DNA-Bound peptide radicals generated through DNA-mediated electron transport

Flash-quench experiments were carried out to explore peptide/DNA electron-transfer reactions. DNA-bound [Ru(phen)(2)(dppz)](3+) (phen = 1,10-phenanthroline; dppz = dipyridophenazine) and [Ru(phen)(bpy')(dppz)](3+) [bpy' = 4-(4'-methyl-2, 2'-bipyridyl)valerate], generated in situ by flash-quench methodology, are powerful ground-state oxidants, capable of oxidizing guanine or tyrosine intercalated in DNA. In flash-quench experiments with mixed-sequence oligonucleotides in the presence of Lys-Tyr-Lys, transient absorption spectroscopy yielded a spectrum with a sharp maximum at 405 nm assigned to the tyrosine radical. Experiments with poly(dG.dC) suggested the intermediacy of the guanine radical, since the rise of the 405 nm signal occurred with the same kinetics as the disappearance of the guanine radical, as monitored at 510 nm. In oligonucleotide duplexes containing [Ru(phen)(bpy')(dppz)](2+) tethered at one end, damage to distant guanines was observed by gel electrophoresis, consistent with the mobility of the electron hole through the DNA duplex; the presence of the peptide did not inhibit but instead altered the distribution of guanine damage. Covalent adducts of the DNA and Lys-Tyr-Lys were detected as final irreversible products of this peptide-to-DNA electron-transfer chemistry by mass spectrometric and enzymatic digestive analysis. From these different assays and comparison of reactions of Lys-Trp-Lys and Lys-Tyr-Lys, the reactivity of the DNA-bound tyrosine radical was found to differ considerably from that of the tryptophan radical. These results establish that Lys-Tyr-Lys and Lys-Trp-Lys can participate in long-range electron-transfer reactions through the DNA from a distinct binding site. On that basis, proposals for functional roles for these peptide radicals may be considered.     

A 500 MHz proton NMR study of interaction of tripeptides Lys-Tyr-Lys and Lys-Phe-Lys with deoxydinucleotide d-CpG.

The binding of di- and tetranucleotides with tri- and tetrapeptides containing Tyr, Trp, Phe having lysine on both ends has been studied using a 500 MHz proton NMR. The results show that d-CpG exists as a right-handed B-DNA structure with both sugars in 01'-endo sugar conformation and glycosidic bond angle as in anti domain. On binding to tripeptide Lys-Tyr-Lys, the Tyr ring protons shift upfield by 0.015 ppm at 285 degrees K, while the conformation of d-CpG remains unchanged. Change in chemical shift of Tyr and nucleotide protons decreases with temperature. This upfield shift is attributed to stacking with bases/base-pairs. The presence of intermolecular NOE's also supports this. Results of binding of d-CpG to Lys-Phe-Lys are similar to those with Lys-Tyr-Lys except that the chemical shift changes occur to a lesser extent. On comparing the results obtained with three different peptides, it is found that interaction decreases in the order Trp > Tyr > Phe which is similar to that found by theoretical energy calculations (reported elsewhere) and fluorescence measurements. The results also exhibit a specificity in recognition of these amino acid residues by dinucleotides.     

Synthesis and DNA nicking studies of a novel cyclic peptide: cyclo[Lys-Trp-Lys-Ahx-].

