Crystallography Experiments Research Articles

Crystal structure of a bacterial photoactivated adenylate cyclase determined by serial femtosecond and serial synchrotron crystallography.

OaPAC is a recently discovered blue-light-using flavin adenosine dinucleotide (BLUF) photoactivated adenylate cyclase from the cyanobacterium Oscillatoria acuminata that uses adenosine triphosphate and translates the light signal into the production of cyclic adenosine monophosphate. Here, we report crystal structures of the enzyme in the absence of its natural substrate determined from room-temperature serial crystallography data collected at both an X-ray free-electron laser and a synchrotron, and we compare these structures with cryo-macromolecular crystallography structures obtained at a synchrotron by us and others. These results reveal slight differences in the structure of the enzyme due to data collection at different temperatures and X-ray sources. We further investigate the effect of the Y6W mutation in the BLUF domain, a mutation which results in a rearrangement of the hydrogen-bond network around the flavin and a notable rotation of the side chain of the critical Gln48 residue. These studies pave the way for picosecond-millisecond time-resolved serial crystallography experiments at X-ray free-electron lasers and synchrotrons in order to determine the early structural intermediates and correlate them with the well studied picosecond-millisecond spectroscopic intermediates.

Target Discovery of Dhilirane-Type Meroterpenoids by Biosynthesis Guidance and Tailoring Enzyme Catalysis.

Dhilirane-type meroterpenoids (DMs) featuring a 6/6/6/5/5 ring system represent a rare group of fungal meroterpenoids. To date, merely 11 DMs have been isolated or derived, leaving their chemical diversity predominantly unexplored. Herein, we leverage an understanding of biosynthesis to develop a workflow for discovery of DMs by genome mining, metabolite analysis, and tailoring enzyme catalysis. Twenty-three new DMs, including seven unprecedented scaffolds, were consequently identified. An α-ketoglutarate (α-KG)-dependent oxygenase DhiD was found to catalyze the stereodivergent ring contraction of dhilirolide D to form the dhilirane skeleton; while the cytochrome P450 DhiH reshaped the structural diversity by establishing diverse C-C bonds and oxidation. Crystallographic and mutagenesis experiments provide a molecular basis for the DhiD reaction and its stereodivergent products. Notably, DhiD exhibits substrate-controlled catalytic versatility in the chemical expansion of DMs through ring contraction, hydroxylation, dehydrogenation, epoxidation, isomerization, epimerization, and α-ketol cleavage. Bioassay results demonstrated that the obtained meroterpenoids exhibited anti-inflammatory and insecticidal activities. Our work provides insight into nature's arsenal for DM biosynthesis and the functional versatility of α-KG-dependent oxygenase and P450, which can be applied for target discovery and diversification of DM-type natural products.

Synthesis, crystal structure, Hirshfeld surface analysis, DFT computations and protein binding efficiency of a 1-D Ni(II) chain derived from a tridentate Schiff base ligand

A new Ni(II)-azido 1-D coordination polymer, [Ni2L2(μ1,1-N3)(μ1,3-N3)]n, was obtained through reaction of 1-[(3-dimethylamino-propylimino)-methyl]-naphthalen-2-ol (HL) and the perchlorate salt of nickel(II) in the presence of pseudohalide azide. X-ray crystallography and spectroscopic experiments (IR and UV-Vis) were used to describe this coordination polymer (CP). Single crystal X-ray studies revealed that the CP is a one-dimensional chain of Ni(II) in which the neighboring dimeric units (triply bridged by di-μ2-phenoxidoand µ1,1-N3) are further connected by μ1,3-azido bridges in a zig-zag fashion. The cooperative participation of N···H hydrogen bonding, π···π stacking and C-H···π interactions occur during crystal packing. A 2-D supramolecular architecture with star-shaped voids results from additional C–H···π stacking interactions. Hirshfeld surface analysis was used to look at the intermolecular interactions. DFT studies were carried out to calculate the HOMO-LUMO band gap of the ligand as well as the coordination polymer. Interaction of the CP with bovine serum albumin (BSA) protein was investigated spectroscopically by absorption and fluorescence titration methods. The result showed that the CP could quench the intrinsic fluorescence of BSA. Fluorescence resonance energy transfer (FRET) studies revealed that energy transfer takes place from BSA to the CP. Cyclic voltammetry of the CP indicated an irreversible cathodic redox couple assigned to Ni(II)/Ni(I).

