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Enzymes are conformationally dynamic, and their dynamical properties play an important role in regulating their specificity and evolvability. In this context, substantial attention has been paid to the role of ligand-gated conformational changes in enzyme catalysis; however, such studies have focused on tremendously proficient enzymes such as triosephosphate isomerase and orotidine 5'-monophosphate decarboxylase, where the rapid (μs timescale) motion of a single loop dominates the transition between catalytically inactive and active conformations. In contrast, the (βα)

Enzymes are conformationally dynamic, and their dynamical properties play an important role in regulating their specificity and evolvability. In this context, substantial attention has been paid to the role of ligand-gated conformational changes in enzyme catalysis; however, such studies have focused on tremendously proficient enzymes such as triosephosphate isomerase and orotidine 5’-monophosphate decarboxylase, where the rapid (μs timescale) motion of a single loop dominates the transition between catalytically inactive and active conformations. In contrast, the (βα)8-barrels of tryptophan and histidine biosynthesis, such as the specialist isomerase enzymes HisA and TrpF, and the bifunctional isomerase PriA, are decorated by multiple long loops that undergo conformational transitions on the ms (or slower) timescale. Studying the interdependent motions of multiple slow loops, and their role in catalysis, poses a significant computational challenge. This work combines conventional and enhanced molecular dynamics simulations with empirical valence bond simulations to provide rich detail of the conformational behavior of the catalytic loops in HisA, PriA and TrpF, and the role of their plasticity in facilitating bifunctionality in PriA and evolved HisA variants. In addition, we demonstrate that, similar to other enzymes activated by ligand-gated conformational changes, loops 3 and 4 of HisA and PriA act as gripper loops, facilitating the isomerization of the large bulky substrate ProFAR, albeit now on much slower timescales. This hints at convergent evolution on these different (βα)8-barrel scaffolds. Finally, our work highlights the potential of engineering loop dynamics as a powerful tool to artificially manipulate the diverse catalytic repertoire of TIM-barrel proteins.

The structures of two bis-ethylpyrrolidinoadducts of Gd3N@Ih-C80, obtained by regioselective 1,3-dipolar cycloadditions, were elucidated by single crystal X-ray, visible-near infrared (vis-NIR) spectra, studies on their thermal isomerization, and theoretical calculations. The structure of the minor-bis-adduct reveals a C2-symmetric carbon cage with [6,6][6,6]-addition sites and with an endohedral Gd3N cluster that is completely flattened. This is the first example of a crystal structure of Gd3N@Ih-C80 derivatives. The structure of the major-bis-adduct was inferred by the vis-NIR spectrum being corresponded to the structure of a previously reported major-bis-adduct of Y3N@Ih-C80 known to have an asymmetric [6,6][6,6]-structure. Based on experimental results showing that the minor-bis-adduct of Gd3N@Ih-C80 isomerized to the major-adduct, a possible second addition site was elucidated with support from density functional theory calculations.

Three Prato monoadduct isomers were synthesized and structurally characterized by 1H, 13C NMR spectra and single-crystal X-ray diffraction, and one adduct on the dd-[5,6]-bond was found as the first example of a Prato [5,6]-adduct of C70. To investigate the mechanism in the generation of this dd-[5,6]-adduct, computational studies were employed to show that it was thermodynamically obtained by sigmatropic rearrangement from the presumed initial kinetic product de-[6,6]-adduct.

[EN] Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ∼5500 reported crystallographic structures of ∼1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed., his work was supported by Human Frontier Science Program Grant RGP0041 (J.M.S.-R., E.A.G., B.S., and S.C.L.K.), NIH grant R01AR069137 (E.A.G.), Department of Defense grant MURI W911NF-16-1-0372 (E.A.G.), the Swedish Research Council (2019-03499) (S.C.L.K.), the Knut and Alice Wallenberg Foundation (2018.0140 and 2019.0431) (S.C.L.K.), Spanish Ministry of Economy and Competitiveness/FEDER Funds Grants BIO2015-66426-R (J.M.S.-R.) RTI2018-097142-B-100 (J.M.S.-R.) and BIO2016-74875-P (J.A.G.). The simulations were enabled by resources provided by the Swedish National Infrastructure for Computing (SNIC) at UPPMAX partially funded by the Swedish Research Council through grant agreement no. 2016-07213. We acknowledge the Spanish Synchrotron Radiation Facility (ALBA, Barcelona) for the provision of synchrotron radiation facilities and the staff at XALOC beamline for their invaluable support. We are also grateful to Victoria Longobardo Polanco (Proteomic Unit, Institute of Parasitology and Biomedicine “López-Neyra”) for help with mass spectrometry experiments and data analyses and to Juan Román Luque Ortega (Molecular Interactions Facility, Centro de Investigaciones Biológicas Margarita Salas) for help with ultracentrifugation experiments and data analyses.

