Accurate positioning of functional residues with robotics-inspired computational protein design.

SignificanceComputational protein design promises to advance applications in medicine and biotechnology by creating proteins with many new and useful functions. However, new functions require the design of specific and often irregular atom-level geometries, which remains a major challenge. Here, we develop computational methods that design and predict local protein geometries with greater accuracy than existing methods. Then, as a proof of concept, we leverage these methods to design new protein conformations in the enzyme ketosteroid isomerase that change the protein's preference for a key functional residue. Our computational methods are openly accessible and can be applied to the design of other intricate geometries customized for new user-defined protein functions.

Design of Efficient Artificial Enzymes Using Crystallographically Enhanced Conformational Sampling.

The ability to create efficient artificial enzymes for any chemical reaction is of great interest. Here, we describe a computational design method for increasing the catalytic efficiency of de novo enzymes by several orders of magnitude without relying on directed evolution and high-throughput screening. Using structural ensembles generated from dynamics-based refinement against X-ray diffraction data collected from crystals of Kemp eliminases HG3 (kcat/KM 125 M-1 s-1) and KE70 (kcat/KM 57 M-1 s-1), we design from each enzyme ≤10 sequences predicted to catalyze this reaction more efficiently. The most active designs display kcat/KM values improved by 100-250-fold, comparable to mutants obtained after screening thousands of variants in multiple rounds of directed evolution. Crystal structures show excellent agreement with computational models, with catalytic contacts present as designed and transition-state root-mean-square deviations of ≤0.65 Å. Our work shows how ensemble-based design can generate efficient artificial enzymes by exploiting the true conformational ensemble to design improved active sites.

Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis.

How changes in enzyme structure and dynamics facilitate passage along the reaction coordinate is a fundamental unanswered question. Here, we use time-resolved mix-and-inject serial crystallography (MISC) at an X-ray free electron laser (XFEL), ambient-temperature X-ray crystallography, computer simulations, and enzyme kinetics to characterize how covalent catalysis modulates isocyanide hydratase (ICH) conformational dynamics throughout its catalytic cycle. We visualize this previously hypothetical reaction mechanism, directly observing formation of a thioimidate covalent intermediate in ICH microcrystals during catalysis. ICH exhibits a concerted helical displacement upon active-site cysteine modification that is gated by changes in hydrogen bond strength between the cysteine thiolate and the backbone amide of the highly strained Ile152 residue. These catalysis-activated motions permit water entry into the ICH active site for intermediate hydrolysis. Mutations at a Gly residue (Gly150) that modulate helical mobility reduce ICH catalytic turnover and alter its pre-steady-state kinetic behavior, establishing that helical mobility is important for ICH catalytic efficiency. These results demonstrate that MISC can capture otherwise elusive aspects of enzyme mechanism and dynamics in microcrystalline samples, resolving long-standing questions about the connection between nonequilibrium protein motions and enzyme catalysis.

Identification of Isoprene Oxidation Reaction Products via Anion Photoelectron Spectroscopy.

We present a study on the oxidation of isoprene under several different conditions that may model both atmospheric and combustion chemistry. Anions, formed by passing isoprene/oxidant gas mixtures through a pulsed discharge generating a range of species, are separated via mass spectrometry and characterized by anion photoelectron (PE) spectroscopy supported by computations. Specifically, a UV-irradiated isoprene/O2 mixture, which additionally produces O3, and an isoprene/O2/H2 mixture, which generates •OH when passed through the discharge, were sampled. The mass spectra of ions generated under both conditions show the production of intact molecular ions, ion-molecule complexes (e.g., O2-, O4-, and O2-·isoprene), and singly deprotonated species (e.g., deprotonated isoprene, C5H7-). In addition, both smaller and oxidized fragments are observed using both gas mixtures, though relative abundances differ. From the UV-irradiated isoprene/O2 gas mixture, additional intact molecular products of reactions initiated by ozonolysis of isoprene, methylglyoxal, and dimethylglyoxal were observed. Fragmentation and oxidation of isoprene observed in both gas mixtures included species with m/z 39, 53, 67, 69, and 83 that we attribute to a series of alkyl- and alkenoxide-based anions. The coexistence of intact molecules and complexes with fragments and reaction products demonstrates the versatility of this ion source as a simple and efficient anion formation method for studying species that may be relevant in atmospheric and combustion chemistry.

Emerging Nonvalence Anion States of [Isoprene-H·]·H2O Accessed via Detachment of OH-·Isoprene.

