Protein Structure:

Secondary Structure
Motifs and Protein Domains
Laksmi Ambarsari
 I
Supersecondary Structure
Motifs of Proteins
 Types of Secondary Structure
Types of Secondary Structure
-helix 310 helix -helix

Struktur sekunder protein:

alpha helix, beta sheets, and
turns

alpha helix,
distabilkan oleh ikatan
Hidrogen

ikatan H: ggs -NH aa 1

dengan ggs -C=O aa ke-4
 The
TheAlpha
Alpha()
()Helix
Helix

1. Struktur tulang2. Unit peptida? 3. 1 turn coil 3,6 aa

punggung ???
 The
TheAlpha
Alpha()
()Helix
Helix
- Heliks: struktur sekunder berulang dengan struktur
tulang punggung sudut phi dan sudut psi

Psi () the
angle of
rotation about
the C-C bond.

Phi () the
angle of
rotation about
the N-C bond.

The planar bond angles and bond

lengths are fixed.
The
TheHelical
HelicalWheels
Wheels

Helical wheels atau Spiral.

Residu asam amino diplot
setiap (360/3.6) atau
setiap100 diplot aa.

Hijau adalah asam amino

hidrofobik, biru adalah asam
amino polar, dan merah
asam amino bermuatan
Helix
HelixWheels
Wheels
Some
SomeAmino
AminoAcids
Acidsare
arePreferred
PreferredininaaHelix
Helix
Eight Most Common Residues as Helix Formers:
Glu, Met, Ala, Leu, Lys, Phe, Gln, Trp
Eight Least Common Residues as Helix Formers:
Gly, Pro, Asn, Tyr, Cys, Ser, Thr, Arg
 3310 Helix & -Helix
10 Helix & -Helix

alpha 3.10 pi
Ik. H 310-helix,
Ikatan H antara (C=Oi ...
H-Ni+3)

Ik. H -helix,
Ikatan H antara (C=Oi ...
H-bonding H-Ni+5)

Ik. H -helix,
amino acids Ikatan H antara (C=Oi ...
per turn: 3.6 3.0 4.4 H-Ni+4)
frequency ~97% ~3% rare
 Perbedaan , 3 , - Helix
Perbedaan , 310 , - Helix
10

phi Psi H-bond

(deg) (deg) pattern
right-handed alpha-helix -57,8 -47,0 i+4
pi-helix -57.1 -69.7 i+5
3-10 helix -74.0 -4.0 i+3
 -Sheet
-Sheet
phi Psi Omega
(deg) (deg) (deg)
Beta strand -120 120 180

Hydrogen bond patterns in beta sheets. Here a four-stranded

beta sheet is drawn schematically which contains three
antiparallel and one parallel strand. Hydrogen bonds are
indicated with red lines (antiparallel strands) and green lines
(parallel strands) connecting the hydrogen and receptor oxygen.
 Turns/loops
Turns/loops
Secondary structure elements
are
connected by regions of turns
and loops
Loop
Beta-Turn

Loops larger stretches with

Turns short regions no secondary structure.
of non-, non- Often disordered.
conformation Random coil
Sequences vary much
more than secondary
structure regions
 Turns
Turns

there are various types of

turns, differing in the
number of residues and
H-bonding pattern
A -turn is defined by four consecutive residues i, i+1, i+2 and i+3
that do not form a helix and have a C(i)-C(i+3) distance less than
7 and the turn lead to reversal in the protein chain. (Richardson,
1981).
The conformation of -turn is defined in terms of and of two
central residues, i+1 and i+2 and can be classified into different
types on the basis of and .
 Turns
Turns

Type No. of residues H-bonding

-turn 2 NH(i)-CO(i+1)

-turn 3 CO(i)-NH(i+2)

-turn 4 CO(i)-NH(i+3)

-turn 5 CO(i)-NH(i+4)

-turn 6 CO(i)-NH(i+5)
 Loops
Loops
Connect the
secondary structure
elements.
Have various length
and shapes.
Loops are typically
longer, they are
often called coils and
do not have a
regular or
repeating structure Located at the surface of the
folded protein and therefore
may have important role in
biological recognition
processes.
Loops often have polar aa
Preferred
PreferredResidues forSheet
Residuesfor Sheetand
andTurns
Turns

Eight most Eight most

common residues common
for beta-sheet residues for
Val, Ile, Tyr, Trp, turns
Phe, Leu, Cys, Thr Gly, Asn, Pro,
Eight least Asp,
common residues Ser, Cys, Tyr, Lys
for beta-sheet Eight least
Glu, Asp, Pro, Ser, common
Lys, Gly, Ala, Asn residues for
turns
Ile, Val, Met, Leu,
Amino Acid Sequence Reflects Structure

Amino acid sequence of strands 2, 3, and 4 in human

plasma retinol-binding protein.
The sequences are listed in such a way that residues which
point into the barrel are aligned.
These hydrophobic residues are shown by arrows and are
colored green. The remaining residues are exposed to the
solvent.
Supersecondary Structures (Motifs)
Supersecondary Structures (Motifs)
2-10

Simple combinations of a few secondary structure

elements with a specific geometric arrangement
are called super secondary structures or motifs.
They may have functional and structural
significance.
Common motifs:
- Helix-turn-helix
- -hairpin, -meander
- -barrel, Geek key
-
 Helix-loop-helix (Motifs)
Helix-loop-helix (Motifs)

DNA binding motif Calcium binding motif

EF-hand Calcium-binding Motif
 The Hairpin Motif

Bovine Trypsin Inhibitor Snake Venom Erabutoxin

Greek Key Motif
 Motif

Handedness
Leucine-rich Motifs

Consensus amino acid sequence and

secondary structure of the leucine-rich
motifs of type A and type B. X denotes
any amino acid; a denotes an aliphatic
amino acid. Conserved residues are shown
in bold in type B.
In the ribonuclease inhibitor, leucine
residues 2, 5, and 7 from the strand pack
against leucine residues 17, 20, and 24
from the helix as well as leucine residue
12 from the loop to form a hydrophobic
core between the strand and the helix.
Zinc Finger Motifs
 II
Secondary Structure:
Protein Domains
 What are protein domains?
Domain:Polypeptidechain(orapartofit)
thatcanindependentlyfoldintostabletertiary
structure(Baranden&Tooze;IntroductiontoProteinStructure)

Two-domain protein.
 Proteins Domains
Bundle structural domain

A Domain is a compact, semi-independent region of

100-150 amino acids that has a hydrophobic core
and hydrophilic exterior. Domains can be structural
and/or functional
 Proteins Domains

Protein1

Protein2

Protein3

A protein is a combination of domains

 Domain Structures
TIM Barrel Barrel Active Site
 Domain Structures

Open / /horseshoe
Sheet Fold
(Domain) Folds of Protein
Terimakasih
Terimakasih