Structural analysis of the protein phosphatase 1 docking motif: molecular description of binding specificities identifies interacting proteins

The interplay between kinases and phosphatases represents a fundamental regulatory mechanism in biological systems. Being less numerous than kinases, phosphatases increase their diversity by the acquisition of a variety of binding partners, thereby forming a large number of holoenzymes. Proteins interacting with protein phosphatase 1 (PP1) often bind via a so-called docking motif to regulate its enzymatic activity, substrate specificity, and subcellular localization. Here, we systematically determined structural elements that mediate the binding specificity of PP1 interacting proteins, and propose a refined consensus sequence for high-affinity PP1 ligands. Applying this pattern to database searches, we predicted and experimentally confirmed several previously unknown PP1 interactors. Thus, the suggested PP1 docking motif enables a highly specific prediction of PP1 binding partners, thereby facilitating the genome-wide identification of PP1 interactors.     

Crystallographic analysis of metal-ion binding to human ubiquitin

The metal-binding ability of human ubiquitin (hUb) towards a selection of biologically relevant metal ions and complexes has been probed. Different techniques have been used to obtain crystals suitable for crystallographic analysis. In the first type of experiments, crystals of hUb have been soaked in solutions containing copper(II) acetate and two metallodrugs, Zeise salt (K[PtCl(3)(η(2)-C(2)H(4))]·H(2)O) and cisplatin (cis-[PtCl(2)(NH(3))(2)]). The Zeise salt is used in a test for hepatitis, whereas cisplatin is one of the most powerful anticancer drugs in clinical use. The Zeise salt readily reacts with hUb crystals to afford an adduct with three platinum residues per protein molecule, Pt(3)-hUb. In contrast, copper(II) acetate and cisplatin were found to be unreactive for contact times up to one hour and to cause degradation of the hUb crystals for longer times. In the second type of experiments, hUb was cocrystallized with a solution of copper(II) or zinc(II) acetate or cisplatin. Zinc(II) acetate gives, at low metal-to-protein molar ratios (8:1), crystals containing one metal ion per three molecules of protein, Zn-hUb(3) (already reported in previous work), whereas at high metal-to-protein ratios (70:1) gives crystals containing three Zn(II) ions per protein molecule, Zn(3)-hUb. In contrast, once again, copper(II) acetate and cisplatin, even at low metal-to-protein ratios, do not give crystalline material. In the soaking experiment, the Zeise anion leads to simultaneous platination of His68, Met1, and Lys6. Present and previous results of cocrystallization experiments performed with Zn(II) and other Group 12 metal ions allow a comprehensive understanding of the metal-ion binding properties of hUb with His68 as the main anchoring site, followed by Met1 and carboxylic groups of Glu16, Glu18, Glu64, Asp21, and Asp32, to be reached. In the case of platinum, Lys6 can also be a binding site. The amount of bound metal ion, with respect to that of the protein, appears to be a relevant parameter influencing crystal packing.     

DNA binding and photocleavage specificities of a group of tricationic metalloporphyrins

The interactions of 5,10,15-tris(1-methylpyridinium-4-yl)-20-(4-hydroxyphenyl)porphyrinatozinc(II) Zn[TMPyHP]³⁺ (2) along with Cu[TMPyHP]³⁺ (3), Co[TMPyHP]⁴⁺ (4), Mn[TMPyHP]⁴⁺ (5) and the free base porphyrin H₂[TMPyHP]³⁺ (1) with duplex DNA have been studied by using a combination of absorption, fluorescence titration, surface-enhanced Raman spectroscopy (SERS), induced circular dichroism (ICD) spectroscopy, thermal DNA denaturation, viscosity measurements as well as gel electrophoresis experiment. Their binding modes and intrinsic binding constants (K_b) to calf DNA (CT DNA) were comparatively studied and were found significantly influenced by different metals coordinated with the porphyrin plane. Except 3, which has four-coordination structure at the metal, all the metal derivatives showed non-intercalative DNA-binding mode and lower K_b than the free base porphyrin 1, most probably due to the steric hindrance results from the axial ligands of the inserted metals which are five or six-coordination structures. Meanwhile, the insertion of metals into cationic porphyrin greatly removed the self-aggregation of the metal-free porphyrins, and thus fully enhanced the singlet oxygen (¹O₂) productivities in the DNA photocleavage experiments. Therefore, these metalloporphyrins have comparable DNA cleavage ability with the free base porphyrin.     

