Distance measurements between paramagnetic ligands bound to parallel stranded guanine quadruplexes.

Aside from a double helix, deoxyribonucleic acid (DNA) folds into non-canonical structures, one of which is the guanine quadruplex. Cationic porphyrins bind guanine quadruplexes, but the effects of ligand binding on the structure of guanine quadruplexes with more than four contiguous guanine quartets remains to be fully elucidated. Double electron-electron resonance (DEER) spectroscopy conducted at 9.5 GHz (X-band) using broadband, shaped inversion pulses was used to measure the distances between cationic copper porphyrins bound to model parallel-stranded guanine quadruplexes with increasing numbers of guanine quartets. A single Gaussian component was found to best model the time domain datasets, characteristic of a 2 : 1 binding stoichiometry between the porphyrins and each quadruplex. The measured Cu(2+)-Cu(2+) distances were found to be linearly proportional with the number of guanines. Rather unexpectedly, the ligand end-stacking distance was found to monotonically decreases the overall quadruplex length was extended, suggesting a conformational change in the quadruplex secondary structure dependent upon the number of successive guanine quartets.

Effects of tail-like substituents on the binding of competitive inhibitors to the Q(B) site of photosystem II.

The QB quinone-binding site of photosystem II is an important target for herbicides. Two major classes of herbicides are based on s-triazine and phenylurea moieties. A small library of triazine and phenylurea compounds has been synthesized which have tail-like substituents in order to test the effects of charge, hydrophobicity and size of the tail on binding properties. It is found that a tail can be attached to one of the alkylamino groups of triazine-type herbicides or to the para position of phenylurea-type herbicides without loss of binding, provided that the tail is hydrophobic. This indicates that the herbicides must be oriented in the QB site such that these positions point toward the natural isoprenyl tail-binding pocket that extends out of the Q(B) site. In turn, the requirement that the tail must extend out of the QB site constrains the size of the other herbicide substituents in the pocket. This is in agreement with the presumed orientation and fit of ligands in the QB site. When longer hydrophobic tails are used, the binding penalty that occurs upon adding a charged substituent at the distal end is reduced. This allows the use of a series of tail substituents possessing a distal charge as an approximate molecular ruler to measure the distance from the QB site to the aqueous phase. Even a 10-carbon alkyl chain still shows a 4-fold effect from the presence or absence of a distal charge. Such a chain does not appear to be long enough to extend from the bulk aqueous phase to the QB site because binding is completely lost when a large hydrophilic domain (PEG(4000)) is attached to the distal end. Longer tails are effective only if they are sufficiently hydrophobic. An effort was made to use tailed herbicides for affinity binding of photosystem II. It was found that hydrophobic linkers promote nonspecific binding, but careful choice of solvent conditions, such as the use of excess nonionic detergent well above its critical micelle concentration, might obviate this problem during affinity-binding applications.

Competitive binding of acetate and chloride in photosystem II.

The binding of chloride and acetate to photosystem II (PSII) was examined to elucidate the mechanism of acetate inhibition. The mode of inhibition was studied, and individual binding sites were assigned by steady-state O2 evolution measurements in correlation with electron paramagnetic resonance (EPR) results. Two binding sites were found for acetate, one chloride-sensitive on the electron donor side and one chloride-insensitive on the electron acceptor side. The respective binding constants were as follows: KCl = 0.5 +/- 0.2 mM (chloride binding to the donor side), KI = 16 +/- 5 mM (acetate binding to the donor side), and KI' = 130 +/- 40 mM (acetate binding to the acceptor side). When acetate was bound to the acceptor side of PSII, 200 K illumination induced a narrowed form of the QA-FeII EPR signal, the yield of which was independent of the chloride concentration. When acetate was bound to the donor side, room-temperature illumination produced the S2YZ* state. EPR measurements showed that both the yield and formation rate of this state increased with acetate concentration. Increasing chloride concentrations slowed the rate of formation of the S2YZ* state, but did not affect the steady-state yield of the S2YZ* state. These findings indicate that the light-induced reactions in acetate-inhibited PSII are modulated by both donor side and acceptor side binding of acetate, while the steady-state yield of the S2YZ* state at the high PSII concentrations used for EPR measurements depends primarily on acceptor side turnover. Our data further support a close proximity of chloride to YZ*, indicating a possible role for chloride in the electron-transfer mechanism at the O2-evolving complex.

Characterization of the interaction between manganese and tyrosine Z in acetate-inhibited photosystem II.

