Stereochemical Constraints Research Articles

ARCIMBOLDO at low resolution: Verification for coiled coils and globular proteins.

Crystallography at low resolution must determine the atomic model from less experimental observations, which is challenging in the absence of a model. In addition, model bias is more severe when independent experimental data are scarce. Our methods solve the phase problem by combining the location of accurate model fragments using Phaser with density modification and interpretation of the resulting maps using SHELXE. From a partial, correct structure, the density modification process and the stereochemical constraints draw the rest of the structure, validating the result. This same principle is now exploited at low resolution. Coiled coils are important, ubiquitous structures but notoriously difficult to phase and to predict. Both correct solutions and incorrect ones are poorly discriminated by the crystallographic figures of merit as long as helices are correctly oriented. We incorporate coiled-coil verification, designed to set up competing, incompatible structural hypotheses to probe both the results and establish the power of the data to discriminate them. Efficiency of coiled-coil phasing and validation in test cases from 3 to 4 Å is demonstrated in ARCIMBOLDO_LITE, placing single helices, and in ARCIMBOLDO_SHREDDER, with fragments derived from AlphaFold models. SHELXE tracing at low resolution has been enhanced, maintaining its local character but extending the environment assessment. For non-helical structures, verification is demonstrated in the fragment location process. Its use is exemplified with the solution of the VSR1 structure at 3.5 Å, depending on LLG optimization and the emergence of new features in the electron density. Relying on verification, we have extended the use of the ARCIMBOLDO software to low resolution.

Aminobenzoic Acid Derivatives Obstruct Induced Fit in the Catalytic Center of the Ribosome.

The Escherichia coli (E. coli) ribosome can incorporate a variety of non-l-α-amino acid monomers into polypeptide chains in vitro but with poor efficiency. Although these monomers span a diverse set of compounds, there exists no high-resolution structural information regarding their positioning within the catalytic center of the ribosome, the peptidyl transferase center (PTC). Thus, details regarding the mechanism of amide bond formation and the structural basis for differences and defects in incorporation efficiency remain unknown. Within a set of three aminobenzoic acid derivatives-3-aminopyridine-4-carboxylic acid (Apy), ortho-aminobenzoic acid (oABZ), and meta-aminobenzoic acid (mABZ)-the ribosome incorporates Apy into polypeptide chains with the highest efficiency, followed by oABZ and then mABZ, a trend that does not track with the nucleophilicity of the reactive amines. Here, we report high-resolution cryo-EM structures of the ribosome with each of these three aminobenzoic acid derivatives charged on tRNA bound in the aminoacyl-tRNA site (A-site). The structures reveal how the aromatic ring of each monomer sterically blocks the positioning of nucleotide U2506, thereby preventing rearrangement of nucleotide U2585 and the resulting induced fit in the PTC required for efficient amide bond formation. They also reveal disruptions to the bound water network that is believed to facilitate formation and breakdown of the tetrahedral intermediate. Together, the cryo-EM structures reported here provide a mechanistic rationale for differences in reactivity of aminobenzoic acid derivatives relative to l-α-amino acids and each other and identify stereochemical constraints on the size and geometry of non-monomers that can be accepted efficiently by wild-type ribosomes.

Fragment-Based Ab Initio Phasing of Peptidic Nanocrystals by MicroED.

Electron diffraction (MicroED/3DED) can render the three-dimensional atomic structures of molecules from previously unamenable samples. The approach has been particularly transformative for peptidic structures, where MicroED has revealed novel structures of naturally occurring peptides, synthetic protein fragments, and peptide-based natural products. Despite its transformative potential, MicroED is beholden to the crystallographic phase problem, which challenges its de novo determination of structures. ARCIMBOLDO, an automated, fragment-based approach to structure determination, eliminates the need for atomic resolution, instead enforcing stereochemical constraints through libraries of small model fragments, and discerning congruent motifs in solution space to ensure validation. This approach expands the reach of MicroED to presently inaccessible peptide structures including fragments of human amyloids, and yeast and mammalian prions. For electron diffraction, fragment-based phasing portends a more general phasing solution with limited model bias for a wider set of chemical structures.

