Dr. Ofer 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

 Three projects focusing on related aspects of voltage-gated potassium channel function are currently being addressed in my lab.  These projects are entitled:

1. Conformational transitions underlying information transduction along allosteric communication networks of voltage-activated potassium channels

2.  Activation gating of potassium channel pores controlled by hydrophobic interactions: does a unified mechanism exist?

3. Intrinsically disordered protein domain of voltage-activated potassium channel mediates its binding to scaffold proteins: implication for synapse assembly, maintenance and function.

These 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


1. Allosteric communication networks of voltage-activated potassium channels.

The 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 allosterically-regulated proteins.

2.  Activation gating of potassium channel pores controlled by hydrophobic interactions.

Potassium 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.

In 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.  


3. Intrinsically disordered protein segments underlying Kv channel clustering: implication for synapse assembly, maintenance and function.

The 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 elucidated.

Last Updated: 19/03/2007