Quantum Chemical Study of the Enzymatic Repair of T(6‐4)C/C(6‐4)T UV‐Photolesions by DNA Photolyases

Several strategies have evolved to repair one of the abundant UV radiation‐induced damages caused to DNA, namely the mutagenic pyrimidine (6‐4) pyrimidone photolesions. DNA (6‐4)‐photolyases are enzymes repairing these lesions by a photoinitiated electron transfer. An important aspect of a possible repair mechanism is its generality and transferability to different (6‐4) lesions. Therefore, previously suggested mechanisms for the repair of the T(6‐4)T lesion are here transferred to the T(6‐4)C and C(6‐4)T lesions and investigated theoretically using quantum chemical methods. Despite the different functional groups of the pyrimidine bases involved, a general valid molecular mechanism was identified, in which the initial step is an electron transfer coupled to a proton transfer from the protonated HIS365 to the N3^′ nitrogen of the 3^′ pyrimidine, followed by an intramolecular OH/NH₂ transfer in one concerted step, which does not require an oxetane/azetidine or isolated water/ammonia intermediate.     

DNA Photosensitization by an “Insider”: Photophysics and Triplet Energy Transfer of 5‐Methyl‐2‐pyrimidone Deoxyribonucleoside

The main chromophore of (6‐4) photoproducts, namely, 5‐methyl‐2‐pyrimidone (Pyo), is an artificial noncanonical nucleobase. This chromophore has recently been reported as a potential photosensitizer that induces triplet damage in thymine DNA. In this study, we investigate the spectroscopic properties of the Pyo unit embedded in DNA by means of explicit solvent molecular‐dynamics simulations coupled to time‐dependent DFT and quantum‐mechanics/molecular‐mechanics techniques. Triplet‐state transfer from the Pyo to the thymine unit was monitored in B‐DNA by probing the propensity of this photoactive pyrimidine analogue to induce a Dexter‐type triplet photosensitization and subsequent DNA damage.     

New QM/MM implementation of the DFTB3 method in the gromacs package

The approximate density‐functional tight‐binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free‐energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) electron‐induced repair of a DNA lesion. Also discussed is the further development of the framework, regarding mostly the options for parallelization. © 2015 Wiley Periodicals, Inc.     

Quantum Mechanics/Molecular Mechanics Study on the Oxygen Binding and Substrate Hydroxylation Step in AlkB Repair Enzymes

AlkB repair enzymes are important nonheme iron enzymes that catalyse the demethylation of alkylated DNA bases in humans, which is a vital reaction in the body that heals externally damaged DNA bases. Its mechanism is currently controversial and in order to resolve the catalytic mechanism of these enzymes, a quantum mechanics/molecular mechanics (QM/MM) study was performed on the demethylation of the N¹‐methyladenine fragment by AlkB repair enzymes. Firstly, the initial modelling identified the oxygen binding site of the enzyme. Secondly, the oxygen activation mechanism was investigated and a novel pathway was found, whereby the catalytically active iron(IV)–oxo intermediate in the catalytic cycle undergoes an initial isomerisation assisted by an Arg residue in the substrate binding pocket, which then brings the oxo group in close contact with the methyl group of the alkylated DNA base. This enables a subsequent rate‐determining hydrogen‐atom abstraction on competitive σ‐ and π‐pathways on a quintet spin‐state surface. These findings give evidence of different locations of the oxygen and substrate binding channels in the enzyme and the origin of the separation of the oxygen‐bound intermediates in the catalytic cycle from substrate. Our studies are compared with small model complexes and the effect of protein and environment on the kinetics and mechanism is explained.     

DNA光解酶模型研究的近期进展

用模型化合物来模拟DNA光解酶与底物的作用, 有助于认识DNA光复活作用机理. 评述了环丁烷型嘧啶二聚体光解酶和(6-4)光产物光解酶的模型研究进展, 并展望了该领域的发展前景．     

Repair of a Dimeric Azetidine Related to the Thymine–Cytosine (6‐4) Photoproduct by Electron Transfer Photoreduction

Photolyases are intriguing enzymes that take advantage of sunlight to restore lesions like cyclobutane pyrimidine dimers or (6‐4) photoproducts. This work focused on the photoreductive process responsible for splitting of the azetidine ring proposed to occur during (6‐4) photoproduct repair at a thymine–cytosine sequence. A model compound formed by photocycloaddition between thymine and 6‐azauracil has been designed to mimic the elusive azetidine intermediate. The photoinduced electron transfer process has been investigated by means of steady‐state and time‐resolved fluorescence using photosensitizers with oxidation potentials in the singlet excited state ranging from ?3.3 to ?2.1 V vs. SCE. Azetidine ring splitting and recovery of “repaired” bases were proven by HPLC analysis.     

