Loading in 5 sec....

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

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

- By
**trinh** - Follow User

- 60 Views
- Uploaded on

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.

Presentation Transcript

Local geometry of polypeptidechainsElements of secondarystructure (turns)

Chirality

Enantiomers

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

Representation of geometry of molecular systems Internalcoordinates

- Cartesiancoordinates
- describeabsolute geometry of a system,
- versatilewith MD/minimizing energy,
- need a moleculargraphics program to visualize.

- describelocal geometry of an atom wrt a selectedreferenceframe,
- withsomeexperience, local geometry can be imaginedwithout a moleculargraphics software,
- mightcauseproblemswhendoing MD/minimizing energy (curvilinearspace).

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)

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)

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

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)

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

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).

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)

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

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

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

side chain

main chain

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

Skan z wykresem energii

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

Side chain conformations is effectively defined by the

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

Some disulfide bridgesandpairs are not allowed due to steric overlap (e.g, ==0o)

The Ramachandran map disulfide bridges

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

E

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

C7eq

C7ax

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

Types of ECEPP/2 force fieldb-turns in proteins

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

Older classification ECEPP/2 force field

Download Presentation

Connecting to Server..