Genetic switching by the Lac repressor is based on two-state Monod-Wyman-Changeux allostery.

High-resolution NMR spectroscopy enabled us to characterize allosteric transitions between various functional states of the dimeric Escherichia coli Lac repressor. In the absence of ligands, the dimer exists in a dynamic equilibrium between DNA-bound and inducer-bound conformations. Binding of either effector shifts this equilibrium toward either bound state. Analysis of the ternary complex between repressor, operator DNA, and inducer shows how adding the inducer results in allosteric changes that disrupt the interdomain contacts between the inducer binding and DNA binding domains and how this in turn leads to destabilization of the hinge helices and release of the Lac repressor from the operator. Based on our data, the allosteric mechanism of the induction process is in full agreement with the well-known Monod-Wyman-Changeux model.

Single-stranded DNA Binding by the Helix-Hairpin-Helix Domain of XPF Protein Contributes to the Substrate Specificity of the ERCC1-XPF Protein Complex.

The nucleotide excision repair protein complex ERCC1-XPF is required for incision of DNA upstream of DNA damage. Functional studies have provided insights into the binding of ERCC1-XPF to various DNA substrates. However, because no structure for the ERCC1-XPF-DNA complex has been determined, the mechanism of substrate recognition remains elusive. Here we biochemically characterize the substrate preferences of the helix-hairpin-helix (HhH) domains of XPF and ERCC-XPF and show that the binding to single-stranded DNA (ssDNA)/dsDNA junctions is dependent on joint binding to the DNA binding domain of ERCC1 and XPF. We reveal that the homodimeric XPF is able to bind various ssDNA sequences but with a clear preference for guanine-containing substrates. NMR titration experiments and in vitro DNA binding assays also show that, within the heterodimeric ERCC1-XPF complex, XPF specifically recognizes ssDNA. On the other hand, the HhH domain of ERCC1 preferentially binds dsDNA through the hairpin region. The two separate non-overlapping DNA binding domains in the ERCC1-XPF heterodimer jointly bind to an ssDNA/dsDNA substrate and, thereby, at least partially dictate the incision position during damage removal. Based on structural models, NMR titrations, DNA-binding studies, site-directed mutagenesis, charge distribution, and sequence conservation, we propose that the HhH domain of ERCC1 binds to dsDNA upstream of the damage, and XPF binds to the non-damaged strand within a repair bubble.

Spin polarization transfer mechanisms of SABRE: A magnetic field dependent study.

We have investigated the magnetic field dependence of Signal Amplification By Reversible Exchange (SABRE) arising from binding of para-hydrogen (p-H2) and a substrate to a suitable transition metal complex. The magnetic field dependence of the amplification of the (1)H Nuclear Magnetic Resonance (NMR) signals of the released substrates and dihydrogen, and the transient transition metal dihydride species shows characteristic patterns, which is explained using the theory presented here. The generation of SABRE is most efficient at low magnetic fields due to coherent spin mixing at nuclear spin Level Anti-Crossings (LACs) in the SABRE complexes. We studied two Ir-complexes and have shown that the presence of a (31)P atom in the SABRE complex doubles the number of LACs and, consequently, the number of peaks in the SABRE field dependence. Interestingly, the polarization of SABRE substrates is always accompanied by the para-to-ortho conversion in dihydride species that results in enhancement of the NMR signal of free (H2) and catalyst-bound H2 (Ir-HH). The field dependences of hyperpolarized H2 and Ir-HH by means of SABRE are studied here, for the first time, in detail. The field dependences depend on the chemical shifts and coupling constants of Ir-HH, in which the polarization transfer takes place. A negative coupling constant of -7Hz between the two chemically equivalent but magnetically inequivalent hydride nuclei is determined, which indicates that Ir-HH is a dihydride with an HH distance larger than 2Å. Finally, the field dependence of SABRE at high fields as found earlier has been investigated and attributed to polarization transfer to the substrate by cross-relaxation. The present study provides further evidence for the key role of LACs in the formation of SABRE-derived polarization. Understanding the spin dynamics behind the SABRE method opens the way to optimizing its performance and overcoming the main limitation of NMR, its notoriously low sensitivity.

The Cerebro-oculo-facio-skeletal Syndrome Point Mutation F231L in the ERCC1 DNA Repair Protein Causes Dissociation of the ERCC1-XPF Complex.

