BAHAN KULIAH BIOKIMIA POWER POINT BAGIAN 1 /BIOCHEMISTRY POWER POINT LECTURES PART 1 | Karya Tulis Ilmiah

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Protein Secondary Structure II

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Principles of Protein Structure

Using the Internet

• Useful online resource:

http://www.cryst.bbk.ac.uk/PPS2/

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Peptide Torsion Angles

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Rammachandran plot for L amino acids

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Sidechain torsion rotamers

• named chi1, chi2, chi3,

etc

.

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chi1 angle is restricted

• Due to steric hindrance between the gamma side chain atom(s) and the main chain

• The different conformations referred to as gauche(+), trans

and gauche(-)

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Regular Secondary Structure

Pauling and Corey

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Helices

A repeating spiral, right handed (clockwise twist)

helix

pitch = p

Number of repeating units per turn = n

d = p/n = Rise per repeating unit

Fingers of a right hand.

Several types



, 2.2

₇

ribbon, 3

₁₀

,



helicies, or

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The N

_m

nomenclature for helices

N = the number of repeating units per turn

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The 2.2

₇

Ribbon

•

Atom (1) -O- hydrogen bonds to the 7th atom in the

chain with an N = 2.2 (2.2 residues per turn)

3.0

₁₀

helix

•

Atom (1) -O- hydrogen bonds to the 10th residue in

the chain with an N= 3.

•

Pitch = 6.0 Å occasionally observed but torsion

angles are slightly forbidden. Seen as a single

turn at the end of an



helix.

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The



helix

The most favorable  and  angles with little steric

hindrance.

Forms repeated hydrogen bonds.

N = 3.6 residues per turn

P = 5.4 Å ( What is the d for an  helix?)

The C=O of the nth_{residue points towards the N-H of the}

(N+4)th_residue.

The

N H O

hydrogen bond is 2.8 Å and the atoms are 180o in plane. This is almost optimal with

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Properties of the



helix

• 3.6 amino acids per turn • Pitch of 5.4 Å

• O(i) to N(i+4) hydrogen bonding • Helix dipole

• Negative  and  angles,

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Distortions of alpha-helices

• The packing of buried helices against other

secondary structure elements in the core of the

protein.

• Proline residues induce distortions of around 20

degrees in the direction of the helix axis. (causes

two H-bonds in the helix to be broken)

• Solvent. Exposed helices are often bent away from

the solvent region. This is because the exposed

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3

10

helix

• Three residues per turn

• O(i) to N(i+3) hydrogen bonding

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Proline helix

Left handed helix

3.0 residues per turn

pitch = 9.4 Å

No hydrogen bonding in the backbone but helix

still forms.

Poly glycine also forms this type of helix

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Peptide helicity prediction

• AGADIR

http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html

Agadir predicts the helical behaviour of

monomeric peptides

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Beta sheets

•Hydrogen bonding between adjacent peptide chains.

•Almost fully extended but have a buckle or a pleat.

Much like a Ruffles potato chip

Two types

Parallel

Antiparallel

N N C C N N C C

7.0 Å between pleats on the sheet

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beta () sheet

• Extended zig-zag conformation