1D Radical Motion in Protein Pocket: Proton-Coupled Electron Transfer in Human Serum Albumin

Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning

Metalloproteins require metal ions as cofactors to catalyze specific reactions with remarkable efficiency and specificity. In various electron transfer reactions, metals in the active sites change their oxidation states to facilitate the biochemical reactions. Cryogenic electron microscopy, X-ray, and X-ray free electron laser (XFEL) crystallography are used to image metalloproteins to understand the reaction mechanisms. However, radiation damage in cryoEM and X-ray crystallography, and the challenge of generating homogeneous crystals and keeping the appropriate experimental conditions for all the crystals in XFEL crystallography, may alter the oxidation states. Here, we build machine learning models trained on a large data set from the Cambridge Crystallographic Data Center to evaluate the metal oxidation states. The models yield high accuracy scores (from 82% to 94%) for all metals in the small molecules. Then, they were used to predict the oxidation states of more than 30 000 metal clusters in metalloproteins with Fe, Mn, Co, and Cu in their active sites. We found that most of the metals exist in the lower oxidation states (Fe2+ 77%, Mn2+ 85%, Co2+ 65%, and Cu+ 64%), and these populations correlate with the standard reduction potentials of the metal ions. Furthermore, we found no clear correlation between these populations and the resolution of the structures, which suggests no significant dependence of these predictions on the resolution. Our models represent a valuable tool for evaluating the oxidation states of the metals in metalloproteins imaged with different techniques. The data files and the machine learning code are available in a public GitHub repository: https://github.com/mamin03/OxitationStatesMetalloprotein.git.

Formation mechanisms and supervisory prediction of scaling in water supply pipelines: A review

The scaling problem in the water supply pipeline will increase the resistance coefficient of the pipeline and the pressure of the water supply pipeline, which will not only affect the operation safety of the water supply pipeline, but also cause energy waste. The scale in the pipeline will also enrich heavy metal ions and pathogenic microorganisms, affecting the safety of water supply water quality and causing secondary pollution of water quality. At present, a lot of research has been done on the composition structure and crystallization process of the scale. The study found that calcite is the main component of the scale; the scale process is a heterogeneous nucleation process induced by heavy metal particles and their corrosion products in the pipeline. The introduction of electrochemical detection technology, density functional theory and molecular dynamics simulation has greatly improved the accuracy and timeliness of water scaling conditions detection and realized the visualization of scaling mechanism. In this paper, the measurement methods of the scale in the water supply pipeline and the corresponding material composition and crystal structure characteristics are reviewed, and the mechanism of the scale and the water quality conditions are summarized. At the end of this paper, based on summarizing the existing water quality scaling tendency evaluation methods, it is proposed to establish a water quality potential scaling risk assessment framework based on Puckorius scaling index (PSI) and electrochemical impedance spectroscopy (EIS) in the future.

First principles study of photostability within hydrogen-bonded amino acids

The photochemistry and photophysics of a two-glycine minimal model is studied at the CASPT2//CASSCF level of theory. Different photoinduced processes are discussed, on the basis of the calculated minimum energy paths and the characterization of the electronic state crossings. Two main processes could provide UV-photostability to the hydrogen-bonded peptide system: (i) forward-backward photoinduced electron/proton transfer involving the H in the hydrogen bond, (ii) singlet-singlet energy transfer between two amino acids, providing ultrafast population of the low-energy n,π* state.

Protein surface interactions probed by magnetic field effects on chemical reactions

Here we have employed the effects of weak static magnetic fields (not exceeding 46 mT) on radical recombination reactions to investigate protein-substrate interactions. Pulsed laser excitation of an aqueous solution of anthraquinone-2,6-disulfonate (AQDS(2-)) and either hen egg white lysozyme (HEWL) or bovine serum albumin (BSA) produces the triplet state of the radical pair (T)[AQDS(3-*) Trp(*)] by a photoinduced electron transfer reaction from tryptophan residues. Time-resolved absorption techniques were employed to study the recombination characteristics of these radical pairs at different static magnetic fields and ionic strengths. The experimental data in connection with the simulated curves unequivocally show that the radical pair has a lifetime of the order of microseconds in both systems (HEWL and BSA). However, the radical pair is embedded within a binding pocket of the BSA protein, while the (otherwise identical) radical pair, being subject to attractive Coulomb forces, resides on the protein surface in the HEWL system.

