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At least 181 records · Page 10

On the Sensitivity to Density-Functional Approximations for CO Binding Energies of Single-Atom Catalysts in Nitrogen-Doped Graphene

Density functional theory (DFT) methods are the working horse in screening new catalytic materials. They are widely used to predict trends in binding energies, which are then used to compare the activity of different materials. Here, the binding strength of CO is an important descriptor to the CO 2 reduction catalytic activity of the single transition metal atoms embedded on nitrogen-doped graphene (TM/NG). In this work, however, we show that CO binding strengths in different TM/NG has very different sensitivity to DFT methods. Specifically, Fe/NG CO binding energy changes dramatically with the percentage of exact exchange in the functional; Co/NG does less so, while Ni/NG nearly has no change. Such varying behaviors is a direct result of different local spin configurations, similar to the performance of DFT methods for metal porphyrin complexes. Therefore, caution should be exercised when using DFT binding energies for quantitative predictions in TM/NG single atom catalysis.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Crystal Structures of Diaryl Hydrazone and Sulfone Stabilizers in Complex with an Amyloidogenic Light Chain Reveal an Alternate Ligand‐Binding Cavity

Abstract Stabilization of amyloidogenic immunoglobulin light chains (LCs) by binding of small molecule “kinetic stabilizers” is under development as a novel treatment for light chain amyloidosis. From a high‐throughput screen, we previously identified 16 full‐length (FL) LC stabilizers from five distinct chemotypes. We then obtained structural biological information on two classes of hits, coumarins and hydantoins, revealing that both chemotypes bind to a pocket at the V L −V L interface of the FL LC dimer. Here, we report crystal structures of three screening hits from two other chemotypes, diaryl hydrazones and sulfones, in complex with an amyloidogenic FL LC. While two of these hits bind to the previously identified pocket, one diaryl hydrazone binds to a different pocket bisected by the C 2 symmetry axis of the dimer. These data further expand on the FL LC stabilizer‐binding surface that could be used in design of more potent FL LC aggregation inhibitors.

Chemistry↗

De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV -2 spike receptor binding domain ( RBD )

The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of “human Abs” based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed “forward folding” with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.

59 BASIC BIOLOGICAL SCIENCES↗

Site heterogeneity and broad surface-binding isotherms in modern catalysis: Building intuition beyond the Sabatier principle

Learning the science of heterogeneous catalysis and electrocatalysis always starts with the simple case of a flat, uniform surface with an ideal adsorbate. It has of course been recognized for a century that real catalysts are more complicated. For the increasingly complex catalysts of the 21st century, this Perspective argues that surface heterogeneity and non-ideal binding isotherms are central features, and their implications need to be incorporated in current thinking. A variety of systems are described herein where catalyst complexity leads to broad, non-Langmuirian surface isotherms for the binding of hydrogen atoms – and this occurs even for ideal, flat Pt(111) surfaces. Modern catalysis employs nanoscale materials whose surfaces have substantial step, edge, corner, impurity, and other defect sites, and they increasingly have both metallic and non-metallic elements M n X m , including metal oxides, chalcogenides, pnictides, carbides, doped carbons, etc. The surfaces of such catalysts are often not crystal facets of the bulk phase underneath, and they typically have a variety of potential active sites. Catalytic surfaces in operando are often non-stoichiometric, amorphous, dynamic, and impure, and often vary from one part of the surface to another. Understanding of the issues that arise at such nanoscale, multi-element catalysts is just beginning to emerge. Yet these catalysts are widely discussed using Brønsted/Bell-Evans-Polanyi (BEP) relations, volcano plots, Tafel slopes, the Butler-Volmer equation, and other linear free energy relations (LFERs), which all depend on the implicit assumption that the active sites are “similar” and that surface adsorption is close to ideal. These assumptions underly the ubiquitous intuition based on the Sabatier Principle, that the fastest catalysis will occur when key intermediates have free energies of adsorption that are not too strong nor too weak. Current catalysis research often aims to minimize the complexity of non-ideal isotherms through experimental and computational design (e.g., the use of single crystal surfaces), and these studies are the foundation of the field. In contrast, this Perspective argues that the heterogeneity of binding sites and binding energies is an inherent strength of these catalysts. Here, this diversity makes many nanoscale catalysts inherently a high-throughput screen wrapped in a tiny package. Only by making the heterogeneity part of the foundation of catalysis models, sorting the types of active sites and dissecting non-ideal binding isotherms, will modern catalysis learn to harness the inherent diversity of real catalysts. Controlling and exploiting diversity rather than avoiding it will help to optimize complex modern catalysts and catalytic conditions.

