Exploiting the basis of proline recognition by SH3 and WW domains: design of N-substituted inhibitors

Encodamers: unnatural peptide oligomers encoded in RNA

Conventional display libraries are generally limited to the 20 naturally occurring amino acids. Here, we demonstrate that novel unnatural amide-linked oligomers can be constructed and encoded in an attached RNA for the purpose of mRNA display library design. To do this, we translated templates of various lengths in a protein synthesis system modified to promote sense codon suppression. Unnatural residues were escorted to the ribosome as chemically acylated tRNAs added to the translation mixture. Our experiments reveal that unnatural peptide oligomers ("encodamers") consisting of an N-substituted amino acid are readily generated as mRNA-peptide fusions with excellent stepwise efficiency. The N-substituted polyamides have strikingly improved proteolytic stability relative to their naturally encoded counterparts. Overall, our work indicates that the ribosome can be used as a synthesis platform to generate encoded combinatorial chemistry outside the universal genetic code.

A Miniprotein Scaffold Used to Assemble the Polyproline II Binding Epitope Recognized by SH3 Domains

SH3 domains are molecular-recognition modules that function by interacting with proteins containing sequences in polyproline II (PPII) conformation. The main limitation in designing short-ligand peptides to interact with these domains is the preservation of this helical arrangement, for which a high content of proline is needed. We have overcome this limitation by using a protein scaffold provided by the avian pancreatic polypeptide (APP), a natural hormone of 36 amino acid residues. The APP protein contains a PPII stretch packed against an alpha-helix. We have designed a structure in which some residues of the APP PPII helix are replaced by a sequence motif, named RP1, which interacts with the SH3 domain of the Abelson tyrosine kinase (Abl-SH3). This design, which we call APP-RP1, is folded and, as shown by circular dichroism, has a structural content similar to that of natural APP (APP-WT). The stability of both miniproteins has been compared by unfolding experiments; the designed APP-RP1 is almost 20 deg. C more stable than the wild-type and has a higher Gibbs energy function. This increase in stability has an entropic origin. Isothermal titration calorimetry and fluorescence spectroscopy show that the thermodynamics of the binding of the APP-RP1 molecule to Abl-SH3 is comparable to that of the shorter RP1 peptide. Furthermore, the mutation by Tyr of two proline residues in APP-RP1, which are essential for the binding of some linear peptides to Abl-SH3, demonstrates the effectiveness of the scaffold in enhancing the variability in the design of high-affinity and high-specificity ligands for any SH3 domain. The application of this strategy may help in the design of ligands for other polyproline-recognition domains such as WW, PX or EVH1, and even for the in vivo application of these miniproteins.

Common mechanism of ligand recognition by group II/III WW domains: redefining their functional classification

WW domain is a well known protein module that mediates protein to protein interactions by binding to proline-containing ligands. Based on the ligand predilections, the WW domains have been classified into four major groups. Group II and III WW domains have been reported to bind the proline-leucine and proline-arginine motifs, respectively. In the present study, using surface plasmon resonance technique we have shown that these WW domains have almost indistinguishable ligand preferences and kinetic properties. Hence, we propose that Group II and III WW domains should be joined together as one group (Group II/III). Unlike Group I and IV WW domains, Group II/III WW domains can bind simple polyprolines as well as the proline-leucine and proline-arginine motifs, and they possess two Xaa-proline (where Xaa is any amino acid) binding grooves similar to SH3 domains. Our work assigns Group II and III WW domains to a larger family of polyproline-binding modules and proteins, which includes SH3 domains and profilin. Because polyprolines belong to the most frequently found peptide motifs in several genomes, our study implies the versatile importance of Group II/III WW domains in signaling.

Ligand-regulated association of ErbB-4 to the transcriptional co-activator YAP65 controls transcription at the nuclear level

It has been proposed that ligand-dependent Regulated Intramembrane Proteolysis (RIP) of ErbB-4 receptors generates 80 kDa Intra-Cellular Domains (E4.ICDs) that relocate to the nuclear compartments where they implement the signaling abilities of the ErbB-4 receptors. The E4.ICD may directly regulate gene transcription or, in an alternative scenario, the tyrosine kinase activity of E4.ICDs may target proteins involved in transcriptional regulation upon its relocation into the nucleus. We have identified the transcriptional coactivator YAP65, here referred as YAP (Yes Associated Protein), as binding partner of ErbB-4 in a two hybrid screening in yeast. Interaction between YAP and ErbB-4 occurs via the WW domain of YAP and the PPPPY at positions 1297-1301 and the PPPAY at positions 1052-1056 of the amino acid sequence of the Cyt-1 isoform of ErbB-4. Stechiometry of binding is regulated by the ligand-dependent phosphorylation of Tyr 1056 in the PPPAYTPM module that function as "biochemical switch" to decrease the association of YAP to ErbB-4. In principle, this novel interaction highlights new mechanisms of signaling propagation from the ErbB-4 receptors, offering supporting evidences that the E4.ICDs forms released following ligand-receptor engagement may recruit YAP and relocate to the nucleus to implement or regulate transcription.

Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain

Because of the association of beta-sheet formation with the initiation and propagation of amyloid diseases, model systems have been sought to further our understanding of this process. WW domains have been proposed as one such model system. Whereas the folding of the WW domains from human Yes-associated protein (YAP) and Pin have been shown to obey single-exponential kinetics, the folding of the WW domain from formin-binding protein (FBP) 28 has been shown to proceed via biphasic kinetics. From an analysis of free-energy landscapes from atomic-level molecular dynamics simulations, the biphasic folding kinetics observed in the FBP WW domain may be traced to the ability of this WW domain to adopt two slightly different forms of packing in its hydrophobic core. This conformational change is propagated along the peptide backbone and affects the position of a tryptophan residue shown in other WW domains to play a key role in binding. The WW domains of Pin and YAP do not support more than one type of packing each, leading to monophasic folding kinetics. The ability of the FBP WW domain to assume two different types of packing may, in turn, explain the capacity of this WW domain to bind two classes of ligand, a property that is not shared by other WW domains. These findings lead to the hypothesis that lability with respect to conformations separated by an observable barrier as a requirement for function is incompatible with the ability of a protein to fold via single-exponential kinetics.

