Loops - Protein Structure

Dr.Satyavani
IIITA

Different Levels of Protein

Structures

The primary structure is the sequence

of residues in the polypeptide chain.
Secondary structure is a local
regularly occurring structure in proteins.
Alpha helices
Beta sheets
Loops (Coils, Turns)

Loops of Protein Structures

Most protein
structures are
built up from
Alpha helices
and beta
strands which
are connected
by loop regions.
3

Loops exhibit greater structural variability

than Beta-sheets and Alpha helices.
Loop structure therefore is considerably
more difficult to predict than the structure of
the geometrically highly regular Beta-sheets
and Alpha helices.
Loops are often exposed to the surface of
proteins and contribute to active and
binding sites. Consequently, loops are
crucial for protein function.

A combination of secondary
structure elements forms the stable
hydrophobic core of the molecule.
The loop regions are at the surface
of the molecule.
The main Chain C-O and N-H groups
of the loop regions, which do not
form hydrogen bonds to each other.
5

The loop regions are exposed to

the solvent and can form hydrogen
bonds to water molecules.
Loop regions exposed to solvents
are rich in charged and polar
hydrophilic residues.

This has been used in several

predictions schemes, and it has
proved possible to predict loop
regions from an amino acid
sequence with high degree of
confidence than alpha helices or
beta sheets, which is ironic since
loops have irregular shapes.
7

When homologous amino acid

sequences from different species
are compared, it is found that
insertions and deletions of a few
residues occur almost exclusively
in the loop regions.
During evolution cores are much
more stable than loops.
8

Intron positions are also often found at

sites in structural genes that correspond
to loop regions in the protein structure.

Since proteins that exhibit sequence

homology in general have similar core
structures, it is apparent that the
specific arrangement of secondary
structure elements in the core is rather
insensitive to the lengths of the loop
regions.
9

In addition to their function as

connecting units between secondary
structure elements, loop regions
frequently participate in forming
binding sites and enzyme active
sites.
Thus antigen binding sites in
antibodies are built up from six loop
regions, which vary in both in length
and in amino acid sequence between
different antibodies
10

Modelling antigen binding site from

a known antibody sequence is thus
essentially a problem of modelling
three-Dimensional structures of
loop regions since the core
structures of all antibodies are
very similar.
11

Such model building has been

facilitated by the recent findings that
loop regions have preferred structures.
Surveys of known 3-D structures of
loops have shown that they fall into a
rather limited set of structures and are
not a random collection of possible
structures.
12

Loop regions that connect two

adjacent antiparallel beta strands
are called hairpin loops.
Short hairpin loops are usually
called reverse turns or simply
turns.

13

Long loop regions are often flexible and

can frequently adopt several different
conformations, making them invisible
in X-Ray structure determinations and
undetermined in NMR studies.
Such loops are frequently involved in in
the function of the protein and can
switch from an open confirmation.
14

which allows access to the active

site,
to the closed confirmation, which
sheilds reactive groups in the active
site from water.
Long loops are in many cases
susceptable to proteolytic
degradation.
15

One specific type of long loop, the

omega loop, is compact with good
internal packing interactions and is
therefor quite stable.
Other long loops, which by themselves
would be attacked by proteolytic
enzymes, are stabilized and protected
by binding metal ions, especially
calcium.
16

Turns

Turns are the third of the three "classical"

secondary structures. Approximately onethird of all residues in globular proteins are
contained in turns that serve to reverse the
direction of the polypeptide chain.
This is perhaps not so surprising since the
diameter of the average globular protein
domain is roughly 25 (an extended
polypeptide conformation would require ~7
residues to traverse the domain before
having to change directions).

Turns are located primarily on the

protein surface and accordingly
contain polar and charged
residues. Antibody recognition,
phosphorylation, glycosylation,
hydroxylation, and intron/exon
splicing are found frequently at or
adjacent to turns.
18

Gamma Turn

The hydrogen bond

between CO of
residue i and NH of
residue i+2.
The dihedral angles
of residue i+1 are
(70, -60) and (-70,
60) for phi and psi
of the classical and
inverse gamma
turns.

Type I Turn.

The hydrogen bond

between CO of
residue i and NH of
residue i+3.
The backbone
dihedral angles are (60, -30) and (-90, 0)
of residues i+1 and
i+2, respectively, for
the type I turn.

