Correct Nucleotide Selection Is Confined at the Binding Site of Polymerase Enzymes.

DNA polymerases (Pols) add incoming nucleotides (deoxyribonucleoside triphosphate (dNTPs)) to growing DNA strands, a crucial step for DNA synthesis. The insertion of correct (vs incorrect) nucleotides relates to Pols' fidelity, which defines Pols' ability to faithfully replicate DNA strands in a template-dependent manner. We and others have demonstrated that reactant alignment and correct base pairing at the Pols catalytic site are crucial structural features to fidelity. Here, we first used equilibrium molecular simulations to demonstrate that the local dynamics at the protein-DNA interface in the proximity of the catalytic site is different when correct vs incorrect dNTPs are bound to polymerase ß (Pol ß). Formation and dynamic stability of specific interatomic interactions around the incoming nucleotide influence the overall binding site architecture. This explains why certain Pols' mutants can affect the local catalytic environment and influence the selection of correct vs incorrect nucleotides. In particular, this is here demonstrated by analyzing the interaction network formed by the residue R283, whose mutant R283A has an experimentally measured lower capacity of differentiating correct (G:dCTP) vs incorrect (G:dATP) base pairing in Pol ß. We also used alchemical free-energy calculations to quantify the G:dCTP →G:dATP transformation in Pol ß wild-type and mutant R283A. These results correlate well with the experimental trend, thus corroborating our mechanistic insights. Sequence and structural comparisons with other Pols from the same family suggest that these findings may also be valid in similar enzymes.

Targeting the conserved active site of splicing machines with specific and selective small molecule modulators.

The self-splicing group II introns are bacterial and organellar ancestors of the nuclear spliceosome and retro-transposable elements of pharmacological and biotechnological importance. Integrating enzymatic, crystallographic, and simulation studies, we demonstrate how these introns recognize small molecules through their conserved active site. These RNA-binding small molecules selectively inhibit the two steps of splicing by adopting distinctive poses at different stages of catalysis, and by preventing crucial active site conformational changes that are essential for splicing progression. Our data exemplify the enormous power of RNA binders to mechanistically probe vital cellular pathways. Most importantly, by proving that the evolutionarily-conserved RNA core of splicing machines can recognize small molecules specifically, our work provides a solid basis for the rational design of splicing modulators not only against bacterial and organellar introns, but also against the human spliceosome, which is a validated drug target for the treatment of congenital diseases and cancers.

Cation Chloride Cotransporter NKCC1 Operates through a Rocking-Bundle Mechanism.

The sodium, potassium, and chloride cotransporter 1 (NKCC1) plays a key role in tightly regulating ion shuttling across cell membranes. Lately, its aberrant expression and function have been linked to numerous neurological disorders and cancers, making it a novel and highly promising pharmacological target for therapeutic interventions. A better understanding of how NKCC1 dynamically operates would therefore have broad implications for ongoing efforts toward its exploitation as a therapeutic target through its modulation. Based on recent structural data on NKCC1, we reveal conformational motions that are key to its function. Using extensive deep-learning-guided atomistic simulations of NKCC1 models embedded into the membrane, we captured complex dynamical transitions between alternate open conformations of the inner and outer vestibules of the cotransporter and demonstrated that NKCC1 has water-permeable states. We found that these previously undefined conformational transitions occur via a rocking-bundle mechanism characterized by the cooperative angular motion of transmembrane helices (TM) 4 and 9, with the contribution of the extracellular tip of TM 10. We found these motions to be critical in modulating ion transportation and in regulating NKCC1's water transporting capabilities. Specifically, we identified interhelical dynamical contacts between TM 10 and TM 6, which we functionally validated through mutagenesis experiments of 4 new targeted NKCC1 mutants. We conclude showing that those 4 residues are highly conserved in most Na+-dependent cation chloride cotransporters (CCCs), which highlights their critical mechanistic implications, opening the way to new strategies for NKCC1's function modulation and thus to potential drug action on selected CCCs.