A Native Ternary Complex Trapped in a Crystal Reveals the Catalytic Mechanism of a Retaining Glycosyltransferase

Glycosyltransferases (GTs) comprise a prominent family of enzymes that play critical roles in a variety of cellular processes, including cell signaling, cell development, and host–pathogen interactions. Glycosyl transfer can proceed with either inversion or retention of the anomeric configuration with respect to the reaction substrates and products. The elucidation of the catalytic mechanism of retaining GTs remains a major challenge. A native ternary complex of a GT in a productive mode for catalysis is reported, that of the retaining glucosyl‐3‐phosphoglycerate synthase GpgS from M. tuberculosis in the presence of the sugar donor UDP‐Glc, the acceptor substrate phosphoglycerate, and the divalent cation cofactor. Through a combination of structural, chemical, enzymatic, molecular dynamics, and quantum‐mechanics/molecular‐mechanics (QM/MM) calculations, the catalytic mechanism was unraveled, thereby providing a strong experimental support for a front–side substrate‐assisted S_Ni‐type reaction.     

The role of the alien proton acceptor on the formation of LC structure in H-bonded monomeric and polymeric derivatives of alkoxybenzoic acids

The formation of the complex between 4-cyanopyridine and 4-(6-acryloyloxy-hexyloxy) benzoic acid and its polymeric analog proceeds due to the proton transfer with the H-bond formation. The presence of two proton acceptor groups within one molecule provides a strong shift of the electron density along the complex molecule due to the conjugation within the proton acceptor molecule. The dielectric relaxation process in a symmetric associate experimentally observed is explained as a kinetic effect related to the formation and destruction of the associate.

Transition from a monomer to a polymer proton donor leads to the formation of the characteristic 1:1 complex with SmC layered structure different from that of a polymer itself.     

One‐carbon unit transfer quantum study of 1,10‐CH+‐tetrahydroquinoxaline analog

Quantum mechanics is used in this article to study one‐carbon unit's transfer from 1,10‐tetrahydroquinoxaline analog to methylamine. The computation result shows this reaction can be completed via two paths. Each path experiences two processes of proton transferring and bond rupturing. The structures and energies of all possible stationary points have been calculated by different methods. By analyzing the result, we can find that along the reaction route the proton transfer reaction has the highest energy barrier, which indicates that a general‐acid catalysis exists in this reaction. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Photophysical Properties of Ruthenium(II) Polypyridyl DNA Intercalators: Effects of the Molecular Surroundings Investigated by Theory

The environmental effects on the structural and photophysical properties of [Ru(L)₂(dppz)]²⁺ complexes (L=bpy=2,2′‐bipyridine, phen=1,10‐phenanthroline, tap=1,4,5,8‐tetraazaphenanthrene; dppz=dipyrido[3,3‐a:2′,3′‐c]phenazine), used as DNA intercalators, have been studied by means of DFT, time‐dependent DFT, and quantum mechanics/molecular mechanics calculations. The electronic characteristics of the low‐lying triplet excited states in water, acetonitrile, and DNA have been investigated to decipher the influence of the environment on the luminescent behavior of this class of molecules. The lowest triplet intra‐ligand (IL) excited state calculated at λ≈800 nm for the three complexes and localized on the dppz ligand is not very sensitive to the environment and is available for electron transfer from a guanine nucleobase. Whereas the lowest triplet metal‐to‐ligand charge‐transfer (³MLCT) states remain localized on the ancillary ligand (tap) in [Ru(tap)₂(dppz)]²⁺, regardless of the environment, their character is drastically modified in the other complexes [Ru(phen)₂(dppz)]²⁺ and [Ru(bpy)₂(dppz)]²⁺ upon going from acetonitrile (MLCT_dppz/phen or MLCT_dppz/bpy) to water (MLCT_dppz) and DNA (MLCT_phen and MLCT_bpy). The change in the character of the low‐lying ³MLCT states accompanying nuclear relaxation in the excited state controls the emissive properties of the complexes in water, acetonitrile, and DNA. The light‐switching effect has been rationalized on the basis of environment‐induced control of the electronic density distributed in the lowest triplet excited states.     

