Model for the porphyrin-DNA binding site: ENDOR investigations of Cu-porphyrins binding to DNA.

Proton ENDOR has been observed from frozen solutions (ca. 38K degrees) of copper meso-(4-N-tetra-methylpyridyl)porphyrin (CuTMpyP(4)) complexed with Salmon sperm DNA in water and D2O. Lines from exchangeable protons of the DNA bases have been observed in these ENDOR spectra. Analyses of these ENDOR data show that the separations of these DNA protons from the copper atom are between 3.76 and 3.84 A with angles of 19.5 to 22.5 degrees between the Cu-H vectors and the gz axis. A distant ENDOR response has also been observed from phosphorous nuclei in the DNA backbone. We estimate that the phosphorous atoms producing this ENDOR signal are 7.5-10 A from the copper center of the porphyrin. These ENDOR data combined with results from an earlier NMR investigation have been used to construct a computer simulated model of the binding site in which the porphyrin is partially intercalated and extends into the major groove of DNA. The two GC base pairs at this site are slightly inequivalent. For each, the G imino proton and one of the C amino protons are at appropriate positions to account for the ENDOR signals arising from exchangeable protons. It is unlikely that this inequivalence would persist at room temperature where dynamic processes would give an apparently symmetric interaction. Although the model accounts for all reported experimental data involving tetracationic porphyrin species which have been suggested to be intercalators, it is not a unique solution.     

Structural Model for the Trialkyltin Binding Site on Cat Hemoglobin

Abstract

The binding site for trialkyltin complexes on the alpha- chain of cat oxyhemoglobins is proposed to involve the SG and NE2 atoms of Cys-13 and His-113 respectively. On deoxygenation, the conformation of this region changes substantially, allowing complexation only through the ND1 nitrogen atom of His-113, a much less favorable interaction. Thus the model presented explains the preferential binding of trialkyltin complexes to R-state cat hemoglobin and suggests the type of interaction that is likely to occur between these compounds and a variety of less well-characterized enzymes to produce the metabolic effects that trialkyltin complexes are known to produce in vivo.     

Investigations of Amino Acids in the ATP Binding Site of 5,10-Methenyltetrahydrofolate Synthetase

5-Formyltetrahydrofolate is a compound that is administered as a rescue agent in methotrexate chemotherapy and in 5-fluorouracil chemotherapy for synergistic effects. It has also recently been suggested to play a role in bacterial resistance to antifolate therapy. 5,10-methenyltetrahydrofolate synthetase (MTHFS) is the only enzyme known to catalyze the conversion of this compound to 5,10-methenyltetrahydrofolate along with the hydrolysis of ATP to ADP. To better understand the roles of specific amino acids in the ATP binding pocket of this enzyme, we used site-directed mutagenesis to create 10 modified forms of the Mycoplasma pneumoniae ortholog. The Michaelis constant (K_m) for each substrate and the turnover number (k_cat) was determined for each mutant to help elucidate the role of individual amino acids. Data were compared to crystal structures of human and M. pneumoniae orthologs of MTHFS. Results were largely consistent with a simple coulombic and proximity model; the larger the predicted charges of an interaction and the closer those interactions were to the phosphate transferred between the substrates, the greater the reduction in ATP binding and catalytic activity of the enzyme.     

Blind Prediction of Charged Ligand Binding Affinities in a Model Binding Site

Predicting absolute protein–ligand binding affinities remains a frontier challenge in ligand discovery and design. This becomes more difficult when ionic interactions are involved because of the large opposing solvation and electrostatic attraction energies. In a blind test, we examined whether alchemical free-energy calculations could predict binding affinities of 14 charged and 5 neutral compounds previously untested as ligands for a cavity binding site in cytochrome c peroxidase. In this simplified site, polar and cationic ligands compete with solvent to interact with a buried aspartate. Predictions were tested by calorimetry, spectroscopy, and crystallography. Of the 15 compounds predicted to bind, 13 were experimentally confirmed, while 4 compounds were false negative predictions. Predictions had a root-mean-square error of 1.95 kcal/mol to the experimental affinities, and predicted poses had an average RMSD of 1.7 Å to the crystallographic poses. This test serves as a benchmark for these thermodynamically rigorous calculations at predicting binding affinities for charged compounds and gives insights into the existing sources of error, which are primarily electrostatic interactions inside proteins. Our experiments also provide a useful set of ionic binding affinities in a simplified system for testing new affinity prediction methods.     

