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Thymine electron configuration..
α-helix
Fig.4.13. The a-helix. A. Polypeptide backbone showing the arrangements of the H-bonds. The N-H
of the peptide bond make an H-bond with the C=O of a peptide bond 3+ a bit residues further along
the chain. And this pattern repeats for every next peptide bond in the chain. B. Ribbon diagram with
the polypeptide backbone drawn in. C. The ribbon symbolizing the a-helix.
Myoglobin
Fig 4.15 3-D Structure of Myoglobin, a
small oxygen binding protein in muscle. Only
the backbone of protein is indicated plus the
hemegroup. The tube like structures
represent a-helices. Myoglobin consists for
70% of a-helices.
Helices are extremely popular in compact globular proteins because they allow the
packing of an essentially very polar polypeptide chain into a protein with a very
hydrophobic interior. The first protein for which a 3-D structure was obtained,
myoglobin (Perutz and Kendrew 1956-1961, Nobel Prize Chemistry in 1962) showed
70% of a–helix (see figs 4.14 and 4.15).
Myoglobin
Fig. 4.16 Fe(II) heme
(ferroprotoporphyrin IX) shown liganded
to a protein His and O2 as it is in
oxygenated myoglobin and oxygenated
hemoglobin. Note that the heme is a
conjugated system so that all of the Fe-N
bonds are equivalent. Due to the
presence of a second histidine close to
the O2 molecule, the O2 must bind at an
angle of about 45o, thereby lowering the
binding constant for O2, but much more
so for CO.
Fig. 4.18. Structure of
Rhodopsin, the visual protein.
Purple cylinders reflect ahelices, which span the
membrane of a visual cell. The
chromophore, retinal,is
indicated in the center (light
blue). Upon excitation the
retinal chrompohore isomerizes
around its C11-C12 double
bond, which leads to a
rearrangement of H-bonds in
the protein structure, eventually
leading to a small
conformational change that
eventually produces a signal to
the brain.
Membrane proteins:
rhodopsin
Membrane proteins:
photosynthetic reaction center
Fig 4.19. Structure of the bacterial photosynthetic reaction center. The transmembrane part consists of 11 a-helices: 5 from
the L-subunit (yellow), 5 from the M-subunit (red) and 1 from the H-subunit (green). The blue protein is a 4-heme
cytochrome, linked to the reaction center, this cytochrome subunit is only there in some photosynthetic bacteria. The L and
M-subunits are intrinsic membrane proteins, the H-subunit is mainly in the cytoplasm, the cytochrome is mainly in the
periplasmic space. Upon excitation by a photon an electron is transferred by the bacteriochlorophyll cofactors from the
periplasmic side of the protein to the cytosolic side.
Antiparallel and parallel β-sheet
The energetically preferred
dihdreal angles are (φ, ψ) =
(–135°, 135°)
(φ, ψ) about (–140°, 135°) (φ, ψ) about (–120°, 115°)
Anti-parallel β-sheet
The second most-frequently occurring element of secondary structure is the
antiparallel β-sheet. The N-H and C=O groups of a certain strand are hydrogen
bonded to C=O and N-H groups of adjacent chains that run parallel to it, but in the
opposite direction. The R-side groups in each strand alternately project above and
below the plane of the sheet (see fig 4.20)
Anti-parallel β-sheet example:
fibroin
Fig 4.21 Silk fibroin is organized in an anti-parallel b-sheet.
Protein folding
Proteins fold into a unique 3-D structure with a unique biological function. Even a
mutation of one single amino acid may perturb this process in the sense that no
longer a stable structure can be formed, or if it is formed it has no, or a much
reduced, biological activity.
Folded state → minimum in energy
‘Simple’ rules:
1. Two atoms can never be in the same place.
Steric hindering is one of the major driving
forces for the formation of secondary structure
Protein folding
2. Covalent connections between different parts of the chain can be made by disulfide bridges, involving two cysteines (see fig 4.25 and 4.26).
A disulfide bridge in a protein is exceptionally stable.
When a protein is being produced by the ribosome, a certain
number of cysteine residues will be present.