Structural basis of leukotriene B4 12-hydroxydehydrogenase/15-Oxo-prostaglandin 13-reductase catalytic mechanism and a possible Src homology 3 domain binding loop

The bifunctional leukotriene B(4) 12-hydroxydehydrogenase/15-oxo-prostaglandin 13-reductase (LTB(4) 12-HD/PGR) is an essential enzyme for eicosanoid inactivation. It is involved in the metabolism of the E and F series of 15-oxo-prostaglandins (15-oxo-PGs), leukotriene B(4) (LTB(4)), and 15-oxo-lipoxin A(4) (15-oxo-LXA(4)). Some nonsteroidal anti-inflammatory drugs (NSAIDs), which primarily act as cyclooxygenase inhibitors also inhibit LTB(4) 12-HD/PGR activity. Here we report the crystal structure of the LTB(4) 12-HD/PGR, the binary complex structure with NADP(+), and the ternary complex structure with NADP(+) and 15-oxo-PGE(2). In the ternary complex, both in the crystalline form and in solution, the enolate anion intermediate accumulates as a brown chromophore. PGE(2) contains two chains, but only the omega-chain of 15-oxo-PGE(2) was defined in the electron density map in the ternary complex structure. The omega-chain was identified at the hydrophobic pore on the dimer interface. The structure showed that the 15-oxo group forms hydrogen bonds with the 2'-hydroxyl group of nicotine amide ribose of NADP(+) and a bound water molecule to stabilize the enolate intermediate during the reductase reaction. The electron-deficient C13 atom of the conjugated enolate may be directly attacked by a hydride from the NADPH nicotine amide in a stereospecific manner. The moderate recognition of 15-oxo-PGE(2) is consistent with a broad substrate specificity of LTB(4) 12-HD/PGR. The structure also implies that a Src homology domain 3 may interact with the left-handed proline-rich helix at the dimer interface and regulate LTB(4) 12-HD/PGR activity by disruption of the substrate binding pore to accommodate the omega-chain.

The tryptophan switch: changing ligand-binding specificity from type I to type II in SH3 domains

The ability of certain Src homology 3 (SH3) domains to bind specifically both type I and type II polyproline ligands is perhaps the best characterized, but also the worst understood, example in the family of protein-interaction modules. A detailed analysis of the structural variations in SH3 domains, with respect to ligand-binding specificity, together with mutagenesis of SH3 Fyn tyrosine kinase, reveal the structural basis for types I and II binding specificity by SH3 domains. The conserved Trp in the SH3 binding pocket can adopt two different orientations that, in turn, determine the type of ligand (I or II) able to bind to the domain. The only exceptions are ligands with Leu at positions P(-1) and P(2), that deviate from standard poly-Pro angles. The motion of the conserved Trp depends on the presence of certain residues located in a key position (132 for Fyn), near the binding pocket. SH3 domains placing aromatic residues in this key position are promiscuous. By contrast, those presenting beta-branched or long aliphatic residues block the conserved Trp in one of the two possible orientations, preventing binding in a type I orientation. This is experimentally demonstrated by a single mutation in Fyn SH3 (Y132I) that abolishes type I ligand binding, while preserving binding to type II ligands. Thus, simple conformational changes, governed by simple rules, can have profound effects on protein-protein interactions, highlighting the importance of structural details to predict protein-protein interactions.

Thermodynamic Dissection of the Binding Energetics of Proline-rich Peptides to the Abl-SH3 Domain: Implications for Rational Ligand Design

The inhibition of the interactions between SH3 domains and their targets is emerging as a promising therapeutic strategy. To date, rational design of potent ligands for these domains has been hindered by the lack of understanding of the origins of the binding energy. We present here a complete thermodynamic analysis of the binding energetics of the p41 proline-rich decapeptide (APSYSPPPPP) to the SH3 domain of the c-Abl oncogene. Isothermal titration calorimetry experiments have revealed a thermodynamic signature for this interaction (very favourable enthalpic contributions opposed by an unfavourable binding entropy) inconsistent with the highly hydrophobic nature of the p41 ligand and the Abl-SH3 binding site. Our structural and thermodynamic analyses have led us to the conclusion, having once ruled out any possible ionization events or conformational changes coupled to the association, that the establishment of a complex hydrogen-bond network mediated by water molecules buried at the binding interface is responsible for the observed thermodynamic behaviour. The origin of the binding energetics for proline-rich ligands to the Abl-SH3 domain is further investigated by a comparative calorimetric analysis of a set of p41-related ligands. The striking effects upon the enthalpic and entropic contributions provoked by conservative substitutions at solvent-exposed positions in the ligand confirm the complexity of the interaction. The implications of these results for rational ligand design are discussed.

Structural insight into modest binding of a non-PXXP ligand to the signal transducing adaptor molecule-2 Src homology 3 domain

Although some exceptional motifs have been identified, it is well known that the PXXP motif is the motif of ligand proteins generally recognized by the Src homology 3 (SH3) domain. SH3-ligand interactions are usually weak, with ordinary KD approximately 10 microM. The structural basis for a tight and specific association (KD = 0.24 microm) between Gads SH3 and a novel motif, PX(V/I)(D/N)RXXKP, was revealed in a previous structural analysis of the complex formed between them. In this paper, we report the crystal structure of the signal transducing adaptor molecule-2 (STAM2) SH3 domain in complex with a peptide with a novel motif derived from a ligand protein, UBPY. The derived KD value for this complex is 27 microM. The notable difference in affinity for these parallel complexes may be explained because the STAM2 SH3 structure does not provide a specificity pocket for binding, whereas the Gads SH3 structure does. Instead, the structure of STAM2 SH3 is analogous to that of Grb2 SH3 which, in addition to normal PXXP ligands, has also been shown to moderately recognize the novel motif discussed herein. Thus, the extremely tight interaction observed between Gads SH3 and the novel motif is caused not by an innate ability of the novel motif but rather by an evolutionary change in the Gads SH3 domain. Instead, SH3 domains of STAM2 and Grb2 retain the moderate characteristics of recognizing their ligand proteins like other SH3 domains for appropriate transient interactions between signaling molecules.

