Identification of a surface actin-binding site on myosin.

The surface accessibility of mobile domains of rabbit fast muscle myosin subfragment-1 isoenzymes (subfragment-1(A1), (A2)) influenced by interaction with actin has been investigated by proton magnetic resonance spectroscopy using the soluble paramagnetic reagents Cr(CN)6(3-), Fe(CN)6(3-), Mn2+ and the Gd3+ salt of 1,4,7,10-tetraazacyclododecane-N,N',N",N"'-tetraacetic acid as probes. Anionic probes interact principally with lysine residues disposed close to other non-charged sidechains in both isoenzymes. Additional resonances in subfragment-1(A1) not present in subfragment-1(A2) are also observed to be affected, notably the sharp signal at 3.23 ppm which derives from a -N+ (CH3)3 group found in the N-terminal segment of the A1 light chain, showing that this domain of interaction with actin (Prince et al. (1981) Eur. J. Biochem. 121, 213-219) is situated at a surface location. Different probes identify a heterogeneity in the location and function of mobile sidechains. These results suggest a configurational lability in the various parts of the myosin head, differentially constrained upon interaction with actin and consistent with a structure composed of relatively rigid domains linked by more flexible regions.

Characterization of the actin-binding site on the alkali light chain of myosin.

1H-NMR experiments on myosin subfragment-1 (S1) isoenzymes, containing either the A1 or the A2 alkali light chains (S1(A1) or S1(A2)), have previously suggested the 41-residue proline, alanine and lysine-rich N-terminal extension of A1 to constitute a mobile 'domain' in solution. This segment of the molecule is immobilised in the presence of actin (Prince et al. (1981) Eur. J. Biochem. 121, 213-219). We now establish that the A1 light chain interacts with actin directly, and furthermore, that the binding site appears to be restricted to the terminal 41 residues. This observation carries important consequences for both the structure of the actomyosin complex and the role of myosin isoenzymes. Using the proteinase, thrombin, a technique has been developed in which the A1 light chain is cleaved, releasing the N-terminal 'tail' from an A2-like fragment. The method is shown to be widely applicable to light chains from a variety of sources. The isolated N-terminal fragments from rabbit skeletal and bovine cardiac muscle have been shown to interact directly with actin by a combination of affinity chromatography and 1H-NMR experiments. The 1H-NMR results are similar to those obtained earlier with S1 (ibid) and suggest the terminal alpha-N-trimethylalanine residue (Henry et al. (1982) FEBS Lett. 144, 11-15) to participate in the interaction.

The nature of the trifluoperazine binding sites on calmodulin and troponin-C.

We have employed 1H-nuclear magnetic resonance spectroscopy to study the interaction of the drug trifluoperazine with calmodulin and troponin-C. Distinct trifluoperazine-binding sites exist in the N- and C-terminal halves of both proteins. Each site consists of a group of hydrophobic side-chains brought into proximity by the Ca2+-dependent juxtaposition of two alpha-helical segments of the protein, each, in turn, belonging to a different Ca2+-binding site in the protein half. The trifluoperazine-induced inhibition of the biological activating ability of calmodulin appears to result from conformational restrictions conferred upon the protein by the bound drug.

Protein phosphorylation and signal transduction modulation: chemistry perspectives for small-molecule drug discovery.

Protein phosphorylation has been exploited by Nature in profound ways to control various aspects of cell proliferation, differentiation, metabolism, survival, motility and gene transcription. Cellular signal transduction pathways involve protein kinases, protein phosphatases, and phosphoprotein-interacting domain (e.g., SH2, PTB, WW, FHA, 14-3-3) containing cellular proteins to provide multidimensional, dynamic and reversible regulation of many biological activities. Knowledge of cellular signal transduction pathways has led to the identification of promising therapeutic targets amongst these superfamilies of enzymes and adapter proteins which have been linked to various cancers as well as inflammatory, immune, metabolic and bone diseases. This review focuses on protein kinase, protein phosphatase and phosphoprotein-interacting cellular protein therapeutic targets with an emphasis on small-molecule drug discovery from a chemistry perspective. Noteworthy studies related to molecular genetics, signal transduction pathways, structural biology, and drug design for several of these therapeutic targets are highlighted. Some exemplary proof-of-concept lead compounds, clinical candidates and/or breakthrough medicines are further detailed to illustrate achievements as well as challenges in the generation, optimization and development of small-molecule inhibitors of protein kinases, protein phosphatases or phosphoprotein-interacting domain containing cellular proteins.