Two novel cyclic tetrapeptides: cyclo[Lys-Tyr-Lys-Ahx-] 7a and cyclo[Lys-Trp-Lys-Ahx-] 7b were synthesized by coupling protected amino acid in solution and the subsequent cyclization effected by the pentafluorophenyl ester method as described in previous papers. These cyclic peptides were designed and synthesized to study their interaction with DNA, based on previous reports that linear peptides Lys-Tyr-Lys and Lys-Trp-Lys could bind to various forms of DNA and cleaved supercoiled DNA at apurinic sites. Ethidium bromide displacement assay showed that the apparent DNA binding constant of linear Lys-Tyr-Lys and cyclic peptide 7a are far below 1 x 10(3) M(-1), whereas those of cyclic peptide 7b and linear Lys-Trp-Lys are 1.9 x 10(4) M(-1) and 9.5 x 10(3) M(-1), respectively. Kinetic studies using agarose gel electrophoresis showed that cyclic peptide 7b and Lys-Trp-Lys possessed DNA nicking activity on natural supercoiled phi X174 DNA with nicking rate of 50.7 and 75.6 pM min(-1) at 65 degrees C, respectively, whereas cyclic peptide 7a and linear Lys-Tyr-Lys were devoid of the corresponding activity. The DNA nicking rate increased significantly with increase in reaction temperature. At reaction temperatures lower than 65 degrees C, the DNA nicking rate of cyclic peptide 7b exceeded that of linear Lys-Trp-Lys. The addition of 1 microM ferrous ion did not give significant enhancement effect on the DNA nicking rate by the peptides. UV irradiation gave a marked rate enhancement on the DNA nicking rate of linear Lys-Trp-Lys and a moderate enhancement on the DNA nicking rate of cyclic peptide 7b.     

The effect of adjacent residues on the reactivity of tyrosyl with iodine

The effect of the adjacent amino acid side chain groups on the iodination rate of the tyrosine was studied. The model peptides used were Gly-Tyr-Gly, Leu-Tyr-Leu, Glu-Tyr-Glu, and Lys-Tyr-Lys, in which the tyrosine is sandwiched between two hydrophobic, two negatively charged, or two positively charged residues. The results show only minor differences in the iodination rate of tyrosine in these four peptides. These differences are very small in comparison with those previously observed between the tyrosines of kappa Bence-Jones proteins.     

Photosensitized formation of thymine dimers in DNA by tyramine, tyrosine and tyrosine-containing peptides.

The formation of Thy-Thy in DNA in the presence of tyramine, tyrosine and tyrosine-containing peptides such as Lys-Tyr and Lys-Tyr-Lys was studied with monochromatic UV irradiation. The formation of Thy-Thy by UV irradiation was enhanced in the presence of these compounds. The action spectrum of the photosensitization has a peak near 280 nm corresponding to the absorption spectrum of tyrosine. The triplet quencher reduced the sensitization substantially. The sensitization in native DNA was more than six times larger than that in denatured DNA. increasing the concentration of salts suppressed the sensitization. The nature of the interaction between DNA and the sensitizer is discussed.     

β-catenin takes a HIT

Histidine triad (HIT) proteins represent a small family of nucleotide-binding and -hydrolyzing proteins, which attracted the attention of cancer biologists because their expression is lost in multiple human malignancies. To some of the family members including Fhit, Hint1 and Hint2, a tumor suppressive activity was assigned. Although highly similar in structure, their mode of action appears to be different as they are not able to compensate each other’s function. Surprisingly, in any reported assay system the enzymatic activity of the histidine triad proteins was not required for their tumor suppressor function. Until recently, little was known about the molecular mechanisms mediating the tumor suppressor activities of histidine triad proteins. The identification of new interaction partners started to shed light on the signaling pathways modulated by the HIT proteins. Here, we summarize these findings with special emphasis on the histidine triad proteins Hint1 and Fhit and their repressive activity on the β-catenin signaling function.     

A 500 MHz proton NMR study of stacking interactions: binding of tripeptide Lys-Tyr-Lys to tetradeoxynucleotide d-GpCpGpC.

The complete sequential assignment and conformation of d-GpCpGpC in D2O has been determined from 1D NMR spectra at 285-320 K and room temperature 2D-COSY and NOESY spectra. The tetradeoxynucleotide exists primarily as a right handed double helix at 285 K, having Tm as 314 K. On binding to a tripeptide Lys-Tyr-Lys in a concentration equimolar to tetranucleotide duplex, the Tyr ring protons shift upfield by 0.14 ppm at 285 K. The increase in Tm on binding suggests stabilization of duplex. The existence of intermolecular NOEs between C4 sugar protons and Tyr alpha C and Lys alpha C protons give direct evidence of proximity of Tyr residue to the C4 base of d-GpCpGpC. The conformation of d-GpCpGpC remains unchanged on binding. The observed results are interpreted in terms of preferential stacking of aromatic ring of Tyr residue with proximal base-pair of d-GpCpGpC, stabilized by electrostatic interaction of Lysine side chains with backbone phosphates. This is in contrast to intercalculation of aromatic dyes within base-pairs resulting in a change in sugar conformation at the binding site.     

