Secondary Structure Comparisons

• Secondary Structure Analysis using DSSP
• Sequence Similarity Comparisons of All Secondary Elements
• Sequence Similarity Comparisons of Helical Residue

Secondary Structure Analysis

The different secondary structure elements are identified from the pdb file using DSSP run on the NCSA Biology Workbench at University of Illinois - Urbana Champaign.

DSSP is a program which defines secondary structure and solvent exposure of proteins from atomic coordinates given Protein Data Bank format. DSSP algorithm citation : W. Kabsch and C. Sander (1983) Biopolymers 22: 2577-2637.

IL-4 (1rcb)

1

H

K

C

D

I

T

L

Q

E

I

I

K

T

L

N

S

L

T

E

Q

K

T

L

C

T

E

L

T

V

T

D

I

F

A

A

S

K

N

T

T

E

K

E

T

F

C

R

A

A

T

t

t

s

t

h

h

h

h

h

h

h

h

h

t

t

t

t

s

e

e

e

g

g

g

s

s

h

h

h

h

h

h

h

h

h

h

51

V

L

R

Q

F

Y

S

H

H

E

K

D

T

R

C

L

G

A

T

A

Q

Q

F

H

R

H

K

Q

L

I

R

F

L

K

R

D

L

R

N

L

W

G

L

A

G

L

N

S

C

P

h

h

h

h

h

h

t

t

t

t

t

s

s

s

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

101

V

K

E

A

N

Q

S

T

L

E

N

F

L

E

R

L

K

T

I

M

R

E

K

Y

S

K

C

S

S

e

e

e

h

h

h

h

h

h

h

h

h

h

h

h

h

h = alpha helix, e = beta sheet, g = 3-10 helix, t = hydrogen bonded turn and s = bend.

IL-2 (3ink)

1

A

P

T

S

S

S

T

K

K

T

Q

L

Q

L

E

H

L

L

L

D

L

Q

M

I

L

N

G

I

N

N

Y

K

N

P

K

L

T

R

M

L

T

F

K

F

Y

M

P

K

K

A

h

h

h

h

h

h

h

h

h

h

h

t

t

t

t

h

h

h

h

t

t

s

e

e

e

e

s

51

T

E

L

K

H

L

Q

C

L

E

E

E

L

K

P

L

E

E

V

L

N

L

A

Q

S

K

N

F

H

L

R

P

R

D

L

I

S

N

I

N

V

I

V

L

E

L

K

G

S

E

s

g

g

g

g

h

h

h

h

t

t

h

h

h

h

h

h

h

t

t

s

g

g

g

s

s

s

h

h

h

h

h

h

h

h

h

h

h

h

h

101

T

T

F

M

C

E

Y

A

D

E

T

A

T

I

V

E

F

L

N

R

W

I

T

F

A

Q

S

I

I

S

T

L

T

e

e

e

e

e

e

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

t

t

GMCSF (1gmf)

1

A

P

A

R

S

P

S

P

S

T

Q

P

W

E

H

V

N

A

I

Q

E

A

R

R

L

L

N

L

S

R

D

T

A

A

E

M

N

E

T

V

E

V

I

S

E

M

F

D

L

Q

t

t

t

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

h

t

e

e

e

e

e

s

s

t

t

51

E

P

T

C

L

Q

T

R

L

E

L

Y

K

Q

G

L

R

G

S

L

T

K

L

K

G

P

L

T

M

M

A

S

H

Y

K

Q

H

C

P

P

T

P

E

T

S

C

A

T

Q

I

s

s

h

h

h

h

h

h

h

h

h

h

t

g

g

g

g

g

g

h

h

h

h

h

h

h

h

h

h

h

h

h

h

s

s

s

e

e

e

101

I

T

F

E

S

F

K

E

N

L

K

D

F

L

L

V

I

P

F

D

C

W

E

P

V

Q

E

e

e

h

h

h

h

h

h

h

h

h

h

h

h

h

s

s

s

Sequence Similarity Comparisons

The comparison was done with LALIGN run on the NCSA Biology Workbench at University of Illinois - Urbana Champaign.

LALIGN Algorithm Citation : X. Huang and W. Miller (1991) Adv. Appl. Math. 12 : 373-381.

	IL-4	IL-2	GMCSF
IL-4	---	22.6%	16.1%
IL-2	22.6%	---	17.2%
GMCSF	16.1%	17.2%	---

There is higher sequence similarity between IL-4 and IL-2 than between the interleukins and GMCSF. However, none of these sequence similarity comparisons indicate significant structural or functional relationship among the 3 proteins.

Sequence Comparison of Helical Residues

The similarity was computed again with LALIGN using only residues involved in helices.

	IL-4	IL-2	GMCSF
IL-4	---	15.6%	24.2%
IL-2	15.6%	---	36.8%
GMCSF	24.2%	36.8%	---

In summary, the sequence similarity appears to be higher in the heclical comparisons. It is interesting to note that the helical sequence similarity is higher between the ILs and GMCSF than that between the 2 ILs.

Content

Introduction

Primary

Tertiary

Kingman Ng  

October 25, 1996.