The anion photoelectron imaging spectra of an ion with m/z 85, generated under ion source conditions that optimize •OH production in a coexpansion with isoprene, are presented and analyzed with supporting calculations. A spectroscopic feature observed at a vertical electron detachment energy of 2.45 eV, which dominates the photoelectron spectrum measured at 3.495 eV photon energy, is consistent with the OH-·isoprene ion-molecule complex, while additional signal observed at lower electron binding energy can be attributed to other constitutional isomers. However, spectra measured over a 2.2-2.6 eV photon energy range, i.e., from near threshold of the predominant OH-·isoprene detachment feature through the vertical detachment energy, exhibit sharp features with common electron kinetic energies, suggesting autodetachment from a temporary anion prepared by photoexcitation. The photon energy independence of the electron kinetic energy of these features along with the low dipole moment predicted for the neutral •OH·isoprene van der Waals complex, suggest a complex photon-driven process. We present calculations supporting a hypothesis that near-threshold production of the •OH···isoprene reactive complex results in hydrogen abstraction of the isoprene molecule. The newly formed activated complex anion supports a dipole bound state that temporarily traps the near zero-kinetic energy electron and then autodetaches, encoding the low-frequency modes of the dehydrogenated neutral isoprene radical in the electron kinetic energies.

Temporary anion states of fluorine substituted benzenes probed by charge transfer in O2 -·C6H6-xFx (x = 0-5) ion-molecule complexes.

The broadband photoelectron source realized by detaching O2 -·X (X = neutral unsaturated molecule) complexes offers a unique opportunity to probe temporary anion states of the unsaturated species. Detachment of the ion molecule complex typically accesses a dissociative portion of the neutral potential, creating a continuum electron source that can undergo scattering with X. We present the application of this new approach to electron-neutral scattering toward a study of the series of fluorinated benzenes via photoelectron spectroscopy of O2 -·C6H6-xFx (x = 0-6) measured with several photon energies. We compare these spectra to the reference O2 -·hexane spectrum and observe evidence of temporary anion states of C6H6-xFx for species with x = 0-5 in the form of enhanced signal intensity at electron kinetic energies coinciding with the energies of the temporary anions. Furthermore, we observe autodetachment features in the x = 3, 5 spectra. Results of calculations on the isolated symmetric isomer of C6H3F3 suggest that the molecule cannot support a weakly-bound non-valence state that could be associated with the observed autodetachment. However, C6HF5 - is predicted to support a valence bound state, which, if produced by charge transfer from O2 - with sufficient vibrational energy, may undergo autodetachment. Finally, the [O2·C6F6]- spectrum is unique insofar as the spectrum is substantially higher in binding energy and qualitatively different from the x = 0-5 spectra. This result suggests much stronger interactions and charge delocalization between O2 - and C6F6.

Characterization of Intermediate Oxidation States in CO2 Activation.

Redox chemistry during the activation of carbon dioxide involves changing the charge state in a CO2 molecular unit. However, such changes are usually not well described by integer formal charges, and one can think of COO functional units as being in intermediate oxidation states. In this article, we discuss the properties of CO2 and CO2-based functional units in various charge states. Besides covering isolated CO2 and its ions, we describe the CO2-based ionic species formate, oxalate, and carbonate. Finally, we provide an overview of CO2-based functional groups and ligands in clusters and metal-organic complexes.

Probing alkenoxy radical electronic structure using anion PEI spectroscopy.

Photoelectron imaging spectra of three alkenoxide radical anions (3-buten-1-oxide, 3-buten-2-oxide, and 2-propenoxide) are presented and analyzed with supporting results of density functional theory calculations. In all spectra, intense detachment features are observed at approximately 2 eV electron binding energy, which is similar to the electron affinities of saturated neutral alkoxy radicals [Ramond et al., J. Chem. Phys. 112, 1158 (2000)]. Photoelectron angular distributions suggest the presence of several overlapping transitions which are assigned to the X̃ and à states of multiple energetically competitive conformers. The term energy of the à state of the 2-propenoxy radical, 0.17 eV, is higher than that of 3-buten-2-oxy (0.13 eV) and 3-buten-1-oxy (0.05 eV) radicals. Comparing the butenoxy radicals, we infer that stronger interactions between the non-bonding O 2p orbitals and the π bond increase the splitting between the ground and the first excited state in the 3-buten-2-oxy radical relative to the 3-buten-1-oxy radical.

Infrared Photodissociation Spectra of [Sn(CO2) n]- Cluster Ions.

We present infrared spectra and density functional theory calculations of mass selected [Sn(CO2) n]- cluster anions ( n = 2-6). The spectra and structures of these clusters exhibit less structural diversity than those of analogous clusters with first-row transition metals, but are more complex than those for the heavy coinage metals or for the related [Bi(CO2) n]- clusters. The most favorable core ion structure for all cluster sizes can be characterized as a Sn-oxalate complex, Sn[C2O4]-. Higher energy isomers based on a bidentate η2-(C,O) CO2 ligand tightly bound to the metal atom in SnCO2- complexes are also observed, even for the largest cluster sizes studied here. For n = 2, another high energy isomer is found, featuring a CO2 ligand weakly bound to the metal atom in a SnCO2- ion.

