Local geometry of polypeptide chains elements of secondary structure turns
Download
1 / 38

Local geometry of polypeptide chains Elements of secondary structure ( turns ) - PowerPoint PPT Presentation


  • 60 Views
  • Uploaded on

Local geometry of polypeptide chains Elements of secondary structure ( turns ). Levels of protein structure organization. Atom symbols and numbering in amino acids. Chirality. Enantiomers.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about 'Local geometry of polypeptide chains Elements of secondary structure ( turns )' - trinh


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript
Local geometry of polypeptide chains elements of secondary structure turns
Local geometry of polypeptidechainsElements of secondarystructure (turns)




Chirality
Chirality

Enantiomers

Phenomenological manifestation of chiraliy: optical dichroism (rotation of the plane of polarized light).


Representation of geometry of molecular systems
Representation of geometry of molecular systems

  • Cartesiancoordinates

    • describeabsolute geometry of a system,

    • versatilewith MD/minimizing energy,

    • need a moleculargraphics program to visualize.

  • Internalcoordinates

    • describelocal geometry of an atom wrt a selectedreferenceframe,

    • withsomeexperience, local geometry can be imaginedwithout a moleculargraphics software,

    • mightcauseproblemswhendoing MD/minimizing energy (curvilinearspace).


  • Local geometry of polypeptide chains elements of secondary structure turns

    Cartesian coordinate system

    z

    Atom x (Å) y (Å) z (Å)

    C(1) 0.000000 0.000000 0.000000

    O(2) 0.000000 0.000000 1.400000

    H(3) 1.026719 0.000000 -0.363000

    H(4) -0.513360 -0.889165 -0.363000

    H(5) -0.513360 0.889165 -0.363000

    H(6) 0.447834 0.775672 1.716667

    zH(6)

    H(6)

    O(2)

    H(4)

    C(1)

    yH(6)

    xH(6)

    x

    H(5)

    y

    H(3)


    Local geometry of polypeptide chains elements of secondary structure turns

    Internal coordinate system

    i dijaijkbijkl j k l

    C(1)

    O(2) 1.40000 * 1

    H(3) 1.08900 * 109.47100 * 1 2

    H(4) 1.08900 * 109.47100 * 120.00000 * 1 2 3

    H(5) 1.08900 * 109.47100 * -120.00000 * 1 2 3

    H(6) 0.95000 * 109.47100 * 180.00000 * 2 1 5

    H(6)

    O(2)

    H(4)

    C(1)

    H(5)

    H(3)




    Local geometry of polypeptide chains elements of secondary structure turns

    Dihedral (torsional) angle

    The C-O-H plane is rotated counterclockwise about the C-O bond from the H-C-O plane.



    Local geometry of polypeptide chains elements of secondary structure turns

    Bond length calculation

    zj

    zi

    xi

    yi

    xj

    xj




    Local geometry of polypeptide chains elements of secondary structure turns

    Calculation of Cartesian coordinates in a local reference frame from internal coordinates

    H(5)

    z

    H(6)

    d26

    C(1)

    a426

    H(3)

    b3426

    O(2)

    y

    x

    H(4)



    Local geometry of polypeptide chains elements of secondary structure turns

    Polymer chains system

    qi+2

    qi+2

    wi+1

    wi+1

    qi+1

    i+1

    i+1

    di+1

    di+1

    i

    i

    wi

    pi-1

    di

    ai

    wi-1

    wi-1

    qi-1

    qi-1

    i-1

    i-1

    di-1

    di-1

    qi

    i-2

    i-2


    Local geometry of polypeptide chains elements of secondary structure turns

    For regular polymers (when there are „blocks” inside such as in the right picture, pi is a full translation vector and TiRi is a full transformation matrix).


    Local geometry of polypeptide chains elements of secondary structure turns

    Ring closure such as in the right picture,

    3

    4

    q3

    w4

    2

    d2

    n-3

    1

    a21n

    d1n

    a1 n n-1

    wn

    n

    n-2

    dn

    qn

    n-1

    N. Go and H.A. Scheraga, Macromolecules, 3, 178-187 (1970)


    Peptide bond geometry
    Peptide bond geometry such as in the right picture,

    Hybrid of two canonical structures

    60% 40%


    Local geometry of polypeptide chains elements of secondary structure turns

    Electronic structure of peptide bond such as in the right picture,


    Local geometry of polypeptide chains elements of secondary structure turns

    Peptide bond: planarity such as in the right picture,

    • The partially double character of the peptide bond results in

    • planarity of peptide groups

    • their relatively large dipole moment


    Side chain conformations the c angles
    Side chain conformations: the such as in the right picture, c angles

    c1

    c2

    c3

    c1=0


    Dihedrals with which to describe polypeptide geometry
    Dihedrals with which to describe polypeptide geometry such as in the right picture,

    side chain

    main chain


    Local geometry of polypeptide chains elements of secondary structure turns

    Peptide group: such as in the right picture, cis-trans isomerization

    Skan z wykresem energii


    Local geometry of polypeptide chains elements of secondary structure turns

    Because of peptide group planarity, main chain conformation is effectively defined by the f and y angles.


    Side chain conformations
    Side chain conformations is effectively defined by the



    Some and pairs are not allowed due to steric overlap e g 0 o
    Some disulfide bridgesandpairs are not allowed due to steric overlap (e.g, ==0o)


    The ramachandran map
    The Ramachandran map disulfide bridges


    Conformations of a terminally blocked amino acid residue
    Conformations of a terminally-blocked amino-acid residue disulfide bridges

    E

    Zimmerman, Pottle, Nemethy, Scheraga, Macromolecules, 10, 1-9 (1977)

    C7eq

    C7ax



    G and b turns
    g ECEPP/2 force field- and b-turns

    g-turn (fi+1=-79o, yi+1=69o)

    b-turns


    Types of b turns in proteins
    Types of ECEPP/2 force fieldb-turns in proteins

    Hutchinson and Thornton, Protein Sci., 3, 2207-2216 (1994)


    Older classification
    Older classification ECEPP/2 force field