Structural Insights and Reaction Profile of a New Unspecific Peroxygenase from Marasmius wettsteinii Produced in a Tandem-Yeast Expression System.

Fungal unspecific peroxygenases (UPOs) are gaining momentum in synthetic chemistry. Of special interest is the UPO from Marasmius rotula (MroUPO), which shows an exclusive repertoire of oxyfunctionalizations, including the terminal hydroxylation of alkanes, the α-oxidation of fatty acids and the C-C cleavage of corticosteroids. However, the lack of heterologous expression systems to perform directed evolution has impeded its engineering for practical applications. Here, we introduce a close ortholog of MroUPO, a UPO gene from Marasmius wettsteinii (MweUPO-1), that has a similar reaction profile to MroUPO and for which we have set up a directed evolution platform based on tandem-yeast expression. Recombinant MweUPO-1 was produced at high titers in the bioreactor (0.7 g/L) and characterized at the biochemical and atomic levels. The conjunction of soaking crystallographic experiments at a resolution up to 1.6 Å together with the analysis of reaction patterns sheds light on the substrate preferences of this promiscuous biocatalyst.

Robust and automatic beamstop shadow outlier rejection: combining crystallographic statistics with modern clustering under a semi-supervised learning strategy.

During the automatic processing of crystallographic diffraction experiments, beamstop shadows are often unaccounted for or only partially masked. As a result of this, outlier reflection intensities are integrated, which is a known issue. Traditional statistical diagnostics have only limited effectiveness in identifying these outliers, here termed Not-Excluded-unMasked-Outliers (NEMOs). The diagnostic tool AUSPEX allows visual inspection of NEMOs, where they form atypical pattern: clusters at the low-resolution end of the AUSPEX plots of intensities or amplitudes versus resolution. To automate NEMO detection, a new algorithm was developed by combining data statistics with a density-based clustering method. This approach demonstrates a promising performance in detecting NEMOs in merged data sets without disrupting existing data-reduction pipelines. Re-refinement results indicate that excluding the identified NEMOs can effectively enhance the quality of subsequent structure-determination steps. This method offers a prospective automated means to assess the efficacy of abeamstop mask, as well as highlighting the potential of modern pattern-recognition techniques for automating outlier exclusion during data processing, facilitating future adaptation to evolving experimental strategies.

Single pulse data collection with an X-ray chopper at in situ room temperature Laue crystallography beamline BL03HB

in situ room temperature Laue crystallography has gained increasing attention. This method is suitable for time-resolved Laue crystallography experiments to get crystal structure with only several single-frame data collections. To improve the diffraction efficiency of protein crystals at room temperature, a simple X-ray chopper combined with a fast shutter has been successfully developed and tested at in situ room temperature Laue crystallography beamline BL03HB of the Shanghai Synchrotron Radiation Facility (SSRF). This chopper is built with two aluminum blades. There are two windows on both blades, as well as an internal lead block. The width of windows for transmission of beam can be flexibly adjusted by a steel block coated with lead. The chopping frequency is controlled independently. The device allows chopping frequencies ranging from 0 to 10 Hz, and exposure times down to 100 μs can be obtained for our Laue diffraction experiment with the combination of a fast shutter. Moreover, a single pulse data collection strategy has been developed at BL03HB. The performance of our single pulse data collection method with the designed chopper for the improvement of data quality has been analyzed. Results show that the quality of diffraction data obtained from the single pulse data collection method is significantly improved, and the developed chopper is very suitable for room temperature Laue crystallography experiments at the synchrotron beamline with super bending magnet as light source.

A Tetranuclear copper(II) Complex with a Pyridine‐2,6‐dicarboxamide Ligand: Structural and Magnetic Properties and In vitro Antiproliferative Activity Against Human Cancer Cells

