Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly

Role of Conformational Dynamics in the Evolution of Retro-Aldolase Activity

Enzymes exist as ensembles of conformations that are important for function. Tuning these populations of conformational states through mutation enables evolution toward additional activities. Here we computationally evaluate the population shifts induced by distal and active site mutations in a family of computationally designed and experimentally optimized retro-aldolases. The conformational landscape of these enzymes was significantly altered during evolution, as pre-existing catalytically active conformational substates became major states in the most evolved variants. We further demonstrate that key residues responsible for these substate conversions can be predicted computationally. Significantly, the identified residues coincide with those positions mutated in the laboratory evolution experiments. This study establishes that distal mutations that affect enzyme catalytic activity can be predicted computationally and thus provides the enzyme (re)­design field with a rational strategy to determine promising sites for enhancing activity through mutation

Engineered P450 Atom-Transfer Radical Cyclases are Bifunctional Biocatalysts: Reaction Mechanism and Origin of Enantioselectivity

New-to-nature radical biocatalysis has recently emerged as a powerful strategy to tame fleeting open-shell intermediates for stereoselective transformations. In 2021, we introduced a novel metalloredox biocatalysis strategy that leverages the innate redox properties of the heme cofactor of P450 enzymes, furnishing new-to-nature atom-transfer radical cyclases (ATRCases) with excellent activity and stereoselectivity. Herein, we report a combined computational and experimental study to shed light on the mechanism and origins of enantioselectivity for this system. Molecular dynamics and quantum mechanics/molecular mechanics (QM/MM) calculations revealed an unexpected role of the key beneficial mutation I263Q. The glutamine residue serves as an essential hydrogen bond donor that engages with the carbonyl moiety of the substrate to promote bromine atom abstraction and enhance the enantioselectivity of radical cyclization. Therefore, the evolved ATRCase is a bifunctional biocatalyst, wherein the heme cofactor enables atom-transfer radical biocatalysis, while the hydrogen bond donor residue further enhances the activity and enantioselectivity. Unlike many enzymatic stereocontrol rationales based on a rigid substrate binding model, our computations demonstrate a high degree of rotational flexibility of the allyl moiety in an enzyme-substrate complex and succeeding intermediates. Therefore, the enantioselectivity is controlled by the radical cyclization transition states rather than the substrate orientation in ground-state complexes in the preceding steps. During radical cyclization, anchoring effects of the Q263 residue and steric interactions with the heme cofactor concurrently control the π-facial selectivity, allowing for highly enantioselective C-C bond formation. Our computational findings are corroborated by experiments with ATRCase mutants generated from site-directed mutagenesis

Endohedral Metal-Induced Regioselective Formation of Bis-Prato Adduct of Y₃N@<i>I</i>_<i>h</i>‑C₈₀ and Gd₃N@<i>I</i>_<i>h</i>‑C₈₀

Regioselective bisaddition of M₃N@<i>I</i>_<i>h</i>-C₈₀ (M = Y, Gd) was observed for the first time in the Prato reaction with <i>N</i>-ethylglycine and formaldehyde. The main kinetic bisadduct of Y₃N@C₈₀ was determined to be a [6,6],[6,6] adduct by ¹H and ¹³C NMR and vis/NIR spectroscopy, and it converted to a mixture of regioisomers upon heating via a sigmatropic rearrangement. The main kinetic bisadduct of Gd₃N@C₈₀ (the [6,6],[6,6] adduct on the basis of vis/NIR data) existed stably under thermal conditions without isomerization. The likely position of the second addition of the Gd₃N@C₈₀ bisadduct was predicted by DFT calculations

Electronic and Vibrational Nonlinear Optical Properties of Five Representative Electrides

The electrides have a very special electronic structure with diffuse excess electrons not localized on any specific atom. Such systems are known to have huge electronic nonlinear optical (NLO) properties. Here, we determine and analyze the vibrational, as compared to the electronic, NLO properties for a representative set of electrides: Li@Calix, Na@Calix, Li@B₁₀H₁₄, Li₂^•+TCNQ^•–, and Na₂^•+TCNQ^•–. The static and dynamic vibrational (hyper)­polarizabilities are computed by the nuclear relaxation method (with field-induced coordinates and the infinite optical frequency approximation) at the UB3LYP level using a hybrid Pople basis set. In general, the static vibrational β_vec and γ_∥ exceed the corresponding static electronic property values by up to an order of magnitude. The same comparison for dynamic vibrational hyperpolarizabilities shows a smaller ratio. For the intensity-dependent refractive index (IDRI) and dc-Kerr processes, the ratio is on the order of unity or somewhat larger; it is less for the dc-Pockels and the electric field induced second harmonic (EFISH) effects (as well as the static α̅) but still important. The role of anharmonicity, motion of the alkali atoms, and substitution of Na for Li is discussed along with specific aspects of the charge distribution associated with the excess electron

