Download Amino acid

Nucleic Acids
Central dogma of biology
replication
transcription
DNA
translation
RNA
PROTEIN
folding,
assembly,
targeting
FUNCTIONAL
(NATIVE)
PROTEIN
Nucleic acid
• DNA (Deoxyribo Nucleic Acid)
~Store genetic information, Called the blue
print of life
• RNA (Ribo Nucleic Acid)
~Helps in protein synthesis, sometime also
act as enzyme
The pattern of X-ray diffraction by DNA
fibers reveals a helical structure with
steps of 3.4 and 34 Å
This x-ray diffraction by
calf thymus DNA was
measured by Franklin &
Gosling in 1952. The X
pattern is indicative of a
helix with a pitch of 34 Å
per turn. The strong
spots at the top and
bottom reveal internal
steps of 3.4 Å.
http://osulibrary.oregonstate.edu/specialcollections/coll/pauling/dna/pictures/franklin-typeBphoto.html
Structure
• The DNA Molecule consist
of two unbranched
polynucleotides chains
(strands) held together in
an antiparallel manner by
hydrogen bonds formed
between specific pairs of
bases [Adenine-Thymine]
[Guanosine-Cytosine].
DNA
Basic DNA and
RNA Structure
Components
•Sugar
•Base
•Phosphate
• 5’ to 3’ direction
• RNA
ribose extra –OH at 2’ of
ribose
• DNA
deoxyribose
• Numbering
•
Structure of DNA/RNA
Bases and Sugars and Phosphates
pyrimidines
C
T
U
purines
G
A
Ribose
sugars
PDB (http://www.rcsb.org/)
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
ATOM
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
O5'
C5'
C4'
O4'
C3'
O3'
C2'
C1'
N1
C2
O2
N3
C4
N4
C5
C6
P
OP1
OP2
O5'
C5'
DC A
DC A
DC A
DC A
DC A
DC A
DC A
DC A
DC A
DC A
DC A
DC A
DC A
DC A
DC A
DC A
DG A
DG A
DG A
DG A
DG A
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
1
2
2
2
2
2
18.935
19.130
19.961
19.360
20.172
21.350
18.948
19.231
18.070
18.224
19.360
17.143
15.917
14.828
15.719
16.843
22.409
23.536
21.822
22.840
23.543
34.195
33.921
32.668
31.583
32.122
31.325
31.223
30.482
29.661
28.454
28.014
27.761
28.226
27.477
29.442
30.171
31.286
32.157
31.459
29.751
29.175
25.617
24.219
24.100
24.852
22.694
22.681
22.647
23.944
24.380
25.015
25.214
25.377
25.120
25.444
24.471
24.101
21.483
21.851
20.139
21.498
22.594
1.00 64.35
1.00 44.69
1.00 31.28
1.00 37.45
1.00 46.72
1.00 48.89
1.00 30.88
1.00 36.58
1.00 40.51
1.00 16.62
1.00 27.75
1.00 20.55
1.00 34.72
1.00 40.31
1.00 30.78
1.00 25.90
1.00 58.85
1.00 57.82
1.00 78.33
1.00 40.36
1.00 47.19
O
C
C
O
C
O
C
C
N
C
O
N
C
N
C
C
P
O
O
O
C
Standard (Watson-Crick) type base
pairing
Geometry of
Watson Crick
Base Pairs
• A:T and G:C pairs are
spatially similar
• 3 H-bonds vs 2
• Sugar groups are attached
asymmetrically on the same
side of the pair
• Leads to a major and
minor grove
• Bases are flat but the
hydrogen bonding leads to
considerable flexibility
• Base stacking is flexible
Backbone
Conformation
Canonical B DNA
The B-form DNA helix has a diameter of
about 20 Å
Base pairs fill the center of the helix; the phosphates ( ) are on the outside.
A base pair is more exposed to the solvent on one side (the “major groove”,
at the top in these views) than the other (the “minor groove”, bottom).
Canonical B DNA
• First determined experimentally by fiber
diffraction (Arnott)
• C2’-endo sugar puckers
• High anti glycosidic angles
• Right handed – 10 base pairs per turn
• Bases perpendicular to the helix axis and
stacked over the axis
• Overall bending as much as 15 degrees
• Over 230 structures 25 with base mispairing – only cause local perturbations
A DNA
Canonical A DNA
• C3’-endo sugar puckers – brings
consecutive phosphates closer together
5.9Å rather than 7.0Å
• Glycosidic angle from high anti to anti
• Base pairs twisted and nearly 5Å from
helix axis
• Helix rise 2.56 Å rather than 3.4Å
• Helix wider and 11 base pairs per repeat
• Major groove now deep and narrow
• Minor grove wide and very shallow
Z-DNA
•
•
•
•
•
•
Helix has left-handed sense
Narrower, more elongated helix than A or B.
