Is there a dynamic protein contribution to the substrate trigger in coenzyme B12-dependent ethanolamine ammonia lyase?

Factors that Impact Photochemical Cage Escape Yields

The utilization of visible light to mediate chemical reactions in fluid solutions has applications that range from solar fuel production to medicine and organic synthesis. These reactions are typically initiated by electron transfer between a photoexcited dye molecule (a photosensitizer) and a redox-active quencher to yield radical pairs that are intimately associated within a solvent cage. Many of these radicals undergo rapid thermodynamically favored "geminate" recombination and do not diffuse out of the solvent cage that surrounds them. Those that do escape the cage are useful reagents that may undergo subsequent reactions important to the above-mentioned applications. The cage escape process and the factors that determine the yields remain poorly understood despite decades of research motivated by their practical and fundamental importance. Herein, state-of-the-art research on light-induced electron transfer and cage escape that has appeared since the seminal 1972 review by J. P. Lorand entitled "The Cage Effect" is reviewed. This review also provides some background for those new to the field and discusses the cage escape process of both homolytic bond photodissociation and bimolecular light induced electron transfer reactions. The review concludes with some key goals and directions for future research that promise to elevate this very vibrant field to even greater heights.

Investigating radical pair reaction dynamics of B12 coenzymes 1: Transient absorption spectroscopy and magnetic field effects

B₁₂ coenzymes are vital to healthy biological function across nature. They undergo radical chemistry in a variety of contexts, where spin-correlated radical pairs can be generated both thermally and photochemically. Owing to the unusual magnetic properties of B₁₂ radical pairs, however, most of the reaction and spin dynamics occur on a timescale (picoseconds-nanoseconds) that cannot be resolved by most measurement techniques. Here, we describe a method that combines femtosecond transient absorption spectroscopy with magnetic field exposure, which enables the direct scrutiny of such rapid processes. This approach should provide a means by which to investigate the apparently profound effect protein environments have on the generation and reactivity of B₁₂ radical pairs.

Photolytic properties of B12-dependent enzymes: A theoretical perspective

The biologically active vitamin B₁₂ derivates, methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), are ubiquitous organometallic cofactors. In addition to their key roles in enzymatic catalysis, B₁₂ cofactors have complex photolytic properties which have been the target of experimental and theoretical studies. With the recent discovery of B₁₂-dependent photoreceptors, there is an increased need to elucidate the underlying photochemical mechanisms of these systems. This book chapter summarizes the photolytic properties of MeCbl- and AdoCbl-dependent enzymes with particular emphasis on the effect of the environment of the cofactor on the excited state processes. These systems include isolated MeCbl and AdoCbl as well as the enzymes, ethanolamine ammonia-lyase (EAL), glutamate mutase (GLM), methionine synthase (MetH), and photoreceptor CarH. Central to determining the photodissociation mechanism of each system is the analysis of the lowest singlet excited state (S₁) potential energy surface (PES). Time-dependent density functional theory (TD-DFT), employing BP86/TZVPP, is widely used to construct such PESs. Regardless of the environment, the topology of the S₁ PES of AdoCbl or MeCbl is marked by characteristic features, namely the metal-to-ligand charge transfer (MLCT) and ligand field (LF) regions. Conversely, the relative energetics of these electronic states are affected by the environment. Applications and outlooks for Cbl photochemistry are also discussed.