Lamellar Tetragonal Symmetry of Amphiphilic Thermotropic Ionic Liquid Crystals in the Framework of Other Closely Related Highly Ordered Structures

An overview of the chemical compounds forming the rare smectic T phases is presented with references to the historical context. Thermodynamics (transition temperatures, enthalpies) along with the factors (stereochemical constraints, electrostatic interactions, aliphatic chain stacking, intermolecular forces) contributing to the adoption of tetragonal scaffolds are also discussed. Characteristic optical microscopy textures and X-ray diffraction patterns are presented. In parallel, a comparison of the geometrical parameters such as distances between atoms, molecular areas, volumes, and lattice parameters with the closest two-dimensional and three-dimensional organizations, is performed.

Catalyst: Challenges in development of adsorbents for recovery of uranium from seawater

Sheng Dai is currently a section head of separations and polymer chemistry and a UT-Battelle Corporate Fellow at the Chemical Sciences Division of the Oak Ridge National Laboratory and a professor of chemistry at the University of Tennessee, Knoxville. He served as a national technical director for a US Department of Energy project aimed at recovering uranium from seawater (2010–2016). His current research interests include ionic liquids, porous materials, and their applications for separation sciences and energy storage, as well as catalysis by nanomaterials.

The emerging structural complexity of G-quadruplex RNAs.

G-quadruplexes (G4s) are four-stranded nucleic acid structures that arise from the stacking of G-quartets, cyclic arrangements of four guanines engaged in Hoogsteen base-pairing. Until recently, most RNA G4 structures were thought to conform to a sequence pattern in which guanines stacking within the G4 would also be contiguous in sequence (e.g., four successive guanine trinucleotide tracts separated by loop nucleotides). Such a sequence restriction, and the stereochemical constraints inherent to RNA (arising, in particular, from the presence of the 2′-OH), dictate relatively simple RNA G4 structures. Recent crystallographic and solution NMR structure determinations of a number of in vitro selected RNA aptamers have revealed RNA G4 structures of unprecedented complexity. Structures of the Sc1 aptamer that binds an RGG peptide from the Fragile-X mental retardation protein, various fluorescence turn-on aptamers (Corn, Mango, and Spinach), and the spiegelmer that binds the complement protein C5a, in particular, reveal complexity hitherto unsuspected in RNA G4s, including nucleotides in syn conformation, locally inverted strand polarity, and nucleotide quartets that are not all-G. Common to these new structures, the sequences folding into G4s do not conform to the requirement that guanine stacks arise from consecutive (contiguous in sequence) nucleotides. This review highlights how emancipation from this constraint drastically expands the structural possibilities of RNA G-quadruplexes.

Insight into the antioxidant and antiradical properties of colorotane sesquiterpenes extracted from Warburgia ugandensis: theoretical evaluation

The present work is focused on the examination of two biological activities (antioxidant and antiradical properties) of colorotane sesquiterpenes extracted from Warburgia ugandensis. The geometrical optimizations of structures studied were performed in gas phase and water at B3PW91/6-311+G(d,p)// B3PW91/6-31+G(d,p) level under stereochemical constraints. The stability of chemical systems has been elaborated according to thermodynamic and kinetic approaches. Additional descriptors referred to global reactivity descriptors (electronegativity, global hardness, global softness, and electrophilicity index) have also been integrated. Predictions of antioxidant power were exclusively based on the calculation of the enthalpy change of the single-electron transfer (SET) mechanism named IP. Electrodonating (ω−), electroaccepting (ω+) powers, donor Rd and Ra indexes are used as antiradical descriptors. Our results demonstrated that 1,4,4a,5,6,7,8,8a-octahydro-1,4-dihydroxy-4a,5,5,8a-tetramethylnaphthalene-1,2-dicarbaldehyde in the absolute configuration (1R,4R) bearing one hydrogen bond exhibits the highest antioxidant profile. This compound that exhibited the lowest hardness values η (1.517 eV) has shown to be the less stable. Collectively, all colorotane sesquiterpenes have exhibited a good electron donor than sodium (Na). The location of the vitamin C above the colorotane sesquiterpenes in the donor-acceptor map illustrates better antiradical behaviour than the vitamin C in the gas phase. But, these compounds have presented worse antiradical behaviour with respect to gallic acid in the gas phase. In water, the Rd of the compound examined is higher than that of gallic acid (0.178 eV) with exception of 1,4,4a,5,6,7,8,8a-octahydro-1,4-dihydroxy-4a,5,5,8a-tetramethylnaphthalene-1,2-dicarbaldehyde in the absolute configuration (1R,4R) that have shown to be the best antiradical activity due to its highest Ra value (0.904 eV) and lowest Rd value (0.169 eV).