Major "groove" not really groove
Narrow minor groove
Base pairs nearly perpendicular to helix axis
GpC repeat, not single base-pair
– GpC stack: good base overlap
– CpG: less overlap.
• Zigzag backbone due to C sugar conformation
compensating for G glycosidic bond conformation
• Conformations:
– G; syn, C3'-endo
– C; anti, C2'-endo
The two strands of the double helix
separate reversibly at high temperatures
If the temperature is
lowered, the strands
recombine. The rate of
reassociation is inversely
proportional to the
complexity of the DNA.
100
80
% Denatured
The temperature at which
this “denaturation” or
“melting” occurs depends
on the pH and salt
concentration, and
increases with the GC
content of the DNA. (The
curves drawn here are
schematic.)
60
40
40 50 60 70% GC
20
0
70
80
90
100
o
Temperature / C
110
Introduction to Protein
structures
Proteins:Heteropolymers of Amino
acids(aa)
Amino acid nomenclature
• What do we call the pieces?
R-group side chain,
?Ca
?
specific for each
amino acid type
R
CH
?
Amino group
N
C
H
O
Carbonyl
carbon (C’)
?
Carbonyl
oxygen
?
Geometry - bond lengths
(covalent)
• X--H ~ 1 Å
• all others ~ 1.5 Å (approximately),
– e.g. C--O, C--N.
– don’t worry about the differences
– Stretching and compression of bonds is
negligible.
Geometry - bond angles
• Flexibility small: ~ 2.5º.
• Geometry predictable according to valence.
• Where do you find examples of sp³, sp²
hybridization?
Atom
Valence
Nitrogen
3?
4?
Carbon - Ca
Carbon
carbonyl
–
?
4
Hybridization
?2
sp
sp?3
? 2
sp
Coodinat- Bond
ion
angle
?
Trigonal
planar
?
120°
?
tetrahedral
?
109°
?
Trigonalplanar
?
120°
Concepts of Torsion angle
Trigonometric
Representation
The distances and the angle
determine the structure.
dihedral angle
a
b
c
c2  a 2  b2  2ab cos(a^ b)
c
N
a
bond angle
C
b
Cα
N
Basics of Protein Structure
• Primary
• Secondary
• Tertiary
primary structure
ACDEFGHIKLMNPQRSTVWY
Primary structure
PDB Text
ATOM 31 N ARG 5
21.425 -21.153 48.328 1.00 43.65
ATOM 32 CA ARG 5
22.707 -21.847 48.226 1.00 45.28
ATOM 33 C ARG 5
22.546 -23.350 48.428 1.00 46.85
ATOM 34 O ARG 5
22.093 -23.844 49.467 1.00 48.28
ATOM 35 CB ARG 5
23.675 -21.287 49.268 1.00 43.67
ATOM 36 CG ARG 5
25.103 -21.733 49.027 1.00 44.97
ATOM 37 CD ARG 5
26.092 -21.095 50.002 1.00 47.52
ATOM 38 NE ARG 5
27.449 -21.261 49.493 1.00 43.50
ATOM 39 CZ ARG 5
28.418 -20.364 49.676 1.00 41.17
ATOM 40 NH1 ARG 5
28.191 -19.238 50.358 1.00 41.97
ATOM 41 NH2 ARG 5
29.611 -20.613 49.137 1.00 35.84
ATOM 42 N GLN 6
22.916 -24.055 47.360 1.00 48.95
ATOM 43 CA GLN 6
22.845 -25.500 47.291 1.00 52.08
ATOM 44 C GLN 6
23.991 -25.969 46.401 1.00 54.80
ATOM 45 O GLN 6
24.101 -25.571 45.233 1.00 55.99
• (Format A4, 1X, I6, 1X, A4, A4,1X, A1,I4, 4X, 3F8.3)
N
C
C
O
C
C
C
N
C
N
N
N
C
C
http://www.wwpdb.org/documentation/changesv3.20.pdf
Amino acid
Aliphatic (except Gly) – Non-Zwitterionic state;
ESS: Essential
Alanine = Ala = A
Valine = Val = V
M = 71.09; sa = 115; Res. Vol =
88.6; Cry. Den = 1.401
M = 99.4, sa = 155, Res.vol. =
140, Cry. Den = 1.23 ESS
Leucine = Leu = L
Isoleucine = Ile = I
M = 113.16; sa = 170; Res.vol =
166.7; Cry.den = 1.191 ESS
M = 113.16; sa = 175; Res.vol = 166.7;
ESS
Amino acid
Nonpolar – Non-Zwitterionic state
Glycine = Gly = G
Cysteine = Cys = C
M = 57.05; sa = 75;
M = 103.5, sa = 135, Res.vol = 108.5, d
=?
Res.vol= 60.1; d= 1.607
Methionine = Met = M
Proline = Pro= P
M = 131.19; sa = 185; Res.vol = 162.9;
d = 1.34 ESS
M = 97.12; sa = 145; Res. vol
= 112.7; d = ?