Conformational Behavior of β-Proline Oligomers

Conformations of the monomer, dimer, and hexamer of beta-proline ((S) pyrrolidine-3-carboxylic acid) were determined using ab initio molecular orbital calculations at the RHF/6-31G level of theory. The calculated minima are in good agreement with experimental data for the system and imply that the conformations could be controlled through chemical modification at Calpha, Cgamma, or Cdelta. The monomer and dimer are small and flexible with many low-energy minima. In the hexamer, two forms of regular secondary structure are preferred: left-handed helices with cis-peptide bonds and right-handed helices with trans-peptide bonds. This is similar to the behavior of alpha-proline helices, except that the relationship between the peptide rotamer and the handedness of the helix is reversed. Therefore, helices of the enantiomer of beta-proline ((R)-pyrrolidine-3-carboxylic acid) should exhibit the same behavior as alpha-proline helices. Through understanding the conformational behavior of beta-proline in various environments, it may be possible to use these protein mimics to inhibit various protein-protein recognition events. To estimate these effects, SCRF energies for the conformers were determined in dielectrics corresponding to water, methanol, and chloroform. It appears that the cis helices are more favorably solvated than the trans helices, but the cause is not clear.

Exploration of the P6/P7 region of the peptide-binding site of the human class II major histocompatability complex protein HLA-DR1

Crystal structures of the class II major histocompatibilty complex (MHC) protein, HLA-DR1, generally show a tight fit between MHC and bound peptide except in the P6/P7 region of the peptide-binding site. In this region, there is a shallow water-filled pocket underneath the peptide and between the pockets that accommodate the P6 and P7 side chains. We investigated the properties of this pocket with the idea of engineering substitutions into the corresponding region of peptide antigens to increase their binding affinity for HLA-DR1. We investigated d-amino acids and N-alkyl modifications at both the P6 and P7 positions of the peptide and found that binding of peptides to HLA-DR1 could be increased by incorporating an N-methyl substitution at position 7 of the peptide. The crystal structure of HLA-DR1 bound to a peptide containing a P7 N-methyl alanine was determined. The N-methyl group orients in the P6/P7 pocket, displacing one of the waters usually bound in this pocket. The structure shows that the substitution does not alter the conformation of the bound peptide, which adopts the usual polyproline type II helix. An antigenic peptide carrying the N-methyl modification is taken up by antigen-presenting cells and loaded onto endogenous class II MHC molecules for presentation, and the resultant MHC-peptide complexes activate antigen-specific T-cells. These results suggest a possible strategy for increasing the affinity of weakly immunogenic peptides that might be applicable to the development of vaccines and diagnostic reagents.

Formation of an Endophilin-Ca2+ Channel Complex Is Critical for Clathrin-Mediated Synaptic Vesicle Endocytosis

A tight balance between synaptic vesicle exocytosis and endocytosis is fundamental to maintaining synaptic structure and function. Calcium influx through voltage-gated Ca2+ channels is crucial in regulating synaptic vesicle exocytosis. However, much less is known about how Ca2+ regulates vesicle endocytosis or how the endocytic machinery becomes enriched at the nerve terminal. We report here a direct interaction between voltage-gated Ca2+ channels and endophilin, a key regulator of clathrin-mediated synaptic vesicle endocytosis. Formation of the endophlin-Ca2+ channel complex is Ca2+ dependent. The primary Ca2+ binding domain resides within endophilin and regulates both endophilin-Ca2+ channel and endophilin-dynamin complexes. Introduction into hippocampal neurons of a dominant-negative endophilin construct, which constitutively binds to Ca2+ channels, significantly reduces endocytosis-mediated uptake of FM 4-64 dye without abolishing exocytosis. These results suggest an important role for Ca2+ channels in coordinating synaptic vesicle recycling by directly coupling to both exocytotic and endocytic machineries.

Design of N-substituted peptomer ligands for EVH1 domains

Ena/VASP proteins are implicated in cytoskeletal reorganization during actin-dependent motility processes. Recruitment to subcellular sites of actin polymerization is mediated by the highly conserved N-terminal EVH1 domain, which interacts with target proteins containing proline-rich motifs. The VASP EVH1 domain specifically binds peptides with the consensus motif FPPPP present in all its binding partners, including the Listerial ActA protein. Previous studies have shown that the Phe and first and final Pro residues are highly conserved and cannot be substituted with any other natural amino acid without significant loss of binding affinity. We have incorporated peptoid building blocks (sarcosine derived, non-natural amino acids) into the peptide SFEFPPPPTEDEL from the Listerial ActA protein and were able to substitute the most highly conserved residues of this motif while maintaining binding to the VASP EVH1 domain with affinities in the range of 45-180 microm. We then used NMR chemical shift perturbations to locate specific domain residues involved in particular interactions. These studies may open up the way for designing selective modulators of VASP function for biological studies and for the development of novel therapeutics for diseases involving pathologically altered cell adhesion or cell motility.

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.