Photocatalytic generation of oxygen radicals by the water-soluble bacteriochlorophyll derivative WST11, noncovalently bound to serum albumin

Light-induced radical generation is the hallmark of fundamental processes and many applications including photosynthesis and photodynamic therapy (PDT). In this manuscript, we present two novel observations made upon monitoring light-induced generation of reactive oxygen species (ROS) in aqueous solutions by WST11, a water-soluble derivative of the photosynthetic pigment Bacteriochlorophyll a (Bchl). Using a host of complementary experimental techniques including time-resolved spectroscopy at the subpicosecond to the millisecond range, ESR spectroscopy, electrochemistry, spectroelectrochemistry, oximetry, and protein mass spectroscopy, we first show that in aqueous solutions WST11 generates only superoxide (O(2)(-*)) and hydroxyl (OH*) radicals with no detectable traces of singlet oxygen. Second, we show that WST11 makes a noncovalent complex with human serum albumin (HSA) and that this complex functions as a photocatalytic oxidoreductase at biologically relevant concentrations enabling approximately 15 cycles of electron transfer from the associated HSA protein to molecular oxygen in the solution. These findings rule out the paradigm that porphyrin and chlorophyll based PDT is mainly mediated by formation of singlet oxygen, particularly in vascular targeted photodynamic therapy (VTP) with sensitizers that undergo photoactivation during circulation in the plasma, like [Pd]-Bacteriopheophorbide (WST09, Tookad). At the same time, our findings open the way for new design paradigms of novel sensitizers, since O(2)(-*) and OH* radicals are well-recognized precursors of important pathophysiological processes that can be activated for achieving tumor eradication. Moreover, the finding that promiscuous protein scaffolds become sinks for holes and electrons when holding light-activated pigments provides a new insight to the evolution and action mechanism of natural light activated oxidoreductases (such as photosynthetic reaction centers) and new guidelines for the preparation of synthetic-light converting machineries.

Real-time observation of the spin-state mixing process of a micellized radical pair in weak magnetic fields by nanosecond fast field switching

The singlet-triplet spin-state mixing process of a singlet-born radical pair confined in a sodium dodecyl sulfate (SDS) micelle was studied by observing the nanosecond switched external magnetic field (SEMF) effect on the transient absorption signals. A long-lived singlet radical pair is generated by the photoinduced bond cleavage reaction of tetraphenylhydrazine in an SDS micelle. Application of off-on type SEMF results in the increase of the free radical yield contrary to the decrease produced by an applied static magnetic field. The S-T mixing process in low magnetic field was observed by means of a delay-shift SEMF experiment. Observed incoherent mixing processes are explained in terms of the interplay between coherent hyperfine interaction and fast dephasing processes caused by the fluctuation of electron-spin interactions. Singlet-triplet and triplet-triplet dephasing rate constants are determined independently to be 2 x 10(8) and 0.2 x 10(8) s(-)1, respectively, by a simulation based on a modified single-site Liouville equation. This is the first direct observation of the incoherent spin-state mixing process at magnetic fields comparable to the hyperfine interactions of the radical pair.

H and13C Hyperfine Coupling Constants of the Tryptophanyl Cation Radical in Aqueous Solution from Microsecond Time-Resolved CIDNP

Relative values of the 1H and 13C isotropic hyperfine couplings in the cationic oxidized tryptophan radical TrpH*+ in aqueous solution are determined. The data are obtained from the photo-CIDNP (chemically induced dynamic nuclear polarization) enhancements observed in the microsecond time-resolved NMR spectra of the diamagnetic products of photochemical reactions in which TrpH*+ is a transient intermediate. The method is validated using the tyrosyl neutral radical Tyr*, whose 1H and 13C hyperfine couplings have previously been determined by electron paramagnetic resonance spectroscopy. Good agreement is found with hyperfine coupling constants for TrpH*+ calculated using density functional theory methods but only if water molecules are explicitly included in the calculation.