Overriding Traditional Electronic Effects in Biocatalytic Baeyer–Villiger Reactions by Directed Evolution

Controlling the regioselectivity of Baeyer-Villiger (BV) reactions remains an ongoing issue in organic chemistry, be it by synthetic catalysts or enzymes of the type Baeyer-Villiger monooxygenases (BVMOs). Herein, we address the challenging problem of switching normal to abnormal BVMO regioselectivity by directed evolution using three linear ketones as substrates, which are not structurally biased toward abnormal reactivity. Upon applying iterative saturation mutagenesis at sites lining the binding pocket of the thermostable BVMO from Thermocrispum municipale DSM 44069 (TmCHMO) and using 4-phenyl-2-butanone as substrate, the regioselectivity was reversed from 99:1 (wild-type enzyme in favor of the normal product undergoing 2-phenylethyl migration) to 2:98 in favor of methyl migration when applying the best mutant. This also stands in stark contrast to the respective reaction using the synthetic reagent m-CPBA, which provides solely the normal product. Reversal of regioselectivity was also achieved in the BV reaction of two other linear ketones. Kinetic parameters and melting temperatures revealed that most of the evolved mutants retained catalytic activity, as well as thermostability. In order to shed light on the origin of switched regioselectivity in reactions of 4-phenyl-2-butanone and phenylacetone, extensive QM/MM and MD simulations were performed. It was found that the mutations introduced by directed evolution induce crucial changes in the conformation of the respective Criegee intermediates and transition states in the binding pocket of the enzyme. In mutants that destabilize the normally preferred migration transition state, a reversal of regioselectivity is observed. This conformational control of regioselectivity overrides electronic control, which normally causes preferential migration of the group that is best able to stabilize positive charge. The results can be expected to aid future protein engineering of BVMOs

Origin and Control of Chemoselectivity in Cytochrome c Catalyzed Carbene Transfer into Si–H and N–H bonds

A cytochrome c heme protein was recently engineered to catalyze the formation of carbon-silicon bonds via carbene insertion into Si-H bonds, a reaction that was not previously known to be catalyzed by a protein. High chemoselectivity toward C-Si bond formation over competing C-N bond formation was achieved, although this trait was not screened for during directed evolution. Using computational and experimental tools, we now establish that activity and chemoselectivity are modulated by conformational dynamics of a protein loop that covers the substrate access to the iron-carbene active species. Mutagenesis of residues computationally predicted to control the loop conformation altered the protein's chemoselectivity from preferred silylation to preferred amination of a substrate containing both N-H and Si-H functionalities. We demonstrate that information on protein structure and conformational dynamics, combined with knowledge of mechanism, leads to understanding of how non-natural and selective chemical transformations can be introduced into the biological world

A Full Dimensionality Approach to Evaluate the Nonlinear Optical Properties of Molecules with Large Amplitude Anharmonic Tunneling Motions

Previously, a reduced dimensionality approach was used to determine the vibrational contribution to nonlinear optical properties for molecules with large amplitude anharmonic modes that takes into account tunneling between potential wells (Luis, J. M.; Reis, H.; Papadopoulos, M. G.; Kirtman, B. <i>J. Chem. Phys.</i> <b>2009</b>, <i>131</i>, 034116). Here, the treatment is extended, again using ammonia as an example, to include the remaining modes at several approximate levels. It is shown that this extension is essential to obtaining the correct results. Our new approach fully accounts for tunneling and avoids possible convergence problems associated with the normal coordinate expansion of the potential energy surface in a single-well treatment. For accurate numerical values, a good treatment of electron correlation is required along with a flexible basis set including diffuse functions

An Enzymatic Platform for Primary Amination of 1‑Aryl-2-alkyl Alkynes

Propargyl amines are versatile synthetic intermediates with numerous applications in the pharmaceutical industry. An attractive strategy for efficient preparation of these compounds is nitrene propargylic C(sp3)-H insertion. However, achieving this reaction with good chemo-, regio-, and enantioselective control has proven to be challenging. Here, we report an enzymatic platform for the enantioselective propargylic amination of alkynes using a hydroxylamine derivative as the nitrene precursor. Cytochrome P450 variant PA-G8 catalyzing this transformation was identified after eight rounds of directed evolution. A variety of 1-aryl-2-alkyl alkynes are accepted by PA-G8, including those bearing heteroaromatic rings. This biocatalytic process is efficient and selective (up to 2610 total turnover number (TTN) and 96% ee) and can be performed on preparative scale