Titanium Insertion into CO Bonds in Anionic Ti-CO2 Complexes.

We explore the structures of [Ti(CO2) y]- cluster anions using infrared photodissociation spectroscopy and quantum chemistry calculations. The existence of spectral signatures of metal carbonyl CO stretching modes shows that insertion of titanium atoms into C-O bonds represents an important reaction during the formation of these clusters. In addition to carbonyl groups, the infrared spectra show that the titanium center is coordinated to oxalato, carbonato, and oxo ligands, which form along with the metal carbonyls. The presence of a metal oxalato ligand promotes C-O bond insertion in these systems. These results highlight the affinity of titanium for C-O bond insertion processes.

Interactions of Molecular Titanium Oxides TiO x ( x = 1-3) with Carbon Dioxide in Cluster Anions.

We study small titanium oxide-CO2 cluster anions in vacuo to understand the fundamental interactions between TiO x and CO2 in the presence of an excess electron. Infrared spectra of [TiO x(CO2) y]- ( x = 1-3, y > 1) were obtained using photodissociation spectroscopy and assigned through quantum chemistry calculations, identifying the formation of carbonato, oxalato, oxo, η2-(O,O), and carbonyl ligands in the core ions of these clusters, with carbonato ligands being the dominant ligand species.

Allosteric Inhibitors, Crystallography, and Comparative Analysis Reveal Network of Coordinated Movement across Human Herpesvirus Proteases.

Targeting of cryptic binding sites represents an attractive but underexplored approach to modulating protein function with small molecules. Using the dimeric protease (Pr) from Kaposi's sarcoma-associated herpesvirus (KSHV) as a model system, we sought to dissect a putative allosteric network linking a cryptic site at the dimerization interface to enzyme function. Five cryogenic X-ray structures were solved of the monomeric protease with allosteric inhibitors bound to the dimer interface site. Distinct coordinated movements captured by the allosteric inhibitors were also revealed as alternative states in room-temperature X-ray data and comparative analyses of other dimeric herpesvirus proteases. A two-step mechanism was elucidated through detailed kinetic analyses and suggests an enzyme isomerization model of inhibition. Finally, a representative allosteric inhibitor from this class was shown to be efficacious in a cellular model of viral infectivity. These studies reveal a coordinated dynamic network of atomic communication linking cryptic binding site occupancy and allosteric inactivation of KHSV Pr that can be exploited to target other members of this clinically relevant family of enzymes.

Interaction of CO2 with Atomic Manganese in the Presence of an Excess Negative Charge Probed by Infrared Spectroscopy of [Mn(CO2)n]- Clusters.

We report infrared photodissociation spectra of manganese-CO2 cluster anions, [Mn(CO2)n]- (n = 2-10) to probe structural motifs characterizing the interaction between Mn and CO2 in the presence of an excess electron. We interpret the experimental spectra through comparison with infrared spectra predicted from density functional theory calculations. The cluster anions consist of core ions combining a Mn atom with a variety of ligands, solvated by additional CO2 molecules. Structural motifs of ligands evolve with increasing cluster size from simple monodentate and bidentate CO2 ligands to oxalate ligands and combinations of these structural themes.

Structural Motifs of [Fe(CO2)n]- Clusters (n = 3-7).

We present IR spectra and quantum chemical calculations for anionic iron-CO2 clusters of the form [Fe(CO2)n]- (n = 3-7). All observed clusters have at least two CO2 units strongly bound to the metal atom. These strongly bound iron-CO2 complexes form the core ions of the clusters and are solvated by additional, weakly bound CO2 molecules. Larger clusters show clear infrared signatures of core ion isomers with three CO2 moieties as well. Dominant structural motifs are based on bidentate CO2 ligands with Fe-O/Fe-C bonds, oxalate ligands, and metal insertion into a CO bond.

Infrared spectroscopic studies on the cluster size dependence of charge carrier structure in nitrous oxide cluster anions.

We report infrared photodissociation spectra of nitrous oxide cluster anions of the form (N2O)(n)O(-) (n = 1-12) and (N2O)n(-) (n = 7-15) in the region 800-1600 cm(-1). The charge carriers in these ions are NNO2(-) and O(-) for (N2O)(n)O(-) clusters with a solvation induced core ion switch, and N2O(-) for (N2O)n(-) clusters. The N-N and N-O stretching vibrations of N2O(-) (solvated by N2O) are reported for the first time, and they are found at (1595 ± 3) cm(-1) and (894 ± 5) cm(-1), respectively. We interpret our infrared spectra by comparison with the existing photoelectron spectroscopy data and with computational data in the framework of density functional theory.

