Alkane monooxygenase (AlkB) is the dominant enzyme that catalyzes oxidation of liquid alkanes in environment. Two recent structural models derived from cryo-electron microscopy (cryo-EM) reveal an unusual active site: a histidine-rich center binds two iron ions without bridging ligand. To ensure potential photoreduction and radiation damage are not responsible for absence ligand cryo-EM structures, spectroscopic methods needed. We present results extended X-ray absorption fine structure...

The proton-coupled electron transfer (PCET) reactions of tyrosine (Y) are instrumental to many redox in nature. This study investigates how the local environment and thermodynamic properties Y influence its PCET characteristics. Herein, 2- 4-mercaptophenol (MP) placed well-folded α3C protein (forming 2MP-α3C 4MP-α3C) oxidized by external light-generated [Ru(L)3]3+ complexes. resulting neutral radicals long-lived (>100 s) with distinct optical EPR spectra. Calculated spin-density...

Ribonucleotide reductase (RNR) catalyzes the reduction of ribonucleotides to deoxyribonucleotides and is critical for DNA synthesis repair in all organisms. Its mechanism requires radical transfer along a ∼32 Å pathway through series proton-coupled electron (PCET) steps. Previous simulations suggested that glutamate residue (E623) mediates PCET reaction between two stacked tyrosine residues (Y730 Y731) proton relay mechanism. This work focuses on adjacent Y730 cysteine (C439). Quantum...

Purified alkane monooxygenase (AlkB) from Fontimonas thermophila (FtAlkB) catalyzes the defluorination of 1-fluorooctane, producing octanal, which is partially reduced under reaction conditions to generate 1-octanol. This occurs preferentially at monofluorinated methyl group, with only a minor amount oxidation nonfluorinated end molecule. The dehalogenation chemistry specific as neither 1-chlorooctane or 1-bromooctane are dehalogenated an appreciable extent. Furthermore, P. putida cells...

N,N-Dimethylformamide (DMF) is a pollutant that can be metabolized naturally by DMF-utilizing microorganisms, via the non-heme iron enzyme N,N-dimethylformamidase (DMFase). We investigated unusual protein fold and Tyr-Tyr-Glu coordination sphere of DMFase performing molecular dynamics simulations studying DMF binding substrate positioning. Our docking studies support directly coordinates center through its carbonyl group, with Fe-DMF distances consistent structures inorganic complexes....

N,N-Dimethylformamide (DMF) is a solvent that can be metabolized naturally by DMF-utilizing microorganisms via non-heme iron enzyme N,N-dimethylformamidase (DMFase). DMF small molecule with very few hydrogen bond donors or acceptors, and thus must bound in the active site through other noncovalent interactions. We investigated unusual protein fold, role of residues, substrate positioning performing molecular dynamics (MD) simulations studying binding. Our docking studies support idea...

Proton-coupled electron transfer (PCET) from tyrosine produces a neutral tyrosyl radical (Y•) that is vital to many catalytic redox reactions. To better understand how the protein environment influences PCET properties of tyrosine, we have studied formation behavior Y32 in α3Y model protein. The previously solved solution NMR structure shows sequestered ∼7.7 ± 0.3 Å below surface without any primary proton acceptors nearby. Here present transient absorption kinetic data and molecular...

Ribonucleotide reductases (RNRs) catalyze the conversion of all four ribonucleotides to deoxyribonucleotides and are essential for DNA synthesis in organisms. The active form E. coli Ia RNR is composed two homodimers that α2β2 complex. Catalysis initiated by long-range radical translocation over a ∼32 Å proton-coupled electron transfer (PCET) pathway involving Y356β Y731α at interface. Resolving PCET α/β interface has been long-standing challenge due lack structural data. Herein, molecular...

Ribonucleotide reductase (RNR) regulates DNA synthesis and repair in all organisms. The mechanism of Escherichia coli RNR requires radical transfer over a proton-coupled electron (PCET) pathway spanning ∼32 Å across two protein subunits. A key step along this is the interfacial PCET reaction between Y356 β subunit Y731 α subunit. Herein, tyrosines an aqueous interface explored with classical molecular dynamics quantum mechanical/molecular mechanical (QM/MM) free energy simulations....

Photoreceptor proteins play a vital role in wide range of light-regulated processes. The formation the light-adapted state blue light using flavin (BLUF) photoreceptors is thought to involve rearrangements hydrogen-bonding networks upon photoexcitation. Free energy simulations with partial charges corresponding relevant ground and excited states Slr1694 BLUF domain characterize conformations prior following indicate that Trp91 thermodynamically favored be active site, although it also able...