On the Role of Molecular Conformation of the 8-Oxoguanine Lesion in Damaged DNA Processing by Polymerases.

A common and insidious DNA damage is 8-oxoguanine (8OG), bypassed with low catalytic efficiency and high error frequency by polymerases (Pols) during DNA replication. This is a fundamental process with far-reaching implications in cell function and diseases. However, the molecular determinants of how 8OG exactly affects the catalytic efficiency of Pols remain largely unclear. By examining ternary deoxycytidine triphosphate/DNA/Pol complexes containing the 8OG damage, we found that 8OG consistently adopts different conformations when bound to Pols, compared to when in isolated DNA. Equilibrium molecular dynamics and metadynamics free energy calculations quantified that 8OG is in the lowest energy conformation in isolated DNA. In contrast, 8OG adopts high-energy conformations often characterized by intramolecular steric repulsion when bound to Pols. We show that the 8OG conformation can be regulated by mutating Pol residues interacting with the 8OG phosphate group. These findings propose the 8OG conformation as a factor in Pol-mediated processing of damaged DNA.

Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106.

The antiviral pseudo-base T705 and its de-fluoro analog T1106 mimic adenine or guanine and can be competitively incorporated into nascent RNA by viral RNA-dependent RNA polymerases. Although dispersed, single pseudo-base incorporation is mutagenic, consecutive incorporation causes polymerase stalling and chain termination. Using a template encoding single and then consecutive T1106 incorporation four nucleotides later, we obtained a cryogenic electron microscopy structure of stalled influenza A/H7N9 polymerase. This shows that the entire product-template duplex backtracks by 5 nt, bringing the singly incorporated T1106 to the +1 position, where it forms an unexpected T1106:U wobble base pair. Similar structures show that influenza B polymerase also backtracks after consecutive T1106 incorporation, regardless of whether prior single incorporation has occurred. These results give insight into the unusual mechanism of chain termination by pyrazinecarboxamide base analogs. Consecutive incorporation destabilizes the proximal end of the product-template duplex, promoting irreversible backtracking to a more energetically favorable overall configuration.

Alchemical Free Energy Calculations to Investigate Protein-Protein Interactions: the Case of the CDC42/PAK1 Complex.

Here, we show that alchemical free energy calculations can quantitatively compute the effect of mutations at the protein-protein interface. As a test case, we have used the protein complex formed by the small Rho-GTPase CDC42 and its downstream effector PAK1, a serine/threonine kinase. Notably, the CDC42/PAK1 complex offers a wealth of structural, mutagenesis, and binding affinity data because of its central role in cellular signaling and cancer progression. In this context, we have considered 16 mutations in the CDC42/PAK1 complex and obtained excellent agreement between computed and experimental data on binding affinity. Importantly, we also show that a careful analysis of the side-chain conformations in the mutated amino acids can considerably improve the computed estimates, solving issues related to sampling limitations. Overall, this study demonstrates that alchemical free energy calculations can conveniently be integrated into the design of experimental mutagenesis studies.

Structure of the human cation-chloride cotransport KCC1 in an outward-open state.

Cation-chloride cotransporters (CCCs) catalyze electroneutral symport of Cl- with Na+ and/or K+ across membranes. CCCs are fundamental in cell volume homeostasis, transepithelia ion movement, maintenance of intracellular Cl- concentration, and neuronal excitability. Here, we present a cryoelectron microscopy structure of human K+-Cl- cotransporter (KCC)1 bound with the VU0463271 inhibitor in an outward-open state. In contrast to many other amino acid-polyamine-organocation transporter cousins, our first outward-open CCC structure reveals that opening the KCC1 extracellular ion permeation path does not involve hinge-bending motions of the transmembrane (TM) 1 and TM6 half-helices. Instead, rocking of TM3 and TM8, together with displacements of TM4, TM9, and a conserved intracellular loop 1 helix, underlie alternate opening and closing of extracellular and cytoplasmic vestibules. We show that KCC1 intriguingly exists in one of two distinct dimeric states via different intersubunit interfaces. Our studies provide a blueprint for understanding the mechanisms of CCCs and their inhibition by small molecule compounds.