Molecular mechanisms and therapeutical implications of intramembrane receptor/receptor interactions among heptahelical receptors with examples from the striatopallidal GABA neurons

The molecular basis for the known intramembrane receptor/receptor interactions among G protein-coupled receptors was postulated to be heteromerization based on receptor subtype-specific interactions between different types of receptor homomers. The discovery of GABAB heterodimers started this field rapidly followed by the discovery of heteromerization among isoreceptors of several G protein-coupled receptors such as delta/kappa opioid receptors. Heteromerization was also discovered among distinct types of G protein-coupled receptors with the initial demonstration of somatostatin SSTR5/dopamine D2 and adenosine A1/dopamine D1 heteromeric receptor complexes. The functional meaning of these heteromeric complexes is to achieve direct or indirect (via adapter proteins) intramembrane receptor/receptor interactions in the complex. G protein-coupled receptors also form heteromeric complexes involving direct interactions with ion channel receptors, the best example being the GABAA/dopamine D5 receptor heteromerization, as well as with receptor tyrosine kinases and with receptor activity modulating proteins. As an example, adenosine, dopamine, and glutamate metabotropic receptor/receptor interactions in the striatopallidal GABA neurons are discussed as well as their relevance for Parkinson's disease, schizophrenia, and drug dependence. The heterodimer is only one type of heteromeric complex, and the evidence is equally compatible with the existence of higher order heteromeric complexes, where also adapter proteins such as homer proteins and scaffolding proteins can exist. These complexes may assist in the process of linking G protein-coupled receptors and ion channel receptors together in a receptor mosaic that may have special integrative value and may constitute the molecular basis for some forms of learning and memory.

Incorporation of unprotected heterocyclic side chains into peptoid oligomers via solid-phase submonomer synthesis

Peptoids (N-substituted glycines) are an important class of biomimetic oligomers that have made a significant impact in the areas of combinatorial drug discovery, gene therapy, drug delivery, and biopolymer folding in recent years. Sequence-specific peptoid oligomers are easily assembled from primary amines by the solid-phase submonomer method. However, most amines that contain heterocyclic nitrogens in the side chain do not incorporate efficiently. We present here a straightforward revision of the submonomer method that allows efficient incorporation of unprotected imidazoles, pyridines, pyrazines, indoles, and quinolines into oligomers as long as 15 monomers in length. This improved method uses chloroacetic acid instead of bromoacetic acid in the acylation step of the monomer addition cycle, and allows for the incorporation of new side chains that should enable the synthesis of peptoids with entirely new properties.

Peptides with anticancer use or potential

This review is an attempt to illustrate the diversity of peptides reported for a potential or an established use in cancer therapy. With 612 references, this work aims at covering the patents and publications up to year 2000 with many inroads in years 2001-2002. The peptides are classed according to four categories of effective (or plausible) biological mechanisms of action: receptor-interacting compounds; inhibitors of protein-protein interaction; enzymes inhibitors; nucleic acid-interacting compounds. The fifth group is made of the peptides for which no mechanism of action has been found yet. Incidentally this work provides an overview of many of the modern targets of anticancer research.

Molecular mechanisms of filovirus cellular trafficking

The filoviruses, Ebola and Marburg, are two of the most pathogenic viruses, causing lethal hemorrhagic fever in humans. Recent discoveries suggest that filoviruses, along with other phylogenetically or functionally related viruses, utilize a complex mechanism of replication exploiting multiple cellular components including lipid rafts, endocytic compartments, and vacuolar protein sorting machinery. In this review, we summarize these recent findings and discuss the implications for vaccine and therapeutics development.

The structure and function of proline recognition domains

One particularly abundant group of modular recognition domains consists of those that bind proline-rich motifs. Such modules, including the SH3, WW, and EVH1 domains, play a critical role in the assembly and regulation of many intracellular signaling complexes. These domains use strikingly similar molecular mechanisms of proline recognition. We discuss some of the potential biological advantages conferred by proline recognition, which may explain its widespread use in 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.

Structure of a gametocyte protein essential for sexual development in Plasmodium falciparum

Malaria transmission is dependent on the development of sexual forms of Plasmodium falciparum, called gametocytes, in the vertebrate host. Pfg27 is an abundantly expressed sexual stage-specific protein that is essential for gametocytogenesis in P. falciparum. We describe the crystal structure of Pfg27, which reveals a novel fold composed of two pseudo dyad-related repeats of the helix-turn-helix motif. Structurally equivalent helices of each repeat either form a dimer interface or interact with RNA in vitro. One side of the dimer presents an unprecedented juxtaposition of four polyproline (PXXP) motifs. Preliminary binding data indicate that these sites are capable of binding Src homology-3 (SH3) modules. Molecular modeling suggests that the dimer can accommodate two SH3 modules simultaneously, potentially enabling molecular crosstalk between SH3-containing proteins. The structural and initial biochemical evidence suggests that Pfg27 may serve as a platform for RNA and SH3 binding.

The receptor binding protein P2 of PRD1, a virus targeting antibiotic-resistant bacteria, has a novel fold suggesting multiple functions

Bacteriophage PRD1 is unusual, with an internal lipid membrane, but has striking resemblances to adenovirus that include receptor binding spikes. The PRD1 vertex complex contains P2, a 590 residue monomer that binds to receptors on antibiotic-resistant strains of E. coli and so is the functional counterpart to adenovirus fiber. P2 structures from two crystal forms, at 2.2 and 2.4 A resolution, reveal an elongated club-shaped molecule with a novel beta propeller "head" showing pseudo-6-fold symmetry. An extended loop with another novel fold forms a long "tail" containing a protruding proline-rich "fin." The head and fin structures are well suited to recognition and attachment, and the tail is likely to trigger the processes of vertex disassembly, membrane tube formation, and subsequent DNA injection.