The ERCC1-XPF heterodimer, a structure-specific DNA endonuclease, is best known for its function in the nucleotide excision repair (NER) pathway. The ERCC1 point mutation F231L, located at the hydrophobic interaction interface of ERCC1 (excision repair cross-complementation group 1) and XPF (xeroderma pigmentosum complementation group F), leads to severe NER pathway deficiencies. Here, we analyze biophysical properties and report the NMR structure of the complex of the C-terminal tandem helix-hairpin-helix domains of ERCC1-XPF that contains this mutation. The structures of wild type and the F231L mutant are very similar. The F231L mutation results in only a small disturbance of the ERCC1-XPF interface, where, in contrast to Phe(231), Leu(231) lacks interactions stabilizing the ERCC1-XPF complex. One of the two anchor points is severely distorted, and this results in a more dynamic complex, causing reduced stability and an increased dissociation rate of the mutant complex as compared with wild type. These data provide a biophysical explanation for the severe NER deficiencies caused by this mutation.

The role of level anti-crossings in nuclear spin hyperpolarization.

Nuclear spin hyperpolarization is an important resource for increasing the sensitivity of NMR spectroscopy and MRI. Signal enhancements can be as large as 3-4 orders of magnitude. In hyperpolarization experiments, it is often desirable to transfer the initial polarization to other nuclei of choice, either protons or insensitive nuclei such as (13)C and (15)N. This situation arises primarily in Chemically Induced Dynamic Nuclear Polarization (CIDNP), Para-Hydrogen Induced Polarization (PHIP), and the related Signal Amplification By Reversible Exchange (SABRE). Here we review the recent literature on polarization transfer mechanisms, in particular focusing on the role of Level Anti-Crossings (LACs) therein. So-called "spontaneous" polarization transfer may occur both at low and high magnetic fields. In addition, transfer of spin polarization can be accomplished by using especially designed pulse sequences. It is now clear that at low field spontaneous polarization transfer is primarily due to coherent spin-state mixing under strong coupling conditions. However, thus far the important role of LACs in this process has not received much attention. At high magnetic field, polarization may be transferred by cross-relaxation effects. Another promising high-field technique is to generate the strong coupling condition by spin locking using strong radio-frequency fields. Here, an analysis of polarization transfer in terms of LACs in the rotating frame is very useful to predict which spin orders are transferred depending on the strength and frequency of the B1 field. Finally, we will examine the role of strong coupling and LACs in magnetic-field dependent nuclear spin relaxation and the related topic of long-lived spin-states.

Level anti-crossings are a key factor for understanding para-hydrogen-induced hyperpolarization in SABRE experiments.

Various hyperpolarization methods are able to enhance the sensitivity of nuclear magnetic resonance (NMR) spectroscopy and magnetic resonance imaging (MRI) by several orders of magnitude. Among these methods are para-hydrogen-induced polarization (PHIP) and signal amplification by reversible exchange (SABRE), which exploit the strong nuclear alignment of para-hydrogen. Several SABRE experiments have been reported but, so far, it has not been possible to account for the experimentally observed sign and magnetic-field dependence of substrate polarization. Herein, we present an analysis based on level anti-crossings (LACs), which provides a complete understanding of the SABRE effect. The field-dependence of both net and anti-phase polarization is measured for several ligands, which can be reproduced by the theory. The similar SABRE field-dependence for different ligands is also explained. In general, the LAC concept allows complex spin dynamics to be unraveled, and is crucial for optimizing the performance of novel hyperpolarization methods in NMR and MRI techniques.

Exploiting level anti-crossings for efficient and selective transfer of hyperpolarization in coupled nuclear spin systems.

Spin hyperpolarization can be coherently transferred to other nuclei in field-cycling NMR experiments. At low magnetic fields spin polarization is redistributed in a strongly coupled network of spins. Polarization transfer is most efficient at fields where level anti-crossings (LACs) occur for the nuclear spin-states. A further condition is that field switching to the LAC positions is non-adiabatic in order to convert the starting population differences into spin coherences that cause time-dependent mixing of states. The power of this method has been demonstrated by studying transfer of photo-Chemically Induced Dynamic Nuclear Polarization (photo-CIDNP) in N-acetyl-tryptophan. We have investigated the magnetic field dependence and time dependence of coherent CIDNP transfer and directly assessed nuclear spin LACs by studying polarization transfer at specific field positions. The proposed approach based on LACs is not limited to CIDNP but is advantageous for enhancing NMR signals by spin order transfer from any type of hyper-polarized nuclei.