The tris- and tetra-adducts of M3N@Ih-C80 metallofullerenes were synthesized and characterized for the first time. The 1,3-dipolar cycloaddition (Prato reaction) of Y3N@Ih-C80 and Gd3N@Ih-C80 with an excess of N-ethylglycine and formaldehyde provided tris- and tetra-fulleropyrrolidine adducts in a regioselective manner. Purification by HPLC and analyses of the isolated peaks by NMR, MS, and vis-NIR spectra revealed that the major products were four tris- and one tetra-isomers for both Y3N@Ih-C80 and Gd3N@Ih-C80. Considering the large number of possible isomers (e.g., at least 1140 isomers for the tris-adduct), the limited number of isomers obtained indicated that the reactions proceeded with high regioselectivity. NMR analyses of the Y3N@Ih-C80 adducts found that the tris-adducts were all-[6,6]- or [6,6][6,6][5,6]-isomers and that some showed mutual isomerization or remained intact at room temperature. The tetra-adduct obtained as a major product was all-[6,6] and stable. For the structural elucidation of Gd3N@Ih-C80 tris- and tetra-adducts, density functional theory (DFT) calculations were performed to estimate the relative stabilities of tris- and tetra-adducts formed upon Prato functionalization of the most pyramidalized regions of the fullerene structure. The most stable structures corresponded to additions on the most pyramidalized (i.e., strained) bonds. Taking together the experimental vis-NIR spectra, NMR assignments, and the computed relative DFT stabilities of the potential tris- and tetra-adducts, the structures of the isolated adducts were elucidated. Electron resonance (ESR) measurements measurements of pristine, bis-, and tris-adducts of Gd3N@C80 suggested that the rotation of the endohedral metal cluster slowed upon increase of the addition numbers to C80 cage, which is favored for accommodating the Gd atoms of the relatively large Gd3N cluster inner space at the sp3 addition sites. This is presumably related to the high regioselectivity in the Prato addition reaction driven by the strain release of the Gd3N@C80 fullerene structure. Copyright © 2020 American Chemical Society ISSN:0002-7863 ISSN:1520-5126

Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains sluggish, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib is a novel approach which uses phylogenetic analysis and Rosetta design to rank enzyme variants with multiple mutations, on the basis of predicted stability. Here, we use it to target the active site region of a minimalist-designed, de novo Kemp eliminase. The similarity between the Michaelis complex and transition state for the enzymatic reaction makes this system particularly challenging to optimize. Yet, experimental screening of a small number of active-site variants at the top of the predicted stability ranking leads to catalytic efficiencies and turnover numbers ( 2 104 M 1 s 1 and 102 s 1) for this anthropogenic reaction that compare favorably to those of modern natural enzymes. This result illustrates the promise of FuncLib as a powerful tool with which to speed up directed evolution, even on scaffolds that were not originally evolved for those functions, by guiding screening to regions of the sequence space that encode stable and catalytically diverse enzymes. Empirical valence bond calculations reproduce the experimental activation energies for the optimized eliminases to within 2 kcal mol 1 and indicate that the enhanced activity is linked to better geometric preorganization of the active site. This raises the possibility of further enhancing the stabilityguidance of FuncLib by computational predictions of catalytic activity, as a generalized approach for computational enzyme design, Knut and Alice Wallenberg Foundation (Wallenberg Academy Fellowship) 2018.0140, Human Frontier Science Program RGP0041/2017, FEDER Funds/Spanish Ministry of Science, Innovation and Universities BIO2015-66426-R RTI2018-097142-B-100, FEDER/Junta de Andalucia - Consejeria de Economia y Conocimiento E.FQM.113.UGR18, Swedish National Infrastructure for computing (SNAC) 2018/2-3 2019/2-1