Mechanism of Rate Acceleration of Radical C-C Bond Formation Reaction by a Radical SAM GTP 3',8-Cyclase

While the number of characterized radical S-adenosyl-l-methionine (SAM) enzymes is increasing, the roles of these enzymes in radical catalysis remain largely ambiguous. In radical SAM enzymes, the slow radical initiation step kinetically masks the subsequent steps, making it impossible to study the kinetics of radical chemistry. Due to this kinetic masking, it is unknown whether the subsequent radical reactions require rate acceleration by the enzyme active site. Here, we report the first evidence that a radical SAM enzyme MoaA accelerates the radical-mediated C-C bond formation. MoaA catalyzes an unprecedented 3',8-cyclization of GTP into 3',8-cyclo-7,8-dihydro-GTP (3',8-cH₂GTP) during the molybdenum cofactor (Moco) biosynthesis. Through a series of EPR and biochemical characterizations, we found that MoaA catalyzes a shunt pathway in which an on-pathway intermediate, GTP C-3' radical, abstracts H-4' atom from (4'R)-5'-deoxyadenosine (5'-dA) to transiently generate 5'-deoxyadenos-4'-yl radical (5'-dA-C4'^•) that is subsequently reduced stereospecifically to yield (4'S)-5'-dA. Detailed kinetic characterization of the shunt and the main pathways provided the comprehensive view of MoaA kinetics and determined the rate of the on-pathway 3',8-cyclization step as 2.7 ± 0.7 s^-1. Together with DFT calculations, this observation suggested that the 3',8-cyclization by MoaA is accelerated by 6-9 orders of magnitude. Further experimental and theoretical characterizations suggested that the rate acceleration is achieved mainly by constraining the triphosphate and guanine base positions while leaving the ribose flexible, and a transition state stabilization through H-bond and electrostatic interactions with the positively charged R17 residue. This is the first evidence for rate acceleration of radical reactions by a radical SAM enzyme and provides insights into the mechanism by which radical SAM enzymes accelerate radical chemistry.

Observation of the Δg mechanism resulting from the ultrafast spin dynamics that follow the photolysis of coenzyme B12

Throughout nature, both free radicals and transient radical reaction intermediates are vital to many biological functions. Coenzyme B₁₂ is a case in point. This organometallic cofactor generates a radical pair upon activation in its dependent enzymes by substrate binding and following photolysis. The resulting cob(ii)alamin/5'-deoxyadenosyl radical pair has unusual magnetic properties that present a challenge to detailed investigation at ambient temperatures. Here, we use femtosecond transient absorption spectroscopy adapted for magnetic field exposure to reveal that the spin dynamics of the B₁₂ radical pair are sufficiently fast for magnetic field effects to be observed on the ultrafast reaction kinetics. Moreover, the large difference in g-values between the radicals of the pair means that effects of the Δg mechanism are observed for the first time for a radical pair system exposed to magnetic fields below 1 T. Spin dynamic simulations allow a value of the cob(ii)alamin radical g-value (2.105) at ambient temperature to be extracted and, because the spin dynamic time scale is faster than the diffusional rotation of the cob(ii)alamin radical, the observed value corresponds to the anisotropic g_|| value for this radical.

Photochemical Spin Dynamics of the Vitamin B12 Derivative, Methylcobalamin

Derivatives of vitamin B₁₂ are six-coordinate cobalt corrinoids found in humans, other animals, and microorganisms. By acting as enzymatic cofactors and photoreceptor chromophores, they serve vital metabolic and photoprotective functions. Depending on the context, the chemical mechanisms of the biologically active derivatives of B₁₂-methylcobalamin (MeCbl) and 5'-deoxyadenosylcobalamin (AdoCbl)-can be very different from one another. The extent to which this chemistry is tuned by the upper axial ligand, however, is not yet clear. Here, we have used a combination of time-resolved Fourier transform-electron paramagnetic resonance (FT-EPR), magnetic field effect experiments, and spin dynamic simulations to reveal that the upper axial ligand alone only results in relatively minor changes to the photochemical spin dynamics of B₁₂. By studying the photolysis of MeCbl, we find that, similar to AdoCbl, the initial (or "geminate") radical pairs (RPs) are born predominantly in the singlet spin state and thus originate from singlet excited-state precursors. This is in contrast to the triplet RPs and precursors proposed previously. Unlike AdoCbl, the extent of geminate recombination is limited following MeCbl photolysis, resulting in significant distortions to the FT-EPR signal caused by polarization from spin-correlated methyl-methyl radical "f-pairs" formed following rapid diffusion. Despite the photophysical mechanism that precedes photolysis of MeCbl showing wavelength dependence, the subsequent spin dynamics appear to be largely independent of excitation wavelength, again similar to AdoCbl. Our data finally provide clarity to what in the literature to date has been a confused and contradictory picture. We conclude that, although the upper axial position of MeCbl and AdoCbl does impact their reactivity to some extent, the remarkable biochemical diversity of these fascinating molecules is most likely a result of tuning by their protein environment.