Structural basis for inhibition of the Cation-chloride cotransporter NKCC1 by the diuretic drug bumetanide.

Cation-chloride cotransporters (CCCs) NKCC1 and NKCC2 catalyze electroneutral symport of 1 Na+, 1 K+, and 2 Cl- across cell membranes. NKCC1 mediates trans-epithelial Cl- secretion and regulates excitability of some neurons and NKCC2 is critical to renal salt reabsorption. Both transporters are inhibited by the so-called loop diuretics including bumetanide, and these drugs are a mainstay for treating edema and hypertension. Here, our single-particle electron cryo-microscopy structures supported by functional studies reveal an outward-facing conformation of NKCC1, showing bumetanide wedged into a pocket in the extracellular ion translocation pathway. Based on these and the previously published inward-facing structures, we define the translocation pathway and the conformational changes necessary for ion translocation. We also identify an NKCC1 dimer with separated transmembrane domains and extensive transmembrane and C-terminal domain interactions. We further define an N-terminal phosphoregulatory domain that interacts with the C-terminal domain, suggesting a mechanism whereby (de)phosphorylation regulates NKCC1 by tuning the strength of this domain association.

Influence of Steric Effect on the Pseudo-Multicomponent Synthesis of N-Aroylmethyl-4-Arylimidazoles.

A pseudo-three-component synthesis of N-aroylmethylimidazoles 3 with three new C-N bonds formed regioselectively under microwave conditions was developed. Products were obtained by reacting two equivalents of aroylmethyl bromide (ArCOCH2Br, 1) with the appropriate amidine salt (RCN2H3.HX, 2) and with K2CO3 as a base in acetonitrile. The bicomponent reaction also occurred, giving the expected 4(5)-aryl-1H-imidazoles 4. Notably, the ratio of products 3 and 4 is governed by steric factors of the amidine 2 (i.e., R = H, CH3, Ph). Therefore, a computational study was carried out to understand the reaction course regarding product ratio (3/4), regioselectivity, and the steric effects of the amidine substituent group.

Modeling Kinetics and Thermodynamics of Guest Encapsulation into the [M4L6]12- Supramolecular Organometallic Cage.

The encapsulation of molecular guests into supramolecular hosts is a complex molecular recognition process in which the guest displaces the solvent from the host cavity, while the host deforms to let the guest in. An atomistic description of the association would provide valuable insights on the physicochemical properties that guide it. This understanding may be used to design novel host assemblies with improved properties (i.e., affinities) toward a given class of guests. Molecular simulations may be conveniently used to model the association processes. It is thus of interest to establish efficient protocols to trace the encapsulation process and to predict the associated magnitudes ΔGbind and ΔGbind⧧. Here, we report the calculation of the Gibbs energy barrier and Gibbs binding energy by means of explicit solvent molecular simulations for the [Ga4L6]12- metallocage encapsulating a series of cationic molecules. The ΔGbind⧧ for encapsulation was estimated by means of umbrella sampling simulations. The steps involved were identified, including ion-pair formation and naphthalene rotation (from L ligands of the metallocage) during the guest's entrance. The ΔGbind values were computed using the attach-pull-release method. The results reveal the sensitivity of the estimates on the force field parameters, in particular on atomic charges, showing that higher accuracy is obtained when charges are derived from implicit solvent quantum chemical calculations. Correlation analysis identified some indicators for the binding affinity trends. All computed magnitudes are in very good agreement with experimental observations. This work provides, on one side, a benchmarked way to computationally model a highly charged metallocage encapsulation process. This includes a nonstandard parameterization and charge derivation procedure. On the other hand, it gives specific mechanistic information on the binding processes of [Ga4L6]12- at the molecular level where key motions are depicted. Taken together, the study provides an interesting option for the future design of metal-organic cages.