The tris- and tetra-adducts of M

Glycerol-3-phosphate dehydrogenase is a biomedically important enzyme that plays a crucial role in lipid biosynthesis. It is activated by a ligand-gated conformational change that is necessary for the enzyme to reach a catalytically competent conformation capable of efficient transition-state stabilization. While the human form (hlGPDH) has been the subject of extensive structural and biochemical studies, corresponding computational studies to support and extend experimental observations have been lacking. We perform here detailed empirical valence bond and Hamiltonian replica exchange molecular dynamics simulations of wild-type hlGPDH and its variants, as well as providing a crystal structure of the binary hlGPDH center dot NAD R269A variant where the enzyme is present in the open conformation. We estimated the activation free energies for the hydride transfer reaction in wild-type and substituted hlGPDH and investigated the effect of mutations on catalysis from a detailed structural study. In particular, the K120A and R269A variants increase both the volume and solvent exposure of the active site, with concomitant loss of catalytic activity. In addition, the R269 side chain interacts with both the Q295 side chain on the catalytic loop, and the substrate phosphodianion. Our structural data and simulations illustrate the critical role of this side chain in facilitating the closure of hlGPDH into a catalytically competent conformation, through modulating the flexibility of a key catalytic loop (292-LNGQKL-297). This, in turn, rationalizes a tremendous 41,000 fold decrease experimentally in the turnover number, k(cat), upon truncating this residue, as loop closure is essential for both correct positioning of key catalytic residues in the active site, as well as sequestering the active site from the solvent. Taken together, our data highlight the importance of this ligand-gated conformational change in catalysis, a feature that can be exploited both for protein engineering and for the design of allosteric inhibitors targeting this biomedically important enzyme.

Glycosidases are phylogenetically widely distributed enzymes that are crucial for the cleavage of glycosidic bonds. Here, we present the exceptional properties of a putative ancestor of bacterial and eukaryotic family-1 glycosidases. The ancestral protein shares the TIM-barrel fold with its modern descendants but displays large regions with greatly enhanced conformational flexibility. Yet, the barrel core remains comparatively rigid and the ancestral glycosidase activity is stable, with an optimum temperature within the experimental range for thermophilic family-1 glycosidases. None of the ~5500 reported crystallographic structures of ~1400 modern glycosidases show a bound porphyrin. Remarkably, the ancestral glycosidase binds heme tightly and stoichiometrically at a well-defined buried site. Heme binding rigidifies this TIM-barrel and allosterically enhances catalysis. Our work demonstrates the capability of ancestral protein reconstructions to reveal valuable but unexpected biomolecular features when sampling distant sequence space. The potential of the ancestral glycosidase as a scaffold for custom catalysis and biosensor engineering is discussed.

Directed evolution has revolutionized protein engineering. Still, enzyme optimization by random library screening remains a sluggish process, in large part due to futile probing of mutations that are catalytically neutral and/or impair stability and folding. FuncLib (funclib-weizmann.ac.il) is a novel automated computational procedure which uses phylogenetic analysis and Rosetta design to rank enzyme variants with multiple mutations, on the basis of a stability metric. Here, we use it to target the active site region of a minimalist-designed, de novo Kemp eliminase. The similarity between the Michaelis complex and transition state for the enzymatic reaction makes this a particularly challenging system to optimize. Yet, experimental screening of a very small number of active-site, multi-point variants at the top of the predicted stability ranking leads to catalytic efficiencies and turnover numbers (~2·104 M-1 s-1 and ~102 s-1) that compare well with modern natural enzymes, and that approach the catalysis levels for the best Kemp eliminases derived from extensive screening. This result illustrates the promise of FuncLib as a powerful tool with which to speed up directed evolution, by guiding screening to regions of the sequence space that encode stable and catalytically diverse enzymes. Empirical valence bond calculations reproduce the experimental activation energies for the optimized eliminases to within ~2 kcal·mol-1 and indicate that the improvements in activity are linked to better geometric preorganization of the active site. This raises the possibility of further enhancing the stability-guidance of FuncLib by EVB-based computational predictions of catalytic activity, as a generalized approach for computational enzyme design.

