Structure of a regulatory complex involving the Abl SH3 domain, the Crk SH2 domain, and a Crk-derived phosphopeptide

Specificity and versatility of SH3 and other proline-recognition domains: structural basis and implications for cellular signal transduction

Protein-protein interactions occurring via the recognition of short peptide sequences by modular interaction domains play a central role in the assembly of signalling protein complexes and larger protein networks that regulate cellular behaviour. In addition to spatial and temporal factors, the specificity of signal transduction is intimately associated with the specificity of many co-operative, pairwise binding events upon which various pathways are built. Although protein interaction domains are usually identified via the recognition code, the consensus sequence motif, to which they selectively bind, they are highly versatile and play diverse roles in the cell. For example, a given interaction domain can bind to multiple sequences that exhibit no apparent identity, and, on the other hand, domains of the same class or different classes may favour a given consensus motif. This promiscuity in ligand selection is typified by the SH3 (Src homology 3) domain and several other interaction modules that commonly recognize proline-rich sequences. Furthermore, interaction domains are highly adaptable, a property that is essential for the evolution of novel pathways and modulation of signalling dynamics. The ability of certain interaction domains to perform multiple tasks, however, poses a challenge for the cell to control signalling specificity when cross-talk between pathways is undesired. Extensive structural and biochemical analysis of many interaction domains in recent years has started to shed light on the molecular basis underlying specific compared with diverse binding events that are mediated by interaction domains and the role affinity plays in affecting domain specificity and regulating cellular signal transduction.

Weak protein-protein interactions as probed by NMR spectroscopy

Weak protein-protein interactions (PPIs) are fundamental to many cellular processes, such as reversible cell-cell contact, rapid enzyme turnover and transient assembly and/or reassembly of large signaling complexes. However, structural and functional characterizations of weak PPIs have been technically challenging and lagged behind those for strong PPIs. Here, we describe nuclear magnetic resonance (NMR) spectroscopy as a highly effective tool for unraveling the atomic details of weak PPIs. We highlight the recent advances of how NMR can be used to rapidly detect and structurally determine extremely weak PPIs (K(d)>10(-4)M). Coupled with functional approaches, NMR has the potential to look into a wide variety of biologically important weak PPIs at the detailed molecular level, thereby facilitating a thorough view of how proteins function in living cells.

Uncoupling Crk signal transduction by Pseudomonas exoenzyme T

Exoenzyme T (ExoT) is a bifunctional type III cytotoxin of Pseudomonas aeruginosa that possesses both Rho GTPase-activating protein and ADP-ribosyltransferase activities. The ADP-ribosyltransferase activity of ExoT stimulated depolymerization of the actin cytoskeleton independent of Rho GTPase-activating protein function, and ExoT was subsequently shown to ADP-ribosylate Crk (CT10 regulator of kinase)-I and Crk-II. Crk proteins are eukaryotic adaptor proteins comprising SH2 and SH3 domains that are components of the integrin signaling pathway leading to Rac1 and Rap1 functions. Mass spectroscopic analysis identified Arg20 as the site of ADP-ribosylation by ExoT. Arg20 is a conserved residue located within the SH2 domain that is required for interactions with upstream signaling molecules such as paxillin and p130cas. Glutathione S-transferase pull-down and far Western assays showed that ADP-ribosylated Crk-I or Crk-I(R20K) failed to bind p130cas or paxillin. This indicates that ADP-ribosylation inhibited the direct interaction of Crk with these focal adhesion proteins. Overexpression of wild-type Crk-I reduced cell rounding by ExoT, whereas expression of dominant-active Rac1 interfered with the ability of ExoT to round cells. Thus, the ADP-ribosylation of Crk uncouples integrin signaling by direct inhibition of the binding of Crk to focal adhesion proteins.