1H and 15N assignments and secondary structure of the PI3K SH3 domain.

The sequential 1H and 15N assignments of the SH3 domain of human phosphatidyl inositol 3'-kinase (PI3K) were determined by a combination of homonuclear and heteronuclear NMR experiments. With the exception of several protons belonging to lysine and proline residues, all proton and proton-bearing amide nitrogen resonances were assigned. Based on the sequential nuclear Overhauser effects (NOEs), 3JNH-C alpha H coupling constants and locations of slowly exchanging amide protons, we determined that the secondary structures of the protein consists of six beta-strands, two beta-turns and four short helices. Additional long range NOEs indicate that these beta-strands form two antiparallel beta-sheets. The topology of secondary structural elements of the PI3K SH3 domain is similar to those of the SH3 domains from c-Src and alpha-spectrin, suggesting that the SH3 family has a common tertiary structural motif.

Bone-targeted Src SH2 inhibitors block Src cellular activity and osteoclast-mediated resorption.

Src, a nonreceptor tyrosine kinase, is an important regulator of osteoclast-mediated resorption. We have investigated whether compounds that bind to the Src SH2 domain inhibit Src activity in cells and decrease osteoclast-mediated resorption. Compounds were examined for binding to the Src SH2 domain in vitro using a fluorescence polarization binding assay. Experiments were carried out with compounds demonstrating in vitro binding activity (nmol/L range) to determine if they inhibit Src SH2 binding and Src function in cells, demonstrate blockade of Src signaling, and lack cellular toxicity. Cell-based assays included: (1) a mammalian two-hybrid assay; (2) morphological reversion and growth inhibition of cSrcY527F-transformed cells; and (3) inhibition of cortactin phosphorylation in csk-/- cells. The Src SH2 binding compounds inhibit Src activity in all three of these mechanism-based assays. The compounds described were synthesized to contain nonhydrolyzable phosphotyrosine mimics that bind to bone. These compounds were further tested and found to inhibit rabbit osteoclast-mediated resorption of dentine. These results indicate that compounds that bind to the Src SH2 domain can inhibit Src activity in cells and inhibit osteoclast-mediated resorption.

Structural information from NMR secondary chemical shifts of peptide alpha C-H protons in proteins.

The secondary chemical shift experienced by the 1H-NMR resonances of the alpha C-H protons in proteins can be correlated with their backbone torsional angles psi, which dictate the orientation of the alpha C-H proton to the adjacent carbonyl group. It is shown that alpha C-H protons present in beta-sheet regions experience downfield secondary shifts, whereas those in alpha-helix regions experience upfield secondary shifts. The predictive use of this correlation in assignment studies is illustrated for the calcium-binding protein paravalbumin, for which a crystal structure is available, and troponin C, for which no crystallographic data are available.

SH3 domains and drug design: ligands, structure, and biological function.

The ligand binding preferences, structural features, and biological function of SH3 (Src homology 3) domains are discussed. SH3 domains bind "core" Pro-rich peptide ligands (7-9 amino acids in length) in a polyproline II helical conformation in a highly conserved aromatic rich patch on the protein surface (approximately 390 A2). The ligands can interact with the protein in one of two orientations, depending on the position (N- vs C-terminal) of ligand residues binding to the SH3 selectivity pocket. Core SH3 ligands are characterized by relatively weak interactions (KD = 5-100 microM) that show little binding selectivity within SH3 families. Higher affinity, more selective contiguous ligands require additional flanking residues that bind to less conserved portions of the SH3 surface, with corresponding increase in ligand size and complexity. In contrast to peptide ligands, protein ligands of SH3 domains can exploit multiple discontiguous interactions to enhance affinity and selectivity. A protein-SH3 interaction that utilizes unique interactions may permit the design of small high affinity SH3 ligands. At present, the extended nature of the binding site and homologous nature of the core binding region among SH3 domains present key challenges for structure-based drug design.

