BURs as Targets for Anticancer Therapy

SIDD profiles (i.e. plots of G versus map position) are potent predictive tools for localizing base-unpairing regions (BURs), which are the hallmarks of S MARs. BURs either consist of one dominant G(x) minimum exceeding a threshold extension of 200-300 bp (see inserts to Figs. 1 and 2) or of a succession of multiple, evenly spaced, but moderately destabilized unpairing elements (UEs). In the latter case, if spacing between restricted UEs exceeds 500 bp, individual elements lose their capacity...

Transmembrane Adaptor Proteins

Transmembrane adaptor proteins (TRAPs) are a group of integral membrane proteins that recruit and assemble signaling molecules proximal to the antigen receptors (Horejsi et al. 2004). These molecules are characterized by short extracellular domains followed by a transmembrane domain and long cytoplasmatic tails containing mainly tyrosine-based interaction motifs. The phosphorylation status of these motifs changes after immunoreceptor ligation and Zap-70 activation, thereby regulating their...

Atypical PKCs A World Apart

Much of what has been discussed to this point applies only to the DAG-responsive PKC isoforms, which include the conventional (a, pi, piI, y) and novel (5, e, 8, n) subgroups. Two atypical PKC isoforms (X and Z) live in a world of their own, including a unique set of scaffolds and a distinct relationship with lipids (Suzuki et al. 2003 Moscat and Diaz-Meco 2000 Hirai and Chida 2003). The atypical PKCs are classified within the PKC family on the basis of modest sequence homol-ogy in the kinase...

Regulation of PDE4

PDE4 activity appears to be regulated at a number of levels, including post-translationally by multi-site phosphorylation (Lim et al. 1999 MacKenzie et al. 2000 MacKenzie et al. 2002), at the transcriptional level (Vicini and Conti 1997 Rena et al. 2001 Wallace et al. 2005) and through regulation of mRNA stability (Liu et al. 2000). Central to coordinating the functional output of regulation by phosphorylation are the UCR1 and UCR2 domains. These interact to, presumably, alter the conformation...

SNARE Proteins

Proteins, lipids, and other biomolecules are transferred among different cellular compartments by transport vesicles, which carry hydrophilic cargoes in the aqueous lumen or hydrophobic ones in the lipid membrane. Crucially, each vesicle must pinch off from the membrane of its parent compartment and recognize and fuse with that of its target compartment in a highly specific and tightly regulated way, such as to release its contents at the right place at the right time (Bennett 1995). In...

Ligand Design for PRDs

A first strategy for PRM PRD inhibition was based on the introduction of non-natural amino acids into the known wild-type peptides (Nguyen et al. 1998, 2000). They demonstrated that the second proline residue of the PxxP motif recognized by SH3 domains could be replaced with -alkylated glycine derivatives to create ligands exhibiting enhanced affinities. Their strategy for inhibitor design can be outlined as follows maintain the required hybrid Ca- and N-substituted scaffold, but vary...

References

Aoki M, Hecht A, Kruse U, Kemler R, Vogt PK (1999) Nuclear endpoint of Wnt signaling neoplastic transformation induced by transactivating lymphoid-enhancing factor 1. Proc Natl Acad Sci USA 96 139-144 Arce L, Yokoyama NN, Waterman ML (2006) Diversity of LEF TCF action in development and disease. Oncogene 25 7492-7504 Barker N, Hurlstone A, Musisi H, Miles A, Bienz M, Clevers H (2001) The chromatin remodelling factor Brg-1 interacts with beta-catenin to promote target gene activation. EMBO J 20...

Mechanism of Nwasp Inhibition by Wiskostatin

Since wiskostatin inhibits the activity of full-length N-WASP, but not that of the isolated VCA domain, this suggested that wiskostatin might perturb the conforma-tional changes in N-WASP that accompany activation. How it might do so was of particular interest because N-WASP is a scaffolding protein not previously known to bind a small molecule. Available three-dimensional structural data for N-WASP that could facilitate prediction of binding sites for wiskostatin are limited to crystal...

