proteins - lecture 3
Dihydrofolate reductase
This is an enzyme that reduces dihydrofolate to tetrahydrofolate
In cancer cells, uncontrolled cell growth and division require higher levels of nucleotides for DNA synthesis. Inhibiting DHFR disrupts the production of THF, leading to reduced nucleotide synthesis and inhibiting cancer cell proliferation.
myoglobin
153 amino acids
the abilty of myoglobin to bnd to oxygen depends on the presence of heme
its an extremely compact molecule
70% of the chain is in alpha helixes
the interiori is complex and devoid of symetry
shokcingly the inside consists mostly of non polar residues
there are only two polar residues - hisatdines on the inside - these play a vital role in bonding oxygen
it is a globular protein
characteristics of globular proteins - highly compact lacking symetry, souble in water
fibouruos proteins
they use special helixes to facilitate their length
keratin is an example and it consists of two right handed alpha helies which are coiled around each toher to form a left handed superhelix called an alpha helical coiled coil
this creates a very stable structure
collagen
collagen - the most abundent protein in mammals - three helical polypeptide chains
glycine is every third amino acid
Rod shaped 3000Å long 15 Å diameter - 1000 residue polypeptide chains
the collagen helix has different properties to that of the normal alpha helix
there are no hydrogen bonds within the structure
the three sttrands wind around one another to forma superhelical cable
which is then stableised by hyrogen bonds between strands
the interior of this is very crowded and thats why there a glycine every third amino acid
its the only amino acid that can fit on the inside
protein folding and function - disease impact from this
the sharp denaturing of proteins suggest that protein folding is an all or nothing process
that results from cooperative transtion - this is molcularly impossible there will always be transistion states
ie if u have a protein at a tempature where ie of its usbunits is thermodynamically unstable then the entire protein will not work properly due to the loss of the interactions destabilising the rest of the proteins
the essense of protein folding is that it maintains partially correct intermediates
however correct intermediates can be lost particualrly those folded at the beginning
it is almost impossible to predict the folding of a protein from its amino acid sequence
Chaperone Proteins:
Molecular chaperones assist in the folding process, ensuring that proteins reach their functional conformation.
Chaperones prevent misfolding and aggregation and can facilitate correct folding pathways.
Energy Considerations:
Protein folding is energetically favorable, as the folded state is often associated with lower free energy compared to the unfolded state.
Denaturation and Renaturation:
Denaturation involves the disruption of a protein's native structure due to factors like heat or chemical denaturants.
Renaturation, when possible, involves the restoration of the native structure, showcasing the intrinsic ability of proteins to refold.
Protein Folding:
Primary Structure:
The process of protein folding begins with the linear sequence of amino acids, known as the primary structure, which is determined by the genetic code.
Secondary Structure Formation:
Localized folding patterns emerge, forming secondary structures like alpha helices and beta sheets through hydrogen bonding between amino acid residues.
Tertiary Structure Formation:
Interactions between amino acid side chains (R groups) lead to the formation of the protein's three-dimensional tertiary structure.
Hydrophobic interactions, hydrogen bonding, disulfide bonds, and van der Waals forces contribute to the folding.
Quaternary Structure (if applicable):
For proteins consisting of multiple polypeptide chains, the quaternary structure arises as these chains associate with each other.
Chaperone Proteins:
Molecular chaperones assist in the folding process, ensuring that proteins reach their functional conformation.
Chaperones prevent misfolding and aggregation and can facilitate correct folding pathways.
Energy Considerations:
Protein folding is energetically favorable, as the folded state is often associated with lower free energy compared to the unfolded state.
Denaturation and Renaturation:
Denaturation involves the disruption of a protein's native structure due to factors like heat or chemical denaturants.
Renaturation, when possible, involves the restoration of the native structure, showcasing the intrinsic ability of proteins to refold.
Cellular Locations of Protein Folding:
Cytosol:
Many proteins fold in the cytosol, the gel-like substance that fills the cell. These include proteins that function in the cytosol or are destined for organelles such as the nucleus or mitochondria.
Endoplasmic Reticulum (ER):
Proteins targeted for secretion or insertion into membranes often fold in the lumen of the endoplasmic reticulum. This is crucial for quality control and proper post-translational modifications.
Mitochondria and Chloroplasts:
Proteins destined for these organelles fold in the cytosol before being transported and completing their folding inside the organelles.
proteins may undergo further modfications and folding in the golgi apparatus
how a protein folds properly
What is needed for a protein to fold properly
Unfolding of ribonulcease A
Addition of a chemical denaturant - urea
Reducing agent beta -Mercaptoethanol)
Refolding of RnaseA
disease and proteins
Protein folding also serves as a form of quality control for the cell - once the protein has been put into extracellular space there is no return- misfolded or incorrect proteins will cause deposits and this will cause diseases such as parkinsons and
Eat the meat of the damaged protein - crosses blood brain barrier - reaches cells and removed the comfortably souble human cells - causes neurological diseases
Mad cow disease - misfolded proteins become transulent
thermodynamics of protein folding
hydrophilic collapse that occurs in protein folding