Mayer, James M.↗

Intramolecular Electrostatic Effects on O 2 , CO 2 , and Acetate Binding to a Cationic Iron Porphyrin

Noncovalent electrostatic interactions are important in many biological and chemical reactions, especially those that involve charged intermediates. There has been a growing interest in using electrostatic ligand designs—placing charges in the second coordination sphere—to improve molecular reactivity, catalysis, and electrocatalysis. For instance, an iron porphyrin bearing four cationic ortho -trimethylanilinium groups, Fe( o -TMA), has been reported to be an exceptional electrocatalyst for both the carbon dioxide reduction reaction (CO 2 RR) and the oxygen reduction reaction (ORR). These reactions involve many different steps, and it is not evident which steps are affected by the four positive charges, or why. By comparing Fe( o -TMA) with the related iron-tetraphenylporphyrin, this work examines how covalently positioned charged groups affect substrate binding and other key pre-equilibria of both the ORR and CO 2 RR, specifically acetate, dioxygen, and carbon dioxide binding. This study is among the first to directly measure the effects of electrostatics on ligand-binding. The results show that adding electrostatic groups to a catalyst design often results in a complex interplay of multiple effects, including changes in pre-equilibria prior to substrate binding, combinations of through-space and inductive contributions, and effects of ionic strength and solution dielectric. The inverse half-order dependence of binding constant on ionic strength is proposed as a clear marker for an electrostatic effect. Overall, the conclusions provide guidance for the increasingly popular electrostatic ligand designs in catalysis and other reactivity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phosphine Ligand Binding and Catalytic Activity of Group 10–14 Heterobimetallic Complexes

We report heterobimetallic complexes have attracted much interest due to their broad range of structures and reactivities as well as unique catalytic abilities. Additionally, these complexes can be utilized as single-source precursors for the synthesis of binary intermetallic compounds. An example is the family of bis(pyridine-2-thiolato)dichloro-germanium and tin complexes of group 10 metals (Pd and Pt). The reactivity of these heterobimetallic complexes is highly tunable through substitution of the group 14 element and the neutral ligand bound to the transition metal. Here, we study the binding energies of three different phosphorous-based ligands, PR 3 (R = Bu, Ph, and OPh) by density functional theory and restricted Hartree–Fock methods. The PR 3 ligand-binding energies follow the trend of PBu 3 > PPh 3 > P(OPh) 3 , in agreement with their sigma-bonding ability. These results are confirmed by ligand exchange experiments monitored with 31 P NMR spectroscopy, in which a weaker binding PR 3 ligand is replaced with a stronger one. Furthermore, we demonstrate that the heterobimetallic complexes are active catalysts in the Negishi coupling reaction, where stronger binding PR 3 ligands inhibit access to an active site at the metal center. Similar strategies could be applied to other complexes to better understand their ligand-binding energetics and predict their reactivity as both precursors and catalysts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Direct Observation of Methylmercury and Auranofin Binding to Selenocysteine in Thioredoxin Reductase

Selenoenzymes, containing a selenocysteine (Sec) residue, fulfill important roles in biology. The mammalian thioredoxin reductase selenoenzymes are key regulators of antioxidant defense and redox signaling and are inhibited by methylmercury species and by the gold-containing drug auranofin. It has been proposed that such inhibition is mediated by metal binding to Sec in the enzyme. However, direct structural observations of these classes of inhibitors binding to selenoenzymes have been few to date. Here we therefore have used extended X-ray absorption fine structure as a direct structural probe to investigate binding to the selenium site in recombinant rat thioredoxin reductase 1 (TrxR1). The results demonstrate for the first time the direct and complete binding of the metal atom of the inhibitors to the selenium atom in TrxR1 for both methylmercury and auranofin, indicating that TrxR1 inhibition indeed can be attributed to such direct metal–selenium binding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Studying the Collective Functional Response of a Receptor in Alchemical Ligand Binding Free Energy Simulations with Accelerated Solvation Layer Dynamics