Disruption of Akappka Interactions by Genetically Encoded Peptides

In order to study the function of PKA anchoring in cell and animal models, disruptor peptides have been genetically encoded for expression. Generally, this approach overcomes limitations of peptides, such as their short half-life if applied to animals parenterally. In addition, this technique allows for introduction of peptides into cells and possibly animals that are not or are only limitedly accessible to chemical synthesis. Furthermore, encoding peptides genetically permits labelling with...

PDE4 Associates with Different Scaffolding Proteins Modulating Interactions as Treatment for Certain Diseases

Li, and M.D. Houslay(*) 2.1 Structure of 2.2 Regulation of 2.3 Therapeutic Uses and Limitations of PDE4 of 2.5 Intracellular Targeting via Protein-Protein 3 Alternatives to PDE4 Catalytic Site 3.1 Peptide Array Analyses to Identify Protein-Protein Interaction Sites 151 3.2 Disruptor 3.3 Dominant Negative Approach to Inhibition by Abstract cAMP is an ubiquitous second messenger that is crucial to many cellular processes. The sole means of terminating the cAMP signal...

Scaffolds That Regulate Cardiac Hypertrophy 51 mAkappkapde4D3 Complexes

Several AKAPs have been implicated in the coordination of cardiac hypertrophy. The muscle-specific AKAP (mAKAP, the 255-kDa muscle A-kinase anchoring protein) is a multivalent scaffold that binds PDE4D3 (and other signaling proteins, see below), is tethered to the nuclear envelope (through a protein-protein interaction with the integral nuclear membrane protein nesprin-1a), and plays a crucial role to synchronize PKA and PDE4D3 activity in cardiomyocytes (Fig. 3 Pare et al. 2005 Dodge-Kafka et...

Molecular Interactions of Shank Scaffolds Signaling Proteins

Several interactors of the Shank PDZ domains have been suggested to play a role in morphogenic signaling within spines. Most notable, the guanine nucleotide exchange factor PPIX is attached to Shank via this type of interaction, involving the C-terminal PDZ ligand motif of PIX and an additional leucine zipper, also located in the C-terminal region of PPIX (Park et al. 2003). PPIX is an exchange factor for rho GTPases, in particular for cdc42 and rac. Both GTPases have been implicated in the...

IKKgModification Triggers NFkB Activation in Response to DNA Damage

Atm Kinase Interactions

DNA-damaging agents belong to the most widely used anti-cancer drugs. Depending on the extent of damage, the cells are either arrested in the cell cycle to allow DNA repair or the cells undergo apoptosis. The tumor suppressor p53 is a primary sensor of genotoxic stress and induces cell-cycle arrest or apoptosis (Vousden 2002). A major obstacle to an efficient anti-cancer therapy is the activation of NF-KB-mediated pro-survival signaling by DNA-damaging agents. There is a complex crosstalk...

Disruption of AKAP Function by Gene Targeting

Although knockout and RNA strategies have revealed crucial functions of AKAPs in elementary processes whose dysregulation causes disease, it is not clear to which degree the loss of the AKAP function of a protein, i.e. its ability to interact with R subunits of PKA, contributes to the phenotypes because gene knockout deletes all functions of a protein. Knockout of AKAP149 (also termed AKAP1) decreases fertility in female null mutant mice, but not in heterozygotes (Newhall et al. 2006). Oocytes...

Arrestin Binding Sites for the Non Receptor Partners

Selective targeting of arrestin interactions with individual non-receptor partners has a tremendous therapeutic potential. Arrestin functions affect a huge variety of signaling mechanisms (Lefkowitz and Shenoy 2005 Gurevich and Gurevich 2006a), some of which may underlie the pathology of multiple diseases. For example, increases in arrestin expression in the brain of MPTP-treated monkeys with Parkinsonian symptoms (Bezard et al. 2005) and human patients with Parkinson's disease-dementia...