Metal Binding at the Deinococcus radiodurans Dps-1 N-Terminal Metal Site Controls Dodecameric Assembly and DNA Binding

The prokaryotic DNA protection during starvation (Dps) proteins typically protect macromolecules against damaging agents via physical association with DNA and by oxidizing and sequestering iron. However, Deinococcus radiodurans Dps-1, which binds DNA with high affinity, fails to protect DNA against hydroxyl radicals due to iron leakage from the core, raising the question of how (?)OH-mediated damage to Dps-1-bound DNA is avoided. As shown here, Mn(II) inhibits ferroxidase activity, suggesting that ferroxidation may be prevented in vivo as D. radiodurans accumulates a high ratio of Mn:Fe. Dps-1 has an N-terminal extension with a unique metal-binding site, an extension that has been proposed to be important for DNA binding and dodecameric assembly. Electrophoretic mobility shift assays show that Mn(II) restores DNA binding to bipyridyl-treated Dps-1, whereas Fe(II) fails to do so in the presence of H(2)O(2), thus preventing DNA binding under conditions of ongoing ferroxidase activity. We also show that disruption of the N-terminal metal site leads to a significant reduction in DNA binding and to compromised oligomeric assembly, with the mutant protein assembling into a hexamer in the presence of divalent metal. We propose that securing the N-terminal loop by metal binding is required to initiate dodecameric assembly by contacting the neighboring dimer and that the absence of such optimal contacts results in formation of a hexameric assembly intermediate in which three dimers associate about one of the 3-fold axes. Once dodecameric Dps-1 is assembled, metal binding no longer affects oligomeric state; instead, differential metal binding controls DNA interaction under conditions of oxidative stress.     

Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site

We present a combined experimental and modeling study of organic ligand molecules binding to a slightly polar engineered cavity site in T4 lysozyme (L99A/M102Q). For modeling, we computed alchemical absolute binding free energies. These were blind tests performed prospectively on 13 diverse, previously untested candidate ligand molecules. We predicted that eight compounds would bind to the cavity and five would not; 11 of 13 predictions were correct at this level. The RMS error to the measurable absolute binding energies was 1.8 kcal/mol. In addition, we computed “relative” binding free energies for six phenol derivatives starting from two known ligands: phenol and catechol. The average RMS error in the relative free energy prediction was 2.5 kcal/mol (phenol) and 1.1 kcal/mol (catechol). To understand these results at atomic resolution, we obtained x-ray co-complex structures for nine of the diverse ligands and for all six phenol analogs. The average RMSD of the predicted pose to the experiment was 2.0 Å (diverse set), 1.8 Å (phenol-derived predictions), and 1.2 Å (catechol-derived predictions). We found that predicting accurate affinities and rank-orderings required near-native starting orientations of the ligand in the binding site. Unanticipated binding modes, multiple ligand binding, and protein conformational change all proved challenging for the free energy methods. We believe that these results can help guide future improvements in physics-based absolute binding free energy methods.     