Visualizing group II intron dynamics between the first and second steps of splicing.

Group II introns are ubiquitous self-splicing ribozymes and retrotransposable elements evolutionarily and chemically related to the eukaryotic spliceosome, with potential applications as gene-editing tools. Recent biochemical and structural data have captured the intron in multiple conformations at different stages of catalysis. Here, we employ enzymatic assays, X-ray crystallography, and molecular simulations to resolve the spatiotemporal location and function of conformational changes occurring between the first and the second step of splicing. We show that the first residue of the highly-conserved catalytic triad is protonated upon 5'-splice-site scission, promoting a reversible structural rearrangement of the active site (toggling). Protonation and active site dynamics induced by the first step of splicing facilitate the progression to the second step. Our insights into the mechanism of group II intron splicing parallels functional data on the spliceosome, thus reinforcing the notion that these evolutionarily-related molecular machines share the same enzymatic strategy.

A resorcinarene-based tetrabenzoimidazolylidene complex of rhodium.

A tetrabenzoimidazolium-resorcinarene cavitand was used for the preparation of a tetra-benzoimidazolylidene of rhodium, which is unprecedented in the field of poly-NHC metal complexes. Both the experimental and computational analyses of the molecule reveal a distorted vase conformation as the most stable one, although several non-interconverting conformational isomers due to the restricted rotation about the Rh-C(carbene) bond coexist in the product. There is a fluxional behaviour involving the vase-kite interconversion. The main interactions between the arms of the cavitand are mostly concentrated on the terminal organometallic fragments attached to NHC, along with those between -CH3 and a N-heterocyclic carbene ring from benzoimidazoles.

Reversible carbon-boron bond formation at platinum centers through σ-BH complexes.

A reversible carbon-boron bond formation has been observed in the reaction of the coordinatively unsaturated, cyclometalated, Pt(ii) complex [Pt(I t BuiPr')(I t BuiPr)][BArF], 1, with tricoordinated boranes HBR2. X-ray diffraction studies provided structural snapshots of the sequence of reactions involved in the process. At low temperature, we observed the initial formation of the unprecedented σ-BH complexes [Pt(HBR2)(I t BuiPr')(I t BuiPr)][BArF], one of which has been isolated. From -15 to +10 °C, the σ-BH species undergo a carbon-boron coupling process leading to the platinum hydride derivative [Pt(H)(I t BuiPr-BR2)(I t BuiPr)][BArF], 4. Surprisingly, these compounds are thermally unstable undergoing carbon-boron bond cleavage at room temperature that results in the 14-electron Pt(ii) boryl species [Pt(BR2)(I t BuiPr)2][BArF], 2. This unusual reaction process has been corroborated by computational methods, which indicate that the carbon-boron coupling products 4 are formed under kinetic control whereas the platinum boryl species 2, arising from competitive C-H bond coupling, are thermodynamically more stable. These findings provide valuable information about the factors governing productive carbon-boron coupling reactions at transition metal centers.

Bonding rearrangements in organometallic reactions: from orbitals to curly arrows.

Reaction mechanisms include a description of both the nuclear and electronic rearrangements along the energetically most favourable pathway. Extracting the nuclear rearrangements from the outcome of quantum chemical calculations is straightforward, while it is more intricate for the electronic rearrangements. This is particularly true when changes in the bonding pattern are of interest, just as in the arrow-pushing formalism used in chemical schemes. Here, we report on our use of a simple and highly visual procedure to recover the bonding rearrangements along a reaction pathway from DFT calculations and to draw curly arrows. We show that the procedure allows us discern among mechanistic proposals in the context of organometallic reactions featuring the forming and breaking of bonds.

