Download Amino acid

Struktura proteinů
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Aminokyseliny
Primární
Sekundární
Terciární (Geometrie)
Kvarterní
• Domény, Motivy
Struktura proteinů
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Hlavní řetězec
Vedlejší (boční) řetězce
Het – grupy (hem, Fe4S4 ,Zn2+)
Sacharidy
Solvent
Protein Function in Cell
1. Enzymes
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Catalyze biological reactions
2. Structural role
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Cell wall
Cell membrane
Cytoplasm
General Amino Acid Structure
H
H2N
α
C
R
COOH
General Amino Acid Structure
At pH 7.0
H
+H
N
3
α
C
R
COO-
General Amino Acid Structure
Atom numbering
Cα, Cβ, Cγ, Cδ, Nε, Cζ, Nκ
CA, CB, CG,CD, NE,CZ, NK
A: -CB
I: -CB(CG1)-CG2-CD
R: -CB-CG-CD-NE-CZ(NK1)-NK2
Chirality: Glyceraldehyde
D-glyderaldehyde
L-glyderaldehyde
CORN
20 Naturally-occurring Amino Acids
Single and 3-Letter Codes
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Alanine
Aspartic AciD
Phenylalanine
Histidine
Lysine
Methionine
Proline
ARginine
Threonine
Tryptophan
Ala A
Asp D
Phe F
His H
Lys K
Met M
Pro P
Arg R
Thr T
Trp W
Cysteine
Glutamic Acid
Glycine
Isoleucine
Leucine
AsparagiNe
Glutamine
Serine
Valine
TYrosine
Cys C
Glu E
Gly G
Ile I
Leu L
Asn N
Gln Q
Ser S
Val V
Tyr Y
Properties of the amino acids
aliphatic and aromatic
Side chain
pKa
Amino acid
Occurrence
Molecular
weighta
Volume Å3
Aliphatic
Glycine
Gly
G
7.2
57.05
48
Alanine
Ala
A
7.8
71.09
67
Valine
Val
V
6.6
99.14
105
Leucine
Leu
L
9.1
113.6
124
Isoleucine
Ile
I
5.3
113.6
124
Proline
Pro
P
5.2
97.12
90
Phenylalanine
Phe
F
3.9
147.18
135
Tyrosine
Tyr
Y
3.2
163.18
141
Tryptophan
Trp
W
1.4
186.21
163
Aromatic
aMolecular
10.5
weight of nonionized amino acid minus that of water.
Properties of the amino acids
polar-uncharged and charged
Side chain pKa
Amino acid
Occurrence
Molecular weighta
Vol. Å3
Polar uncharged
Serine
Ser
S
~13
6.8
87.08
73
Threonine
Thr
T
~13
5.9
101.11
93
Cysteine
Cys
C
8.4
1.9
103.15
86
Methionine
Met
M
2.2
131.19
124
Asparagine
Asn
N
4.3
114.11
96
Glutamine
Gln
Q
4.3
128.14
114
Lysine
Lys
K
10.5
5.9
128.17
135
Arginine
Arg
R
12.5
5.1
156.19
148
Histidine
His
H
6.0
2.3
137.14
118
Aspartate
Asp
D
3.9
5.3
115.09
91
Glutamate
Glu
E
4.1
6.3
129.12
109
Positively Charged
Negatively Charged
aMolecular
weight of nonionized amino acid minus that of water.
Polypeptid
Peptide Bond
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The peptide bond influences all aspects of protein structure and function.
Key features:
– 1. Planar
– 2. Fairly rigid, due to partial double bond character.
– 3. Almost always in trans configuration.
– 4. Polar. Can form at least two hydrogen bonds.
– 5. Places restrictions on the conformation of the polypeptide chain.
Geometrie peptidu
Peptidická vazba
Cis - trans
Chemické modifikace
Syntéza
Genetický kód
Acetylace terminální aminoskupiny
Odštěpování částí peptidů (insulin)
Hydroxylace prolinu (hydroxyprolin, Hyp)
Karboxylace glutamové kyseliny
Fosforylace (serin, tyrozin)
Glykoproteiny (glukóza, galaktóza)
Zelené proteiny (medúza)
Disulfide Bonds
• Side chain of cysteine contains highly
reactive thiol group
• Two thiol groups form a disulfide bond
Disulfide Bridge
Disulfide Bridge –
Linking Distant Amino Acids
Protein Structure
Protein Structure
Hemoglobin – Primary Structure
NH2-Val-His-Leu-Thr-Pro-Glu-Glu-
Lys-Ser-Ala-Val-Thr-Ala-Leu-TrpGly-Lys-Val-Asn-Val-Asp-Glu-ValGly-Gly-Glu-…..
beta subunit amino acid sequence
Konformace
Bond Rotation Determines
Protein Folding
G.N. Ramachandran
• Used computer models of small polypeptides to
systematically vary φ and ψ with the objective of finding
stable conformations
• For each conformation, the structure was examined for
close contacts between atoms
• Atoms were treated as hard spheres with dimensions
corresponding to their van der Waals radii
• Therefore, φ and ψ angles which cause spheres to collide
correspond to sterically disallowed conformations of the
polypeptide backbone
Computed Ramachandran Plot
White = sterically
disallowed
conformations (atoms
come closer than sum of
van der Waals radii)
Blue = sterically
allowed conformations
Ramachandran Plot
Experimental Ramachandran Plot
φ, ψ distribution in 42 high-resolution
protein structures (x-ray crystallography)
Specificita Aa
Alanine Ramachandran Plot
Glycine Ramachandran Plot
Note more allowed regions due to less steric hindrance - Turns
Proline Ramachandran Plot
Note less allowed regions due to structure rigidity
Secondary Structural Elements
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α-helices
β-sheets
Turns
Random coil
φ, ψ and Secondary Structure
Name
φ
ψ
Structure
------------------- ------- ------- --------------------------------αR
-57 -47 right-handed alpha helix.
