1 / 38

Local geometry of polypeptide chains Elements of secondary structure ( turns )

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

kalb
Download Presentation

Local geometry of polypeptide chains Elements of secondary structure ( turns )

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. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Local geometry of polypeptidechainsElements of secondarystructure (turns)

  2. Levels of protein structure organization

  3. Atom symbols and numbering in amino acids

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

  5. 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).

  6. 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)

  7. 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)

  8. Bond length

  9. Bond (valence) angle

  10. Dihedral (torsional) angle The C-O-H plane is rotated counterclockwise about the C-O bond from the H-C-O plane.

  11. Improper dihedral (torsional) angle

  12. Bond length calculation zj zi xi yi xj xj

  13. Bond angle calculation j aijk i k

  14. Dihedral angle calculation i bijkl k j l

  15. 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)

  16. Need to bring the coordinates to the global coordinate system

  17. Polymer chains 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

  18. 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).

  19. Ring closure 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)

  20. Peptide bond geometry Hybrid of two canonical structures 60% 40%

  21. Electronic structure of peptide bond

  22. Peptide bond: planarity • The partially double character of the peptide bond results in • planarity of peptide groups • their relatively large dipole moment

  23. Side chain conformations: the c angles c1 c2 c3 c1=0

  24. Dihedrals with which to describe polypeptide geometry side chain main chain

  25. Peptide group: cis-trans isomerization Skan z wykresem energii

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

  27. Side chain conformations

  28. The dihedral angles with which to describe the geometry of disulfide bridges

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

  30. The Ramachandran map

  31. Conformations of a terminally-blocked amino-acid residue E Zimmerman, Pottle, Nemethy, Scheraga, Macromolecules, 10, 1-9 (1977) C7eq C7ax

  32. Energy minima of therminally-blocked alanine with the ECEPP/2 force field

  33. g- and b-turns g-turn (fi+1=-79o, yi+1=69o) b-turns

  34. Types of b-turns in proteins Hutchinson and Thornton, Protein Sci., 3, 2207-2216 (1994)

  35. Older classification

More Related