High affinity molecules disrupting GRB2 protein complexes as a therapeutic strategy for chronic myelogenous leukaemia

Chronic myelogenous leukaemia (CML) is one of the most intensively studied human malignancies. It has been the focus of major efforts to develop potent drugs for several decades, but until recently cure rates remained low. A breakthrough in CML therapy was very likely accomplished with the clinical introduction of STI-571 [imatinib mesylate; Gleevec (USA); Glivec (other countries)] in 2000/2001. Despite the hope that STI-571 has generated for many CML patients, development of resistance to this drug is already apparent in some cases, especially if the CML is diagnosed in its later stages. Therefore, novel drugs which can be used alone or in combination with STI-571 are highly desirable. This review briefly summarises the current understanding and therapy of CML and then discusses in more detail basic laboratory research that attempts to target Grb2, an adaptor protein known to directly interact with the Bcr portion of the Bcr-Abl fusion protein. Blocking the binding of Grb2 to the GDP-releasing protein SoS is well known to abrogate the activation of the GTPase Ras, a major driving force of the central mitogenic (MAP kinase) pathway. Additional Grb2 effector proteins may also contribute to the proliferation-inhibiting effects observed upon uncoupling Grb2 from its downstream signalling system. Since Grb2 is a known signal transducer for several major human oncogenes, this approach may have applications for a wider range of human cancers.

The HIV-TSG101 interface: recent advances in a budding field

Efficient budding of HIV from the plasma membrane requires a small peptide motif, Pro-Thr/Ser-Ala-Pro (PTAP), located near the amino terminus of the p6 Gag protein. Studies from several laboratories have demonstrated that the ability of p6 to stimulate HIV budding requires a direct interaction between the PTAP motif and the host endosomal sorting protein TSG101. The structure of the PTAP-TSG101 binding site has recently been solved, providing valuable insights into this crucial protein-protein interaction.

Structural basis for specific binding of the Gads SH3 domain to an RxxK motif-containing SLP-76 peptide: a novel mode of peptide recognition

The SH3 domain, which normally recognizes proline-rich sequences, has the potential to bind motifs with an RxxK consensus. To explore this novel specificity, we have determined the solution structure of the Gads T cell adaptor C-terminal SH3 domain in complex with an RSTK-containing peptide, representing its physiological binding site on the SLP-76 docking protein. The SLP-76 peptide engages four distinct binding pockets on the surface of the Gads SH3 domain and upon binding adopts a unique structure characterized by a right-handed 3(10) helix at the RSTK locus, in contrast to the left-handed polyproline type II helix formed by canonical proline-rich SH3 ligands. The structure, and supporting mutagenesis and peptide binding data, reveal a novel mode of ligand recognition by SH3 domains.

Palladium(II) complex as a sequence-specific peptidase: hydrolytic cleavage under mild conditions of X-Pro peptide bonds in X-Pro-Met and X-Pro-His segments

The X-Pro peptide bond (in which X represents any amino acid residue) in peptides and proteins is resistant to cleavage by most proteolytic enzymes. We show that [Pd(H(2)O)(4)](2+) ion can selectively hydrolyze this tertiary peptide bond within the X-Pro-Met and X-Pro-His sequence segments. The hydrolysis requires an equimolar amount of the Pd(II) reagent and occurs under mild conditions-at temperature as low as 20 degrees C (with half-life of 1.0 h at pH 2.0) and at pH as high as 7.0 (with half-life of 4.2 h at pH 7.0 and 40 degrees C). The secondary peptide bond, exemplified by X-Gly in the X-Gly-Met and X-Gly-His sequence segments, however, is cleaved only in weakly acidic solution (pH < 4.0) and more slowly (half-life is 4.2 h at pH 2.0 and 60 degrees C). We explain the sequence-specificity of X-Pro cleavage by NMR spectroscopic analysis of the coordination of the X-Pro-Met segment to the Pd(II) ion. We give indirect evidence for the mechanism of cleavage by analyzing the conformation of the scissile X-Pro peptide bond, and by comparing the rate constants for the cleavage of the tertiary X-Pro peptide bond, the tertiary X-Sar peptide bond (Sar is N-methyl glycine), and the typical secondary X-Gly peptide bond in a set of analogous oligopeptides. Methionine and histidine side chains provide the recognition by selectively binding (anchoring) the Pd(II) ion. The proline residue provides the enhanced activity because its tertiary X-Pro peptide bond favors the cleavage-enhancing binding of the Pd(II) ion to the peptide oxygen atom and prevents the cleavage-inhibiting binding of the Pd(II) ion upstream of the anchoring (histidine or methionine) residue. Cleavage can be switched from the residue-selective to the sequence-specific mode by simply adjusting the pH of the aqueous solution. In acidic solutions, any X-Y bond in X-Y-Met and X-Y-His segments is cleaved because the cleavage is directed by anchoring methionine and histidine residues. In mildly acidic and neutral solutions, only the X-Pro bond in X-Pro-Met and X-Pro-His sequences is cleaved because of an interplay between the anchoring residue and the proline residue preceding it. Because Pro-Met and Pro-His sequences are rare in proteins, this sequence-specific cleavage is potentially useful for the removal of the fusion tags from the bioengineered fusion proteins.

Topography for independent binding of alpha-helical and PPII-helical ligands to a peroxisomal SH3 domain

While the function of most small signaling domains is confined to binary ligand interactions, the peroxisomal Pex13p SH3 domain has the unique capacity of binding to two different ligands, Pex5p and Pex14p. We have used this domain as a model to decipher its structurally independent ligand binding sites. By the combined use of X-ray crystallography, NMR spectroscopy, and circular dichroism, we show that the two ligands bind in unrelated conformations to patches located at opposite surfaces of this SH3 domain. Mutations in the Pex13p SH3 domain that abolish interactions within the Pex13p-Pex5p interface specifically impair PTS1-dependent protein import into yeast peroxisomes.