Magnetic resonance imaging (MRI) study of the water content and transport in rat lenses.

NMR micro-imaging technique has been used for the measurement of the water content distribution in lenses of senescence-accelerated OXYS rats and age-matched Wistar rats, as well as for the study of water and phosphate transport in rat lenses. The water content in the lens cortex is significantly higher than in the nucleus; the spatial gradient of the water content becomes steeper with age. No difference in the water content distribution has been found between Wistar and OXYS rat lenses of matching ages, although cataract onset in the OXYS rat lens occurs much earlier due to the enhanced generation of reactive oxygen species associated with oxidative stress. This finding implies that cataract development does not lead to significant changes in water content distribution inside the lens. The water transport in rat lenses slows down with age, and in OXYS lenses it is somewhat faster than in lenses of Wistar rats, probably due to the compensatory response to oxidative stress. The application of (31)P MRI for the monitoring of phosphate penetration into a lens has been performed for the first time. It is found that phosphate transport in a lens is significantly slower than that of water.

The Fanconi anemia associated protein FAAP24 uses two substrate specific binding surfaces for DNA recognition.

To maintain the integrity of the genome, multiple DNA repair systems exist to repair damaged DNA. Recognition of altered DNA, including bulky adducts, pyrimidine dimers and interstrand crosslinks (ICL), partially depends on proteins containing helix-hairpin-helix (HhH) domains. To understand how ICL is specifically recognized by the Fanconi anemia proteins FANCM and FAAP24, we determined the structure of the HhH domain of FAAP24. Although it resembles other HhH domains, the FAAP24 domain contains a canonical hairpin motif followed by distorted motif. The HhH domain can bind various DNA substrates; using nuclear magnetic resonance titration experiments, we demonstrate that the canonical HhH motif is required for double-stranded DNA (dsDNA) binding, whereas the unstructured N-terminus can interact with single-stranded DNA. Both DNA binding surfaces are used for binding to ICL-like single/double-strand junction-containing DNA substrates. A structural model for FAAP24 bound to dsDNA has been made based on homology with the translesion polymerase iota. Site-directed mutagenesis, sequence conservation and charge distribution support the dsDNA-binding model. Analogous to other HhH domain-containing proteins, we suggest that multiple FAAP24 regions together contribute to binding to single/double-strand junction, which could contribute to specificity in ICL DNA recognition.

Sliding and target location of DNA-binding proteins: an NMR view of the lac repressor system.

In non-specific lac headpiece-DNA complexes selective NMR line broadening is observed that strongly depends on length and composition of the DNA fragments. This broadening involves amide protons found in the non-specific lac-DNA structure to be interacting with the DNA phosphate backbone, and can be ascribed to DNA sliding of the protein along the DNA. This NMR exchange broadening has been used to estimate the 1D diffusion constant for sliding along non-specific DNA. The observed 1D diffusion constant of 4×10(-12) cm(2)/s is two orders of magnitude smaller than derived from previous kinetic experiments, but falls in the range of values determined more recently using single molecule methods. This strongly supports the notion that sliding could play at most a minor role in the association kinetics of binding of lac repressor to lac operator and that other processes such as hopping and intersegment transfer contribute to facilitate the DNA recognition process.

Ligand-directed acid-sensitive amidophosphate 5-trifluoromethyl-2'-deoxyuridine conjugate as a potential theranostic agent.