Structural aspects of some organoselenium compounds

The crystal structures of four organoselenium compounds, viz. bis(2-formylphenyl)diselenide (5), bis(2-methylnaphthyl)diselenide (6), organoselenenyl sulfide (7), and spiroselenurane (8) are described. Crystal data for 5: space group Pca2₁, crystal system orthorhombic, a=7.9969(4) Å, b=20.8794(12) Å, c=15.8307(13) Å, Z=8, R=0.0292. Owing to the presence of a strong Se···O interaction in compound 5 the geometry around the selenium atom may be considered as T-shaped. Crystal data for 6: space group Pna2₁, crystal system orthorhombic, a=18.2253(12) Å, b=13.0714(8) Å, c=7.7355(5) Å, Z=4, R=0.0570. The molecule has a cisoid conformation. Crystal data for 7: space group Pbcn, crystal system orthorhombic, a=22.2144(13) Å, b=8.0255(4) Å, c=15.4496(9) Å, Z=8, R=0.0292. Due to intramolecular Se···N interaction in 7 the geometry around selenium is T- shaped. Crystal data for 8: space group P2₁/c, crystal system monoclinic, a=7.4585(5) Å, b=19.5634(13) Å, c=8.0428(5) Å, β=97.1320(10)°, Z=4, R=0.0254. The O?Se?O angle is 172.86(6)°.     

Structural aspects of deformation of amorphous polymers

Experimental and theoretical data on the inelastic deformation of amorphous glassy polymers were analyzed. The decisive role of direct structural methods in determination of the deformation mechanism of glassy polymers was established. A new mechanism of deformation and thermally stimulated recovery of strained glassy polymers was considered on the basis of structural data analysis.__________Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 1, pp. 1–6, January, 2005.     

Anion binding to ubiquitin and its relevance to the Hofmeister effects

Although the non-covalent interactions between proteins and salts contributing to the Hofmeister effects have been generally mapped, there are many questions regarding the specifics of these interactions. We report here studies involving the small protein ubiquitin and salts of polarizable anions. These studies reveal a complex interplay between the reverse Hofmeister effect at low pH, the salting-in Hofmeister effect at higher pH, and six anion binding sites in ubiquitin at the root of these phenomena. These sites are all located at protuberances of preorganized secondary structure, and although stronger at low pH, are still apparent when ubiquitin possesses no net charge. These results demonstrate the traceability of these Hofmeister phenomena and suggest new strategies for understanding the supramolecular properties of proteins.

Studying the supramolecular properties of Ubiquitin reveals six anion binding sites that contribute to the reverse Hofmeister effect at low pH and the salting-in Hofmeister effect at higher pH.     

Structural aspects of mononuclear Mo/W-enzymes

This review provides an overview of the contributions of protein X-ray crystallography to the field of pyranopterin-containing W/Mo-enzymes. Several crystal structures for all of the four different families of pyranopterin-containing enzymes have been determined in recent years allowing one to compare overall folds and active site architectures. Especially within the dimethylsulfoxide reductase family and the Mo-containing hydroxylases a diversity of Mo/W-ligands has been discovered, challenging the earlier proposed functions of individual active site components. Reinterpretations of structures and the use of enzyme variants and complexes with inhibitors and slow substrate provided further insights, which will be discussed for the individual enzymes.     

Structural aspects of metal–amide complexes

An exhaustive survey of crystal structure data on simple amides and metal complexes containing monodentate amide ligands has been performed. Statistical analysis of structural features are reported as a function of the degree of alkylation of the amide functional group, the type of metal ion in the amide complex, and the type of binding to the metal ion. Average values are reported for bond lengths, bond angles, and torsional angles. Orientational preferences of the coordinated amide ligand are discussed in terms of M–O–C bond angles and M–O–C–N torsion angles.     

