Alexei Kurakin

Atypical recognition consensus of CIN85/SETA/Ruk SH3 domains revealed by target-assisted iterative screening

Target-assisted iterative screening applied to random peptide libraries unveiled a novel and atypical recognition consensus shared by CIN85/SETA/Ruk SH3 domains, PX(P/A)XXR. Confirmed by mutagenesis and in vitro binding experiments, the novel consensus allowed for the accurate mapping of CIN85 SH3 binding sites within known CIN85 interactors, c-Cbl, BLNK, Cbl-b, AIP1/Alix, SB1, and CD2 proteins, as well as the prediction of CIN85 novel-interacting partners in protein databases. Synaptojanin 1, PAK2, ZO-2, and TAFII70, which contain CIN85 SH3 recognition consensus sites, were selectively precipitated from mouse brain lysates by CIN85 SH3 domains in glutathione S-transferase pull-down experiments. A direct interaction of synaptojanin 1 and PAK2 with CIN85 SH3 domains was confirmed by Far Western blotting.

Self-organization vs Watchmaker: stochastic gene expression and cell differentiation.

Cell differentiation and organism development are traditionally described in deterministic terms of program and design, echoing a conventional clockwork perception of the cell on another scale. However, the current experimental reality of stochastic gene expression and cell plasticity is poorly consistent with the ideas of design, purpose and determinism, suggesting that the habit of classico-mechanistic interpretation of life phenomena may handicap our ability to adequately comprehend and model biological systems. An alternative conceptualization of cell differentiation and development is proposed where the developing organism is viewed as a dynamic self-organizing system of adaptive interacting agents. This alternative interpretation appears to be more consistent with the probabilistic nature of gene expression and the phenomena of cell plasticity, and is coterminous with the novel emerging image of the cell as a self-organizing molecular system. I suggest that stochasticity, as a principle of differentiation and adaptation, and self-organization, as a concept of emergence, have the potential to provide an interpretational framework that unites phenomena across different scales of biological organization, from molecules to societies.

Self-organization versus Watchmaker: stochastic dynamics of cellular organization

Abstract The cell, as a molecular system, is often interpreted in terms of complex clockworks, and the design charts of mechanical and electrical engineering are assumed to provide adequate approximations for the description of cellular organization. However, a growing body of experimental evidence obtained through the observation and analysis of real-time dynamics of fluorescently labeled molecules inside living cells is increasingly inconsistent with the classico-mechanistic perception of the cell. An overview of recent studies favors an emerging alternative image of the cell as a dynamic integrated system of interconnected and interdependent metastable molecular organizations realized through stochasticity and self-organization.

Novel Mediators of Amyloid Precursor Protein Signaling

Multiple recent reports implicate amyloid precursor protein (APP) signaling in the pathogenesis of Alzheimers disease, but the APP-dependent signaling network involved has not been defined. Here, we report a novel consensus sequence for interaction with the PDZ-1 and PDZ-2 domains of the APP-interacting proteins Mint1, Mint2, and Mint3 (X11α, X11β, and X11γ), and multiple novel interactors for these proteins, with the finding that transcriptional coactivators are highly represented among these interactors. Furthermore, we show that Mint3 interaction with a set of the transcriptional coactivators leads to nuclear localization and transactivation, whereas interaction of the same set with Mint1 or Mint2 prevents nuclear localization and transactivation. These results define new mediators of the signal transduction network mediated by APP.

Target-Assisted Iterative Screening Reveals Novel Interactors for PSD95, Nedd4, Src, Abl and Crk proteins

Abstract A new in vitro screening method has been developed and applied to commercial phage-dis- played cDNA library to search for novel protein-protein interactions. PDZ, WW and SH3 domains from PSD95, Nedd4, Src, Abl and Crk proteins were used as targets. 12 novel putative and 2 previously reported interactions were identified in test screens. The novel screening format, dubbed TAIS (target-assisted iterative screening), is discussed as an alternative platform to existing technologies for pair-wise characterization of protein-protein interactions.

Target-Assisted Iterative Screening of Phage Surface Display cDNA Libraries

The novel screening format, target-assisted iterative screening (TAIS), comprises a simple and rapid two-step procedure for in vitro affinity selection of specific binders from enormous molecular diversities to the target molecule of interest. This detailed protocol describes the application of TAIS to a T7 phage-displayed complementary DNA (cDNA) library with a protein domain as a target. Protocols for purification of the target as glutathione-S-transferase (GST) fusion protein and modifications of the purified target that are required for the screening complement the TAIS protocol. The described application is a method of choice for the researchers interested in the identification and characterization of novel protein-protein interactions mediated by peptide recognition domains.