Herein, we report a novel strategy to engineer an acid-sensitive anticancer theranostic agent using a vector-drug ensemble. The ensemble was synthesized by directly conjugating the linoleic acid (LA)-modified branched polyethyleneimine with a chemotherapeutic drug trifluorothymidine. Linoleic acid residues were grafted onto 25 kDa polyethyleneimine (PEI) by treating PEI with linoleic acid chloroanhydride. 5-Trifluoromethyl-2'-deoxyuridine (trifluorothymidine, TFT) was introduced into LA-PEI conjugate by phosphorylating the conjugate with amidophosphate of trifluorothymidine 5'-monophosphate (pTFT), which had been activated by its conversion into the N,N-dimethylaminopyridine derivative. The extent of mononucleotide analog incorporation in the polymer was regulated by the ratio of pTFT to the polymer during the synthesis. Samples containing 20-70 TFT residues per PEI molecule were obtained. The cytotoxicity of PEI-LA-pTFT conjugates decreased with increasing nucleotide content, as examined using the MTT method. Due to the presence of fluorine atoms, TFT-based conjugates could be detected directly in the animals by (19)F magnetic resonance imaging. In addition, the presence of the amidophosphate group in PEI-LA-pTFT conjugates allowed their detection by in vivo(31)P NMR spectroscopy. Indeed, the (31)P NMR signal of a phosphoramide (δ ~ 12 ppm) was observed in the mouse muscle tissue treated with PEI-LA-pTFT conjugate along with the signals from endogenous phosphorus-containing compounds. At the same time, the use of PEI-LA-pTFT conjugate for chemotherapeutic drug delivery is limited due to the low release of pTFT from the carrier. To enhance the release of the drug from the conjugate in the endosomes, PEI-LA polymer was coupled with urocanic acid (UA), which bears imidazole ring and thus can form an acid-labile P-N bond with pTFT. The PEI-LA-UA-pTFT conjugate containing 30 residues of UA and 40 residues of pTFT was tested against the murine Krebs-II ascites carcinoma, grown as an ascetic tumor. The intraperitoneal injection of the conjugates resulted in prolongation of the animals' life and to the complete disappearance of the tumor after three injections.

Photochemistry of aqueous solutions of kynurenic acid and kynurenine yellow.

The photophysics and photochemistry of kynurenic acid (KNA) and kynurenine yellow (KNY) in neutral aqueous solutions were investigated using time-resolved optical spectroscopy. Both molecules have similar quinoline-like structures, the only difference being the absence of conjugation in the nitrogen containing cycle in KNY. The main channel of S(1) excited state decay in the case of partially-unconjugated KNY is the solvent assisted S(1) → S(0) radiationless transition via intermolecular hydrogen bonds (Φ(IC) = 0.96), whereas, in the case of fully-conjugated KNA, it is intersystem crossing to the triplet state (Φ(T) = 0.82). The major intermediate products of the singlet excited KNY deactivation are the triplet state (Φ(T) = 0.022) and, most probably, the enol form (Φ(enol) = 0.012), which decay with the formation of 2,3-dihydro-4-hydroxyquinoline and 4-hydroxyquinoline, respectively. The results obtained show that KNA and KNY, which are products of the decomposition of the UV filter kynurenine, are significantly more photoactive and less photostable than the parent molecule.

Evidence for Coherent Transfer of para-Hydrogen-Induced Polarization at Low Magnetic Fields.

We have investigated the mechanism of para-hydrogen-induced polarization (PHIP) transfer from the original strongly aligned protons to other nuclei at low external magnetic fields. Although it is known that PHIP is efficiently transferred at low fields, the nature of the transfer mechanism, that is, coherent spin mixing or cross-relaxation, is not well established. Polarization transfer kinetics for individual protons of styrene was, for the first time, measured and modeled theoretically. Pronounced oscillations were observed indicating a coherent transfer mechanism. Spin coherences were excited by passing through an avoided level crossing of the nuclear spin energy levels. Transfer at avoided level crossings is selective with respect to spin order. Our work provides evidence that the coherent PHIP transfer mechanism is dominant at low magnetic fields.

High resolution NMR study of T1 magnetic relaxation dispersion. III. Influence of spin 1/2 hetero-nuclei on spin relaxation and polarization transfer among strongly coupled protons.

Effects of spin-spin interactions on the nuclear magnetic relaxation dispersion (NMRD) of protons were studied in a situation where spin ½ hetero-nuclei are present in the molecule. As in earlier works [K. L. Ivanov, A. V. Yurkovskaya, and H.-M. Vieth, J. Chem. Phys. 129, 234513 (2008); S. E. Korchak, K. L. Ivanov, A. V. Yurkovskaya, and H.-M. Vieth, ibid. 133, 194502 (2010)], spin-spin interactions have a pronounced effect on the relaxivity tending to equalize the longitudinal relaxation times once the spins become strongly coupled at a sufficiently low magnetic field. In addition, we have found influence of (19)F nuclei on the proton NMRD, although in the whole field range, studied protons and fluorine spins were only weakly coupled. In particular, pronounced features in the proton NMRD were found; but each feature was predominantly observed only for particular spin states of the hetero-nuclei. The features are explained theoretically; it is shown that hetero-nuclei can affect the proton NMRD even in the limit of weak coupling when (i) protons are coupled strongly and (ii) have spin-spin interactions of different strengths with the hetero-nuclei. We also show that by choosing the proper magnetic field strength, one can selectively transfer proton spin magnetization between spectral components of choice.

