BAHAN KULIAH BIOKIMIA POWER POINT BAGIAN 1 /BIOCHEMISTRY POWER POINT LECTURES PART 1 | Karya Tulis Ilmiah
Protein Secondary Structure II
Lecture 2/24/2003
Principles of Protein Structure
Using the Internet
• Useful online resource:
http://www.cryst.bbk.ac.uk/PPS2/
• Web-based protein course
Structural hierarchy in proteins
The Polypeptide Chain
Peptide Torsion Angles
Torsion angles determine flexibility of backbone structure
Rammachandran plot for L amino acids
Indicates energetically favorable / backbone rotamers
Steric hindrance limits backbone flexibility
Side Chain Conformation
Sidechain torsion rotamers
• named chi1, chi2, chi3, etc.
e.g. lysine
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(-)
• gauche(+) most common
Regular Secondary Structure
Pauling and Corey
Helix
Sheet
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 , 2.27 ribbon, 310 , helicies, or
the most common is the helix.
Examples of helices
The Nm nomenclature for helices
N = the number of repeating units per turn
M = the number of atoms that complete the cyclic
system that is enclosed by the hydrogen bond.
The 2.27 Ribbon
•Atom (1) -O- hydrogen bonds to the 7th atom in the
chain with an N = 2.2 (2.2 residues per turn)
3.010 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.
•Pi helix 4.416 4.4 residues per turn. Not seen!!
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
favorable Van der Waals interactions within the helix.
alpha helix
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,
Typically = -60 º and = -50 º
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
C=O groups tend to point towards solvent to
maximize their H-bonding capacity
Top view along helix axis
310 helix
•
•
•
•
Three residues per turn
O(i) to N(i+3) hydrogen bonding
Less stable & favorable sidechain packing
Short & often found at the end of helices
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
Collagen: high in Gly-Pro residues has this type of
helical structure
Helical bundle
Helical propensity
Peptide helicity prediction
• AGADIR
http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html
Agadir predicts the helical behaviour of
monomeric peptides
It only considers short range interactions
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
C
C
N
7.0 Å between pleats on the sheet
Widely found pleated sheets exhibit a right-handed twist,
seen in many globular proteins.
Antiparallel beta sheet
Antiparallel beta sheet side view
Parallel beta sheet
Parallel, Antiparallel and Mixed BetaSheets
beta () sheet
• Extended zig-zag
conformation
• Axial distance 3.5 Å
• 2 residues per repeat
• 7 Å pitch
Lecture 2/24/2003
Principles of Protein Structure
Using the Internet
• Useful online resource:
http://www.cryst.bbk.ac.uk/PPS2/
• Web-based protein course
Structural hierarchy in proteins
The Polypeptide Chain
Peptide Torsion Angles
Torsion angles determine flexibility of backbone structure
Rammachandran plot for L amino acids
Indicates energetically favorable / backbone rotamers
Steric hindrance limits backbone flexibility
Side Chain Conformation
Sidechain torsion rotamers
• named chi1, chi2, chi3, etc.
e.g. lysine
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(-)
• gauche(+) most common
Regular Secondary Structure
Pauling and Corey
Helix
Sheet
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 , 2.27 ribbon, 310 , helicies, or
the most common is the helix.
Examples of helices
The Nm nomenclature for helices
N = the number of repeating units per turn
M = the number of atoms that complete the cyclic
system that is enclosed by the hydrogen bond.
The 2.27 Ribbon
•Atom (1) -O- hydrogen bonds to the 7th atom in the
chain with an N = 2.2 (2.2 residues per turn)
3.010 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.
•Pi helix 4.416 4.4 residues per turn. Not seen!!
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
favorable Van der Waals interactions within the helix.
alpha helix
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,
Typically = -60 º and = -50 º
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
C=O groups tend to point towards solvent to
maximize their H-bonding capacity
Top view along helix axis
310 helix
•
•
•
•
Three residues per turn
O(i) to N(i+3) hydrogen bonding
Less stable & favorable sidechain packing
Short & often found at the end of helices
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
Collagen: high in Gly-Pro residues has this type of
helical structure
Helical bundle
Helical propensity
Peptide helicity prediction
• AGADIR
http://www.embl-heidelberg.de/Services/serrano/agadir/agadir-start.html
Agadir predicts the helical behaviour of
monomeric peptides
It only considers short range interactions
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
C
C
N
7.0 Å between pleats on the sheet
Widely found pleated sheets exhibit a right-handed twist,
seen in many globular proteins.
Antiparallel beta sheet
Antiparallel beta sheet side view
Parallel beta sheet
Parallel, Antiparallel and Mixed BetaSheets
beta () sheet
• Extended zig-zag
conformation
• Axial distance 3.5 Å
• 2 residues per repeat
• 7 Å pitch