Structural aspects of aqueous tetraalkylammonium salt solutions

Various thermodynamic and spectroscopic investigations on aqueous tetraalkylammonium salt solutions are reviewed from a structural viewpoint. At present, it is not yet clear what kind of water structure is formed around the alkyl groups of the large cations. However, the importance of cosphere overlap and ion-ion interaction (cation-anion, cation-cation, cation-anion-cation, etc.) in determining the solution properties are emerging more clearly. In this regard, model calculations based on the approach of Friedman and his coworkers are expected to be of considerable value.This paper was presented at the symposium, The Physical Chemistry of Aqueous Systems, held at the University of Pittsburgh, Pittsburgh, Pennsylvania, June 12–14, 1972, in honor of the 70th birthday of Professor H. S. Frank.     

Structural aspects of water in 1-octanol

Water-saturated 1-octanol, extensively used for studies of the distribution of organic solutes, is subjected to structural analysis in terms of the neighbors each molecule has. This is based on thermodynamic information on the system from the literature. The local composition of a given water molecule is richer in water than the bulk composition, and, conversely, for the local composition near a 1-octanol molecule. At saturation (mole fraction of water of 0.275 in the organic phase) the excess (deficiency) of the mole fraction of water is 0.197 (–0.075) near water (1-octanol) molecules.     

Click synthesis of ubiquitin dimer analogs to interrogate linkage-specific UBA domain binding

A new route to the synthesis of triazole-linked ubiquitin dimers (diUbs) as structural analogs of the seven diUbs is reported. Binding studies with the Lys48-specific UBA domain of the Mud1 protein suggest that they represent functionally suitable surrogates of their native counterparts linked by an isopeptide bond.     

Anion binding with some 22- and 28-membered selenaaza macrocycles: Structural aspects and Se NMR studies

A series of macrocyclic adducts of the 22- and 28-membered selenaaza macrocycles (1 and 2, respectively) with different counter anions such as halides, sulfate, perchlorate, phosphate, trifluoroacetate and nitrate has been prepared. The adducts have been characterized by elemental analysis, IR, ¹H NMR, ⁷⁷Se NMR and ESI-MS analysis. The ⁷⁷Se NMR spectrum of the adduct (7) shows an upfield shift compared to the parent macrocycle. The bromo (5), iodo (6), sulfate (7), trifluroacetate (10) adducts of the 22-membered selenaaza macrocycle and perchlorate (16), trifluroacetate (18) adducts of the 28-membered selenaaza macrocycle have been structurally characterized. The crystal structures show extensive hydrogen bonding networks. The molecular structures of all the compounds show the macrocycle to be fully protonated except the trifluroacetate adduct of the 22-membered macrocycle (10), which is only diprotonated. The binding constants of the neutral 22-membered selenaaza macrocycle towards, fluoride, bromide, iodide and sulfate ion have been determined by the NMR titration method.     

Sugar binding specificities of anti-H(O) lectins disclosed by use of fucose-containing human milk oligosaccharides as binding inhibitors

The binding to normal and sialidase-treated human erythrocytes of six 125I-labeled lectins [Ulex europeus lectin I (UEA-1) and II (UEA-II), Laburnum alpinum lectins I (LAA-I) and II (LAA-II), and Cytisus multiflorus lectins I (CMA-I) and II (CMA-II)], was studied in detail. Quantitative inhibition assays of the lectin binding to the cells were also performed with various human milk oligosaccharides as inhibitors. Based on a comparison of the inhibition constants of the inhibitors thus obtained with the association constants of the lectins to the cells, the relative activities of cell surface blood group antigens toward the lectins are discussed.     

Steroid binding by antibodies and artificial receptors: Exploration of theoretical methods to determine the origins of binding affinities and specificities

Binding mode calculations for complexes between an artificial paracyclophane receptor and digoxins, cholic acids as well as cortisone steroids show encapsulation of different ring combinations. Docking experiments were performed between the 26-10 antibody and digoxins. Coordination affinity arises from hydrophobic desolvation and van der Waals interactions rather than from hydrogen bonds. The specificity and affinity arises mainly from shape complementarity. Computed binding free energies and Kohonen neural network computations both point to physicochemical and structural similarities of natural antibodies and artificial receptors.     