The SH2 domain: versatile signaling module and pharmaceutical target

The Src homology 2 (SH2) domain is the most prevalent protein binding module that recognizes phosphotyrosine. This approximately 100-amino-acid domain is highly conserved structurally despite being found in a wide variety proteins. Depending on the nature of neighboring protein module(s), such as catalytic domains and other protein binding domains, SH2-containing proteins play many different roles in cellular protein tyrosine kinase (PTK) signaling pathways. Accumulating evidence indicates SH2 domains are highly versatile and exhibit considerable flexibility in how they bind to their ligands. To illustrate this functional versatility, we present three specific examples: the SAP, Cbl and SOCS families of SH2-containing proteins, which play key roles in immune responses, termination of PTK signaling, and cytokine responses. In addition, we highlight current progress in the development of SH2 domain inhibitors designed to antagonize or modulate PTK signaling in human disease. Inhibitors of the Grb2 and Src SH2 domains have been extensively studied, with the aim of targeting the Ras pathway and osteoclastic bone resorption, respectively. Despite formidable difficulties in drug design due to the lability and poor cell permeability of negatively charged phosphorylated SH2 ligands, a variety of structure-based strategies have been used to reduce the size, charge and peptide character of such ligands, leading to the development of high-affinity lead compounds with potent cellular activities. These studies have also led to new insights into molecular recognition by the SH2 domain.

Photophysics and Biological Applications of the Environment-Sensitive Fluorophore 6-N,N-Dimethylamino-2,3-naphthalimide

We have synthesized a new environment-sensitive fluorophore, 6-N,N-dimethylamino-2,3-naphthalimide (6DMN). This chromophore exhibits valuable fluorescent properties as a biological probe with emission in the 500-600 nm range and a marked response to changes in the environment polarity. The 6DMN fluorescence is red-shifted in polar protic environments, with the maximum emission intensity shifting more than 100 nm from 491 nm in toluene to 592 nm in water. Additionally, the fluorescence quantum yield decreases more than 100-fold from chloroform (Phi = 0.225) to water (Phi = 0.002). The scope and applications of the 6DMN probe are expanded with the synthesis of an Fmoc-protected amino acid derivative (5), which contains the fluorophore. This unnatural amino acid has been introduced into several peptides, demonstrating that it can be manipulated under standard solid-phase peptide synthesis conditions. Peptides incorporating the new residue can be implemented for monitoring protein-protein interactions as exemplified in studies with Src homology 2 (SH2) phosphotyrosine binding domains. The designed peptides exhibit a significant increase in the quantum yield of the long wavelength fluorescence emission band (596 nm) upon binding to selected SH2 domains (e.g., Crk SH2, Abl SH2, and PI3K SH2). The peptides can be used as ratiometric sensors, since the short wavelength band (460 nm) was found almost invariable throughout the titrations.

Regulation of integrin-mediated cellular responses through assembly of a CAS/Crk scaffold

The molecular coupling of CAS and Crk in response to integrin activation is an evolutionary conserved signaling module that controls cell proliferation, survival and migration. However, when deregulated, CAS/Crk signaling also contributes to cancer progression and developmental defects in humans. Here we highlight recent advances in our understanding of how CAS/Crk complexes assemble in cells to modulate the actin cytoskeleton, and the molecular mechanisms that regulate this process. We discuss in detail the spatiotemporal dynamics of CAS/Crk assembly and how this scaffold recruits specific effector proteins that couple integrin signaling networks to the migration machinery of cells. We also highlight the importance of CAS/Crk signaling in the dual regulation of cell migration and survival mechanisms that operate in invasive cells during development and pathological conditions associated with cancer metastasis.

Sequence, structure and energetic determinants of phosphopeptide selectivity of SH2 domains