Ribonucleotide reductase (RNR) is an essential enzyme in DNA synthesis for all living organisms. It reduces ribonucleotides to the corresponding deoxyribonucleotides by a reversible radical transfer mechanism. The active form of E. coli Ia RNR composed two subunits, α and β, which asymmetric α2β2 complex. pathway involves series proton-coupled electron (PCET) reactions spanning β over ∼32 Å. Herein, quantum mechanical/molecular mechanical free energy simulations PCET between tyrosine...

The enzyme ribonucleotide reductase plays a critical role in DNA synthesis and repair. Its mechanism requires long-range radical transfer through series of proton-coupled electron (PCET) steps. Nuclear quantum effects such as zero-point energy, proton delocalization, hydrogen tunneling are known to be important PCET. We present strategy for efficiently incorporating nuclear into multidimensional free energy surfaces real-time dynamical simulations condensed-phase systems enzymes. This is...

The π–π stacking interaction between lumiflavin and a number of π-electron-rich molecules has been studied by density functional theory using several new-generation functionals. Six known lumiflavin-aromatic adducts were used the models evaluated comparing geometry energetics with experimental results. study found that dispersion-corrected hybrid functionals larger (>50%) Hartree–Fock exchanges produced superior results in modeling thermodynamic characteristics these complexes. producing...

Metal-organic cages form well-defined microenvironments that can enhance the catalytic proficiency of encapsulated transition metal catalysts (TMCs). We introduce a screening protocol to efficiently identify TMCs are promising candidates for encapsulation in Ga4L6-12 nanocage. obtain from Cambridge Structural Database with geometric and electronic characteristics amenable mine text associated manuscripts curate documented functionality. By docking candidate inside nanocage cavity carrying...

Miniature artificial enzymes such as mimochromes provide a simplified platform to extract design principles for engineering rate enhancements beyond that of natural enzymes, although optimizations have largely focused on geometric properties, leaving the impact electronic environment unexplored. To investigate how influences reactivity, we carry out classical and ab initio molecular dynamics (MD) simulations, supervised machine learning (ML), statistical analysis series mimochromes, MC6,...

Metal-organic cages form well-defined microenvironments that can enhance the catalytic proficiency of encapsulated transition metal complexes (TMCs). We introduce a screening protocol to efficiently identify TMCs are promising candidates for encapsulation in Ga

The enzyme ribonucleotide reductase (RNR), which catalyzes the reduction of ribonucleotides to deoxynucleotides, is vital for DNA synthesis, replication, and repair in all living organisms. Its mechanism requires long-range radical translocation over ∼32 Å through two protein subunits intervening aqueous interface. Herein, a kinetic model designed describe reversible transfer Escherichia coli RNR. This based on experimentally studied photoRNR systems that allow photochemical injection at...

Quinone reductases belong to the family of flavin-dependent oxidoreductases. With redox active cofactor, flavin adenine dinucleotide, quinone are known utilize a 'ping-pong' kinetic mechanism during catalysis in which hydride is bounced back and forth between its two substrates. However, continuation this catalytic cycle requires product displacement steps, where one half-cycle displaced by substrate next half-cycle. Using improved hybrid quantum mechanical/molecular mechanical simulations,...

Metalloenzymes catalyze a wide range of chemical transformations, with the active site residues playing key role in modulating reactivity and selectivity. Unlike smaller synthetic catalysts, metalloenzyme is embedded larger protein, which makes interrogation electronic properties geometric features quantum mechanical calculations challenging. Here we implement ability to fetch crystallographic structures from Protein Data Bank analyze metal binding sites program molSimplify. We show...

The New Haven Local Section of the American Chemical Society held a virtual version its annual Student Research Symposium prompted by COVID-19 pandemic. A combination YouTube, Google Drive, Open Broadcaster Software, and Zoom was utilized to hold symposium which included juried oral poster presentations. While our aim preserve as much in-person experience possible despite crisis, we found some very encouraging advantages format designed it. These reduced presenter fatigue, more substantive...

The oxidation of tyrosine to form the neutral radical via proton-coupled electron transfer is essential for a wide range biological processes. precise measurement redox potentials (Y) in complex protein environments challenging mainly because highly oxidizing and reactive nature state. Herein, computational strategy presented predicting environment. In this strategy, both reduced Y-OH oxidized Y-O• forms are sampled with molecular dynamics using mechanical force field. For large number...

Prolyl-tRNA synthetases (ProRSs) catalyze the covalent attachment of proline onto cognate transfer ribonucleic acids (tRNAs), an indispensable step for protein synthesis in all living organisms. ProRSs are modular enzymes and "prokaryotic-like" distinguished from "eukaryotic-like" by presence editing insertion domain (INS) inserted between motifs 2 3 main catalytic domain. Earlier studies suggested that coupled-domain dynamics could contribute to catalysis; however, role distal highly mobile...