Long‐Range Electrostatics‐Induced Two‐Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site

Neutron crystallography was used to directly locate two protons before and after a pH‐induced two‐proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV‐1 protease. The two‐proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low‐pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.     

Photophysics of Acetophenone Interacting with DNA: Why the Road to Photosensitization is Open

Deoxyribonucleic acid photosensitization, i.e. the photoinduced electron‐ or energy‐transfer of chromophores interacting with DNA, is a crucial phenomenon that triggers important DNA lesions such as pyrimidine dimerization, even upon absorption of relatively low‐energy radiation. Oxidative lesions may also be produced via the photoinduced production of reactive oxygen species. Aromatic ketones, and acetophenone in particular, are well known for their sensitization effects. In this contribution we model the structural and dynamical properties of the acetophenone/DNA aggregates as well as their spectroscopic and photophysical properties using high‐level hybrid quantum mechanics/molecular mechanics methods. We show that the key steps of the photochemistry of acetophenone in gas phase are conserved in the macromolecular environment and thus an ultrafast singlet–triplet conversion of acetophenone is expected prior to the transfer to DNA.     

O6‐Alkylguanine DNA Alkyltransferase Repair Activity Towards Intrastrand Cross‐Linked DNA is Influenced by the Internucleotide Linkage

Oligonucleotides containing an alkylene intrastrand cross‐link (IaCL) between the O⁶‐atoms of two consecutive 2′‐deoxyguanosines (dG) were prepared by solid‐phase synthesis. UV thermal denaturation studies of duplexes containing butylene and heptylene IaCL revealed a 20 °C reduction in stability compared to the unmodified duplexes. Circular dichroism profiles of these IaCL DNA duplexes exhibited signatures consistent with B‐form DNA. Human O⁶‐alkylguanine DNA alkyltransferase (hAGT) was capable of repairing both IaCL containing duplexes with slightly greater efficiency towards the heptylene analog. Interestingly, repair efficiencies of hAGT towards these IaCL were lower compared to O⁶‐alkylene linked IaCL lacking the 5′‐3′‐phosphodiester linkage between the connected 2′‐deoxyguanosine residues. These results demonstrate that the proficiency of hAGT activity towards IaCL at the O⁶‐atom of dG is influenced by the backbone phosphodiester linkage between the cross‐linked residues.     

Directional Preference of DNA‐Mediated Electron Transfer in Gold‐Tethered DNA Duplexes: Is DNA a Molecular Rectifier?

Electrical properties of self‐assembling DNA nanostructures underlie the paradigm of nanoscale bioelectronics, and as such require clear understanding. DNA‐mediated electron transfer (ET) from a gold electrode to DNA‐bound Methylene Blue (MB) shows directional preference, and it is sequence‐specific. During the electrocatalytic reduction of [Fe(CN)₆]^3? catalyzed by DNA‐bound MB, the ET rate constant for DNA‐mediated reduction of MB reaches (1.32±0.2)10³ and (7.09±0.4)10³ s^?1 for (dGdC)₂₀ and (dAdT)₂₅ duplexes. The backward oxidation process is less efficient, making the DNA duplex a molecular rectifier. Lower rates of ET via (dGdC)₂₀ agree well with its disturbed π‐stacked sub‐molecular structure. Such direction‐ and sequence‐specific ET may be implicated in DNA oxidative damage and repair, and be relevant to other polarized surfaces, such as cell membranes and biomolecular interfaces.     

Geometrically associative yet electronically dissociative character in the transition state of enzymatic reversible phosphorylation

Reversible phosphorylation of proteins is a post‐translational modification that regulates diverse biological processes. The molecular mechanism underlying phosphoryl transfer catalyzed by enzymes remains a subject of active debate. In particular, the nature of transition state (TS), whether it has an associative or dissociative character, has been one of the most controversial issues. Structural evidence supports associative TS, whereas physical organic studies point to a dissociative character. Here we perform hybrid quantum mechanics/molecular mechanics simulations for the reversible phosphorylation of phosphoserine phosphatase (PSP) to study the nature of the TS. Both phosphorylation and dephosphorylation reactions are investigated based on the two‐dimensional energy surfaces along phosphoryl and proton transfer coordinates. The structures of the active site at TS in both reactions reveal compact geometries, consistent with crystal structures of PSP with phosphate analogues. However, the electron density of the phosphoryl group in both TS structures slightly decreases compared with that in the reactant states. These findings suggest that the TS of PSP has a geometrically associative yet electronically dissociative character and strongly depends on proton transfer being coupled with phosphoryl transfer. Structure and literature database, which searches on phosphotransferases, suggest that such a hybrid TS is consistent with many structures and physical organic studies and likely holds for most enzymes catalyzing phosphoryl transfer. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2011     