Phenol coupling initiated by one-electron oxidation of tyrosine units in peptides and histone

Phenoxyl radicals generated pulse radiolytically by the reaction of N.3 with Gly-Tyr decay biomolecularly (2k = 4.7 X 10(8)M-1 s-1) with efficient formation of 2,2'-dimers, which enolize rapidly (k = 2.7 X 10(4) s-1) to produce the 2,2'-biphenolic product. The build-up of the characteristic 2,2'-biphenol fluorescence (400 nm) and absorption also indicated a delayed (k = 80 s-1) process, probably involving the phenoxyl <-> phenoxy-quinol equilibrium. About 60 per cent of the Gly-Tyr phenoxyls were found to dimerize to the 2,2'-biphenol, and a similarly efficient 2,2'-coupling seems to occur with other tyrosyls, such as Lys-Tyr-Lys and histone. gamma-Radiolysis was applied to estimate relative yields of formation of 2,2'-biphenols under various conditions. Dimerization is almost completely inhibited by cysteine or oxygen, consistent with phenoxyl 'repair' by cysteine or O-.2; disproportionation of O-.2 with SOD prevents repair. The phenol 2,2'-coupling is less efficient for .OH- and inefficient for e-aq-initiation.     

Characterization of a novel Ser-cisSer-Lys catalytic triad in comparison with the classical Ser-His-Asp triad

Amidase signature family enzymes, which are widespread in nature, contain a newly identified Ser-cisSer-Lys catalytic triad in which the peptide bond between Ser131 and the preceding residue Gly130 is in a cis configuration. In order to characterize the property of the novel triad, we have determined the structures of five mutant malonamidase E2 enzymes that contain a Cys-cisSer-Lys, Ser-cisAla-Lys, or Ser-cisSer-Ala triad or a substitution of Gly130 with alanine. Cysteine cannot replace the role of Ser155 due to a hyper-reactivity of the residue, which results in the modification of the cysteine to cysteinyl sulfinic acid, most likely inside the expression host cells. The lysine residue plays a structural as well as a catalytic role, since the substitution of the residue with alanine disrupts the active site structure completely. The two observations are in sharp contrast with the consequences of the corresponding substitutions in the classical Ser-His-Asp triad. Structural data on the mutant containing the Ser-cisAla-Lys triad convincingly suggest that Ser131 plays an analogous catalytic role as the histidine of the Ser-His-Asp triad. The unusual cis configuration of Ser131 appears essential for the precise contacts of this residue with the other triad residues, as indicated by the near invariance of the preceding glycine residue (Gly130), structural data on the G130A mutant, and by a modeling experiment. The data provide a deep understanding of the role of each residue of the new triad at the atomic level and demonstrate that the new triad is a catalytic device distinctively different from the classical triad or its variants.     

Identification and analysis of a new family of bacterial serine proteinases

A family of hypothetical proteins, identified predominantly from archaeal genomes, has been analyzed in order to understand its functional characteristics. Using extensive sequence similarity searches it is inferred that this family is remotely related (best sequence identity is 19%) to ClpP proteinases that belongs to serine proteinase class. This family of hypothetical proteins is referred to as SDH proteinase family based on conserved sequential order of Ser, Asp and His residues and predicted serine proteinase activity. Results of fold recognition of SDH family sequences confirmed the remote relationship between SDH proteinases and Clp proteinases and revealed similar tertiary location of putative catalytic triad residues critical for serine proteinase function. However, the best sequence alignment we could obtain suggests that while catalytic Ser is conserved across Clp and SDH proteinases the location of the other catalytic triad residues, namely, His and Asp are swapped in their amino acid alignment positions and hence in 3-D structure. The evidence of conserved catalytic triad suggests that SDH could be a new family of serine proteinases with the fold of Clp proteinase, however sharing the catalytic triad order of carboxypeptidase clan. Signal peptide sequence identified at the N-terminus of some of the homologues suggests that these might be secretory serine proteinases involved in cleavage of extracellular proteins while the remote homologues, ClpP proteinases, are known to work in intracellular environment.     