Amino acid
Aromatic – Non-Zwitterionic state
Histidine = His = H
M = 137.14; sa = 195;
Res.Vol= 153.2; d= ?
Phenyl alanine = Phe =F
M = 147.18, sa = 210, Res.vol =
189.9, d = ? ESS
Tyrosine = Tyr = T
Tryptophan = Trp = W
M = 163.18; sa = 230; Res. vol = 193.6;
d = 1.456
M = 186.12; sa = 255; Res.vol =
227.8; d = ? ESS
Amino acid
Polar – Non-Zwitterionic state
Asparagine = Asn = N
Glutamine = Gln = Q
M = 115.09; sa = 160;
M = 128.14, sa = 180, Res.vol =
143.8, d = ?
Res.Vol= 114.1; d= 1.54
Serine = Ser = S
Threonine = Thr = T
M = 87.08; sa = 115; Res.vol = 89; d =
1.537
M = 101.11; sa = 140; Res.vol =
116.1; d = ? ESS
Amino acid
Charged – Non-Zwitterionic state
Lysine = Lys = K
Arginine = Arg = R
M = 128.17; sa = 200;
M = 156.19, sa = 225, Res.vol. =
173.4, d = 1.1
Res.Vol= 168.6; d= ? ESS
Aspartic acid = Asp = D
Glutamate = Glu = E
M = 114.11; sa = 150; Res.vol = 111.1; d
= 1.66
M = 129.12; sa = 190; Res.vol =
138.4; d = 1.460
Hydrophobicity Scales
(1) Janin (1979)1; (2) Wolfenden, et al.2; (3) Kyte and
48
Doolittle 3; and (4) Rose, et al.4.
Information about amino acids
http://prowl.rockefeller.edu/aainfo/contents.htm
http://www.realtime.net/anr/aminoacd.html
http://www.people.virginia.edu/~rjh9u/aminacid.html
Hydrophobicity of amino acids
•
J. Janin, Nature, 277(1979)491-492.
•
R. Wolfenden, L. Andersson, P. Cullis and C. Southgate, Biochemistry
20(1981)849-855.
•
J. Kyte and R. Doolite,, J. Mol Biol. 157(1982)105-132.
•
G. Rose, A. Geselowitz, G. Lesser, R. Lee and M. Zehfus, Science
229(1985)834-838.
•
J. Cornette, K. B. Cease, H. Margalit, J. L. Spouge, J. A. Berzofsky and C.
DeLisi, J. Mol. Biol. 195(1987)659-685.
•
M. Charton and B. I. Charton, J. theor. Biol. 99(1982)629-644.
Hydrophobic
Polar
Acidic
Basic
Secondary structure
Secondary Structure:
Phi & Psi Angles Defined
• Rotational constraints emerge from interactions
with bulky groups (ie. side chains).
• Phi & Psi angles define the secondary structure
adopted by a protein.
Ramachandran Plot
a-helix
• Side chains extend outward from helix
• Stabilized by H-bonds between NH and
CO groups of main chain 4 residues apart.
• 1.5 Å between residues along the axis of
the helix. (rise/residue)
• 3.6 amino acid residues per turn.
• helix is right handed (like a right handed
screw).
• Amount of a-helix in a protein varies
• Pauling's discovery
b-Pleated Sheets
• Polypeptide chain is almost fully extended
i.e. not tightly coiled like a-helix.
• 3.5 Å between residues.
• H-bonds occur between directly opposed
strands.
• Antiparallel or parallel: parallel sheets are
less stable since H-bonds are distorted.
• R-groups alternate above and below the
plane of the sheet.
β-pleated sheet
3-10 Helix
p-helix
Type II PP
helix
b-Turns
Structure 
3.613helix -57º

n
-47 º 3.6
p (Å) Atom H-bond
5.4
13
i to i+4
310helix
-50º
-25 º 3
6
10
i to i+3
p-helix
-60º
-70 º 4.4
5.2
16
i to i+5
Poly-P
type II
helix
-75
145
-3
9.3
No
hydrogen
bond
Parallel
b-strand
Antiparallel
-120 115
2.0
6.4
-140 135
2.0
6.8
Inter
strand
Inter
strand
The Ramachandran Representation
of Secondary Structure
Tertiary Structure
Tertiary Structure
Lactate
Dehydrogenase:
Mixed a / b
Immunoglobulin
Fold: b
Hemoglobin B
Chain: a
Protein Structure Databases
• Where does protein structural information
reside?
– PDB:
• http://www.rcsb.org/pdb/
– MMDB:
• http://www.ncbi.nlm.nih.gov/Structure/
– FSSP:
• http://www.ebi.ac.uk/dali/fssp/
– SCOP:
• http://scop.mrc-lmb.cam.ac.uk/scop/
– CATH:
• http://www.biochem.ucl.ac.uk/bsm/cath_new/
Quaternary Structure