The incarceration of o‐benzyne and 27 other guest molecules within hemicarcerand 1, as reported experimentally by Warmuth, and Cram and co‐workers, respectively, has been studied by density functional theory (DFT). 1H‐NMR chemical shifts, rotational mobility and conformational preference of the guests within the supramolecular cage were determined, which showed intriguing correlations of the chemical shifts with structural parameters of the host‐guest system. Furthermore, based on the computed chemical shifts reassignments of some NMR signals are proposed. This affects in particular the putative characterization of the volatile benzyne molecule inside a hemicarcerand, for which our CCSD(T) and KT2 results indicate that the experimentally observed signals are most likely not resulting from an isolated benzyne within the supramolecular host. Instead, we show that the guest reacted with an aromatic ring of the host, and this adduct is responsible for the experimentally observed signals The following organizations are thanked for financial support: MICINN (PhD-scholarship ACC CTQ2011-25086/BQU, projects CTQ2014-59212-P, CTQ2015-70851-ERC, CTQ2017-87392-P), CONACyT project 2014-383560, GenCat (PhD scholarship ARR 2015_FI_B_00165, 2014SGR1202 and XRQTC network) and European Fund for Regional Development (FEDER, UNGI10-4E-801)

The structures of two bis-ethylpyrrolidinoadducts of Gd

Three Prato monoadduct isomers were synthesized and structurally characterized by

Incorporation of biotinylated aminopyridine cobalt complexes derived from the triazacyclononane scaffold into the streptavidin protein leads to formation of artificial metalloenzymes for water reduction to hydrogen. The synthesized artificial metalloenzymes have lower overpotential (at the half-peak up to 100 mV) and higher photocatalytic hydrogen evolution activity (up to 14- and 10-fold increase in TOF and TON, respectively, at pH 12.5) than the free biotinylated cobalt complexes. 1H-NMR, EPR and XAS highlight the presence of the metal complexes upon supramolecular attachment to the streptavidin. pHdependent catalytic studies and molecular dynamics (MD) simulations suggest that the increase in the catalytic activity could be induced by the protein residues positioned close to the metal centers. These findings illustrate the ability of the biotin−streptavidin technology to produce artificial metalloproteins for photo- and electrocatalytic hydrogen evolution reaction.

Turn cool off and stay active: the thermostable alcohol dehydrogenase TbSADH originating from the hot springs of Yellow Stone Park was successfully subjected to directed evolution for inducing high activity at ambient temperatures and enabling short reaction times with minimal tradeoff in thermostability. Reversed enantioselectivity was also evolved (99% ee).

Alcohol Dehydrogenase (ADH) enzymes catalyse the reversible reduction of prochiral ketones to the corresponding alcohols., Alcohol Dehydrogenase (ADH) enzymes catalyse the reversible reduction of prochiral ketones to the corresponding alcohols. These enzymes present two differently shaped active site pockets, which dictate their substrate scope and selectivity. In this study, we computationally evaluate the effect of two commonly reported active site mutations (I86A, and W110T) on a secondary alcohol dehydrogenase from Thermoanaerobacter brockii (TbSADH) through Molecular Dynamics simulations. Our results indicate that the introduced mutations induce dramatic changes in the shape of the active site, but most importantly they impact the substrate–enzyme interactions. We demonstrate that the combination of Molecular Dynamics simulations with the tools POVME and NCIplot corresponds to a powerful strategy for rationalising and engineering the stereoselectivity of ADH variants.

High-valent Fe-OH species are often invoked as key intermediates but have only been observed in Compound II of cytochrome P450s. To further address the properties of non-heme FeIV-OH complexes, we demonstrate the reversible protonation of a synthetic FeIV-oxo species containing a tris-urea tripodal ligand. The same protonated FeIV-oxo species can be prepared via oxidation, suggesting that a putative FeV-oxo species was initially generated. Computational, Mössbauer, XAS, and NRVS studies indicate that protonation of the FeIV-oxo complex most likely occurs on the tripodal ligand, which undergoes a structural change that results in the formation of a new intramolecular H-bond with the oxido ligand that aids in stabilizing the protonated adduct. We suggest that similar protonated high-valent Fe-oxo species may occur in the active sites of proteins. This finding further argues for caution when assigning unverified high-valent Fe-OH species to mechanisms We thank the U.S. National Institutes of Health (GM050781 to A.S.B., GM49970 to M.P.H., and GM101390 to M.T.G.), the Ministerio de Economia y Competitividad (CTQ2014-59212-P, CTQ2015-70851-ERC), GenCat (2014SGR1202, 2015FIB00165), and the European Fund for Regional Development (UNGI10-4E-801) for financial support, and E. E. Alp, J. Zhao, and M. Hu from the APS in the Argonne National Laboratory for support in collecting NRVS spectra