Magnetic field effects on coenzyme B12- and B6-dependent lysine 5,6-aminomutase: switching of the J-resonance through a kinetically competent radical-pair intermediate

External magnetic fields interact with lysine 5,6-aminomutase, through an immobilized radical-pair with constant and large exchange interaction, to switch on J-resonance between singlet and triplet spin states, which have different reactive fates.

The photochemistry and photobiology of vitamin B12

This Perspective provides the first detailed overview of the photoresponse of vitamin B₁₂ and its derivatives, from the early, photophysical events to the burgeoning area of B₁₂-dependent photobiology.

Mechanism of Co-C photodissociation in adenosylcobalamin

A mechanism of Co-C bond photodissociation in the base-on form of adenosylcobalamin (AdoCbl) was investigated by time-dependent density functional theory (TD-DFT). The key mechanistic step involves singlet radical pair (RP) generation from the first electronically excited state (S1). To connect TD-DFT calculations with ultra-fast excited state dynamics, the potential energy surface (PES) of the S1 state was constructed using Co-C and Co-NIm axial coordinates. The S1 PES can be characterized by two minima separated by a seam resulting from the crossing of two surfaces, of metal-to-ligand charge transfer (MLCT) character near the minimum, and a shallow ligand field (LF) surface at elongated axial bond distances. Only one possible pathway for photolysis (path A) was identified based on energetic grounds. This pathway is characterized by the first elongation of the Co-C bond, followed by photolysis from an LF state where the axial base is partially detached. A new perspective on the photolysis of AdoCbl is then gained by connecting TD-DFT results with available experimental observations.

Photolytic properties of cobalamins: a theoretical perspective

This Perspective Article highlights recent theoretical developments, and summarizes the current understanding of the photolytic properties of cobalamins from a computational point of view. The primary focus is on two alkyl cobalamins, methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), as well as two non-alkyl cobalamins, cyanocobalamin (CNCbl) and hydroxocobalamin (HOCbl). Photolysis of alkyl cobalamins involves low-lying singlet excited states where photodissociation of the Co-C bond leads to formation of singlet-born alkyl/cob(ii)alamin radical pairs (RPs). Potential energy surfaces (PESs) associated with cobalamin low-lying excited states as functions of both axial bonds, provide the most reliable tool for initial analysis of their photochemical and photophysical properties. Due to the complexity, and size limitations associated with the cobalamins, the primary method for calculating ground state properties is density functional theory (DFT), while time-dependent DFT (TD-DFT) is used for electronically excited states. For alkyl cobalamins, energy pathways on the lowest singlet surface, connecting metal-to-ligand charge transfer (MLCT) and ligand field (LF) minima, can be associated with photo-homolysis of the Co-C bond observed experimentally. Additionally, energy pathways between minima and seams associated with crossing of S1/S0 surfaces, are the most efficient for internal conversion (IC) to the ground state. Depending on the specific cobalamin, such IC may involve simultaneous elongation of both axial bonds (CNCbl), or detachment of axial base followed by corrin ring distortion (MeCbl). The possibility of intersystem crossing, and the formation of triplet RPs is also discussed based on Landau-Zener theory.