AbstractA pentadentate diamide ligand, N,N′‐di(pyridine‐2‐yl)pyridine‐2,6‐dicarboxamide (L1H2) and its tetranuclear Cu(II) complex [Cu4(L1)2(μ3‐OH)2(H2O)3(ClO4)](ClO4) ⋅ H2O are reported. X‐ray crystal structure of the complex reveals that it has an open‐book type architecture. Two central copper atoms are connected to each other by two hydroxo bridges. Each of these two hydroxo bridges also connects the two central copper atoms to one of the two terminal copper atoms. Variable temperature susceptibility measurements show that χMT decreases with the temperature, indicating a strong antiferromagnetic behavior. With the help of DFT calculations the magnetic data was analyzed using the spin Hamiltonian H=−2 J1S3 ⋅ S4 −2 J2(S3 ⋅ S1+ S3 ⋅ S2+ S4 ⋅ S1+ S4 ⋅ S2)−2 J3S1 ⋅ S2 (where subscripts 1 and 2 refer to the terminal copper atoms and 3 and 4 refer to the central copper atoms). The best fit was obtained with 2 J1=−322 cm−1, 2 J2=+34.8 cm−1, 2 J3=−8.8 cm−1 and g=2.18, indicating a δ‐type interaction between terminal copper atoms. The complex proves to be an avid binder of ct‐DNA, with apparent binding constant (Kapp) value estimated as 1.536×107 M−1. In vitro experiments indicate that the Cu(II) complex reduced the proliferation of HCT116 cells among other cell lines. This reduction of cell proliferation may be attributed to the enhancement of intracellular ROS, along with modulation and disruption of cell cycle associated proteins. SKC conceptualized the project, arranged funding and involved in overall coordination among collaborators, analyzing the data, and writing the paper. AM was involved in doing the experimental work on synthesis of the compounds, carrying out analytical and spectroscopic measurements, collecting X‐ray crystallographic data and DNA binding experiments. MS, SM and KDS were involved in study of anticancer activities of the complex. SS helped in refining X‐ray structure of the complex. MC did the magnetic measurements and analysis whereas AF did the DFT calculations.

Rh-Catalyzed Enantioselective Single-Carbon Insertion of Alkenes.

The interest in the discovery and development of skeletal editing processes that selectively insert, exchange, or delete an atom in organic molecules has significantly increased over the last few years. However, processes of this class that proceed through the creation of a chiral center with high asymmetric induction have been largely unexplored. Herein, we report an enantioselective single-carbon insertion in aryl- and alkyl-substituted alkenes mediated by a catalytically generated chiral Rh-carbynoid and phosphate nucleophiles that produce enantioenriched allylic phosphates (enantiomeric ratio (e.r.) = 89.5:10.5-99.5:0.5). The key to the process was a diastereo- and enantioselective cyclopropanation of the alkene with a chiral Rh-carbynoid and the formation of a transient cyclopropyl-I(III) intermediate. The addition of the phosphate nucleophile provided a cyclopropyl-I(III)-phosphate intermediate that undergoes disrotatory ring opening following the Woodward-Hoffmann-DePuy rules. This process led to a chiral intimate allyl cation-phosphate pair that evolved with excellent enantioretention. The evidence of an SN1-like SNi mechanism is provided by linear free-energy relationship studies, kinetic isotope effects, X-ray crystallography, and control experiments. We demonstrated the utility of the enantioenriched allylic phosphates in late-stage N-H allylations of natural products and drug molecules and in cross-coupling reactions that occurred with excellent enantiospecificity.

Total Synthesis Facilitates In Vitro Reconstitution of the C-S Bond-Forming P450 in Griseoviridin Biosynthesis.

Griseoviridin is a group A streptogramin natural product from Streptomyces with broad-spectrum antibacterial activity. A hybrid polyketide-nonribosomal peptide, it comprises a 23-membered macrocycle, an embedded oxazole motif, and a macrolactone with a unique ene-thiol linkage. Recent analysis of the griseoviridin biosynthetic gene cluster implicated SgvP, a cytochrome P450 monooxygenase, in late-stage installation of the critical C-S bond. While genetic and crystallographic experiments provided indirect evidence to support this hypothesis, the exact function of SgvP has never been confirmed biochemically. Herein, we report a convergent total synthesis of pre-griseoviridin, the putative substrate of P450 SgvP and precursor to griseoviridin. Our strategy features concise and rapid assembly of two fragments joined via sequential peptide coupling and Stille macrocyclization. Access to pre-griseoviridin then enabled in vitro validation of SgvP as the C-S bond-forming P450 during griseoviridin biosynthesis, culminating in a nine-step chemoenzymatic synthesis of griseoviridin.