High valent Fe–OH species are often invoked as key intermediates but have only been observed in Compound II of cytochrome P450s. To further address the properties of non-heme FeIV–OH complexes we demonstrate the reversible protonation of a synthetic FeIV–oxo species containing a tris-urea tripodal ligand. The same protonated FeIV–oxo species can be prepared via oxidation, suggesting a putative FeV–oxo species was initially generated. Computational, Mössbauer, XAS, and NRVS studies indicate that protonation of the FeIV–oxo complex most likely occur on the tripodal ligand, which undergoes a structural change that results in the formation of a new intramolecular hydrogen bond with the oxido ligand that aids in stabilizing the protonated adduct. We suggest that similar species for protonated high valent Fe–oxo species may occur in the active sites of proteins. This finding further argues for caution when assigning unverified high valent Fe–OH species to mechanisms.

Functionalization of endohedral metallofullerenes (EMFs) is an active line of research that is important for obtaining nanomaterials with unique properties that might be used in a variety of fields, ranging from molecular electronics to biomedical applications. Such functionalization is commonly achieved by means of cycloaddition reactions. The scarcity of both experimental and theoretical studies analyzing the exohedral regioselectivity of cycloaddition reactions involving EMFs translates into a poor understanding of the EMF reactivity. From a theoretical point of view, the main obstacle is the high computational cost associated with this kind of studies. To alleviate the situation, we propose an approach named the frozen cage model (FCM) based on single point energy calculations at the optimized geometries of the empty cage products. The FCM represents a fast and computationally inexpensive way to perform accurate qualitative predictions of the exohedral regioselectivity of cycloaddition reactions in EMFs. Analysis of the Dimroth approximation, the activation strain or distortion/interaction model, and the noncluster energies in the Diels–Alder cycloaddition of s-cis-1,3-butadiene to X@D3h-C78 (X = Ti2C2, Sc3N, and Y3N) EMFs provides a justification of the method The following organizations are thanked for financial support: the Ministerio de Ciencia e Innovacion (MICINN, Project Nos. CTQ2011-25086/BQU and CTQ2011-23156), and the DIUE of the Generalitat de Catalunya (Project Nos. 2009SGR637 and 2009SGR528). MG.-B. thanks the Spanish MEC for doctoral fellowship AP2010-2517. S.O. is grateful to the European Community for postdoctoral fellowship PIOF-GA-2009-252856. Excellent service by the Centre de Serveis Cientific i Academics de Catalunya (CESCA) is gratefully acknowledged. The authors also are grateful to the computer resources, technical expertise, and assistance provided by the Barcelona Supercomputing Center-Centro Nacional de Supercomputation. Support for the research of M.S. was received through the ICREA Academia 2009 prize for excellence in research funded by the DIUE of the Generalitat de Catalunya

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.

Understanding directed evolution rules for biocatalyst generation through the lens of a computational microscope., Biocatalysis is based on the application of natural catalysts for new purposes, for which enzymes were not designed. Although the first examples of biocatalysis were reported more than a century ago, biocatalysis was revolutionized after the discovery of an in vitro version of Darwinian evolution called Directed Evolution (DE). Despite the recent advances in the field, major challenges remain to be addressed. Currently, the best experimental approach consists of creating multiple mutations simultaneously while limiting the choices using statistical methods. Still, tens of thousands of variants need to be tested experimentally, and little information is available on how these mutations lead to enhanced enzyme proficiency. This review aims to provide a brief description of the available computational techniques to unveil the molecular basis of improved catalysis achieved by DE. An overview of the strengths and weaknesses of current computational strategies is explored with some recent representative examples. The understanding of how this powerful technique is able to obtain highly active variants is important for the future development of more robust computational methods to predict amino-acid changes needed for activity.