NMR analysis of the structure and metal sequestering properties of metallothioneins.

Multinuclear 1 and 2 dimensional magnetic resonance methods have been used to investigate the structures and metal binding properties of metallothioneins (MTs) isolated from several different sources. 113Cd NMR studies have unambiguously shown that the 7 g-atoms of Cd2+ bound per mole of the mammalian MT are located in two separate metal clusters, one containing 4 metal ions and the other, 3 metal ions. In the invertebrate (Scylla serrata) MT, similar studies have revealed that the 6 g-atoms of bound Cd2+ are distributed in two distinct 3-metal clusters while in Neurospora MT, the 3 g-atoms of bound Cd2+ are arranged in a pseudo 3-metal cluster. With the exception of one of the Cd2+ sites in this latter cluster, all the Cd2+ ions are tetrahedrally coordinated to four cysteine thiolate ligands with single cysteinyl sulfurs bridging adjacent metals. These conclusions are based on the 113Cd chemical shift data and a detailed analysis of the observed 113Cd-113Cd scalar couplings by both homonuclear decoupling and 2D techniques. In addition, the 113Cd NMR studies have revealed significant differences in the affinity of different metal ions for the two mammalian metal clusters. For the 3-metal cluster, the affinity is found to decrease in the order Cu+ greater than Cd2+ greater than Zn2+ with Cd2+ greater than Zn2+ for the 4 metal cluster and Cd2+ (4-metal cluster) greater than Cd2+ (3-metal cluster). The 113Cd NMR data are currently being integrated with 500 MHz 2D 1H and 1H-113Cd chemical shift correlated multiple quantum data sets to more completely define the structural arrangement of the metal clusters in the tertiary structure of these proteins.

1H NMR studies on bovine cyclophilin: preliminary structural characterization of this specific cyclosporin A binding protein.

High-field 1H NMR spectroscopy has been used to study the conformation of the cytosolic cyclosporin A binding protein cyclophilin. For the drug-free form of cyclophilin, spectral editing methods in conjunction with a pH titration were used to identify all four His residues present in the protein, and two-dimensional COSY and RELAY spectroscopy was used to elucidate the scalar connectivities in the aromatic and upfield methyl regions of the spectrum. From these scalar connectivities, it was possible to distinguish between inter- and intraresidue dipolar interactions within the aromatic and upfield methyl regions of cyclophilin in the NOESY spectrum. The results of this analysis showed extensive interresidue cross-relaxation among and between these latter spectral regions indicative of the proximal relationships of several of these residues and the presence of a hydrophobic core within cyclophilin.

Solution conformation of endothelin and point mutants by nuclear magnetic resonance spectroscopy.

Two-dimensional NMR techniques were utilized to determine the secondary structural elements of endothelin-1 (ET-1), a potent vasoconstrictor peptide, and two of its point mutants, Met-7 to Ala-7 (ETM7A), and Asp-8 to Ala-8 (ETD8A) in acetic acid-d3/water solution. Sequence specific NMR assignments were determined for all three peptides, as well as chemical shifts and NOE connectivity patterns. The chemical shifts of ET-1 and ETM7A are identical (+/- 0.05 ppm) except for the site of substitution, whereas marked shift changes were detected between ET-1 and ETD8A. These chemical shift differences imply that the Asp-8 to Ala-8 mutation has induced a conformational change relative to the parent conformation. All three molecules show the same basic nuclear Overhauser effect (NOE) pattern, which suggests that the gross conformation of all three molecules is the same. Small changes in sequential NOE intensities and changes in medium-range NOE patterns indicate that there are subtle conformational differences between ET-1 and ETD8A.

Signal transduction drug discovery: targets, mechanisms and structure-based design.