Assistance of DFT calculations on the design and rationalization of active pharmaceutical ingredients synthesis - Michael addition-isomerization steps in Oseltamivir synthesis.

The Michael addition step and the following C5 isomerization in Hayashi’s synthesis of Oseltamivir was studied by means of a DFT mechanistic study. These steps are crucial for the viability of the process where the formation of a single stereoisomer is required. The results indicate that the addition reaction is under thermodynamic and not kinetic control and that the key factor determining the reaction stereoselectivity are the stereochemical constraints imposed by all substituents in the cyclohexane ring. The DFT results indicate that cyclohexylthiol should behave similarly to p-toluylthiol, the one actually employed, and tert-butylthiol should increase the ratio between isomers favoring the desired S configuration of the C5 atom. This work shows that DFT studies can be useful in the selection of a reactant to improve stereoselectivity of a chemical step.

Heterochiral coupling in non-ribosomal peptide macrolactamization

Heterochiral coupling is favoured in abiotic peptide bond formation, whereas biotic peptide bond formation is dominated by homochiral coupling. Here, we report that heterochiral coupling is a rather general paradigm in the head-to-tail macrolactamization of non-ribosomal peptide biosynthesis. The canonical cis-acting offloading cyclases, such as type I thioesterase (TE) and terminal condensation-like domains, catalyse head-to-tail macrolactamization between N- and C-terminal residues with d- and l-configurations, respectively. In contrast, the penicillin-binding protein-type TEs, a recently identified family of trans-acting cyclases, couple heterochiral residues with complementary stereoselectivity to the canonical one. Thus, a suite of cis- and trans-TE non-ribosomal peptide synthetases could overcome the stereochemical constraints present in heterochiral head-to-tail macrolactam formation in bacterial non-ribosomal peptide biosynthesis. Furthermore, we provide the structural rationale for the C-terminal stereoselectivity of non-canonical offloading cyclases. Penicillin-binding protein-type TEs with broad substrate specificity are potentially applicable as biocatalysts and genetic tools for synthetic biology. Penicillin-binding protein-type thiosterases are recently discovered trans-acting enzymes constructing macrocycles during non-ribosomal peptide biosynthesis. Now, their synthetic potential is explored and a protein crystal structure provides insights into their unusual stereochemical requirement.

Ambidextrous α,γ-Hybrid Peptide Foldamers.

Molecular chirality is ubiquitous in nature. The natural biopolymers, proteins and DNA, preferred a right-handed helical bias due to the inherent stereochemistry of the monomer building blocks. Here, we are reporting a rare co-existence of left- and right-handed helical conformations and helix-terminating property at the C-terminus within a single molecule of α,γ-hybrid peptide foldamers composed of achiral Aib (α-aminoisobutyric acid) and 3,3-dimethyl-substituted γ-amino acid (Adb; 4-amino-3,3-dimethylbutanoic acid). At the molecular level, the left- and right-handed helical screw sense of α,γ-hybrid peptides are representing a macroscopic tendril perversion. The pronounced helix-terminating behaviour of C-terminal Adb residues was further explored to design helix-Schellman loop mimetics and to study their conformations in solution and single crystals. The stereochemical constraints of dialkyl substitutions on γ-amino acids showed a marked impact on the folding behaviour of α,γ-hybrid peptides.

Study of correlations between protein peptide plane dynamics and side chain dynamics.