Changing the direction of intramolecular electron transfer in oxidized dipeptides containing tryptophan and tyrosine.

Intramolecular electron transfer (IET) in the oxidized dipeptide Tyr-Trp was investigated in the pH range from 1.0 to 3.1 by the method of time-resolved chemically induced dynamic nuclear polarization. The results were compared with data obtained earlier for Trp-Tyr. Surprisingly, it was found that the direction of IET changes with the order of the amino acid residues in the peptide. For Tyr-Trp, the rate constant of electron transfer from tyrosine residue to tryptophanyl cation radical is below 1.2 × 10(4) s(-1), whereas for Trp-Tyr, the value of this rate constant is 5.5 × 10(5) s(-1). Conversely, for oxidized Tyr-Trp at pH range 2.1 and lower, electron transfer from tryptophan residue to tyrosyl radical is observed. The rate constant of this reaction is proportional to the concentration of protons in aqueous solution, and at pH 1.0 is equal to 6.5 × 10(5) s(-1). The change in direction of IET observed for oxidized Tyr-Trp dipeptide is presumably due to the positive charge at the N-terminal amino group of the peptide, which promotes electron transfer in the direction of the N-terminus.

Theory of pulsed Reaction Yield Detected Magnetic Resonance.

We propose pulse sequences for Reaction Yield Detected Magnetic Resonance (RYDMR), which are based on refocusing the zero-quantum coherences in radical pairs by non-selective microwave pulses and using the population of a radical pair singlet spin state as an observable. The new experiments are analogues of existing EPR experiments such as the primary echo, Carr-Purcell, ESEEM, stimulated echo and Mims ENDOR. All pulse sequences are supported by analytical results and numerical calculations. The pulse sequences can be used for more efficient and highly detailed characterization of intermediates of chemical reactions and charge carriers in organic semiconductors.

Reduction of guanosyl radical by cysteine and cysteine-glycine studied by time-resolved CIDNP.

As a model for chemical DNA repair, reduction of guanosyl radicals in the reaction with cysteine or the dipeptide cysteine-glycine has been studied by time-resolved chemically induced dynamic nuclear polarization (CIDNP). Radicals were generated photochemically by pulsed laser irradiation of a solution containing the photosensitizer 2,2'-dipyridyl, guanosine-5'-monophosphate, and the amino acid or peptide. In neutral and basic aqueous solution, the neutral guanosyl radical is formed via electron or hydrogen atom transfer to the triplet excited dye. The rate constants for reduction of guanosyl radical were determined by quantitative analysis of the CIDNP kinetics, which are sensitive to the rates of fast radical reactions. The rate constants vary from (1.0 ± 0.3) × 10(7) M(-1) s(-1) for the thiol form of cysteine to (1.6 ± 0.2) × 10(8) M(-1) s(-1) for the thiolate anion. These values are comparable with corresponding rate constants for reduction of neutral guanosyl radical by tyrosine.

The structure of the XPF-ssDNA complex underscores the distinct roles of the XPF and ERCC1 helix- hairpin-helix domains in ss/ds DNA recognition.

Human XPF/ERCC1 is a structure-specific DNA endonuclease that nicks the damaged DNA strand at the 5' end during nucleotide excision repair. We determined the structure of the complex of the C-terminal domain of XPF with 10 nt ssDNA. A positively charged region within the second helix of the first HhH motif contacts the ssDNA phosphate backbone. One guanine base is flipped out of register and positioned in a pocket contacting residues from both HhH motifs of XPF. Comparison to other HhH-containing proteins indicates a one-residue deletion in the second HhH motif of XPF that has altered the hairpin conformation, thereby permitting ssDNA interactions. Previous nuclear magnetic resonance studies showed that ERCC1 in the XPF-ERCC1 heterodimer can bind dsDNA. Combining the two observations gives a model that underscores the asymmetry of the human XPF/ERCC1 heterodimer in binding at an ss/ds DNA junction.