Signal transduction targets include catalytic and/or non-catalytic domains, which are critical to various aspects of cell growth, differentiation, metabolism and function, mitogenesis, motility and gene transcription. Specific examples of molecular targets include the catalytic domains of protein tyrosine kinases (PTKs) and of protein tyrosine phosphatases (PTPases), as well as related protein-protein interaction motifs (eg, SH2, PTB and SH3 domains). From the relationship of tyrosine phosphorylation to intracellular pathway regulation by PTKs and PTPases, the dynamic and reversible binding interactions of SH2 and PTB domain-containing proteins with their cognate phosphotyrosine (pTyr)-containing proteins, provide an additional dimension to the modulation of signal transduction pathways which exist as a result of pTyr formation, degradation and molecular recognition events. This review focuses on our current understanding of key relative to recent reports which have provided further insight into their three-dimensional structure and mechanism. This review also highlights recent progress in the design and optimization of molecular mechanism-based signal transduction inhibitors.

1H-NMR studies of calmodulin. The nature of the Ca2+-dependent conformational change.

Using assignments of resonances in the 1H-NMR spectrum of calmodulin obtained by the use of large tryptic fragments of the molecule [Dalgarno, D. C., Klevit, R. E., Levine, B. A., Williams, R. J. P., Dobrowolski, Z., and Drabikowski, W. (1984) Eur. J. Biochem. 138, 281--289], the spectral changes which occur on Ca2+ binding to calmodulin have been examined in detail. Ca2+ binding occurs in two stages: the first two Ca2+ ions bind at sites III and IV (numbered from the N terminus) and the second two Ca2+ ions bind at sites I and II. The high-affinity binding causes perturbations of residues in both halves of the molecule, whereas binding at the two N-terminal sites only affects sidechains in that half of the molecule. The effects of binding Cd2+ to the Ca2+-binding sites of calmodulin have also been studied by 1H NMR. The cation induces spectral changes which are very similar to those seen for Ca2+, but some important differences do exist.

Structural basis for the binding of proline-rich peptides to SH3 domains.

A common RXL motif was found in proline-rich ligands that were selected from a biased combinatorial peptide library on the basis of their ability to bind specifically to the SH3 domains from phosphatidylinositol 3-kinase (PI3K) or c-Src. The solution structure of the PI3K SH3 domain complexed to one of these ligands, RKLPPRPSK (RLP1), was determined. Structure-based mutations were introduced into the PI3K SH3 domain and the RLP1 ligand, and the influence of these mutations on binding was evaluated. We conclude that SH3 domains recognize proline-rich motifs possessing the left-handed type II polyproline (PPII) helix conformation. Two proline residues directly contact the receptor. Other prolines in the ligands appear to function as a molecular scaffold, promoting the formation of the PPII helix. Three nonproline residues consisting of combinations of arginine and leucine interact extensively with the SH3 domain and appear to confer ligand specificity.

The mobility of calcium-trigger proteins and its function.

Trigger activity implies the transfer of the energy of a signal to some amplified (energy) response. Actions in cells, from calcium concentration changes to major protein reorganization are discussed here. The changes must be fast, so mobile polymers must be involved. The first step is the calcium on/off binding to its receptor, calmodulin, troponin C or a comparable protein. Calcium binding is to a loop, EF-hand, between helices. The structures and internal mobilities of these proteins are described using nuclear magnetic resonance and the temperature dependence of NMR shifts. It is suggested that these proteins illustrate a general working hypothesis that proteins made from interacting helices as opposed to beta-sheet proteins will have relatively easy internal main chain motions. Loops connecting the helices then provide particularly obvious read-out points, for example of the initial message of calcium binding. These and other regions of loose structure appear to be associated with highly charged sequences. The further transfer of the trigger message is to highly mobile sequences in troponin I, troponin T and tropomyosin.

Solution conformation of the C-terminal domain of skeletal troponin C. Cation, trifluoperazine and troponin I binding effects.

Proton magnetic resonance spectroscopy has been used to study the cation (Mg2+, Ca2+)-dependent conformational states of the C-terminal domain of rabbit skeletal troponin C under a variety of solution conditions. Nuclear Overhauser data and paramagnetic probe observations provide definition of the configuration of this region of troponin C. Comparative study of homologous proteins identify common features of the tertiary structure relevant to the cation binding reaction. Complex formation with troponin I and the drug trifluoperazine is observed to adjust the solution conformation of the C-terminal domain of troponin C. The interactive conformational response to cation coordination and the binding of the drug and troponin I are discussed.