Two new types of structures from soft coral-associated epiphytic fungus Aspergillus versicolor CGF9-1-2

Global Natural Products Social (GNPS) molecular networking platform was applied to discovery the undescribed compounds from the common marine fungi Aspergillus versicolor CGF9-1-2, ultimately resulting in isolation of four new polyketides, decumbenone E (1), decumbenone F (2), 2′-epi-8-O-methylnidurufin (6), (−)-phomoindene A (7), one new nucleoside, 3-methyl-9-(2-methylbutene)-xanthine (8), and five known analogues. Their structures were elucidated based on 1D/2D NMR spectroscopic and HRESIMS data analyses, meanwhile, the absolute configurations of new compounds were established based on the X-ray crystallographic experiments, as well as the electronic circular dichroism (ECD) analysis. All compounds were predicted pharmaceutical chemistry with ten commonly disease-related proteins by molecular docking. In addition, all compounds against TDP1 were performed in vitro, which was consistent with the docking result, and compound 6 shown a weak inhibitory activity.

In situ serial crystallography facilitates 96-well plate structural analysis at low symmetry.

The advent of serial crystallography has rejuvenated and popularized room-temperature X-ray crystal structure determination. Structures determined at physiological temperature reveal protein flexibility and dynamics. In addition, challenging samples (e.g. large complexes, membrane proteins and viruses) form fragile crystals that are often difficult to harvest for cryo-crystallography. Moreover, a typical serial crystallography experiment requires a large number of microcrystals, mainly achievable through batch crystallization. Many medically relevant samples are expressed in mammalian cell lines, producing a meager quantity of protein that is incompatible with batch crystallization. This can limit the scope of serial crystallography approaches. Direct in situ data collection from a 96-well crystallization plate enables not only the identification of the best diffracting crystallization condition but also the possibility for structure determination under ambient conditions. Here, we describe an in situ serial crystallography (iSX) approach, facilitating direct measurement from crystallization plates mounted on a rapidly exchangeable universal plate holder deployed at a microfocus beamline, ID23-2, at the European Synchrotron Radiation Facility. We applied our iSX approach on a challenging project, autotaxin, a therapeutic target expressed in a stable human cell line, to determine the structure in the lowest-symmetry P1 space group at 3.0 Å resolution. Our in situ data collection strategy provided a complete dataset for structure determination while screening various crystallization conditions. Our data analysis reveals that the iSX approach is highly efficient at a microfocus beamline, improving throughput and demonstrating how crystallization plates can be routinely used as an alternative method of presenting samples for serial crystallography experiments at synchrotrons.

Crystal structure via fluctuation scattering.

Crystallography is a quintessential method for determining the atomic structure of crystals. The most common implementation of crystallography uses single crystals that must be of sufficient size, typically tens of micrometres or larger, depending on the complexity of the crystal structure. The emergence of serial data-collection methods in crystallography, particularly for time-resolved experiments, opens up opportunities to develop new routes to structure determination for nanocrystals and ensembles of crystals. Fluctuation X-ray scattering is a correlation-based approach for single-particle imaging from ensembles of identical particles, but has yet to be applied to crystal structure determination. Here, an iterative algorithm is presented that recovers crystal structure-factor intensities from fluctuation X-ray scattering correlations. The capabilities of this algorithm are demonstrated by recovering the structure of three small-molecule crystals and a protein crystal from simulated fluctuation X-ray scattering correlations. This method could facilitate the recovery of structure-factor intensities from crystals in serial crystallography experiments and relax sample requirements for crystallography experiments.

Investigation of fast and efficient lossless compression algorithms for macromolecular crystallography experiments.

Structural biology experiments benefit significantly from state-of-the-art synchrotron data collection. One can acquire macromolecular crystallography (MX) diffraction data on large-area photon-counting pixel-array detectors at framing rates exceeding 1000 frames per second, using 200 Gbps network connectivity, or higher when available. In extreme cases this represents a raw data throughput of about 25 GB s-1, which is nearly impossible to deliver at reasonable cost without compression. Our field has used lossless compression for decades to make such data collection manageable. Many MX beamlines are now fitted with DECTRIS Eiger detectors, all of which are delivered with optimized compression algorithms by default, and they perform well with current framing rates and typical diffraction data. However, better lossless compression algorithms have been developed and are now available to the research community. Here one of the latest and most promising lossless compression algorithms is investigated on a variety of diffraction data like those routinely acquired at state-of-the-art MX beamlines.

