j) and Hbond(j,i)]
                                                            i
                        or                                                     j
                                                           i+1
[Hbond(i-1,j+1) and Hbond(j-1,i+1)]




                             http://www.agsci.ubc.ca/courses/fnh/301/protein/proprin8.gif

   Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                      20
          HBondPattern: antiparallel
                  bridge
     Antiparallel Bridge (i,j) :=
                                                           i-1
    [Hbond(i,j) and Hbond(j,i)]
                                                            i
                        or                                                     j
                                                           i+1
[Hbond(i-1,j+1) and Hbond(j-1,i+1)]




                             http://www.agsci.ubc.ca/courses/fnh/301/protein/proprin8.gif

   Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                      21
          HBondPattern: antiparallel
                  bridge
     Antiparallel Bridge (i,j) :=
                                                                                       i-1
    [Hbond(i,j) and Hbond(j,i)]                                    j+1
                                                                                        i
                        or                                          j
                                                                                       i+1
                                                                   j-1
[Hbond(i-1,j+1) and Hbond(j-1,i+1)]




                             http://www.agsci.ubc.ca/courses/fnh/301/protein/proprin8.gif

   Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                       22
          HBondPattern: antiparallel
                  bridge
     Antiparallel Bridge (i,j) :=
                                                                                       i-1
    [Hbond(i,j) and Hbond(j,i)]                                    j+1
                                                                                        i
                        or                                          j
                                                                                       i+1
                                                                   j-1
[Hbond(i-1,j+1) and Hbond(j-1,i+1)]




                             http://www.agsci.ubc.ca/courses/fnh/301/protein/proprin8.gif

   Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                       23
          HBondPattern: antiparallel
                  bridge
     Antiparallel Bridge (i,j) :=
                                                                                       i-1
    [Hbond(i,j) and Hbond(j,i)]                                    j+1
                                                                                        i
                        or                                          j
                                                                                       i+1
                                                                   j-1
[Hbond(i-1,j+1) and Hbond(j-1,i+1)]




                             http://www.agsci.ubc.ca/courses/fnh/301/protein/proprin8.gif

   Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                       24
   Cooperative Hbond patterns:
           (3) Ladders
Ladder: set of one or more consecutive bridges of
                      identical type




              http://www.chembio.uoguelph.ca/educmat/chm730/gif/bturn.gif




Secondary Structure Prediction by Hydrogen Bond Pattern Recognition         25
      Cooperative Hbond patterns:
              (4) Strands
Strand: set of one or more ladders connected by shared
                       residues




         http://www.bmb.psu.edu/faculty/tan/lab/gallery/protg_strand_neon1.jpg
   Secondary Structure Prediction by Hydrogen Bond Pattern Recognition           26
               Geometrical Features
    Bend

                                                                      http://www.answersing

    Chirality                                                        enesis.org/images/chiral
                                                                             ity-rgb.jpg




    SSBonds                                                   http://users.rcn.com/jkimball.ma.ul
                                                               tranet/BiologyPages/P/PrimaryStruc
                                                               ture.html




    Chain Breaks
Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                         27
       Geometrical Features: Bend

Bend(i):=[angle{( Ca (i)- Ca(i-2)), (Ca(i+2),- Ca(i))} > 70°]


                                              a
                                      Ca C
                                    N
                      Ca C                i
                    N
      Ca C
    N
       i-2                                              i+2



  Secondary Structure Prediction by Hydrogen Bond Pattern Recognition   28
 Geometrical Features: Chirality
 a (i) = dihedral angle( Ca                        i-1,   Ca i, Ca     i+1,   Ca   i+2   )

                       +: if             0° < a < 180°
                        -: if –180° < a <                         0°


                                                              Dihedral angle:

                                                                          a

 http://www.ee.ualberta.ca/~vick/GLAD/Jerm's_pics/chirality.jpg
Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                          29
                  Geometrical Features:
                       SSBonds
   SS Bonds:             covalent bond between Sg atoms of two
    residues
    here: databases
    today: algorithm




                              http://www.biologie.uni-hamburg.de/b-online/gdv03/a3_4.jpg
    Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                    30
         Example of the Dictionary
Plastocyanin – electron transport – populus leaves




 Secondary Structure Prediction by Hydrogen Bond Pattern Recognition   31
                               Conclusion
    Secondary structure prediction has
     many important application
    It is possible to compute it using hbond
     patterns
    Other molecular features can be
     computed similary
    Despite this algorithm is pretty old it is
     still in use today

Secondary Structure Prediction by Hydrogen Bond Pattern Recognition   32
                                    Outlook
    Challenge: Tertiary structure prediction
    Implemented in BALL
    More modern Algorithm developed by
     Dmitrij Frishman and Patrick Argos
    Link for Secondary Structure Prediction:
     http://www.cmpharm.ucsf.edu/~nomi/
     nnpredict.html

Secondary Structure Prediction by Hydrogen Bond Pattern Recognition   33
Dictionary of Protein Secondary Structure
Pattern Recognition of Hydrogen-Bonded and
            Geometrical Features
              Wolfgang Kabsch, Christian Sander
                  Biopolymers Vol.22 (1983)


                                      The End

                      Thank You for listening

                                  Anna Dehof

                                  http://pymol.sourceforge.net/pmimag/800/1tii.jpg
Secondary Structure Prediction by Hydrogen Bond Pattern Recognition                  34
                     Additional Information
   Chain breaks
       peptide length (distance C-N) exceeds 2.5 A
       reflects absence of peptide bond or coordinate errors or
        missing density in crystallography map
   Solvent exposure                              H2 O      Solvent accesible surface




                      Server.cd.net/cca/doc
                       uments/molecular-
                       modeling/surface3

        Secondary Structure Prediction by Hydrogen Bond Pattern Recognition             35
                Summary: Hierarchy

                                4 helices

                             single bridges
                                  ladders
                                 3 helices
                                 5 helices
                 residues bracked by hbonds
                      residues with a bend

Secondary Structure Prediction by Hydrogen Bond Pattern Recognition   36
          How to find a secondary structure
                      element?
 Ramachandran-Plot:                          H-Bond characteristic:
 •Vary Backbone torsion                       •Weak nonconvalent
 angles psi and phi                           bond between donor and
                                              acceptor atom
 --> stable conformations
 • grid of torsion angles
                                              •good hbond –3 kcal/mol
 =>difficcult




Secondary Structure Prediction by Hydrogen Bond Pattern Recognition     37

								
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