Ligand binding free energy simulations (LB-FES) that involve sampling of protein functional conformations have been longstanding challenges in research on molecular recognition. Particularly, modeling of the conformational transition pathway and design of the heuristic biasing mechanism are severe bottlenecks for the existing enhanced configurational sampling (ECS) methods. Inspired by the key role of hydration in regulating conformational dynamics of macromolecules, this report proposes a novel ECS approach that facilitates binding-associated structural dynamics by accelerated hydration transitions in combination with the lambda-exchange of free energy perturbation (FEP). Further, two challenging protein-ligand binding processes involving large configurational transitions of the receptor are studied, with hydration transitions at binding sites accelerated by Hamiltonian-simulated annealing of the hydration layer. Without the need for pathway analysis or ad hoc barrier flattening potential, LB-FES were performed with FEP/lambda-exchange molecular dynamics simulation at a minor overhead for annealing of the hydration layer. The LB-FES studies showed that the accelerated rehydration significantly enhances the collective conformational transitions of the receptor, and convergence of binding affinity calculations is obtained at a sweet-spot simulation time scale. Alchemical LB-FES with the proposed ECS strategy is free from the effort of trial and error for the setup and realizes efficient on-the-fly sampling for the collective functional response of the receptor and bound water and therefore presents a practical approach to high-throughput screening in drug discovery.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Amino Acid Sequence Controls Enhanced Electron Transport in Heme-Binding Peptide Monolayers

Metal-binding proteins have the exceptional ability to facilitate long-range electron transport in nature. Despite recent progress, the sequence-structure–function relationships governing electron transport in heme-binding peptides and protein assemblies are not yet fully understood. In this work, the electronic properties of a series of heme-binding peptides inspired by cytochrome bc1 are studied using a combination of molecular electronics experiments, molecular modeling, and simulation. Self-assembled monolayers (SAMs) are prepared using sequence-defined heme-binding peptides capable of forming helical secondary structures. Following monolayer formation, the structural properties and chemical composition of assembled peptides are determined using atomic force microscopy and X-ray photoelectron spectroscopy, and the electronic properties (current density–voltage response) are characterized using a soft contact liquid metal electrode method based on eutectic gallium–indium alloys (EGaIn). Our results show a substantial 1000-fold increase in current density across SAM junctions upon addition of heme compared to identical peptide sequences in the absence of heme, while maintaining a constant junction thickness. These findings show that amino acid composition and sequence directly control enhancements in electron transport in heme-binding peptides. Overall, this study demonstrates the potential of using sequence-defined synthetic peptides inspired by nature as functional bioelectronic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polarity-Tolerant Chloride Binding in Foldamer Capsules by Programmed Solvent-Exclusion

Persistent anion binding in a wide range of solution environments is a key challenge that continues to motivate and demand new strategies in synthetic receptor design. Though strong binding in low-polarity solvents has become routine, our ability to maintain high affinities in high-polarity solvents has not yet reached the standard set by nature. Anions are bound and transported regularly in aqueous environments by proteins that use secondary and tertiary structure to isolate anion binding sites from water. Inspired by this principle of solvent exclusion, we created a sequence-defined foldameric capsule whose global minimum conformation displays a helical folded state and is preorganized for 1:1 anion complexation. The high stability of the folded geometry and its ability to exclude solvent were supported by solid-state and solution phase studies. This capsule then withstood a 4-fold increase in solvent dielectric constant (εr) from dichloromethane (9) to acetonitrile (36) while maintaining a high and solvent-independent affinity of 10 5 M –1 ; ΔG ~ 28 kJ mol –1 . This behavior is unusual. More typical of solvent-dependent behavior, Cl – affinities were seen to plummet in control compounds, such as aryl-triazole macrocycles and pentads, with their solvent-exposed binding cavities susceptible to dielectric screening. Finally, dimethyl sulfoxide denatures the foldamer by putative solvent binding, which then lowers the foldamer’s Cl – affinity to normal levels. Furthermore, the design of this capsule demonstrates a new prototype for the development of potent receptors that can operate in polar solvents and has the potential to help manage hydrophilic anions present in the hydrosphere and biosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

A deubiquitylase with an unusually high-affinity ubiquitin-binding domain from the scrub typhus pathogen Orientia tsutsugamushi

Ubiquitin mediated signaling contributes critically to host cell defenses during pathogen infection. Many pathogens manipulate the ubiquitin system to evade these defenses. Here we characterize a likely effector protein bearing a deubiquitylase (DUB) domain from the obligate intracellular bacterium Orientia tsutsugamushi, the causative agent of scrub typhus. The Ulp1-like DUB prefers ubiquitin substrates over ubiquitin-like proteins and efficiently cleaves polyubiquitin chains of three or more ubiquitins. The co-crystal structure of the DUB (OtDUB) domain with ubiquitin revealed three bound ubiquitins: one engages the S1 site, the second binds an S2 site contributing to chain specificity and the third binds a unique ubiquitin-binding domain (UBD). The UBD modulates OtDUB activity, undergoes a pronounced structural transition upon binding ubiquitin, and binds monoubiquitin with an unprecedented ~5 nM dissociation constant. The characterization and high-resolution structure determination of this enzyme should aid in its development as a drug target to counter Orientia infections.