Six undescribed 23-norursane triterpenoids from the biotransformation of ilexgenin a by endophytic fungi and their vascular protective activity

Biotransformation of ursane-type triterpenoid ilexgenin A by endophytic fungi Lasiodiplodia sp. MQD-4 and Pestalotiopsis sp. ZZ-1, isolated from Ilex pubescences and Callicarpa kwangtungensis respectively, was investigated for the first time. Six previously undescribed metabolites (1–6) with 23-norursane triterpenoids skeleton were isolated and their structures were unambiguously established by the analysis of spectroscopic data and single-crystal X-ray crystallographic experiments. Decarboxylation, oxidation, and hydroxylation reactions were observed on the triterpenoid skeleton. Especially, the decarboxylation of C-23 provided definite evidence to understand the biogenetic process of 23-norursane triterpenoids. Moreover, the qualitative analysis of the extract of I. pubescences showed metabolites 1, 3, 4, and 6 could be detected in the originated plant, indicating biotransformation by endophytic fungi is a practical strategy for the isolation of novel natural products. Finally, all isolates were evaluated for the protective activities against H2O2-induced HUVECs dysfunction in vitro. Compound 5 could improve the viability of endothelial cells and decrease the level of intracellular ROS.

Inertial mixing of acoustically levitated droplets for time‐lapse protein crystallography

AbstractVarying the chemical consistency of acoustically levitated droplets opens up an in situ study of chemical and biochemical reactions in small volumes. However, the optimization of the mixing time and the minimization of the positional instability induced by solution dispensing are necessary for practical applications such as the study of the transient state of macromolecules crystallography during the ligand binding processes. For this purpose, we study the inertial mixing in a configuration compatible with the room‐temperature crystallography using the acoustic levitation diffractometer, therein solution drops ejected at high velocity collide and coalesce with droplets dispensed on acoustically levitated and rotating polymer thin‐film sample holders. With the proposed method, we are able to achieve the mixing time of ∼0.1 s for sub‐micro and a few microliter droplets. The observed short mixing time is ascribed to the rapid penetration of the solution into the droplets and confirmed by a computational fluid dynamic simulation. The demonstrated accelerated solution mixing is tested in a pilot time‐lapse protein crystallography experiment using the acoustic levitation diffractometer. The results indicate the detection of transient ligand binding state within 2 s after the solution dispensing, suggesting the feasibility of the proposed method for studying slow biochemical processes.

Does Acinetobacter calcoaceticus glucose dehydrogenase produce self-damaging H2O2?

The soluble glucose dehydrogenase (sGDH) from Acinetobacter calcoaceticus has been widely studied and is used, in biosensors, to detect the presence of glucose, taking advantage of its high turnover and insensitivity to molecular oxygen. This approach, however, presents two drawbacks: the enzyme has broad substrate specificity (leading to imprecise blood glucose measurements) and shows instability over time (inferior to other oxidizing glucose enzymes). We report the characterization of two sGDH mutants: the single mutant Y343F and the double mutant D143E/Y343F. The mutants present enzyme selectivity and specificity of 1.2 (Y343F) and 5.7 (D143E/Y343F) times higher for glucose compared with that of the wild-type. Crystallographic experiments, designed to characterize these mutants, surprisingly revealed that the prosthetic group PQQ (pyrroloquinoline quinone), essential for the enzymatic activity, is in a cleaved form for both wild-type and mutant structures. We provide evidence suggesting that the sGDH produces H2O2, the level of production depending on the mutation. In addition, spectroscopic experiments allowed us to follow the self-degradation of the prosthetic group and the disappearance of sGDH's glucose oxidation activity. These studies suggest that the enzyme is sensitive to its self-production of H2O2. We show that the premature aging of sGDH can be slowed down by adding catalase to consume the H2O2 produced, allowing the design of a more stable biosensor over time. Our research opens questions about the mechanism of H2O2 production and the physiological role of this activity by sGDH.

Structure, mechanism, and evolution of the last step in vitamin C biosynthesis

Photosynthetic organisms, fungi, and animals comprise distinct pathways for vitamin C biosynthesis. Besides this diversity, the final biosynthetic step consistently involves an oxidation reaction carried out by the aldonolactone oxidoreductases. Here, we study the origin and evolution of the diversified activities and substrate preferences featured by these flavoenzymes using molecular phylogeny, kinetics, mutagenesis, and crystallographic experiments. We find clear evidence that they share a common ancestor. A flavin-interacting amino acid modulates the reactivity with the electron acceptors, including oxygen, and determines whether an enzyme functions as an oxidase or a dehydrogenase. We show that a few side chains in the catalytic cavity impart the reaction stereoselectivity. Ancestral sequence reconstruction outlines how these critical positions were affixed to specific amino acids along the evolution of the major eukaryotic clades. During Eukarya evolution, the aldonolactone oxidoreductases adapted to the varying metabolic demands while retaining their overarching vitamin C-generating function.