Here, we present an approach for the prediction of binding preferences of members of a large protein family for which structural information for a number of family members bound to a substrate is available. The approach involves a number of steps. First, an accurate multiple alignment of sequences of all members of a protein family is constructed on the basis of a multiple structural superposition of family members with known structure. Second, the methods of continuum electrostatics are used to characterize the energetic contribution of each residue in a protein to the binding of its substrate. Residues that make a significant contribution are mapped onto the protein sequence and are used to define a "binding site signature" for the complex being considered. Third, sequences whose structures have not been determined are checked to see if they have binding-site signatures similar to one of the known complexes. Predictions of binding affinity to a given substrate are based on similarities in binding-site signature. An important component of the approach is the introduction of a context-specific substitution matrix suitable for comparison of binding-site residues. The methods are applied to the prediction of phosphopeptide selectivity of SH2 domains. To this end, the energetic roles of all protein residues in 17 different complexes of SH2 domains with their cognate targets are analyzed. The total number of residues that make significant contributions to binding is found to vary from nine to 19 in different complexes. These energetically important residues are found to contribute to binding through a variety of mechanisms, involving both electrostatic and hydrophobic interactions. Binding-site signatures are found to involve residues in different positions in SH2 sequences, some of them as far as 9A away from a bound peptide. Surprisingly, similarities in the signatures of different domains do not correlate with whole-domain sequence identities unless the latter is greater than 50%. An extensive comparison with the optimal binding motifs determined by peptide library experiments, as well as other experimental data indicate that the similarity in binding preferences of different SH2 domains can be deduced on the basis of their binding-site signatures. The analysis provides a rationale for the empirically derived classification of SH2 domains described by Songyang & Cantley, in that proteins in the same group are found to have similar residues at positions important for binding. Confident predictions of binding preference can be made for about 85% of SH2 domain sequences found in SWISSPROT. The approach described in this work is quite general and can, in principle, be used to analyze binding preferences of members of large protein families for which structural information for a number of family members is available. It also offers a strategy for predicting cross-reactivity of compounds designed to bind to a particular target, for example in structure-based drug design.

Assembling atomic resolution views of the immunological synapse

Antigen-dependent T-cell activation is initiated by the organized interactions of a host of cell-surface receptors in the interface between the T cell and an antigen-presenting cell. Recent structural studies of many of the receptors that comprise this 'immunological synapse', including integrins, cadherins and co-stimulatory molecules, reveal in detail the molecular interactions that bridge the synapse. Additionally, structural analyses of the cytoplasmic tails of integrins and co-stimulatory receptors in complex with intracellular signaling proteins are providing insight into the mechanisms that couple receptor clustering on the cell surface with the initiation of cytoplasmic signaling.

Assembly of cell regulatory systems through protein interaction domains

The sequencing of complete genomes provides a list that includes the proteins responsible for cellular regulation. However, this does not immediately reveal what these proteins do, nor how they are assembled into the molecular machines and functional networks that control cellular behavior. The regulation of many different cellular processes requires the use of protein interaction domains to direct the association of polypeptides with one another and with phospholipids, small molecules, or nucleic acids. The modular nature of these domains, and the flexibility of their binding properties, have likely facilitated the evolution of cellular pathways. Conversely, aberrant interactions can induce abnormal cellular behavior and disease. The fundamental properties of protein interaction domains are discussed in this review and in detailed reviews on individual domains at Science's STKE at http://www.sciencemag.org/cgi/content/full/300/5618/445/DC1.

Translocation of CrkL to focal adhesions mediates integrin-induced migration downstream of Src family kinases

The adapter protein Crk-Like (CrkL) can associate with the Src substrate p130(Cas) (Cas). The biological role of CrkL downstream of Cas, however, has been largely obscure. Consistent with the ability of CrkL to biochemically associate with Cas, we found that Src triggers translocation of CrkL to focal adhesions (FAs) in a manner dependent on Cas. Forced localization of CRKL to FAs (FA-CRKL) by itself was sufficient to induce activation of Rac1 and Cdc42 and rescued haptotaxis defects of mouse embryonic fibroblasts (MEFs) lacking Src, Yes, and Fyn, three broadly expressed Src family members required for integrin-induced migration. Consistent with Rac1 activation, FA-CRKL induced cotranslocation of a Rac1 activator, Dock1, to focal adhesions. These results therefore indicate a role for CrkL in mediating Src signaling by activating small G proteins at focal adhesions. Furthermore, MEFs lacking CrkL show impaired integrin-induced migration despite expression of a closely related protein, Crk-II, in these cells. These results therefore provide formal evidence that CrkL plays a specific role in integrin-induced migration as a downstream mediator of Src.