Protein folding
3. Non-covalent interactions.
As a result of ionic interactions, Van der Waals forces and hydrogen bonds,
each type of protein has a particular three dimensional structure, which is
determined by the order of the amino acids in the chain.
Folded proteins
The final folded structure, or conformation, is the one in which the free energy is
minimized (this minimum may not be unique for a system with so many degrees
of freedom).
For globular, water soluble proteins this is generally a compact conformation with
a hydrophobic core and polar/charged residues (such as arginine, glutamine,
histidine etc.) exposed to the aqueous phase
Water → driving force
Folded proteins
When polar residues are
buried in the inside of a
protein they are generally
hydrogen-bonded to other
polar amino acids or to the
polypeptide backbone
Protein folding
A distribution of unfolded species slide on the same
energy surface to reach the minimal free energy
They meet at the saddle point where key residues
have formed their native like contact.
Fig 4.31 Free energy of a
folding protein plotted as a
function of the number of
contacts between residues (not
all are favourable) and the
number of native contacts
(meaning contacts that also
occur in the functional protein).
The potential energy drives the
system to a conformation
where a certain number of
native contacts has been
established, but the chain is not
yet folded. Note that there are
many possible pathways. Once
this point is reached, the chain
folds rapidly.
Denaturation
Protein folding in a living cell is often assisted by special proteins called molecular
chaperones. These proteins bind to partly folded polypeptide chains and help
them progress along the energetically most favorable folding pathway. Chaperones
are vital in the crowded conditions of the cytoplasm, since they prevent the
temporarily exposed hydrophobic regions in newly synthesized proteins from
associating with each other to form protein aggregates.
Structures
In vitro, X-ray
Highly
organised
‘misfolded’
structure
.Disease
Denaturation
Each protein normally folds up into a single stable
configuration. However, this conformation often
changes slightly when the protein interacts with other
proteins in the cell. It is this modulation of the shape of
proteins by its interaction with the ‘environment’ that is
often crucial to the function of the protein.
Membranes
All cells are enclosed in a plasma membrane. This container acts as a selective
barrier that enables the cell to concentrate nutrients gathered from its environment
and retain the products it has synthesized for its own use, while excreting waste
products.
Without its plasma membrane the cell could not maintain its integrity as a
coordinated chemical system.
Integral membrane proteins, like
receptors and channels, cross
the membrane. Receptors often
have specific oligosaccharides
attached to them that play a role
in the recognition of specific
compounds like hormones.
Binding of a hormone then leads
to a conformational change that
is sensed at the cytosolic side of
the membrane.
Transport through membranes
A multitude of
compounds must be
transported into and
out of the cell via the
plasma membrane,
into and out of the
nucleus, mitchondria,
chloroplasts, the
golgi apparatus etc,
including synthesized
proteins!!!
Safety valves
MscL - Structure
Periplasmic side
Transmembrane proteine
Channel proteine forms a large
non-selective ‘safety valve’ to
protect the cell from lysis by
osmotic downshocks
Abundance: Plants, bacteria,
fungi, cardiovascular regulation
in animals (eg. kidneys)
Importance: Highly convenient
molecular system for studies of
elemental principles of
mechanotransduction
Cytoplasmic side
Tb-MscL – ‘closed’ (relaxed) form
Crystal structure: 3.5Å resolution
Crystal Structure: Chang et al Science, 282 (1998), 2220.
Postulated helical structure of S1, also: Sukharev et al., Biophys. J., 81 (2001), 917.
Structure of the
mechanosensitive
sensitive channel MscL.
The channel opens in
response to pressure and
functions as a safety
valve to protect the cell
from lysis by osmotic
pressure.
Cells & membranes
• Nucleus: Genome management
• Mitochondria & chloroplasts: Energy generation
• EP & Golgi complex: protein synthesis and modification
Ion pumps using ATP
3 Na+
[Na+]=140 mM
[K+]=5 mM
2 K+
[Na+]=10 mM
70 mV
[K+]=100 mM
1 ATP
Fig 4.46 The ATP-driven K+-Na+ exchanger. Na+ and K+ are exchanged and
transported across the membrane against their gradients using ATP.