Scaffold Matrix Attachment Regions SMARs DNA at the Scaffold

Obviously, S MARs map to non-random locations in the genome. They occur at the flanks of transcribed regions, in 5'-introns and telomeres, and also at gene breakpoint cluster regions (review Bode et al. 1995). S MARs are association points for common nuclear structural proteins (review Bode et al. 2000b and below) and proved to be required for authentic and efficient chromosomal replication and transcription, for recombination and chromosome condensation. These are the levels of their firmly...

Discovery of AKAP Function

Historically, most AKAPs were initially identified in screens for PKA-binding proteins. Thus, these AKAPs tend to be better characterized. The function and or identity of many other putative AKAPs, however, remains obscure. For cellular processes where it has been suspected that PKA anchoring may be involved, techniques to globally disrupt PKA anchoring in a cell have proven quite useful. A peptide that mimics the Rll-binding domain of AKAP-Lbc (termed Ht31 peptide) competes with AKAP PKA...

EVH1 Domain Structure and Function

The EVH1 domain adopts a structure similar to pleckstrin homology (PH) domains. However, EVH1 domains do not bind to phospholipids. Instead, they mediate specific protein-protein interactions with proline-rich short peptide motifs. This interaction is important for the recruitment of EVH1 domain-harbouring proteins to specific subcellular locations and to membrane receptor complexes. According to their ligand specificity, they can be divided into four classes. Class-I EVH1 domains bind to a...

Role of EnaVASP Proteins in Homeostasis and Disease

1 Domain Structure and Functions of the Ena VASP 1.1 EVH1 Domain Structure and 1.2 Structure and Function of the Proline-Rich Domain 1.3 EVH2 Domain Structure and 2 Protein Complexes Containing Ena VASP 2.1 Listeria 2.2 Focal Adhesions and Stress 2.3 Lamellipodia and Filopodia 2.4 Cell-Cell Junctions 2.5 Immunological Synapse 2.6 Phagosome 3 Regulation of Ena VASP Proteins by 3.1 PKA- and PKG-Dependent Phosphorylation of Ena VASP Proteins 46 3.2 PKA- and PKG-Independent Phosphorylation of Ena...

Role of Coiled Coils in Viral Infection

Coiled-coil interactions are essential not only for vesicular trafficking during intra-cellular protein and lipid transport and intercellular communication using neuro-transmitters (see Sect. 2.2), but they also constitute an indispensable part of the fusion machinery of enveloped viruses. Viruses have to overcome the membrane of the host cell to deliver their genetic material into the cytosol and nucleus so that a new infectious cycle can be established. Viral entry into host cells proceeds...

HnRNPs SAFA

Mattern et al. (1997 and references therein) have identified the most abundant proteins that are exclusively present in the internal nuclear network. In line with earlier reports (Nakayasu and Berezney 1991), many of these belong to the group of heterogeneous nuclear ribonucleoproteins (hnRNPs), the sites of nascent transcripts and RNA maturation. These findings support a model in which major matrix protein constituents are involved in RNA metabolism, packaging and transport. The most abundant...

Molecular Interactions of Shank Scaffolds Anchoring of Postsynaptic Membrane Proteins

Shank proteins interact directly as well as indirectly with postsynaptic membrane proteins and membrane proteins in epithelial tissues, such as kidney and lung direct interactions are mediated by the PDZ domain, which is recognized by type I PDZ ligand motifs (sequence .Xxx-Ser Thr-Xxx-Ile Leu-COO-) at the C-termini of various transmembrane proteins, including G-protein coupled receptors (GPCRs), cell adhesion molecules, ion channels and transport proteins (Kim et al. 2004 Kreienkamp et al....

Proline Rich Sequence Recognition Domains PRD Ligands Function and Inhibition

Sticht, and R. K hne(* ) 1 Small-Molecule Modulators of Protein-Protein Interactions 2 Adaptor Domains as Key Components of PPI-Mediated Signal Complex 3 Properties of the PPII Helix and Principles of PRM 4 Molecular Features of 5 Recognition 6 Regulation of the Binding Function of 7 PRD PRM Complexes as Targets for Pharmacological 7.1 SH3 7.2 WW 7.3 GYF 7.4 EVH1 7.5 UEV 8 Ligand Design for Abstract Low-affinity protein-protein interactions (PPI) between domains...

