Yifrach: Research Interests
Molecular basis for electrical signaling
Voltage-dependent gating of ion channels
Long range effects in proteins: Allostery and
cooperativity in protein function
projects focusing on related aspects of voltage-gated potassium channel function
are currently being addressed in my lab. These
projects are entitled:
Conformational transitions underlying information transduction along allosteric
communication networks of voltage-activated potassium channels
Activation gating of potassium channel pores controlled by hydrophobic
interactions: does a unified mechanism exist?
Intrinsically disordered protein domain of voltage-activated potassium channel
mediates its binding to scaffold proteins: implication for synapse assembly,
maintenance and function.
projects are addressed by integration of a wide range of methodologies including
bioinformatics, theory, molecular biology, cell biology, biochemistry,
biophysics, electrophysiology, thermodynamics and kinetics techniques
Allosteric communication networks of voltage-activated potassium channels.
flow of information between distal elements of a protein may rely on allosteric
communication networks lying along the protein's tertiary or quaternary
structure. Our research in this
project attempts to unravel the underlying features of energy parsing along
allosteric pathways in voltage-gated K+ channels (Kv). We use
high-order thermodynamic coupling analysis (double mutant cycles) to analyze
long-range coupling between the distal functional elements of the Kv channel.
Recent results from our lab highlighted that such allosteric trajectories
are functionally and evolutionary conserved and delineated by sharply-defined
boundaries. Moreover, we demonstrate
that allosteric trajectories assume a hierarchical organization whereby
increasingly stronger layers of cooperative residue interactions act to ensure
efficient and cooperative long-range coupling between distal channel regions.
We suggest that this allosteric trajectory also corresponds to a pathway
of physical deformation. Supported
by theoretical analyses and a striking analogy to studies analyzing the
contribution of long-range residue coupling to protein stability, we suggest
that these experimentally-derived trajectory features are a general property of
Activation gating of potassium channel pores controlled by
channels open and close their pores in response to changes in chemical or
electrical potential. This process
results from mechanical coupling of gating domain movements to pore opening and
closing and is fundamental to many biological processes.
An important, still unresolved, question is whether the gating domain of
a K+ channel exerts a positive force to open or close the pore.
This question is related to the intrinsic stability of the pore domain:
if the pore domain of a K+ channel is detached from its gating
domains, will it stay closed or open? What factors determine the pore's
conformational stability? Possible answers to the latter question may be
provided by sequence, structural and functional comparisons of members of two K+
channel families, the voltage activated K+ channel family (Kv) and
the leak K2P channel family, which demonstrate opposing closed and open pore
conformational stability phenotypes, respectively.
Marked sequence differences at the activation gate region of the two
channel families point to hydrophobic interactions as an important determinant
in modulating conformational stability of K+ channel pores.
this project we aim at testing the
hypothesis that hydrophobic interactions play a crucial role in determining the
conformational stability (open to closed equilibrium) of the K+
channel pore, in a manner analogous to their important role in stabilizing
hydrophobic cores of soluble proteins (unfolded to folded equilibrium).
Preliminary observations imply a general role of hydrophobic interactions
in driving conformational transitions in K+ channels, and suggest a
unified activation gating mechanism for potassium channel pores.
Intrinsically disordered protein segments underlying Kv channel clustering:
implication for synapse assembly, maintenance and function.
interaction of membrane-embedded voltage-activated potassium channels (Kv) with
intracellular scaffold proteins, such as the post-synaptic density 95 (PSD-95)
protein, is mediated by the channel C-terminal segment.
This interaction underlies Kv channel clustering at unique membrane sites
and is important for the proper assembly and functioning of the synapse.
In this project, we address the molecular mechanism underlying Kv-PSD-95
interaction. We have shown that the
isolated C-terminal segment of the archetypical Shaker Kv channel (ShB-C)
is a random coil, suggesting that it belongs to the recently-defined class of
intrinsically disordered proteins. We
further demonstrate that intrinsic disorder in the C-terminal segment of the Shaker
channel modulates its interaction with the PSD-95 protein.
Our results thus far suggest that the C-terminal domain of the Shaker
Kv channel behaves as an entropic chain and support a 'fishing rod' molecular
mechanism for Kv channel binding to scaffold proteins.
The importance of intrinsically disordered protein segments to the
complex processes of synapse assembly, maintenance, and function is now being