Protein dynamics is pivotal to biological processes. However, experiments are very demanding and difficult to perform, and all-atom molecular dynamics simulations can still not provide all the answers. This motivates us to analyze protein dynamics in terms of different reduced coordinate representations. We then need to resolve how to reconstruct the full all-atom dynamics from its coarse grained approximation. Accordingly we scrutinize all-atom molecular dynamics trajectories in terms of crystallographic Protein Data Bank (PDB) structures, and inquire to what extent is it possible to predict the dynamics of side chain Cβ atoms in terms of the static properties of backbone Cα and O atoms. Here we find that simulated Cβ dynamics at near physiological conditions can be reconstructed with very high precision, using the knowledge of the crystallographic backbone Cα and O positions. The precision we can reach with our PDB-based Statistical Method reconstruction exceeds that of popular all-atom reconstruction methods such as Remo and Pulchra, and is fully comparable with the precision of the highly elaborate Scwrl4 all-atom reconstruction method that we have enhanced with the knowledge of the backbone Cα and O atom positions. We then conclude that in a dynamical protein that moves around at physiological conditions, the relative positions of its Cβ atoms with respect to the backbone Cα and O atoms, deviate very little from their relative positions in static crystallographic PDB structures. This proposes that the dynamics of a biologically active protein could remain subject to very similar, stringent stereochemical constraints that dictate the structure of a folded crystallographic protein. Thus, our results provide a strong impetus to the development of coarse grained techniques that are based on reduced coordinate representations.

Design, Synthesis, and Development of Stereochemical Constraints into -Amino Acid Residues: Gabapentin Structural Data Role in Nerve Pain Medication

Over the last 15 years, a growing body of work in the literature has focused on the folded structures formed by peptide sequences containing backbone homologated residues. The work of Seebach in Zurich, and Gellman in Madison, established that oligomers of β amino acid residues can form novel helical structures in solution and in the solid state. These peptides are highly useful for nnaovaccine development. Two distinct types of hydrogen bonded helical structures were demonstrated in these studies for oligomeric β peptides. The C12 helix which is an analog of the canonical 310 helical structure in “all α” sequences, has the same hydrogen bond directionality (C=Oi…..H-Ni+3). The second helical form, the C14 helix, has the opposite directionality (C=Oi…..H-Ni+4), which is unprecedented in α peptide sequences.

Collective repacking reveals that the structures of protein cores are uniquely specified by steric repulsive interactions

Protein core repacking is a standard test of protein modeling software. A recent study of six different modeling software packages showed that they are more successful at predicting side chain conformations of core compared to surface residues. All the modeling software tested have multicomponent energy functions, typically including contributions from solvation, electrostatics, hydrogen bonding and Lennard–Jones interactions in addition to statistical terms based on observed protein structures. We investigated to what extent a simplified energy function that includes only stereochemical constraints and repulsive hard-sphere interactions can correctly repack protein cores. For single residue and collective repacking, the hard-sphere model accurately recapitulates the observed side chain conformations for Ile, Leu, Phe, Thr, Trp, Tyr and Val. This result shows that there are no alternative, sterically allowed side chain conformations of core residues. Analysis of the same set of protein cores using the Rosetta software suite revealed that the hard-sphere model and Rosetta perform equally well on Ile, Leu, Phe, Thr and Val; the hard-sphere model performs better on Trp and Tyr and Rosetta performs better on Ser. We conclude that the high prediction accuracy in protein cores obtained by protein modeling software and our simplified hard-sphere approach reflects the high density of protein cores and dominance of steric repulsion.

Natural [4 + 2]-Cyclases.

[4 + 2]-Cycloadditions are increasingly being recognized in the biosynthetic pathways of many structurally complex natural products. A relatively small collection of enzymes from these pathways have been demonstrated to increase rates of cyclization and impose stereochemical constraints on the reactions. While mechanistic investigation of these enzymes is just beginning, recent studies have provided new insights with implications for understanding their biosynthetic roles, mechanisms of catalysis, and evolutionary origin.

Chiral Cyclobutane β-Amino Acid-Based Amphiphiles: Influence of Cis/Trans Stereochemistry on Condensed Phase and Monolayer Structure.