Mapping the Binding Site of Aflatoxin B1 in DNA: Molecular Modeling of the Binding Sites for the N(7)-Guanine Adduct of Aflatoxin B1 in Different DNA Sequences

Abstract

Aflatoxin B, (AFB₁), a potent mutagen and carcinogen, forms an adduct exclusively at the N(7) position of guanine, but the structure of this adduct in double stranded DNA is not known. Molecular modeling (using the program, PSFRODO) in conjunction with molecular mechanical calculation (using the program, AMBER) are used to assess the binding modes available to this AFB₁ adduct TVvo modes appear reasonable; in one the AFB₁ moiety is intercalated between the base pair containing the adducted guanine and the adjacent base pair on the 5₁-side in reference to the adducted guanine, while in the second it is bound externally in the major groove of DNA Rotational flexibilty appears feasible in the latter providing four, potential binding sites. Molecular modeling reveals that the binding sites around the reactive guanine in different sequences are not uniformly compatible for interaction with AFB₁. As the sequence is changed, one particular external binding site would be expected to give a pattern of reactivities that is reasonably consistent with the observed sequence specificity of binding that AFB₁ shows in its reaction with DNA (Benasutti, M., Ejadi, S., Whitlow, M. D. and Loechler, E. L. (1988) Biochemistry 27, 472–481). The AFB₁ moiety is face-stacked in the major groove with its long axis approximately perpendicular to the helix axis. Favorable interactions are formed between exocyclic amino groups that project into the major groove on cytosines and adenines surrounding the reactive guanine, and oxygens in AFB₁; unfavorable interactions involve van der Waals contacts between the methyl group on thymine and the AFB₁ moiety. “Some of the sequence specificity of binding data can be rationalized more readily if it is assumed that 5′-GG-3′ sequences adopt an A-DNA structure.” Based upon molecular modeling/potential energy minimization calculation, it is difficult to predict how reactivity would change in different DNA sequences in the case of the intercalative binding mode; however, several arguments suggest that intercalation might not be favored. From these considerations a model of the structure for the transition state in reaction of AFB, with DNA is proposed involving one particular external binding site.     

DNA与蛋白质结合的荧光测定

构建了插入λ阻抑蛋白（Ｒｅｐ）的操纵基因（ＯＲ）和ＢｇｌⅡ识别位点的ＰＢＲ３２２重组质粒。阻抑蛋白与该质粒的相互作用可用ＢｇｌⅡ对它的水解作用引起的ＥＢ荧光变化来研究。在Ｅ．ｃｏｌｉ中表达的Ｒｅｐ表现了与该重组质粒结合的活力。核苷酸序列具精确二重对称性的ＯＲ（ＯＲｃｏｎｓ）对Ｒｅｐ的亲和力比天然的ＯＲ１小。     

A Theoretical Model for the Binding of Cis-Pt(NH3)2 +2 to DNA

Abstract

The binding of cis-Pt(NH₃)₂B₁B2 to the bases B₁ and B₂, i.e., guanine (G), cytosine (C), adenine (A), and thymine (T), of DNA is studied theoretically. The components of the binding are analyzed and a model structure is proposed for the intrastrand binding to the dB,pdB₂ sequence of a kinked double helical DNA. Quantum mechanical calculations of the ligand binding energy indicates that cw-Pt(NH₃)₂ ⁺² (cis-PDA) binds to N7(G), N3(C), 02(C), 06(G), N3(A), N7(A), 04(T) and 02(T) in order of decreasing binding energy. Conformational analysis provides structures of kinked DNA in which adjacent bases chelate to cis-PDA. Only bending toward the major groove allows the construction of acceptable square planar complexes. Examples are presented for kinks of ?70° and ?40° at the receptor site to orient the base pairs for ligand binding to B, and B₂ to form a nearly square planar complex. The energies for complex formation of cis-PDA to the various intra-strand base sites in double stranded DNA are estimated. At least 32 kcal/mole separates the energetically favorable dGpdG·cis-PDA chelate from the dCpdG·cis-PDA chelate. All other possible chelate structures are much higher in energy which correlates with their lack of observation in competition with the preferred dGpdG chelate.

