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 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.

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.

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.

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 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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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 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.

Novel strategies to overcome expression problems encountered with toxic proteins: application to the production of Lac repressor proteins for NMR studies.

NMR studies of structural aspects of allosteric regulation by the Lac repressor requires overexpression and isotope labeling of the protein. The size of the repressor makes it a challenging target, putting constraints on both expression conditions and sample preparation methods to overcome problems associated with studies of larger proteins by NMR. We optimized protocols for the production of deuterated functionally active thermostable dimeric Lac repressor and its core domain mutants.

Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes.

The structures of a dimeric mutant of the Lac repressor DNA-binding domain complexed with the auxiliary operators O2 and O3 have been determined using NMR spectroscopy and compared to the structures of the previously determined Lac-O1 and Lac-nonoperator complexes. Structural analysis of the Lac-O1 and Lac-O2 complexes shows highly similar structures with very similar numbers of specific and nonspecific contacts, in agreement with similar affinities for these two operators. The left monomer of the Lac repressor in the Lac-O3 complex retains most of these specific contacts.

The tandem zinc-finger region of human ZHX adopts a novel C2H2 zinc finger structure with a C-terminal extension.

Binding of the nuclear factor-Y complex (NF-Y) to the inverted CCAAT-box interferes with transcription activation through nucleosome reorganization. The three homologous proteins forming the zinc-fingers and homeoboxes (ZHX) family interact with the activation domain of NF-Ya to repress transcription. Each ZHX-protein contains two generic C2H2 zinc-fingers (ZNF1 and ZNF2) followed by five homeodomains.

Solution structure and characterization of the DNA-binding activity of the B3BP-Smr domain.

The MutS1 protein recognizes unpaired bases and initiates mismatch repair, which are essential for high-fidelity DNA replication. The homologous MutS2 protein does not contribute to mismatch repair, but suppresses homologous recombination. MutS2 lacks the damage-recognition domain of MutS1, but contains an additional C-terminal extension: the small MutS-related (Smr) domain.