When acetate-inhibited photosystem II (PSII) membranes are illuminated at temperatures above 250 K and quickly cooled to 77 K, a 240 G-wide electron paramagnetic resonance (EPR) signal is observed at 10 K. This EPR signal arises from a reciprocal interaction between the spin 1/2 ground state of the S2 state of the Mn4 cluster, for which a multiline EPR signal with shifted 55Mn hyperfine peaks is observed, and the oxidized tyrosine residue, YZ*, for which a broadened YZ* EPR spectrum is observed. The S2YZ* EPR signal in acetate-inhibited PSII is the first in which characteristic spectral features from both paramagnets can be observed. The observation of distinct EPR signals from each of the paramagnets together with the lack of a half-field EPR transition indicates that the exchange and dipolar couplings are weak. Below 20 K, the S2YZ* EPR signal in acetate-inhibited PSII is in the static limit. Above 20 K, the line width narrows dramatically as the broad low-temperature S2YZ* EPR signal is converted to a narrow YZ* EPR signal at room temperature. The line width narrowing is interpreted to be due to averaging of the exchange and dipolar interactions between YZ* and the S2 state of the Mn4 cluster by rapid spin-lattice relaxation of the Mn4 cluster as the temperature is increased. Decay of the S2YZ* intermediate at 200 K shows that the g = 4.1 form of the S2 state is formed and that a noninteracting S2-state multiline EPR signal is not observed as an intermediate in the decay. This result shows that a change in the redox state of YZ induces a spin-state change in the Mn4 cluster in acetate-inhibited PSII. The interconversion between spin states of the Mn4 cluster in acetate-inhibited PSII supports the idea that YZ oxidation or YZ* reduction is communicated to the Mn4 cluster through a direct hydrogen-bonding pathway, possibly involving a ligand bound to the Mn4 cluster.

Reversible binding of nitric oxide to tyrosyl radicals in photosystem II. Nitric oxide quenches formation of the S3 EPR signal species in acetate-inhibited photosystem II.

Continuous illumination at temperatures above 250 K of photosystem II samples which have been depleted of calcium or chloride or treated with fluoride, acetate, or ammonia results in production of a broad radical EPR signal centered at g = 2.0. This EPR signal, called the S3 EPR signal, has been attributed to an organic radical interacting with the S2 state of the oxygen-evolving complex to give the species S2X+ (X+ = organic radical). A tyrosine radical has been proposed as the species responsible for the S3 EPR signal. On the basis of experiments demonstrating that nitric oxide binds reversibly to the tyrosyl radical in ribonucleotide reductase, nitric oxide has been used to probe the S3 EPR signal in acetate-treated photosystem II. In experiments using manganese-depleted photosystem II, nitric oxide was found to bind reversibly to both redox-active tyrosines, YD* and YZ*, to form EPR-silent adducts. Next, acetate-treated photosystem II was illuminated to form the S3 EPR signal in the presence of nitric oxide to test whether the S3 EPR signal behaves like YZ*. Under conditions that produce the maximum yield of the S3 EPR signal in acetate-treated photosystem II, no S3 EPR signal was observed in the presence of nitric oxide. Upon removal of nitric oxide, the S3 EPR signal could be induced. Quenching of the S3 EPR signal by nitric oxide yielded an S2-state multiline EPR signal. Its amplitude was 45% of that found for uninhibited photosystem II illuminated at 200 K; this yield is the same as the yield of the S3 EPR signal under equivalent conditions but without nitric oxide. These results suggest that the S3 EPR signal is due to the configuration S2YZ* in which the S2 state of the oxygen-evolving complex gives a broadened multiline EPR signal as a result of exchange and dipolar interactions with YZ*. The binding of nitric oxide to YZ* to form a diamagnetic YZ-NO species uncouples the S2 state from YZ*, yielding a noninteracting S2-state multiline EPR signal species.

Formation and decay of the S3 EPR signal species in acetate-inhibited photosystem II.

A 230-G-wide EPR signal is induced in acetate-treated photosystem II by 30 s of illumination at 277 K followed by freezing under illumination to 77 K [MacLachlan, D. J., & Nugent, J. H. A. (1993) Biochemistry 32, 9772-9780]. This signal, referred to as the S3 EPR signal, has been interpreted to arise from an S2X+ species where X+ is an amino acid radical. Investigation of the factors responsible for the formation and decay of the S3 EPR signal reveals that the yield of the S3 EPR signal is strongly temperature-dependent and depends on the rate of oxidation of QA-. Quantitation of the number of centers contributing to the S3 EPR signal produced by the optimal continuous illumination times of 3 min at 250 K, 30 s at 273 K, and 5 s at 294 K gave values of 13, 38, and 49 +/- 3%, respectively. By using 5 s of illumination at 294 K to induce the S3 EPR signal, and then illumination at 200 K to reduce QA, both the S3 and QA(-)Fe EPR signals were induced in high yield. This result indicates that the S3 EPR signal does not arise from an acceptor-side species. When saturating laser flashes were used to induce the S3 EPR signal in a dark-prepared, dark-adapted, acetate-treated sample, the yield was small after one flash and close to maximal after two flashes. An EPR signal at g = 4.1 was observed to be formed at intermediate times during the decay of the S3 EPR signal in the dark; the rates of decay of the S3 EPR signal at 273 and 294 K corresponded to the rates of formation of the g = 4.1 EPR signal. These results, together with the flash results, indicate that two steps are involved in both the generation and decay of the S3 EPR signal. The rates of formation and decay of both the S3 and QA(-)Fe EPR signals were measured at 250, 273, and 294 K. A kinetic model is presented that accounts for these kinetic data and the yield of the S3 EPR signal.