Small Molecule Inhibitors

In the nucleus, the formation of the Tcf-P-catenin complex is a prerequisite for target gene activation. Targeted interference with this complex formation in colon cancer cells has been shown to effectively abrogate activation of target genes and to inhibit their growth in vitro (Tetsu and McCormick 1999 van de Wetering et al. 2002). Accordingly, small compounds that can specifically disrupt the Tcf-P-catenin complex in vivo hold immense potential for the treatment of Wnt-driven tumors. Earlier...

The Role of PArrestin and AKAPs

The traditional model of PAR activation focuses on the role of the heterotrimeric Gs protein to activate the cAMP pathway. PAR activation also leads to the liberation of GPy dimers that contribute to the recruitment of GRKs to the membrane, leading to phosphorylation of agonist-activated PARs (Fig. 1b). P-arrestin then binds GRK-phosphorylated PARs and acts both to sterically interdict further G protein signaling and to promote PAR desensitization. However, P-arrestins also act as scaffolds for...

Alternatives to PDE4 Catalytic Site Inhibitors

PDE4 enzymes have been the subject of extensive research because of the therapeutic potential of PDE4 inhibitors to treat a number of major disease areas. However, PDE4 inhibitors have been slow to fulfill this therapeutic potential because their use is associated with dose-limiting side effects such as nausea and vomiting. Despite concerted efforts to refine PDE4 inhibitors in order to improve efficacy and minimize side effects, current inhibitors are still largely non-selective. The universal...

AKAPs as Drug Targets

Due to the pleiotropic effects of cAMP signaling, it is no surprise that current therapies for some human diseases include the use of drugs that affect cAMP levels. For example, P-adrenergic agonists are a mainstay of asthma therapy due to cAMP-mediated relaxation of bronchial smooth muscle. In a complementary fashion, caffeine and theophylline have been used to inhibit phosphodiesterases. The problem with current cAMP-directed therapies is that many such drugs have unacceptable side effects....

Relevance of an Allosteric Pakl Inhibitor

Current methods used to eliminate Pak1 function include classical genetic knockout Hofmann et al. 2004 as well as transfection of interfering reagents, such as siRNAs Tang et al. 2005 , constructs encoding the IS and KI sequence elements Beeser and Chernoff 2005 , or catalytically inactive, full-length versions of the kinase Adam et al. 2000 . These approaches, while useful in abrogating Pak1 activity, are limited in their degree of control of Pak1 activity, as well as by a lack of control over...

Autoinhibition of mDial

A number of studies have begun to unravel the mechanism of mDial autoinhibition. Early cellular studies utilizing truncated mDial constructs demonstrated the involvement of both N-terminal and C-terminal domains in the regulation of mDia-mediated actin filament assembly Watanabe et al. 1997 Tominaga et al. 2000 Alberts 2001 . Subsequently, these regulatory activities were discovered to be the result of an interaction between a domain in the amino terminus of mDial termed the diaphanous...

Properties of the PPII Helix and Principles of PRM Recognition

A common property of all PRMs is that they preferentially form a left-handed poly-proline type-II PPII helix with an overall shape resembling a triangular prism Kay et al. 2000 . This structural element has a helical pitch of 9.3 , three residues per turn, and F and Y angles centered around -75 and 145 , respectively Bochicchio and Tamburro 2002 Cubellis et al. 2005 . The PPII helix is characterized by a complete lack of main-chain hydrogen bonding patterns that are commonly used to identify...

Domain Interactions as Potential Drug Targets

Protein-protein interactions preside over the physiological and pathological processes in living organisms. Therefore, the ability to intervene in a controlled manner in the protein interaction network, altering its wiring by specifically favoring certain interactions and blocking others, is crucial for molding the cell response into a desired phenotype. Examples of the efficacy of such strategy is witnessed by the modus operandi of some known pathogens, such as the Epstein-Barr virus EBV...