QM, a putative tumor suppressor, regulates proto-oncogene c-yes

The QM gene encodes a 24.5 kDa ribosomal protein L10 known to be highly homologous to a Jun-binding protein (Jif-1), which inhibits the formation of Jun-Jun dimers. Here we have carried out screening with the c-Yes protein and found that a QM homologous protein showed interactions with c-Yes and other Src family members. We have found that two different regions of QM protein were associated with the SH3 domain of c-Yes. The QM protein does not contain canonical SH3 binding motifs or previously reported amino acid fragments showing interaction with SH3 domains. Several c-Yes kinase activity assays indicated that the QM protein reduced c-Yes kinase activity by 70% and that this suppression is related not only to the two SH3 binding regions but also to the C-terminal region of QM. Moreover, our autophosphorylation assays clarified that this regulation resulted from the inhibition of c-Yes autophosphorylation. Immunofluorescence studies showed that the QM proteins and c-Yes are able to interact in various tumor cell lines in vivo. The increases of the c-Yes protein and mRNA levels were detected when the QM was transfected. These results suggest that the QM protein might be a regulator for various signal transduction pathways involving SH3 domain-containing membrane proteins.

Coordinated folding and association of the LIN-2, -7 (L27) domain. An obligate heterodimerization involved in assembly of signaling and cell polarity complexes

LIN-2, -7 (L27) homology domains are putative protein-protein interaction modules found in several scaffold proteins involved in the assembly of polarized cell-signaling structures. These specific interaction pairs are well conserved across metazoan species, from worms to man. We have expressed and purified L27 domains from multiple species and find that certain domains from proteins such as Caenorhabditis elegans LIN-2 and LIN-7 can specifically heterodimerize. Biophysical analysis of interacting L27 domains demonstrates that the domains interact with a 1:1 stoichiometry. Circular dichroism studies reveal that the domains appear to function as an obligate heterodimer; individually the domains are largely unfolded, but when associated they show a significant increase in helicity, as well as a cooperative unfolding transition. These novel obligate interacting pairs are likely to play a key role in regulating the organization of signaling proteins at polarized cell structures.

In vitro selection of mRNA display libraries containing an unnatural amino acid

The incorporation of unnatural amino acid into selectable, amplifiable peptide and protein libraries expands the chemical diversity of such libraries, thus considerably facilitating the process of obtaining ligands with improved properties (affinity, specificity, and function), particularly against therapeutically interesting targets. Here, we report that biocytin, a biotin derivative of lysine, can be inserted into an mRNA-protein fusion molecule through amber stop codon suppression. We also demonstrate that templates containing the codon corresponding to the biocytin tRNA (a UAG stop codon) can be enriched by iterative cycles of selection against a streptavidin agarose matrix.

Diverse recognition of non-PxxP peptide ligands by the SH3 domains from p67(phox), Grb2 and Pex13p

The basic function of the Src homology 3 (SH3) domain is considered to be binding to proline-rich sequences containing a PxxP motif. Recently, many SH3 domains, including those from Grb2 and Pex13p, were reported to bind sequences lacking a PxxP motif. We report here that the 22 residue peptide lacking a PxxP motif, derived from p47(phox), binds to the C-terminal SH3 domain from p67(phox). We applied the NMR cross-saturation method to locate the interaction sites for the non-PxxP peptides on their cognate SH3 domains from p67(phox), Grb2 and Pex13p. The binding site of the Grb2 SH3 partially overlapped the conventional PxxP-binding site, whereas those of p67(phox) and Pex13p SH3s are located in different surface regions. The non-PxxP peptide from p47(phox) binds to the p67(phox) SH3 more tightly when it extends to the N-terminus to include a typical PxxP motif, which enabled the structure determination of the complex, to reveal that the non-PxxP peptide segment interacted with the p67(phox) SH3 in a compact helix-turn-helix structure (PDB entry 1K4U).

Structural biology in drug design: selective protein kinase inhibitors

Protein kinases have a fundamental role in signal transduction pathways, and aberrant kinase activity has been observed in many diseases. In recent years, kinase inhibition has become a major area for therapeutic intervention and a variety of kinase inhibitor pharmacophores has been described. This review illustrates some of the efforts and results in the field of structure-based design of protein kinase inhibitors. The methods and results discussed here illustrate the power of structure-based design in lead discovery, for example via virtual screening and in guiding the optimization of the pharmacological properties of these molecules.

Toward the synthesis of artificial proteins: the discovery of an amphiphilic helical peptoid assembly

While nature exploits folded biopolymers to achieve molecular recognition and catalysis, comparable abiological heteropolymer systems have been difficult to create. We synthesized and identified abiological peptoid heteroploymers capable of binding a dye. Using combinatorial synthesis, we constructed a library of 3400 amphiphilic 15-mer peptoids on an ultra-high-capacity beaded support. Individual macrobeads, each containing a single peptoid sequence, were arrayed into plates, cleaved, and screened in aqueous solution to locate dye binding heteropolymer assemblies. Resynthesis and characterization demonstrated the formation of defined helical assemblies as judged by size-exclusion chromatography, circular dichroism, and analytical ultracentrifugation. Inspired by nature's process of sequence variation and natural selection, we identified rare abiological sequence-specific heteropolymers that begin to mimic the structure and functional properties of their biological counterparts.

Determination of the interface of a large protein complex by transferred cross-saturation measurements

In an earlier paper, it was shown that the cross-saturation method enables us to identify the contact residues of large protein complexes in a more rigorous manner than is possible using chemical shift perturbation and hydrogen-deuterium exchange experiments. However, there are limitations within the determination of the contact residues by the cross-saturation method, in that the method is difficult to apply to protein complexes with a molecular mass over 150 kDa and/or with weak binding, since the resonances originating from the complexes should be observed directly in the method. In the present work, to overcome these limitations, we carried out the cross-saturation measurements under conditions of a fast exchange between free and bound states on the NMR time-scale, and determined the contact residues of the complex of the B domain of protein A and intact IgG, which has a molecular mass of 164 kDa and shows weak binding.