The molecular mechanism of the open–closed protein conformational cycle transitions and coupled substrate binding, activation and product release events in lysine 5,6-aminomutase

The contributions of Lys370α and Asp298α to the critical Co–C bond cleavage trigger and open–closed cycle transitions of lysine 5,6-aminomutase.

The photochemical mechanism of a B12-dependent photoreceptor protein

The coenzyme B₁₂-dependent photoreceptor protein, CarH, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids in response to light. On binding of coenzyme B₁₂ the monomeric apoprotein forms tetramers in the dark, which bind operator DNA thus blocking transcription. Under illumination the CarH tetramer dissociates, weakening its affinity for DNA and allowing transcription. The mechanism by which this occurs is unknown. Here we describe the photochemistry in CarH that ultimately triggers tetramer dissociation; it proceeds via a cob(III)alamin intermediate, which then forms a stable adduct with the protein. This pathway is without precedent and our data suggest it is independent of the radical chemistry common to both coenzyme B₁₂ enzymology and its known photochemistry. It provides a mechanistic foundation for the emerging field of B₁₂ photobiology and will serve to inform the development of a new class of optogenetic tool for the control of gene expression.

Coenzyme B12 traditionally acts as cofactor to light-independent metabolic enzymes in bacteria and humans. Here, Kutta et al. present a time-resolved photochemical description of a B12-dependent photoreceptor protein, which represents a mechanistic foundation for B12 photobiology.

Probing reversible chemistry in coenzyme B12 -dependent ethanolamine ammonia lyase with kinetic isotope effects

Coenzyme B₁₂-dependent enzymes such as ethanolamine ammonia lyase have remarkable catalytic power and some unique properties that enable detailed analysis of the reaction chemistry and associated dynamics. By selectively deuterating the substrate (ethanolamine) and/or the β-carbon of the 5′-deoxyadenosyl moiety of the intrinsic coenzyme B₁₂, it was possible to experimentally probe both the forward and reverse hydrogen atom transfers between the 5′-deoxyadenosyl radical and substrate during single-turnover stopped-flow measurements. These data are interpreted within the context of a kinetic model where the 5′-deoxyadenosyl radical intermediate may be quasi-stable and rearrangement of the substrate radical is essentially irreversible. Global fitting of these data allows estimation of the intrinsic rate constants associated with CoC homolysis and initial H-abstraction steps. In contrast to previous stopped-flow studies, the apparent kinetic isotope effects are found to be relatively small.

Glutamate 338 is an electrostatic facilitator of C-Co bond breakage in a dynamic/electrostatic model of catalysis by ornithine aminomutase

How cobalamin-dependent enzymes promote C–Co homolysis to initiate radical catalysis has been debated extensively. For the pyridoxal 5′-phosphate and cobalamin-dependent enzymes lysine 5,6-aminomutase and ornithine 4,5-aminomutase (OAM), large-scale re-orientation of the cobalamin-binding domain linked to C–Co bond breakage has been proposed. In these models, substrate binding triggers dynamic sampling of the B₁₂-binding Rossmann domain to achieve a catalytically competent ‘closed’ conformational state. In ‘closed’ conformations of OAM, Glu338 is thought to facilitate C–Co bond breakage by close association with the cobalamin adenosyl group. We investigated this using stopped-flow continuous-wave photolysis, viscosity dependence kinetic measurements, and electron paramagnetic resonance spectroscopy of a series of Glu338 variants. We found that substrate-induced C–Co bond homolysis is compromised in Glu388 variant forms of OAM, although photolysis of the C–Co bond is not affected by the identity of residue 338. Electrostatic interactions of Glu338 with the 5′-deoxyadenosyl group of B₁₂ potentiate C–Co bond homolysis in ‘closed’ conformations only; these conformations are unlocked by substrate binding. Our studies extend earlier models that identified a requirement for large-scale motion of the cobalamin domain. Our findings indicate that large-scale motion is required to pre-organize the active site by enabling transient formation of ‘closed’ conformations of OAM. In ‘closed’ conformations, Glu338 interacts with the 5′-deoxyadenosyl group of cobalamin. This interaction is required to potentiate C–Co homolysis, and is a crucial component of the approximately 10¹² rate enhancement achieved by cobalamin-dependent enzymes for C–Co bond homolysis.