Tissue and subcellular distribution of glucokinase in rat liver and their changes during fasting-refeeding

The distribution of glucokinase in rat liver under both normal feeding and fasting-refeeding conditions was investigated immunohistochemically. Under normal feeding conditions, glucokinase immunoreactivity was observed in both nuclei and cytoplasm of parenchymal cells. The nuclei were stained intensely and evenly, whereas the cytoplasm showed weak immunoreactivity of different degrees of staining intensity depending on the location of the cells. The cytoplasm of perivenous hepatocytes was stained more intensely, though not so much more, than that of periportal hepatocytes. The cytoplasm of hepatocytes surrounding the terminal hepatic venule (THV), of hepatocytes surrounding the portal triad, and of some other hepatocytes showed a stronger immunoreactivity than that of residual hepatocytes. The nuclear immunoreactivity in hepatocytes surrounding the portal triad and in some other hepatocytes was weak or absent, and positive immunoreactivity was detected at the plasma membrane of some of these cells. After 72 h of fasting, glucokinase immunoreactivity was markedly decreased in all hepatocytes. After the start of refeeding, the cytoplasmic immunoreactivity began to increase first in the parenchymal cells surrounding the THV and extended to those in the intermediate zone followed by those in the periportal zone. In contrast, the increase in nuclear immunoreactivity started in hepatocytes situated in the intermediate zone adjacent to the perivenous zone and then extended to those in the perivenous zone followed by those in the periportal zone. Hepatocytes surrounding either THV or portal triad showed a distinctive change in immunoreactivity during the refeeding period. After 10 h of refeeding, strong immunoreactivity was observed in both the cytoplasm and the nuclei of all hepatocytes, and appreciable glucokinase immunoreactivity was detected at the plasma membrane of some hepatocytes. These findings are discussed from the standpoint of a functional role of glucokinase in hepatic glucose metabolism.     

Multiple functions for the invariant AGC triad of U6 snRNA

The invariant AGC triad of U6 snRNA plays an essential, unknown role in splicing. The triad has been implicated in base-pairing with residues in U2, U4, and U6. Through a genetic analysis in S. cerevisiae, we found that most AGC mutants are suppressed both by restoring pairing with U2, supporting the significance of U2/U6 helix Ib, and by destabilizing U2 stem I, indicating that this stem regulates helix Ib formation. Intriguingly, one of the helix Ib base pairs is required specifically for exon ligation, raising the possibility that the entirety of helix Ib is required only for exon ligation. We also found that U4 mutations that reduce complementarity in U4 stem I enhance U2-mediated suppression of an AGC mutant, suggesting that U4 stem I competes with the AGC-containing U4/U6 stem I. Implicating an additional, essential function for the triad, three triad mutants are refractory to suppression--even by simultaneous restoration of pairing with U2, U4, and U6. An absolute requirement for a purine at the central position of the triad parallels an equivalent requirement in a catalytically important AGC triad in group II introns, consistent with a role for the AGC triad of U6 in catalysis.     

Knowledge-based modeling of the serine protease triad into non-proteases.