59 BASIC BIOLOGICAL SCIENCES↗

CryoEM reveals the stochastic nature of individual ATP binding events in a group II chaperonin

Chaperonins are homo- or hetero-oligomeric complexes that use ATP binding and hydrolysis to facilitate protein folding. ATP hydrolysis exhibits both positive and negative cooperativity. The mechanism by which chaperonins coordinate ATP utilization in their multiple subunits remains unclear. Here we use cryoEM to study ATP binding in the homo-oligomeric archaeal chaperonin from Methanococcus maripaludis (MmCpn), consisting of two stacked rings composed of eight identical subunits each. Using a series of image classification steps, we obtained different structural snapshots of individual chaperonins undergoing the nucleotide binding process. We identified nucleotide-bound and free states of individual subunits in each chaperonin, allowing us to determine the ATP occupancy state of each MmCpn particle. We observe distinctive tertiary and quaternary structures reflecting variations in nucleotide occupancy and subunit conformations in each chaperonin complex. Detailed analysis of the nucleotide distribution in each MmCpn complex indicates that individual ATP binding events occur in a statistically random manner for MmCpn, both within and across the rings. Our findings illustrate the power of cryoEM to characterize a biochemical property of multi-subunit ligand binding cooperativity at the individual particle level.

59 BASIC BIOLOGICAL SCIENCES↗

Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer

Broadly-neutralizing antibodies (bNAbs) against HIV-1 Env can protect from infection. We characterize Ab1303 and Ab1573, heterologously-neutralizing CD4-binding site (CD4bs) antibodies, isolated from sequentially-immunized macaques. Ab1303/Ab1573 binding is observed only when Env trimers are not constrained in the closed, prefusion conformation. Fab-Env cryo-EM structures show that both antibodies recognize the CD4bs on Env trimer with an ‘occluded-open’ conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4. The occluded-open Env trimer conformation includes outwardly-rotated gp120 subunits, but unlike CD4-bound Envs, does not exhibit V1V2 displacement, 4-stranded gp120 bridging sheet, or co-receptor binding site exposure. Inter-protomer distances within trimers measured by double electron-electron resonance spectroscopy suggest an equilibrium between occluded-open and closed Env conformations, consistent with Ab1303/Ab1573 binding stabilizing an existing conformation. Studies of Ab1303/Ab1573 demonstrate that CD4bs neutralizing antibodies that bind open Env trimers can be raised by immunization, thereby informing immunogen design and antibody therapeutic efforts.

59 BASIC BIOLOGICAL SCIENCES↗

Photochemical spin-state control of binding configuration for tailoring organic color center emission in carbon nanotubes

Abstract Incorporating fluorescent quantum defects in the sidewalls of semiconducting single-wall carbon nanotubes (SWCNTs) through chemical reaction is an emerging route to predictably modify nanotube electronic structures and develop advanced photonic functionality. Applications such as room-temperature single-photon emission and high-contrast bio-imaging have been advanced through aryl-functionalized SWCNTs, in which the binding configurations of the aryl group define the energies of the emitting states. However, the chemistry of binding with atomic precision at the single-bond level and tunable control over the binding configurations are yet to be achieved. Here, we explore recently reported photosynthetic protocol and find that it can control chemical binding configurations of quantum defects, which are often referred to as organic color centers, through the spin multiplicity of photoexcited intermediates. Specifically, photoexcited aromatics react with SWCNT sidewalls to undergo a singlet-state pathway in the presence of dissolved oxygen, leading to ortho binding configurations of the aryl group on the nanotube. In contrast, the oxygen-free photoreaction activates previously inaccessible para configurations through a triplet-state mechanism. These experimental results are corroborated by first principles simulations. Such spin-selective photochemistry diversifies SWCNT emission tunability by controlling the morphology of the emitting sites.