The second most favorable ligand energy occurs with N3(C). A novel binding site involving dC(N3)pdG(N7) is examined. Denaturation can result in an anti ? syn rotation of C about its glycosidic bond to place N3(C) in the major groove for intrastrand binding in duplex DNA. This novel intrastrand dCpdG complex and the most favored dGpdG structure are illustrated with stereographic projections.     

Porphyrin-DNA: a supramolecular scaffold for functional molecules on the nanometre scale

We are pursuing the aim to use DNA as a supramolecular scaffold for the creation of electronically functional molecules on the nanometre scale. Here, we give a review on our results on porphyrin modified nucleotides used for this purpose. A general synthetic route to porphyrin-nucleotides has been devised, and the building blocks can be incorporated into oligonucleotides using standard solid phase synthesis methods. Up to 11 porphyrins were incorporated into DNA, reaching a length of approximately 4 nm in the array. The spectroscopic data are consistent with a porphyrin induced secondary structure stabilisation in the single strands.     

Location of the T4 Gene 32 Protein Binding Site on Simian Virus 40 DNA

The T4 gene 32 protein, which binds to single-stranded but not duplex DNA, forms a specifically located denaturation loop in covalently closed circular simian virus 40 (SV40) DNA. Cleavage of the SV40 DNA-gene 32 protein complex with a restriction endonuclease from Hemophilus parainfluenzae shows the loop center to be at 0.46 on the SV40 DNA map. This is within one of the regions of SV40 DNA cleaved preferentially by the single-strand-specific nuclease S(1).     

Dual Action of Pentobarbitone on GABA Binding: Role of Binding Site Integrity

The effects of pentobarbitone on the binding of gamma-aminobutyric acid (GABA) to crude synaptosomal rat brain membranes were studied. In extensively washed P2 membranes, pentobarbitone had a biphasic action: at concentrations ranging between 12.5 and 500 microM, pentobarbitone enhanced GABA binding in a concentration-dependent manner; at concentrations greater than 500 microM, this enhancement was progressively reversed towards control levels of GABA binding. The effect of pentobarbitone seen at higher concentrations may reflect a GABA-mimetic action, since similar concentrations enhanced diazepam binding to washed P2 membranes, an effect antagonized by bicuculline methochloride and picrotoxinin. When washed P2 membranes were incubated in 0.5% Triton X-100 (30 min at 37 degrees C), the enhancement of GABA binding by low concentrations of pentobarbitone was abolished, while at higher concentrations GABA binding was progressively inhibited, suggesting that the GABA-mimetic action is retained. When washed P2 membranes were subjected to high-frequency homogenization, the biphasic dose-response relationship for pentobarbitone was markedly shifted to the right. The choice of membrane preparation appears to be a critical factor in examining drug-receptor interactions in vitro, at least for those involving GABA and the barbiturates.     

Binding of 2-acetylaminofluorene to DNA

2-Acetylaminofluorene (2-AAF) is a carcinogenic and mutagenic derivative of fluorene. It is used as a biochemical tool in the study of carcinogenesis. Studies have shown that it induces tumors in a number of species in the liver, bladder, and kidney. It is thought that 2-AAF-DNA adduct formation leads to mutation, and eventually tumor formation. The aim of this study was to examine the interactions of AAF with calf-thymus DNA in aqueous solution at physiological conditions, using constant DNA concentration (12.5 mM) and various AAF/polynucleotide (phosphate) ratios of 1/120, 1/80, 1/40, 1/20, 1/10, 1/5, 1/2, and 1/1. Fourier transform infrared and UV-visible spectroscopic methods and molecular modeling were used to determine the ligand binding mode, the binding constant, and the stability of AAF-DNA complexes in aqueous solution. Spectroscopic evidence showed both intercalation and external binding of AAF to DNA with an overall binding constant of K(AAF-DNA) = 2.33 × 10(7) M(-1). 2-AAF induced a partial B to A-DNA transition and DNA aggregation was observed at high AAF content.