The Asp-His-Ser triad of serine proteases has been regarded, in the present study, as an independent catalytic motif, because in nature it has been incorporated at the active sites of enzymes as diverse as the serine proteases and the lipases. Incorporating this motif into non-protease scaffolds, by rational design and mutagenesis, might lead to the generation of novel catalysts. As an aid to such experiments, a knowledge-based computer modeling procedure has been developed to model the protease Asp-His-Ser triad into non-proteases. Catalytic triads from a set of trypsin family proteases have been analyzed and criteria that characterize the geometry of the triads have been obtained. Using these criteria, the modeling procedure first identifies sites in non-proteases that are suitable for modeling the protease triad. H-bonded Asp-His-Ser triads, that mimic the protease catalytic triad in geometry, are then modeled in at these sites, provided it is stereochemically possible to do so. Thus non-protease sites at which H-bonded Asp-His-Ser triads are successfully modeled in may be considered for mutagenesis experiments that aim at introducing the protease triad into non-proteases. The triad modeling procedure has been used to identify sites for introducing the protease triad in three binding proteins and an immunoglobulin. A scoring function, depending on inter-residue distances, solvent accessibility and the substitution potential of amino acid residues at the modeling sites in the host proteins, has been used to assess the quality of the model triads.     

Fundamental limits on wavelength, efficiency and yield of the charge separation triad

In an attempt to optimize a high yield, high efficiency artificial photosynthetic protein we have discovered unique energy and spatial architecture limits which apply to all light-activated photosynthetic systems. We have generated an analytical solution for the time behavior of the core three cofactor charge separation element in photosynthesis, the photosynthetic cofactor triad, and explored the functional consequences of its makeup including its architecture, the reduction potentials of its components, and the absorption energy of the light absorbing primary-donor cofactor. Our primary findings are two: First, that a high efficiency, high yield triad will have an absorption frequency more than twice the reorganization energy of the first electron transfer, and second, that the relative distance of the acceptor and the donor from the primary-donor plays an important role in determining the yields, with the highest efficiency, highest yield architecture having the light absorbing cofactor closest to the acceptor. Surprisingly, despite the increased complexity found in natural solar energy conversion proteins, we find that the construction of this central triad in natural systems matches these predictions. Our analysis thus not only suggests explanations for some aspects of the makeup of natural photosynthetic systems, it also provides specific design criteria necessary to create high efficiency, high yield artificial protein-based triads.     

C-terminal movement during gating in cyclic nucleotide-modulated channels

Activation of cyclic nucleotide-modulated channels such as CNG and HCN channels is promoted by ligand-induced conformational changes in their C-terminal regions. The primary intersubunit interface of these C termini includes two salt bridges per subunit, formed between three residues (one positively charged and two negatively charged amino acids) that we term the SB triad. We previously hypothesized that the SB triad is formed in the closed channel and breaks when the channel opens. Here we tested this hypothesis by dynamically manipulating the SB triad in functioning CNGA1 channels. Reversing the charge at positions Arg-431 and Glu-462, two of the SB triad residues, by either mutation or application of charged reagents increased the favorability of channel opening. To determine how a charge reversal mutation in the SB triad structurally affects the channel, we solved the crystal structure of the HCN2 C-terminal region with the equivalent E462R mutation. The backbone structure of this mutant was very similar to that of wild type, but the SB triad was rearranged such that both salt bridges did not always form simultaneously, suggesting a mechanism for the increased ease of opening of the mutant channels. To prevent movement in the SB triad, we tethered two components of the SB triad region together with cysteine-reactive cross-linkers. Preventing normal movement of the SB triad region with short cross-linkers inhibited channel opening, whereas longer cross-linkers did not. These results support our hypothesis that the SB triad forms in the closed channel and indicate that this region expands as the channel opens.     

The unraveling architecture of the junctional sarcoplasmic reticulum

The sarcoplasmic reticulum (SR) of skeletal muscle controls the contraction-relaxation cycle by raising and lowering the myoplasmic free-Ca²⁺ concentration. The coupling between excitation, i.e., depolarization of sarcolemma and transvers tubule (TT) and Ca²⁺ release from the terminal cisternae (TC) of SR takes place at the triad. The triad junction is formed by a specialized region of the TC, the junctional SR, and the TT. The molecular architecture and protein composition of the junctional SR are under active investigation. Since the junctional SR plays a central role in excitation-contraction coupling and Ca²⁺ release, some of its protein constituents are directly involved in these processes. The biochemical evidence supporting this contention is reviewed in this article.     

