13 LC Concepts in Molecular Biology 27.10.2022
Phase Separation 2
Last time we said that the problem we are discussing is how cells manage to create different
compartments; procaryotes and eukaryotes have major differences in complexity, and the major
innovation in this transition is the nucleus, the invention of a new compartment that allows cells to carry
out certain functions in a different compartment (gene transcription) and physically separated from
translation that happens in the cytoplasm. Doing so, creates regulatory layers that otherwise would not be
possible.
Goals of this lecture:
Any phase separation of a protein or mixture of proteins or rnas can be described by these phase diagrams
where you plot the concentration of the substance undergoing a phase separation against the interactions
strengths (which could be any parameter that modulates the strength like ions, ph, temperature). You’re
ending up with a point called the saturation concentration of a protein when it will start to form visible
condensates and as you increase the concentration you get more of this protein from one to two phase
regime.
There a ways to modulate a phase separation: increasing the concentration, so a protein outside of the two
phase regime (red point) can be brought into the phase separating regime, or lowering the temperature,
that will increase the attractive forces between the molecule, resulting a two phase system.
Phase separating proteins are mostly intrinsic disordered,
meaning that they don’t have an encoded alpha helixes or beta strands but are rather flexible swinging
molecules with repetitive interaction units, which gives rise to multivalency and networking.
for the exam
There are certain rules :
- Tyrosine and arginine govern the saturation concentration of LLPS these residues appear to be
important for phase separation to occur. These are basically aromatic and basic residues, and
abolishing the number and position of these residues will increase the saturation concentration,
needing more protein to achieve the PS phase separation.
- There are certain residues that are required for a certain liquidity: Glycine
For maintaining the condensate hardening: glutamine and serine.
, 13 LC Concepts in Molecular Biology 27.10.2022
Modes of interaction
The kind of attractive forces used for P:
- Charge-charge +/-
- Cation-pi: the arginine side chains interactingwith the aromatic rings
of a tyr for instance.
- Dipole-dpole
- Aromatic residues, pi-pi
Are all weak interactions, short range and have diferent sensitivity to salt.
Valence and patterning of aromatic residues determine phase
behavior.
Does the position of an aminoacid really matter?
Let’s think of space separating proteins such one protein that has spacers and sticker; the stickers would be
those residues that attract to each other and the spacers would be something else, something that is
intersparced aand is not directly engaged in these interactions. a simple experiment was done with a wt
protein that has a certain regular pattern and later on it was made regular and perfect with all of the
stickers that are aromatic residues spaced evenly with even distance across the intrinsect disordered
domain // or they made them very pattry with all
the aromatic residues clustered together.
Both simulations were used and to the
condensate was seen that there was not such of a
difference what’s interesting is that the pattry
situation where you clust them together also
leads to a pattriness and inhomogeinity in these
condensates making even aggregates.
So there is an actual different behavior with
keeping the sequence the same, varing the
sosition, ending up either with liquidity or
aggregates.
SUMMARY
Phase Separation 2
Last time we said that the problem we are discussing is how cells manage to create different
compartments; procaryotes and eukaryotes have major differences in complexity, and the major
innovation in this transition is the nucleus, the invention of a new compartment that allows cells to carry
out certain functions in a different compartment (gene transcription) and physically separated from
translation that happens in the cytoplasm. Doing so, creates regulatory layers that otherwise would not be
possible.
Goals of this lecture:
Any phase separation of a protein or mixture of proteins or rnas can be described by these phase diagrams
where you plot the concentration of the substance undergoing a phase separation against the interactions
strengths (which could be any parameter that modulates the strength like ions, ph, temperature). You’re
ending up with a point called the saturation concentration of a protein when it will start to form visible
condensates and as you increase the concentration you get more of this protein from one to two phase
regime.
There a ways to modulate a phase separation: increasing the concentration, so a protein outside of the two
phase regime (red point) can be brought into the phase separating regime, or lowering the temperature,
that will increase the attractive forces between the molecule, resulting a two phase system.
Phase separating proteins are mostly intrinsic disordered,
meaning that they don’t have an encoded alpha helixes or beta strands but are rather flexible swinging
molecules with repetitive interaction units, which gives rise to multivalency and networking.
for the exam
There are certain rules :
- Tyrosine and arginine govern the saturation concentration of LLPS these residues appear to be
important for phase separation to occur. These are basically aromatic and basic residues, and
abolishing the number and position of these residues will increase the saturation concentration,
needing more protein to achieve the PS phase separation.
- There are certain residues that are required for a certain liquidity: Glycine
For maintaining the condensate hardening: glutamine and serine.
, 13 LC Concepts in Molecular Biology 27.10.2022
Modes of interaction
The kind of attractive forces used for P:
- Charge-charge +/-
- Cation-pi: the arginine side chains interactingwith the aromatic rings
of a tyr for instance.
- Dipole-dpole
- Aromatic residues, pi-pi
Are all weak interactions, short range and have diferent sensitivity to salt.
Valence and patterning of aromatic residues determine phase
behavior.
Does the position of an aminoacid really matter?
Let’s think of space separating proteins such one protein that has spacers and sticker; the stickers would be
those residues that attract to each other and the spacers would be something else, something that is
intersparced aand is not directly engaged in these interactions. a simple experiment was done with a wt
protein that has a certain regular pattern and later on it was made regular and perfect with all of the
stickers that are aromatic residues spaced evenly with even distance across the intrinsect disordered
domain // or they made them very pattry with all
the aromatic residues clustered together.
Both simulations were used and to the
condensate was seen that there was not such of a
difference what’s interesting is that the pattry
situation where you clust them together also
leads to a pattriness and inhomogeinity in these
condensates making even aggregates.
So there is an actual different behavior with
keeping the sequence the same, varing the
sosition, ending up either with liquidity or
aggregates.
SUMMARY