Mechanisms underlying ubiquitination

The conjugation of ubiquitin to other cellular proteins regulates a broad range of eukaryotic cell functions. The high efficiency and exquisite selectivity of ubiquitination reactions reflect the properties of enzymes known as ubiquitin-protein ligases or E3s. An E3 recognizes its substrates based on the presence of a specific ubiquitination signal, and catalyzes the formation of an isopeptide bond between a substrate (or ubiquitin) lysine residue and the C terminus of ubiquitin. Although a great deal is known about the molecular basis of E3 specificity, much less is known about molecular mechanisms of catalysis by E3s. Recent findings reveal that all known E3s utilize one of just two catalytic domains--a HECT domain or a RING finger--and crystal structures have provided the first detailed views of an active site of each type. The new findings shed light on many aspects of E3 structure, function, and mechanism, but also emphasize that key features of E3 catalysis remain to be elucidated.

Binding interactions between peptides and proteins of the class II major histocompatibility complex

The activation of helper T cells by peptides bound to proteins of the class II Major Histocompatibility Complex (MHC II) is pivotal to the initiation of an immune response. The primary functional requirement imposed on MHC II proteins is the ability to efficiently bind thousands of different peptides. Structurally, this is reflected in a unique architecture of binding interactions. The peptide is bound in an extended conformation within a groove on the membrane distal surface of the protein that is lined with several pockets that can accommodate peptide side-chains. Conserved MHC II protein residues also form hydrogen bonds along the length of the peptide main-chain. Here we review recent advances in the study of peptide-MHC II protein reactions that have led to an enhanced understanding of binding energetics. These results demonstrate that peptide-MHC II protein complexes achieve high affinity binding from the array of hydrogen bonds that are energetically segregated from the pocket interactions, which can then add to an intrinsic hydrogen bond-mediated affinity. Thus, MHC II proteins are unlike antibodies, which utilize cooperativity among binding interactions to achieve high affinity and specificity. The significance of these observations is discussed within the context of possible mechanisms for the HLA-DM protein that regulates peptide presentation in vivo and the design of non-peptide molecules that can bind MHC II proteins and act as vaccines or immune modulators.

Interaction domains: from simple binding events to complex cellular behavior

Many of the signaling pathways and regulatory systems in eukaryotic cells are controlled by proteins with multiple interaction domains that mediate specific protein-protein and protein-phospholipid interactions, and thereby determine the biological output of receptors for external and intrinsic signals. Here, we discuss the basic features of interaction domains, and suggest that rather simple binary interactions can be used in sophisticated ways to generate complex cellular responses.

Protein kinase modulation of a neuronal cation channel requires protein-protein interactions mediated by an Src homology 3 domain

Accumulating evidence suggests that many ion channels reside within a multiprotein complex that contains kinases and other signaling molecules. The role of the adaptor proteins that physically link these complexes together for the purposes of ion channel modulation, however, has been little explored. Here, we examine the protein-protein interactions required for regulation of an Aplysia bag cell neuron cation channel by a closely associated protein kinase C (PKC). In inside-out patches, the PKC-dependent enhancement of cation channel open probability could be prevented by the src homology 3 (SH3) domain, presumably by disrupting a link between the channel and the kinase. SH3 and PDZ domains from other proteins were ineffective. Modulation was also prevented by an SH3 motif peptide that preferentially binds the SH3 domain of src. Furthermore, whole-cell depolarizations elicited by cation channel activation were decreased by the src SH3 domain. These data suggest that the cation channel-PKC association may require SH3 domain-mediated interactions to bring about modulation, promote membrane depolarization, and initiate prolonged changes in bag cell neuron excitability. In general, protein-protein interactions between ion channels and protein kinases may be a prominent mechanism underlying neuromodulation.

A single WW domain is the predominant mediator of the interaction between the human ubiquitin-protein ligase Nedd4 and the human epithelial sodium channel

The activity of the epithelial Na(+) channel (ENaC) is required for the maintenance of salt and water balance in the body. Channel activity is regulated by the ubiquitin-protein ligase Nedd4 ['neuronal precursor cell-expressed developmentally down-regulated (gene 4)'] that interacts with the channel via its WW domains. Mutations in channel subunits that disrupt this interaction cause Liddle's syndrome, a severe inherited form of hypertension. In previous studies we showed that WW domains 2, 3 and 4 of human Nedd4 bound to the human ENaC (hENaC) subunits, whereas WW domain 1 did not. Here we extend this observation to determine the binding affinities of the human Nedd4 WW domains for hENaC C-terminal peptides. We show that WW domains 2, 3 and 4 bind with differing affinities to Na(+) channel subunit peptides. WW domain 3 has the highest affinity and we predict that WW domain 3 contributes most of the binding because a construct containing the three WW domains bound no better than WW domain 3 alone. Further, a single amino acid change (Arg(165)-->Thr) in WW domain 1 enables binding to the alpha subunit of the channel to occur, with an affinity comparable with that of WW domain 4. Differential binding propensities between the various WW domains and Na(+) channel subunit peptides are explained on the basis of quantitative structural modelling of the complexes and their isolated components.

Characterization of a phosphorylated peptide and peptoid and peptoid-peptide hybrids by mass spectrometry

