From DNA to RNA to Protein
- Flow of Information
Monika Oberer
http://strubi.uni-graz.at
WS 2013/14
Strukturbiologie, From DNA to
RNA to Protein
1
Expert of a Letter from Francis
Crick to Sol Spiegelman
http://profiles.nlm.nih.gov/ps/access/
PXBBDP.pdf
Original Repository: Wellcome
Library for the History and
Understanding of Medicine. Francis
Harry Compton Crick PapersURL:
http://archives.wellcome.ac.uk/
Strukturbiologie, From DNA to
RNA to Protein
2
From DNA to RNA to Protein
Interaction of protein with nucleic acids (ProteinDNA interaction, Protein-RNA-interaction)
DNA Replication, DNA Repair
Transcription factors
RNA Transcription
RNA Processing
mRNA Transport
Protein Translation (Ribosome Structure)
http://nobelprize.org/educational_games/medicine/dna/index.html
Strukturbiologie, From DNA to RNA to
Protein
3
Short refresher on DNA, RNA,
and protein structure
Strukturbiologie, DNA-RNA
4
Typical Protein Parameters
5
http://www.imb-jena.de/~rake/Bioinformatics_WEB/basics_peptide_bond.html
Typical Protein Parameters
α-Helix
Diameter: 5.5 Å, (12Å)
6
Typical Protein Parameters
α-Helix
Strukturbiologie, DNA-RNA
7
Typical Protein Parameters
β-Sheet:
Wasserstoffbrückenbindungen zwischen unterschiedlichen Strängen
(Abstand von 7,0 Å). Distanz zwischen vicinalen 3.5 Å.
Strukturbiologie, DNA-RNA
8
Ribonucleotides and
Deoxyribonucleotides
Nucleotides (phosphorylated nucleosides) consist of a ribose ring (-D-ribose
in RNA and -D-2'-deoxyribose in DNA), which is phosphorylated on its 5'position. On its 1'-Position it is connected via a -glycosyl C1'-N bond with one
of 4 heterocyclic bases.
Strukturbiologie, DNA-RNA
9
Nucleotide Bases
Purine nucleotides
DNA, RNA
DNA, RNA
Pyrimidine nucleotides
RNA
DNA
DNA, RNA
Strukturbiologie, DNA-RNA
10
DNA
RNA
5’-3’
direction
Strukturbiologie, DNA-RNA
11
Base pairing and structure in DNA
Most DNA in the cell is double stranded.
Chargaff's rules: %A = %T and %G = %C for double strand
%A ~ %T and %G ~ %C are valid for each of the two DNA strands
DNA is a linear molecule with a diameter of approx. 20-25 Å and a
length of millimeters.
Early diffraction photographs of such DNA fibers (Watson, Crick,
Franklin, Wilkins) revealed two types of DNA structures: B-DNA, which
is obtained when DNA is fully hydrated as it is in vivo and A-DNA,
which is obtained under dehydrated non-physiological conditions.
Furthermore, a third structural form of DNA, called Z-DNA, can be
formed by certain DNA sequences under special circumstances.
Strukturbiologie, DNA-RNA
12
Base pairing and structure in DNA
Watson-Crick
base pairing
%A = %T and %G = %C
for double strand
Strukturbiologie, DNA-RNA
13
Base pairing and structure in RNA
The rule A+C=U+G CAN'T BE
APPLIED THERE
because most RNA is single
stranded and does not form a
double helix.
RNA is not a smooth linear
structure. It has extensive regions
of complementary AU, or GC pairs.
Therefore, the molecule folds on
itself forming structures called
hairpin loops. In the base paired
region, the RNA molecule adopts a
helical structure.
(Some viruses genomes are made of
double stranded RNA)
Strukturbiologie, DNA-RNA
14
DNA double helix occurs as A and B form
Schematic drawing of B-DNA. Each
atom of the sugar-phosphate backbones
of the double helix is represented as
connected circles within ribbons.
In B-DNA the central axis of this double
helix goes through the middle of the
base pairs and the base pairs are
perpendicular to the axis.
Strukturbiologie, DNA-RNA
15
A- and B-DNA
Both A-DNA and B-DNA have the shape of a right-handed
helical staircase. The rails are two antiparallel phosphatesugar chains, and the steps are purine-pyrimidine base
pairs, which are hydrogen bonded to each other.
diameter/
Å
base pairs
per turn
helical twist
angle
spacing/
Å
A-DNA
10.9
33.1
2.9
25.5
B-DNA
10.0
35.9
3.4
23.7
There are considerable variations in individual twist angles
from the average values. These variations are sequence
dependent, and in B-DNA they might be important for the
specificity of interactions with proteins.
Strukturbiologie, DNA-RNA
16
The DNA helix has major and minor grooves
The grooves are of two different widths, reflecting the asymmetrical attachment of the base
pairs to the sugar rings of the backbone, so that the helical molecule has one narrower
groove (minor groove, ca 12 A) and one wider groove (major groove, ca. 22 A). The
edges of the base pairs form the floors of the two grooves. The edge of a base pair furthest
from its attachment points to the sugar-phosphate backbones is the major groove edge;
the one closest is the minor groove edge. These edges are accessible from the outside
and form the basis for the sequence-specific recognition of DNA by proteins.
Strukturbiologie, DNA-RNA
17
DNA recognition
The only regions where the bases are available for
interaction are at the floor of the grooves. These are
paved with nitrogen and oxygen atoms that can make
hydrogen bonds with the side chains of a protein. The
methyl group of thymine and the corresponding
hydrogen in cytosine provide additional discriminatory
recognition groups. These sites form patterns that are
different for the four possible Watson/Crick base pairs.
Strukturbiologie, DNA-RNA
18
DNA recognition
Color codes for the recognition
patterns at the edges of the base
pairs in the major (a) and minor (b)
grooves of B-DNA. Hydrogen-bond
acceptors are red; hydrogen bond
donors are blue. The methyl group
of thymine is yellow, while the
corresponding H atom of cytosine is
white.
W for wide, S for small groove
Strukturbiologie, DNA-RNA
19
DNA recognition
W for wide, S for small groove
Strukturbiologie, DNA-RNA
20
DNA recognition involves the major
groove
The major groove is a much better candidate for sequence-specific
recognition than the minor groove for two reasons. First, the major
groove is wider than the minor, and the bases are thus more
accessible to a protein molecule. Second, the pattern of possible
hydrogen bonds from the edges of the base pairs to a protein are
more specific and discriminatory in the major groove than in the
minor.
Frequently, in order to fit the protein‘s recognition module into the
major groove the B-DNA has to be distorted to be made even wider.
Strukturbiologie, DNA-RNA
21
A small number of base pairs is sufficient for
recognition in the major groove
Color codes for the hexanucleotide recognition sites of
three different restriction enzymes EcoRI, Bal1, and
Sma1 (Nobel Prize1978 to D. Nathans, W. Arber, and H. Smith for the
discovery)—. These patterns are quite different, and each
can be uniquely recognized by specific protein—DNA
interactions.
Strukturbiologie, DNA-RNA
22
Protein-DNA-interaction
Think of numbers or residues (aa, nt), distances, diameters, …
Lambdarepressoroperator complex
(Stayrook et al,
nature, 2008;
pdb-code: 3BDN)
Strukturbiologie, DNA-RNA
23