36 MATERIALS SCIENCE↗

Zika virus RNA structure controls its unique neurotropism by bipartite binding to Musashi-1

Human RNA binding protein Musashi-1 (MSI1) plays a critical role in neural progenitor cells (NPCs) by binding to various host RNA transcripts. The canonical MSI1 binding site (MBS), A/GU (1-3) AG single-strand motif, is present in many RNA virus genomes, but only Zika virus (ZIKV) genome has been demonstrated to bind MSI1. Herein, we identified the AUAG motif and the AGAA tetraloop in the Xrn1-resistant RNA 2 (xrRNA2) as the canonical and non-canonical MBS, respectively, and both are crucial for ZIKV neurotropism. More importantly, the unique AGNN-type tetraloop is evolutionally conserved, and distinguishes ZIKV from other known viruses with putative MBSs. Integrated structural analysis showed that MSI1 binds to the AUAG motif and AGAA tetraloop of ZIKV in a bipartite fashion. Thus, our results not only identified an unusual viral RNA structure responsible for MSI recognition, but also revealed a role for the highly structured xrRNA in controlling viral neurotropism.

60 APPLIED LIFE SCIENCES↗

Crystallographic characterization of a tri-Asp metal-binding site at the three-fold symmetry axis of LarE

Detailed crystallographic characterization of a tri-aspartate metal-binding site previously identified on the three-fold symmetry axis of a hexameric enzyme, LarE from Lactobacillus plantarum, was conducted. By screening an array of monovalent, divalent, and trivalent metal ions, we demonstrated that this metal binding site stoichiometrically binds Ca 2+ , Mn 2+ , Fe 2+ /Fe 3+ , Co 2+ , Ni 2+ , Cu 2+ , Zn 2+ , and Cd 2+ , but not monovalent metal ions, Cr 3+ , Mg 2+ , Y 3+ , Sr 2+ or Ba 2+ . Extensive database searches resulted in only 13 similar metal binding sites in other proteins, indicative of the rareness of tri-aspartate architectures, which allows for engineering such a selective multivalent metal ion binding site into target macromolecules for structural and biophysical characterization.

59 BASIC BIOLOGICAL SCIENCES↗

Mechanism of karyopherin-β2 binding and nuclear import of ALS variants FUS(P525L) and FUS(R495X)

Mutations in the RNA-binding protein FUS cause familial amyotropic lateral sclerosis (ALS). Several mutations that affect the proline-tyrosine nuclear localization signal (PY-NLS) of FUS cause severe juvenile ALS. FUS also undergoes liquid–liquid phase separation (LLPS) to accumulate in stress granules when cells are stressed. In unstressed cells, wild type FUS resides predominantly in the nucleus as it is imported by the importin Karyopherin-β2 (Kapβ2), which binds with high affinity to the C-terminal PY-NLS of FUS. Here, we analyze the interactions between two ALS-related variants FUS(P525L) and FUS(R495X) with importins, especially Kapβ2, since they are still partially localized to the nucleus despite their defective/missing PY-NLSs. The crystal structure of the Kapβ2·FUS(P525L) PY-NLS complex shows the mutant peptide making fewer contacts at the mutation site, explaining decreased affinity for Kapβ2. Biochemical analysis revealed that the truncated FUS(R495X) protein, although missing the PY-NLS, can still bind Kapβ2 and suppresses LLPS. FUS(R495X) uses its C-terminal tandem arginine-glycine-glycine regions, RGG2 and RGG3, to bind the PY-NLS binding site of Kapβ2 for nuclear localization in cells when arginine methylation is inhibited. These findings suggest the importance of the C-terminal RGG regions in nuclear import and LLPS regulation of ALS variants of FUS that carry defective PY-NLSs.

59 BASIC BIOLOGICAL SCIENCES↗

The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase

Optimization of binding affinities for compounds to their target protein is a primary objective in drug discovery. Herein we report on a collaborative study that evaluates a set of compounds binding to ROS1 kinase. We use ESMACS (enhanced sampling of molecular dynamics with approximation of continuum solvent) and TIES (thermodynamic integration with enhanced sampling) protocols to rank the binding free energies. The predicted binding free energies from ESMACS simulations show good correlations with experimental data for subsets of the compounds. Consistent binding free energy differences are generated for TIES and ESMACS. Although an unexplained overestimation exists, we obtain excellent statistical rankings across the set of compounds from the TIES protocol, with a Pearson correlation coefficient of 0.90 between calculated and experimental activities.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