Proline is often found in position i+1 in type I turns as

its phi angle is restricted to -60 and its amide nitrogen
does not require a hydrogen bond. Glycine is favored
in this position in the type II' as it requires a positive
(left-handed) phi value.

Type II Turn.

The hydrogen bond

between CO of residue i
and NH of residue i+3.
The backbone dihedral
angles are (-60, 120)
and (80, 0) of residues
i+1 and i+2,
respectively, for the
type II turn.
Glycine is favored in this
position in the type II' as
it requires a positive
(left-handed) phi value.

Type III Turn.

The hydrogen bond between CO of residue i and

NH of residue i+3.
This is a single turn of right-handed (III) and lefthanded (III') 310 helix. The backbone dihedral
angles are (-60, -30) and (-60, -30) of residues
i+1 and i+2, respectively, for the classical type
III turn.

Preferred Residues for Sheet

and Turns

Eight most common

residues for betasheet
Val, Ile, Tyr, Trp,
Phe, Leu, Cys, Thr
Eight least common
residues for betasheet
Glu, Asp, Pro, Ser,
Lys, Gly, Ala, Asn

Eight most common

residues for turns
Gly, Asn, Pro, Asp,
Ser, Cys, Tyr, Lys
Eight least common
residues for turns
Ile, Val, Met, Leu,
Phe, Ala, Glu, Trp

Loops

In Leszczynski & Rose (1986), out of 67

proteins surveyed, they tabulated 26 %
helix, 19% sheet, 26 % turns and 21 % in
loops.
These loop structures contain between 6
and 16 residues and are compact and
globular in structure. Like turns, they
generally contain polar residues and
hence are predominantly at the protein
surface.

-hairpin Loop

Adjacent antiparallel strands are joined by hairpin loops. Such loops

are frequently short and do not have regular secondary structure.
Nevertheless, many loop regions in different proteins have similar
structures.

Schematic Structural Diagrams of

Myoglobin

Richardson Diagrams

Myoglobin

Triosephosphate isomerase

Cylinder for helices; arrows for strands, which gives the

direction of the strand from N to C; and the ribbons for the
remaining part.

Beta Sheet Topology

Diagrams

transcarbamoylase flavodoxin

plastocyanin

Beta sheets are usually represented simply by arrows in

topology diagrams that show both the direction of each
strand and the way the strands are connected to each other
along the polypeptide chain.

Super Secondary Structures

(Motifs)

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-Turn-Helix Motif

Two helices that are connected by a short loop

region in a specific geometric arrangement
constitute a helix-turn-helix motif. (a) the DNAbinding motif and (b) the calcium-binding motif,
which are present in many proteins whose function
is regulated by calcium.

EF-hand Calcium-binding
Motif

The calcium atom is bound to one of the motifs in the

muscle protein troponin-C through six oxygen atoms:
one each from the side chains of Asp (D) 9, Asn (N) 11,
and Asp (D) 13; one from the main chain of residue 15;
and two from the side chain of Glu (E) 20. In addition, a
water molecule (W) is bound to the calcium atom.

Amino Acid Sequences of EF-hand

Motifs
1

12

The side chains of hydrophobic residues on the flanking helices

form a hydrophobic core between the helices

The Hairpin Motif

Bovine Trypsin Inhibitor

Snake Venom Erabutoxin

The hairpin motif is very frequent in sheets and is built up

from two adjacent strands that are joined by a loop region.

Greek Key Motif

The Greek key motif is found in antiparallel sheets when

four adjacent strands are arranged in the pattern shown
as a topology diagram in (a). The three dimensional
structure of the enzyme Staphylococcus Nuclease shown
in (b) in blue and red is also a Greek key motif.

 Motif

Two adjacent parallel strands are usually

connected by an helix from the C-terminus of
strand 1 to the N-terminus of strand 2.
Most protein structures that contain parallel
sheets are built up from combinations of such
motifs.

 Handedness

The motif can in principle have two "hands."

(a) This connection with the helix above the sheet is
found in almost all proteins and is called righthanded because it has the same hand as a righthanded helix.
(b) The left-handed connection with the helix below
the sheet.

Domain Organization

Small protein molecules like the epidermal growth

factor, EGF, are comprised of only one domain. Others,
like the serine proteinase chymotrypsin, are arranged in
two domains that are required to form a functional unit.
Many of the proteins that are involved in blood
coagulation and fibrinolysis have long polypeptide
chains that comprise different combinations of domains.