New diastereomeric nonionic amphiphiles, cis- and trans-1, based on an optically pure cyclobutane β-amino ester moiety have been investigated to gain insight into the influence exerted by cis/trans stereochemistry and stereochemical constraints on the physicochemical behavior, molecular organization, and morphology of their Langmuir monolayers and dry solid states. All these features are relevant to the rational design of functional materials. trans-1 showed a higher thermal stability than cis-1. For the latter, a higher fluidity of its monolayers was observed when compared with the films formed by trans-1 whose BAM images revealed the formation of condensed phase domains with a dendritic shape, which are chiral, and all of them feature the same chiral sign. Although the formation of LC phase domains was not observed by BAM for cis-1, compact dendritic crystals floating on a fluid subphase were observed beyond the collapse, which are attributable to multilayered 3D structures. These differences can be explained by the formation of hydrogen bonds between the amide groups of consecutive molecules allowing the formation of extended chains for trans-1 giving ordered arrangements. However, for cis-1, this alignment coexists with another one that allows the simultaneous formation of two hydrogen bonds between the amide and the ester groups of adjacent molecules. In addition, the propensity to form intramolecular hydrogen bonds must be considered to justify the formation of different patterns of hydrogen bonding and, consequently, the formation of less ordered phases. Those characteristics are congruent also with the results obtained from SAXS-WAXS experiments which suggest a more bent configuration for cis-1 than for trans-1.

Molecular Spin Crossover in Slow Motion: Light-Induced Spin-State Transitions in Trigonal Prismatic Iron(II) Complexes.

A straightforward access is provided to iron(II) complexes showing exceedingly slow spin-state interconversion by utilizing trigonal-prismatic directing ligands (L(n)) of the extended-tripod type. A detailed analysis of the interrelations between complex structure (X-ray diffraction, density functional theory) and electronic character (SQUID magnetometry, Mössbauer spectroscopy, UV/vis spectroscopy) of the iron(II) center in mononuclear complexes [FeL(n)] reveals spin crossover to occur along a coupled breathing/torsion reaction coordinate, shuttling the complex between the octahedral low-spin state and the trigonal-prismatic high-spin state along Bailar's trigonal twist pathway. We associate both the long spin-state lifetimes in the millisecond domain close to room temperature and the substantial barriers against thermal scrambling (Ea ≈ 33 kJ mol(-1), from Arrhenius analysis) with stereochemical constraints. In particular, the topology of the κ(6)N ligands controls the temporary and structural dynamics during spin crossover.

Chiral Cyclobutane β-Amino Acid-Based Amphiphiles: Influence of Cis/Trans Stereochemistry on Solution Self-Aggregation and Recognition.

Novel diastereomeric anionic amphiphiles based on the rigid cyclobutane β-amino acid scaffold have been synthesized and deeply investigated with the aim of generating new functional supramolecular architectures on the basis of the rational design of original amphiphilic molecules and the control of their self-assembly. The main interest has been focused on the effect that cis/trans stereochemistry exerts on their molecular organization and recognition. In diluted solutions, the relative stereochemistry mainly influences the headgroup solvation and anionic-charge stabilization, i.e., better stabilized in the cis diastereoisomer due to intramolecular hydrogen-bonding and/or charge-dipole interactions. This provokes differences in their physicochemical behavior (pKa, cmc, conductivity) as well as in the structural parameters of the spherical micelles formed. Although both diastereoisomers form fibers that evolve with time from the spherical micelles, they display markedly different morphology and kinetics of formation. In the lyotropic liquid crystal domain, the greatest differences are observed at the highest concentrations and can be ascribed to different hydrogen-bonding and molecular packing imposed by the stereochemical constraints. Remarkably, the spherical micelles of the two anionic surfactants show dramatically diverse enantioselection ability for bilirubin enantiomers. In addition, both the surfactants form heteroaggregates with bilirubin at submicellar concentrations but with a different expression of supramolecular chirality. This points out that the unlike relative configuration of the two surfactants influences their chiral recognition ability as well as the fashion in which chirality is expressed at the supramolecular level by controlling the molecular organization in both micellar aggregates and surfactant/bilirubin heteroaggregates. All these differential features can be appropriate and useful for the design and development of new soft materials with predictable and tunable properties and reveal the cyclobutane motif as a valuable scaffold for the preparation of new amphiphiles.

Equilibrium transitions between side-chain conformations in leucine and isoleucine.