Structural and Biochemical Characterization of an Active Arylamine N-Acetyltransferase Possessing a Non-canonical Cys-His-Glu Catalytic Triad

Arylamine N-acetyltransferases (NATs), a class of xenobiotic-metabolizing enzymes, catalyze the acetylation of aromatic amine compounds through a strictly conserved Cys-His-Asp catalytic triad. Each residue is essential for catalysis in both prokaryotic and eukaryotic NATs. Indeed, in (HUMAN)NAT2 variants, mutation of the Asp residue to Asn, Gln, or Glu dramatically impairs enzyme activity. However, a putative atypical NAT harboring a catalytic triad Glu residue was recently identified in Bacillus cereus ((BACCR)NAT3) but has not yet been characterized. We report here the crystal structure and functional characterization of this atypical NAT. The overall fold of (BACCR)NAT3 and the geometry of its Cys-His-Glu catalytic triad are similar to those present in functional NATs. Importantly, the enzyme was found to be active and to acetylate prototypic arylamine NAT substrates. In contrast to (HUMAN) NAT2, the presence of a Glu or Asp in the triad of (BACCR)NAT3 did not significantly affect enzyme structure or function. Computational analysis identified differences in residue packing and steric constraints in the active site of (BACCR)NAT3 that allow it to accommodate a Cys-His-Glu triad. These findings overturn the conventional view, demonstrating that the catalytic triad of this family of acetyltransferases is plastic. Moreover, they highlight the need for further study of the evolutionary history of NATs and the functional significance of the predominant Cys-His-Asp triad in both prokaryotic and eukaryotic forms.     

Molecular Basis of the General Base Catalysis of an α/β-Hydrolase Catalytic Triad

The serine-histidine-aspartate triad is well known for its covalent, nucleophilic catalysis in a diverse array of enzymatic transformations. Here we show that its nucleophilicity is shielded and its catalytic role is limited to being a specific general base by an open-closed conformational change in the catalysis of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (or MenH), a typical α/β-hydrolase fold enzyme in the vitamin K biosynthetic pathway. This enzyme is found to adopt an open conformation without a functional triad in its ligand-free form and a closed conformation with a fully functional catalytic triad in the presence of its reaction product. The open-to-closed conformational transition involves movement of half of the α-helical cap domain, which causes extensive structural changes in the α/β-domain and forces the side chain of the triad histidine to adopt an energetically disfavored gauche conformation to form the functional triad. NMR analysis shows that the inactive open conformation without a triad prevails in ligand-free solution and is converted to the closed conformation with a properly formed triad by the reaction product. Mutation of the residues crucial to this open-closed transition either greatly decreases or completely eliminates the enzyme activity, supporting an important catalytic role for the structural change. These findings suggest that the open-closed conformational change tightly couples formation of the catalytic triad to substrate binding to enhance the substrate specificities and simultaneously shield the nucleophilicity of the triad, thus allowing it to expand its catalytic power beyond the nucleophilic catalysis.     

Localization of the alpha 1 and alpha 2 subunits of the dihydropyridine receptor and ankyrin in skeletal muscle triads

We have studied the subcellular distribution of the alpha 1 and alpha 2 subunits of the dihydropyridine (DHP) receptor and ankyrin in rat skeletal muscle with immunofluorescence and immunogold labeling techniques. All three proteins were concentrated in the triad junction formed between the T-tubules and sarcoplasmic reticulum. The alpha 1 and alpha 2 subunits of the DHP receptor were colocalized in the junctional T-tubule membrane, supporting their proposed association in a functional complex and the possible participation of the alpha 2 subunit in excitation-contraction coupling. Ankyrin label in the triad showed a distribution different from that of the DHP receptor subunits. In addition, ankyrin was found in longitudinally oriented structures outside the triad. Thus, ankyrin might be involved in organizing the triad and in immobilizing integral membrane proteins in T-tubules and the sarcoplasmic reticulum.