αL
+57 +47 left-handed alpha helix .
310
-49 -26
right-handed helix.
π
-57 -80 right-handed helix.
Type II
-79 150 left-handed helices
formed by polyglycine
and polyproline.
Collagen
-51 153 right-handed coil formed
of three left handed
helicies.
Ramachandran Plot
and Secondary Structure
• Repeating values of φ and ψ along the chain result
in regular structure
• For example,
repeating values of φ ~ -57° and
ψ ~ -47° give a right-handed helical fold (the alphahelix)
The structure of cytochrome C shows many segments
of helix and the Ramachandran plot shows a tight
grouping of φ, ψ angles near -50,-50
alpha-helix
cytochrome C
Ramachandran plot
Similarly, repetitive values in the region of φ = -110 to
–140 and ψ = +110 to +135 give beta sheets. The
structure of plastocyanin is composed mostly of beta
sheets; the Ramachandran plot shows values in the
–110, +130 region:
beta-sheet
plastocyanin
Ramachandran plot
Konformace – „all trans“
α-helices
This is the prototypical
secondary structural
element. It satisfies the
hydrogen bonding
requirements of the
polypeptide chain (except
for the ends).
•Properties
•It is compact and self
contained.
•Right handed
•rise per residue, 1.5 Å,
100o
•Residue per turn, 3.6Å
•H-bond between
C=O(n).... .H-N(n+4)
•period -18 residue, 5 turns
How do you define the start and end of
an α-helix?
α – helix
R-groups are on outside of α-helix
Certain amino acids are "preferred"
& others are rare in α−helices
• Ala, Glu, Leu, Met = good helix formers
• Pro, Gly Tyr, Ser = very poor
Obecné spirály
n/m
n - počet residue na otočku
m - počet atomů v cyklu H-vazby
2.27
310 G
3.613 H αR
4.416 π
310 - helix
Beta-strand
β-sheets
β-sheets fulfill the hydrogen bonding potential of the
main-chain atoms, except at the edges. Adjacent strands
are usually close in sequence.
Properties:
Distance between CA's is ~3.6 Å in an extended strand
Distance between strands ~4.6 Å
Strands are not flat. They have a characteristic righthanded twist
Antiparallel β-sheet
Antiparallel β-sheet
Parallel β-sheet
Mixed β-Sheets also occur
Topologie
Twist
Turns
Turns are a major structural
component of proteins. Without
them there could be no globular
proteins.
They are characterized by an
irregular series of
conformational angles that fold
the chain back on itself.
Turns are often very compact
and well ordered, though they
are hot-spots for evolution.
Sometimes they are sites of
flexibility, at other times they
are quite rigid. Need to look
carefully at the structure.
Turns can be classified into a few
well defined arrangements.
Beta - hairpin
β - vlásenka
Beta-hairpin
Reverse turn
Reverse turn - Rama
Tertiary Structure
• All alpha
• All beta
• Alpha+beta
(mix)
• Alpha/beta
(separated)
Common Structural
Motifs
These simple arrangements of
secondary structural elements
account for most protein
domains. In all cases the
stabilizing interactions occur
within a local area of the
sequence (this is convenient
for evolution). Note also that
all of these motifs are chiral
and are observed almost
exclusively in these
arrangements. Is this a
consequence of the chirality of
the amino acids?
Why are these common?
Domains
• A compact, spatially
distinct unit
• Other definitions
– A region of a protein with
an experimentally
assigned function
– A region of a structure
that recurs in different
contexts in different
proteins
– A region with a separate
hydrophobic core
– …
– Or a combination of these
Quaternary Structure
• Multiple chains form a protein
– collaborate to perform a function
Major secondary
structural elements
of HIV-1 protease
The secondary structure is mostly βstrand and random coil. There is
one small helix and two β-turns.
The β-sheets show their
characteristic twist and associate into
two layers, which is common in βstructures.
The structure is compact, though this
is not apparent in these ribbon
representations.
Space Filling
Representation of
HIV-1 Protease
Ribbon representations are convenient
for showing the path of the
polypeptide chain but are misleading
with respect to the compactness.
What is not evident in this
representation?
Hydrogens? Water? Dynamic
properties?
Hemoglobin: Background
• Protein in red blood cells
• Composed of four subunits, each
containing a heme group: a ring-like
structure with a central iron atom that
binds oxygen
• Picks up oxygen in lungs, releases it in
peripheral tissues (e.g. muscles)
Red Blood Cell (Erythrocyte)
Model Molecule: Hemoglobin
Heme Groups in Hemoglobin
Hemoglobin – Tertiary Structure
One beta subunit (8 alpha helices)
Hemoglobin – Quaternary Structure
Two alpha subunits and two beta subunits
(141 AA per alpha, 146 AA per beta)