Fast protein motions are coupled to enzyme H-transfer reactions

Coupling of fast protein dynamics to enzyme chemistry is controversial and has ignited considerable debate, especially over the past 15 years in relation to enzyme-catalyzed H-transfer. H-transfer can occur by quantum tunneling, and the temperature dependence of kinetic isotope effects (KIEs) has emerged as the "gold standard" descriptor of these reactions. The anomalous temperature dependence of KIEs is often rationalized by invoking fast motions to facilitate H-transfer, yet crucially, direct evidence for coupled motions is lacking. The fast motions hypothesis underpinning the temperature dependence of KIEs is based on inference. Here, we have perturbed vibrational motions in pentaerythritol tetranitrate reductase (PETNR) by isotopic substitution where all non-exchangeable atoms were replaced with the corresponding heavy isotope ((13)C, (15)N, and (2)H). The KIE temperature dependence is perturbed by heavy isotope labeling, demonstrating a direct link between (promoting) vibrations in the protein and the observed KIE. Further we show that temperature-independent KIEs do not necessarily rule out a role for fast dynamics coupled to reaction chemistry. We show causality between fast motions and enzyme chemistry and demonstrate how this impacts on experimental KIEs for enzyme reactions.

Ultrafast infrared spectral fingerprints of vitamin B12 and related cobalamins

Vitamin B(12) (cyanocobalamin, CNCbl) and its derivatives are structurally complex and functionally diverse biomolecules. The excited state and radical pair reaction dynamics that follow their photoexcitation have been previously studied in detail using UV-visible techniques. Similar time-resolved infrared (TRIR) data are limited, however. Herein we present TRIR difference spectra in the 1300-1700 cm(-1) region between 2 ps and 2 ns for adenosylcobalamin (AdoCbl), methylcobalamin (MeCbl), CNCbl, and hydroxocobalamin (OHCbl). The spectral profiles of all four cobalamins are complex, with broad similarities that suggest the vibrational excited states are related, but with a number of identifiable variations. The majority of the signals from AdoCbl and MeCbl decay with kinetics similar to those reported in the literature from UV-visible studies. However, there are regions of rapid (<10 ps) vibrational relaxation (peak shifts to higher frequencies from 1551, 1442, and 1337 cm(-1)) that are more pronounced in AdoCbl than in MeCbl. The AdoCbl data also exhibit more substantial changes in the amide I region and a number of more gradual peak shifts elsewhere (e.g., from 1549 to 1563 cm(-1)), which are not apparent in the MeCbl data. We attribute these differences to interactions between the bulky adenosyl and the corrin ring after photoexcitation and during radical pair recombination, respectively. Although spectrally similar to the initial excited state, the long-lived metal-to-ligand charge transfer state of MeCbl is clearly resolved in the kinetic analysis. The excited states of CNCbl and OHCbl relax to the ground state within 40 ps with few significant peak shifts, suggesting little or no homolysis of the bond between the Co and the upper axial ligand. Difference spectra from density functional theory calculations (where spectra from simplified cobalamins with an upper axial methyl were subtracted from those without) show qualitative agreement with the experimental data. They imply the excited state intermediates in the TRIR difference spectra resemble the dissociated states vibrationally (the cobalamin with the upper axial ligand missing) relative to the ground state with a methyl in this position. They also indicate that most of the TRIR signals arise from vibrations involving some degree of motion in the corrin ring. Such coupling of motions throughout the ring makes specific peak assignments neither trivial nor always meaningful, suggesting our data should be regarded as IR spectral fingerprints.