Nano-electrospray tandem mass spectrometry (nano-ES-MS/MS) was used to record collision-induced dissociation (CID) spectra of a set of peptoid-peptide hybrids and the complete peptoid derived from the phosphopeptide Ac-pTyr-Glu-Thr-Leu-NH(2) (1). The presence of B and Y''-type fragment ions in the tandem mass spectra of the protonated molecular ions [M + H](+) allowed confirmation of sequence similar to mass spectrometric sequence analysis in peptides. In the isomeric peptoid compounds studied, one or several amino acid residues were replaced by peptoid residues (N-substituted glycine residues), which resulted in characteristic tandem mass spectra with differently increased relative abundances of Y''-and B-type fragment ions. The increment of a particular Y''-ion was directly correlated to the position of a peptoid residue present. In addition to these increased peak intensities, other characteristic peaks were also observed compared with the spectrum of reference peptide 1. When a peptoid phosphotyrosine was incorporated, the presence of this residue was apparent from the occurrence of a relatively intense peak at m/z 187 representing the positively charged side-chain of phosphotyrosine, which was almost absent in the spectrum of the reference peptide 1. Since the threonine side-chain had to be translated into the homo peptoid analog this substitution was apparent from the presence of [M + H](+) and fragment ions 14 mass units higher than observed in the spectrum of the reference phosphopeptide 1. The presence of an NLeu peptoid residue could be confirmed by the specific fragmentation of the immonium ion showing an intense peak in its tandem mass spectrum at m/z 57, which results from the loss of an neutral imine molecule leading to a positively charged [C(4)H(9)](+) ion. By means of these mass spectrometric characteristics, all isomeric peptoid compounds could be distinguished from each other and characterized. The methods used appear to be very useful in future studies of peptoids and peptoid-peptide hybrids.

Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins

Membrane-associated guanylate kinases (MAGUKs), such as PSD-95, are modular scaffolds that organize signaling complexes at synapses and other cell junctions. MAGUKs contain PDZ domains, which recruit signaling proteins, as well as a Src homology 3 (SH3) and a guanylate kinase-like (GK) domain, implicated in scaffold oligomerization. The crystal structure of the SH3-GK module from PSD-95 reveals that these domains form an integrated unit: the SH3 fold comprises noncontiguous sequence elements divided by a hinge region and the GK domain. These elements compose two subdomains that can assemble in either an intra- or intermolecular fashion to complete the SH3 fold. We propose a model for MAGUK oligomerization in which complementary SH3 subdomains associate by 3D domain swapping. This model provides a possible mechanism for ligand regulation of oligomerization.

Protein-protein interfaces: mimics and inhibitors

Many biological processes are mediated by specific molecular recognition between proteins. However, the thermodynamic and structural 'rules' for such recognition are incompletely understood, as is the potential for inhibition by small molecules. Recent progress has included the discovery of small-molecule inhibitors for several targets important in cancer.

The hunchback and its neighbours: proline as an environmental modulator

The unique ability of Pro or Pro-rich repeats to affect the stability and function of proteins has recently been highlighted by biophysical studies on fragments from prions, signalling domains and muscle proteins. Pro-rich regions have been observed to either occupy disordered states or adopt various helical structures; some are also able to undergo an environmental-dependent transformation between these states. Such a transformation could explain some of the inherent functional properties of the parent proteins and, additionally, can be efficiently exploited to generate novel temperature- and pH-switches in more conventional globular proteins.

SH2 and SH3 domains as targets for anti-proliferative agents

The Src homology domains SH2 and SH3 are small modular protein motifs about 100 and 60 amino acids long, respectively. SH2 domains interact with phosphotyrosine residues, whereas SH3 domains recognize proline-rich motifs of their interacting partners. SH2 and SH3 domains are frequently found in signaling proteins such as small adaptors and in enzymes such as kinases, lipases and phosphatases, in which they differ from the catalytic motif and constitute recognition modules. SH2 and SH3 domains are also found in oncoproteins and in proteins overexpressed in deregulated signaling pathways in tumor cells. The highly folded structures of these domains have been characterized alone and complexed with the essential fragments of their targets. Therefore, based on molecular data, inhibitors of interactions with SH2 and SH3 domains are considered to be potential antitumor agents. Current results are very promising, as inhibitors with very efficient anti-proliferative activity in tumor cells have been reported. This paper describes SH2 and/or SH3 domain-containing proteins that may constitute targets for anticancer therapeutics. It also deals with the essential structural data concerning SH2 and SH3 domains, and the rational design of inhibitors. Some of the more recent pharmacological results obtained with these compounds are also discussed.

Virtual interaction profiles of proteins

We have developed a new method for the prediction of peptide sequences that bind to a protein, given a three-dimensional structure of the protein in complex with a peptide. By applying a recently developed sequence prediction algorithm and a novel ensemble averaging calculation, we generate a diverse collection of peptide sequences that are predicted to have significant affinity for the protein. Using output from the simulations, we create position-specific scoring matrices, or virtual interaction profiles (VIPs). Comparison of VIPs for a collection of binding motifs to sequences determined experimentally indicates that the prediction algorithm is accurate and applicable to a diverse range of structures. With these VIPs, one can scan protein sequence databases rapidly to seek binding partners of potential biological significance. Overall, this method can significantly enhance the information contained within a protein- peptide crystal structure, and enrich the data obtained by experimental selection methods such as phage display.

Crk family adaptors-signalling complex formation and biological roles

Crk family adaptors are widely expressed and mediate the timely formation of signal transduction protein complexes upon a variety of extracellular stimuli, including various growth and differentiation factors. Selective formation of multi-protein complexes by the Crk and Crk-like (CRKL) proteins depends on specific motifs recognized by their SH2 and SH3 domains. In the case of the first SH3 domains [SH3(1)] a P-x-x-P-x-K motif is crucial for highly selective binding, while the SH2 domains prefer motifs which conform to the consensus pY-x-x-P. Crk family proteins are involved in the relocalization and activation of several different effector proteins which include guanine nucleotide releasing proteins like C3G, protein kinases of the Abl- and GCK-families and small GTPases like Rap1 and Rac. Crk-type proteins have been found not only in vertebrates but also in flies and nematodes. Major insight into the function of Crk within organisms came from the genetic model organism C. elegans, where the Crk-homologue CED-2 regulates cell engulfment and phagocytosis. Other biological outcomes of the Crk-activated signal transduction cascades include the modulation of cell adhesion, cell migration and immune cell responses. Crk family adaptors also appear to play a role in mediating the action of human oncogenes like the leukaemia-inducing Bcr-Abl protein. This review summarizes some key findings and highlights recent insights and open questions.