Despite recent improvements in computational methods for protein design, we still lack a quantitative, predictive understanding of the intrinsic probabilities for amino acids to adopt particular side-chain conformations. Surprisingly, this question has remained unsettled for many years, in part because of inconsistent results from different experimental approaches. To explicitly determine the relative populations of different side-chain dihedral angles, we performed all-atom hard-sphere Langevin Dynamics simulations of leucine (Leu) and isoleucine (Ile) dipeptide mimetics with stereo-chemical constraints and repulsive-only steric interactions between non-bonded atoms. We determine the relative populations of the different χ(1) and χ(2) dihedral angle combinations as a function of the backbone dihedral angles ϕ and ψ. We also propose, and test, a mechanism for inter-conversion between the different side-chain conformations. Specifically, we discover that some of the transitions between side-chain dihedral angle combinations are very frequent, whereas others are orders of magnitude less frequent, because they require rare coordinated motions to avoid steric clashes. For example, to transition between different values of χ(2), the Leu side-chain bond angles κ(1) and κ(2) must increase, whereas to transition in χ(1), the Ile bond angles λ(1) and λ(2) must increase. These results emphasize the importance of computational approaches in stimulating further experimental studies of the conformations of side-chains in proteins. Moreover, our studies emphasize the power of simple steric models to inform our understanding of protein structure, dynamics, and design.

Stereochemical control of nucleosome targeting by platinum-intercalator antitumor agents.

Platinum-based anticancer drugs act therapeutically by forming DNA adducts, but suffer from severe toxicity and resistance problems, which have not been overcome in spite of decades of research. And yet defined chromatin targets have generally not been considered in the drug development process. Here we designed novel platinum-intercalator species to target a highly deformed DNA site near the nucleosome center. Between two seemingly similar structural isomers, we find a striking difference in DNA site selectivity in vitro, which comes about from stereochemical constraints that limit the reactivity of the trans isomer to special DNA sequence elements while still allowing the cis isomer to efficiently form adducts at internal sites in the nucleosome core. This gives the potential for controlling nucleosome site targeting in vivo, which would engender sensitivity to epigenetic distinctions and in particular cell type/status-dependent differences in nucleosome positioning. Moreover, while both compounds yield very similar DNA-adduct structures and display antitumor cell activity rivalling that of cisplatin, the cis isomer, relative to the trans, has a much more rapid cytotoxic effect and distinct impact on cell function. The novel stereochemical principles for controlling DNA site selectivity we discovered could aid in the design of improved site discriminating agents.

A density functional theory and spectroscopic study of intramolecular quenching of metal-to-ligand charge-transfer excited states in some mono-bipyridine ruthenium(II) complexes

The complexes [Ru(NCCH3)4bpy]2+ and [Ru([14]aneS4)bpy]2+ ([14]aneS4 = 1,4,8,11-tetrathiacyclotetradecane, bpy = 2,2′-bipyridine) have similar absorption and emission spectra but the 77 K metal-to-ligand charge-transfer (MLCT) excited state emission lifetime of the latter is less than 0.3% that of the former. Density functional theory modeling of the lowest energy triplet excited states indicates that triplet metal centered (3MC) excited states are about 3500 cm−1 lower in energy than their 3MLCT excited states in both complexes. The differences in excited state lifetimes arise from a much larger coordination sphere distortion for [Ru(NCCH3)4bpy]2+ and the associated larger reorganizational barrier for intramolecular electron transfer. The smaller ruthenium ligand distortions of the [Ru([14]aneS4)bpy]2+ complex are apparently a consequence of stereochemical constraints imposed by the macrocyclic [14]aneS4 ligand, and the 3MC excited state calculated for the unconstrained [Ru(S(CH3)2)4bpy]2+ complex (S(CH3)2 = dimethyl sulfide) is distorted in a manner similar to that of [Ru(NCCH3)4bpy]2+. Despite the lower energy calculated for its 3MC than 3MLCT excited state, [Ru(NCCH3)4bpy]2+ emits strongly in 77 K glasses with an emission quantum yield of 0.47. The emission is biphasic with about a 1 μs lifetime for its dominant (86%) emission component. The 405 nm excitation used in these studies results in a significant amount of photodecomposition in the 77 K glasses. This is a temperature-dependent biphotonic process that most likely involves the bipyridine-radical anionic moiety of the 3MLCT excited state. A smaller than expected value found for the radiative rate constant is consistent with a lower energy 3MC than 3MLCT state.