Zinc(II) complexes of ubiquitin: speciation, affinity and binding features

Intraneuronal inclusions consisting of hypermetallated, (poly-)ubiquitinated proteins are a hallmark of neurodegeneration. To highlight the possible role played by metal ions in the dysfunction of the ubiquitin-proteasome system, here we report on zinc(II)/ubiquitin binding in terms of affinity constants, speciation, preferential binding sites and effects on protein stability and self-assembly. Potentiometric titrations allowed us to establish that at neutral pH only two species, ZnUb and Zn(2)Ub, are present in solution, in line with ESI-MS data. A change in the diffusion coefficient of ubiquitin was observed by NMR DOSY experiments after addition of Zn(II) ions, and thus indicates metal-promoted formation of protein assemblies. Analysis of (1)H, (15)N, (13)Cα and (13)CO chemical-shift perturbation after equimolar addition of Zn(II) ions to ubiquitin outlined two different metal-binding modes. The first involves a dynamic equilibrium in which zinc(II) is shared between a region including Met1, Gln2, Ile3, Phe4, Thr12, Leu15, Glu16, Val17, Glu18, Ile61 and Gln62 residues, which represent a site already described for copper binding, and a domain comprising Ile23, Glu24, Lys27, Ala28, Gln49, Glu51, Asp52, Arg54 and Thr55 residues. A second looser binding mode is centred on His68. Differential scanning calorimetry evidenced that addition of increasing amounts of Zn(II) ions does not affect protein thermal stability; rather it influences the shape of thermograms because of the increased propensity of ubiquitin to self-associate. The results presented here indicate that Zn(II) ions may interact with specific regions of ubiquitin and promote protein-protein contacts.     

Structural aspects for evolution of beta-lactamases from penicillin-binding proteins

Penicillin-binding proteins (PBPs), biosynthetic enzymes of bacterial cell wall assembly, and beta-lactamases, resistance enzymes to beta-lactam antibiotics, are related to each other from an evolutionary point of view. Massova and Mobashery (Antimicrob. Agents Chemother. 1998, 42, 1-17) have proposed that for beta-lactamases to have become effective at their function as antibiotic resistance enzymes, they would have had to undergo structure alterations such that they would not interact with the peptidoglycan, which is the substrate for PBPs. A cephalosporin analogue, 7beta-[N-Acetyl-L-alanyl-gamma-D-glutamyl-L-lysine]-3-acetoxymethyl-3-cephem-carboxylic acid (compound 6), was conceived and synthesized to test this notion. The X-ray structure of the complex of this cephalosporin bound to the active site of the deacylation-deficient Q120L/Y150E variant of the class C AmpC beta-lactamase from Escherichia coli was solved at 1.71 A resolution. This complex revealed that the surface for interaction with the strand of peptidoglycan that acylates the active site, which is present in PBPs, is absent in the -lactamase active site. Furthermore, insertion of a peptide in the beta-lactamase active site at a location where the second strand of peptidoglycan in some PBPs binds has effectively abolished the possibility for such interaction with the beta-lactamase. A 2.6 ns dynamics simulation was carried out for the complex, which revealed that the peptidoglycan surrogate (i.e., the active-site-bound ligand) undergoes substantial motion and is not stabilized for binding within the active site. These factors taken together disclose the set of structure modifications in the antibiotic resistance enzyme that prevent it from interacting with the peptidoglycan, en route to achieving catalytic proficiency for their intended function.     

Structural aspects of photosensitized β,γ-enone isomerizations

Sensitized irradiations of enones 5, 9 and 11 gave the corresponding cyclopropyl ketones 6, 10 and 12, whereas similar irradiation of enone 1 only resulted in recovery of the starting material. Investigation of the steric course of the rearrangement of enone 11 utilizing NOE measurements and deuterio-labeled compounds 11α/11β has shown that the overall isomerization of 11 to 12 proceeded nonstereospecifically. In addition, the positional effect of the enone moiety and influence of an additional keto group, i.e., 3-keto in enone 5, have been investigated. These results can be rationalized and satisfactorily explained on the basis of an oxa-di-π-methane intermediate 19.