Synthesis, Characterization, Spectroscopic Properties of 2-（4-Dimethylaminophenyl）-5-fluoro-6-（morpholin-4-yl）-1H-benzimidazole and its Interaction with Calf Thymus DNA

Benzimidazole compounds have attracted a renewed interest recently owing to theirpotential applications in high-performance composite materials, electronic chemicals,photosensitive materials, and their special potentials in biological and/or medicinalapplication1,2. Typically, aromatic compounds with near planar structures and contain-ing hydrogen-donor groups or groups, which are capable of being protonated, havespecial interactions with DNA via intercalation, hydrogen-bonding, and so on3.Me…     

Theoretical study on the repair mechanism of the (6-4) photolesion by the (6-4) photolyase

UV irradiation of DNA can lead to the formation of mutagenic (6-4) pyrimidine-pyrimidone photolesions. The (6-4) photolyases are the enzymes responsible for the photoinduced repair of such lesions. On the basis of the recently published crystal structure of the (6-4) photolyase bound to DNA [Maul et al. 2008] and employing quantum mechanics/molecular mechanics techniques, a repair mechanism is proposed, which involves two photoexcitations. The flavin chromophore, initially being in its reduced anionic form, is photoexcited and donates an electron to the (6-4) form of the photolesion. The photolesion is then protonated by the neighboring histidine residue and forms a radical intermediate. The latter undergoes a series of energy stabilizing hydrogen-bonding rearrangements before the electron back transfer to the flavin semiquinone. The resulting structure corresponds to the oxetane intermediate, long thought to be formed upon DNA-enzyme binding. A second photoexcitation of the flavin promotes another electron transfer to the oxetane. Proton donation from the same histidine residue allows for the splitting of the four-membered ring, hence opening an efficient pathway to the final repaired form. The repair of the lesion by a single photoexcitation was shown not to be feasible.     

Electron Transfer in DNA at Electrified Interfaces

The ability of the DNA double helix to transport electrons underlies many life‐centered biological processes and bio‐electronic applications. However, there is little consensus on how efficiently the base pair π‐stacks of DNA mediate electron transport. This minireview scrutinizes the current state‐of‐the‐art knowledge on electron transfer (ET) properties of DNA and its long‐range ability to transfer (mediate) electrical signals at electrified interfaces, without being oxidized or reduced. Complex changes an electric field induces in the DNA structure and its electronic properties govern the efficiency of DNA‐mediated ET at electrodes and allow addressing the existing phenomenological riddles, while recently discovered rectifying properties of DNA contribute both to our understanding of DNA′s ET in living systems and to advances in molecular bioelectronics.     

Concerted Asynchronous Hula‐Twist Photoisomerization in the S65T/H148D Mutant of Green Fluorescent Protein

Fluorescence emission of wild‐type green fluorescent protein (GFP) is lost in the S65T mutant, but partly recovered in the S65T/H148D double mutant. These experimental findings are rationalized by a combined quantum mechanics/molecular mechanics (QM/MM) study at the QM(CASPT2//CASSCF)/AMBER level. A barrierless excited‐state proton transfer, which is exclusively driven by the Asp148 residue introduced in the double mutant, is responsible for the ultrafast formation of the anionic fluorescent state, which can be deactivated through a concerted asynchronous hula‐twist photoisomerization. This causes the lower fluorescence quantum yield in S65T/H148D compared to wild‐type GFP. Hydrogen out‐of‐plane motion plays an important role in the deactivation of the S65T/H148D fluorescent state.     

ONIOM study of one‐carbon unit transfer from imidazolidine to dUMP analogue

The ONIOM quantum mechanics method is used in this article to study one‐carbon unit transfer from an imidazolidine to 6‐aminouracil derivates. The computation results show that this reaction can be completed via three paths, owing to the three different proton transfer modes. Each path experiences three processes of nucleophile attacking, proton transferring, and bond rupturing. The focus of discussion falls on the proton transfer process. By analyzing the calculation results, we find that the direct proton transfer is the preferable pathway. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004