Simulation of non-Newtonian gas-focused micro-jets in chocked gas flow regime

Stable liquid jets are crucial for successful serial crystallography experiments. They are produced from gas dynamic virtual nozzles (GDVNs), where the liquid from an inner capillary is focused by a co-flowing gas from an outer converging capillary. Our previously investigated non-Newtonian jets with incompressible and compressible focusing gas under atmospheric conditions were extended towards compressible chocked gas under vacuum conditions. An axisymmetric GDVN was considered with a fixed gas flow rate of 15 mg/min and liquid flow rate of 40 µl/min. A mixture formulation of the laminar compressible multiphase problem was solved within finite volume method and volume of fluid framework. The jet lengths, diameters, velocities, and temperatures were analysed as a function of the power-law non-Newtonian modification of reference water. It is observed that the jets under vacuum conditions are thinner for Newtonian and shear-thickening fluids than those in the atmosphere. The jet length increases from shear-thinning to shear-thickening rheology but is not affected by the pressure. The shear produced at the nozzle outlet is similar for both pressure conditions but increases in downstream directions for vacuum conditions. Gas expanding into vacuum cools by ~100-150 K while the temperature of the liquid jet drops only by a few K.

Targeted isolation of antiviral cinnamoylphloroglucinol-terpene adducts from Cleistocalyx operculatus by building blocks-based molecular networking approach

The building blocks-based molecular network (BBMN) strategy was applied to the phytochemical investigation of Cleistocalyx operculatus, leading to the targeted isolation of eighteen novel cinnamoylphloroglucinol-terpene adducts (CPTAs) with diverse skeleton types (cleistoperones A–R, 1–18). Their structures including absolute configurations were determined by extensive spectroscopic methods, quantum chemical calculations, and single-crystal X-ray crystallographic experiments. Cleistoperone A (1), consisting of a cinnamoylphloroglucinol motif and two linear monoterpene moieties, represents an unprecedented macrocyclic CPTA, whose densely functionalized tricyclo[15.3.1.03,8]heneicosane bridge ring skeleton contains an enolizable β,β′-triketone system and two different kinds of stereogenic elements (including five point and three planar chiralities). Cleistoperones B and C (2 and 3) are two new skeletal CPTAs with an unusual coupling pattern between the (nor)monoterpene moiety and the cinnamoyl chain of the cinnamoylphloroglucinol unit. Cleistoperone D (4) possesses an unprecedented cage-like 6/6/6/4/6-fused heteropentacyclic scaffold. The plausible biosynthetic pathways for 1–18 were also proposed. Notably, compounds 1, 4, 7, 8, and 18 exhibited significant antiviral activity against respiratory syncytial virus (RSV). The most potent one, cleistoperone A (1) with IC50 value of 1.71 ± 0.61 μmol/L, could effectively inhibit virus replication via affecting the Akt/mTOR/p70S6K signaling pathway.

KINNTREX: a neural network to unveil protein mechanisms from time-resolved X-ray crystallography.

Here, a machine-learning method based on a kinetically informed neural network (NN) is introduced. The proposed method is designed to analyze a time series of difference electron-density maps from a time-resolved X-ray crystallographic experiment. The method is named KINNTREX (kinetics-informed NN for time-resolved X-ray crystallography). To validate KINNTREX, multiple realistic scenarios were simulated with increasing levels of complexity. For the simulations, time-resolved X-ray data were generated that mimic data collected from the photocycle of the photoactive yellow protein. KINNTREX only requires the number of intermediates and approximate relaxation times (both obtained from a singular valued decomposition) and does not require an assumption of a candidate mechanism. It successfully predicts a consistent chemical kinetic mechanism, together with difference electron-density maps of the intermediates that appear during the reaction. These features make KINNTREX attractive for tackling a wide range of biomolecular questions. In addition, the versatility of KINNTREX can inspire more NN-based applications to time-resolved data from biological macromolecules obtained by other methods.