Solvent-Driven Reductive Activation of CO2 by Bismuth: Switching from Metalloformate Complexes to Oxalate Products.

In this work, we investigated how the reductive activation of CO2 with an atomic bismuth model catalyst changes under aprotic solvation. IR photodissociation spectroscopy of mass-selected [Bi(CO2 )n ]- cluster ions was used to follow the structural evolution of the core ion with increasing cluster size. We interpreted the IR spectra by comparison with density-functional-theory calculations. The results show that CO2 binds to a bismuth atom in the presence of an excess electron to form a metalloformate ion, BiCOO- . Solvation with additional CO2 molecules leads to the stabilization of a bismuth(I) oxalate complex and results in a core ion switch.

Heavy atom vibrational modes and low-energy vibrational autodetachment in nitromethane anions.

We report infrared spectra of nitromethane anion, CH3NO2 (-), in the region 700-2150 cm(-1), obtained by Ar predissociation spectroscopy and electron detachment spectroscopy. The data are interpreted in the framework of second-order vibrational perturbation theory based on coupled-cluster electronic structure calculations. The modes in the spectroscopic region studied here are mainly based on vibrations involving the heavier atoms; this work complements earlier studies on nitromethane anion that focused on the CH stretching region of the spectrum. Electron detachment begins at photon energies far below the adiabatic electron affinity due to thermal population of excited vibrational states.

A challenging interpretation of a hexagonally layered protein structure.

The carboxysome is a giant protein complex that acts as a metabolic organelle in cyanobacteria and some chemoautotrophs. Its outer structure is formed by the assembly of thousands of copies of hexameric shell protein subunits into a molecular layer. The structure determination of a CcmK1 shell protein mutant (L11K) from the ß-carboxysome of the cyanobacterium Synechocystis PCC6803 led to challenges in structure determination. Twinning, noncrystallographic symmetry and packing of hexameric units in a special arrangement led to initial difficulties in space-group assignment. The correct space group was clarified after initial model refinement revealed additional symmetry. This study provides an instructive example in which broken symmetry requires a new choice of unit-cell origin in order to identify the highest symmetry space group. An additional observation related to the packing arrangement of molecules in this crystal suggests that these hexameric shell proteins might have lower internal symmetry than previously believed.

The C-terminal Region of D-DT Regulates Molecular Recognition for Protein-Ligand Complexes.

Systematic analysis of molecular recognition is critical for understanding the biological function of macromolecules. For the immunomodulatory protein D-dopachrome tautomerase (D-DT), the mechanism of protein-ligand interactions is poorly understood. Here, 17 carefully designed protein variants and wild type (WT) D-DT were interrogated with an array of complementary techniques to elucidate the structural basis of ligand recognition. Utilization of a substrate and two selective inhibitors with distinct binding profiles offered previously unseen mechanistic insights into D-DT-ligand interactions. Our results demonstrate that the C-terminal region serves a key role in molecular recognition via regulation of the active site opening, protein-ligand interactions, and conformational flexibility of the pocket's environment. While our study is the first comprehensive analysis of molecular recognition for D-DT, the findings reported herein promote the understanding of protein functionality and enable the design of new structure-based drug discovery projects.

Structural characterization of ligand binding and pH-specific enzymatic activity of mouse Acidic Mammalian Chitinase.

Chitin is an abundant biopolymer and pathogen-associated molecular pattern that stimulates a host innate immune response. Mammals express chitin-binding and chitin-degrading proteins to remove chitin from the body. One of these proteins, Acidic Mammalian Chitinase (AMCase), is an enzyme known for its ability to function under acidic conditions in the stomach but is also active in tissues with more neutral pHs, such as the lung. Here, we used a combination of biochemical, structural, and computational modeling approaches to examine how the mouse homolog (mAMCase) can act in both acidic and neutral environments. We measured kinetic properties of mAMCase activity across a broad pH range, quantifying its unusual dual activity optima at pH 2 and 7. We also solved high resolution crystal structures of mAMCase in complex with oligomeric GlcNAcn, the building block of chitin, where we identified extensive conformational ligand heterogeneity. Leveraging these data, we conducted molecular dynamics simulations that suggest how a key catalytic residue could be protonated via distinct mechanisms in each of the two environmental pH ranges. These results integrate structural, biochemical, and computational approaches to deliver a more complete understanding of the catalytic mechanism governing mAMCase activity at different pH. Engineering proteins with tunable pH optima may provide new opportunities to develop improved enzyme variants, including AMCase, for therapeutic purposes in chitin degradation.