σ-Silane Platinum(II) Complexes as Intermediates in C-Si Bond-Coupling Processes.

Platinum complexes [Pt(NHC')(NHC)][BArF ] (in which NHC' denotes a cyclometalated N-heterocyclic carbene ligand, NHC) react with primary silanes RSiH3 to afford the cyclometalated platinum(II) silyl complexes [Pt(NHC-SiHR')(NHC)][BArF ] through a process that involves the formation of C-Si and Pt-Si bonds with concomitant extrusion of H2 . Low-temperature NMR studies indicate that the process proceeds through initial formation of the σ-SiH complexes [Pt(NHC')(NHC)(HSiH2 R)][BArF ], which are stable at temperatures below -10 °C. At higher temperatures, activation of one Si-H bond followed by a C-Si coupling reaction generates an agostic SiH platinum hydride derivative [Pt(H)(NHC'-SiH2 R)(NHC)][BArF ], which undergoes a second Si-H bond activation to afford the final products. Computational modeling of the reaction mechanism indicates that the stereochemistry of the silyl/hydride ligands after the first Si-H bond cleavage dictates the nature of the products, favoring the formation of a C-Si bond over a C-H bond, in contrast to previous results obtained for tertiary silanes. Furthermore, the process involves a trans-to-cis isomerization of the NHC ligand before the second Si-H bond cleavage.

Selective Synthesis of Tetrasubstituted Olefins by Copper-Mediated Acetoxythiolation of Internal Alkynes: Scope and Mechanistic Studies.

The Cu-mediated synthesis of tetrasubstituted olefins by the addition of an acetate group and a thiolate to an unactivated internal alkyne is described. The reaction is fully stereoselective, because only the E alkene is obtained. If the alkyne is asymmetric, the reaction also shows a very high degree of regioselectivity. The mechanism of the reaction is elucidated by DFT methods, which show that it takes place through Cu-stabilized radical species. Calculations highlight the crucial role of the dimeric copper(II) diacetate in the process, as it generates the active species in which the sulfur center has an incipient thiyl radical character and accepting, through a series of changes in the oxidation states of the two copper centers, the two electrons released in the addition of two nucleophiles to the alkyne.

Isolation of a Cationic Platinum(II) σ-Silane Complex.

The platinum complex [Pt(It Bui Pr')(It Bui Pr)][BArF ] interacts with tertiary silanes to form stable (<0 °C) mononuclear PtII σ-SiH complexes [Pt(It Bui Pr')(It Bui Pr)(η1 -HSiR3 )][BArF ]. These compounds have been fully characterized, including X-ray diffraction methods, as the first examples for platinum. DFT calculations (including electronic topological analysis) support the interpretation of the coordination as an unusual η1 -SiH. However, the energies required for achieving a η2 -SiH mode are rather low, and is consistent with the propensity of these derivatives to undergo Si-H cleavage leading to the more stable silyl species [Pt(SiR3 )(It Bui Pr)2 ][BArF ] at room temperature.

Calculation of Reaction Free Energies in Solution: A Comparison of Current Approaches.

The result of the application of different approaches based on the ideal gas/rigid rotor/harmonic oscillator (IGRRHO) model, commonly used in popular software packages, for the calculation of free energies in solution is compared with that of ab initio molecular dynamics for a process involving ligand exchange in palladium complexes. The IGRRHO-based approaches considered differ in most cases in the extent to which the rotational and translational contributions are included in the correction. Our study supports the use the free energy values directly obtained from dispersion-corrected DFT functionals without any correction or with minor corrections at most.

Directed Evolution of an Artificial Imine Reductase.

Artificial metalloenzymes, resulting from incorporation of a metal cofactor within a host protein, have received increasing attention in the last decade. The directed evolution is presented of an artificial transfer hydrogenase (ATHase) based on the biotin-streptavidin technology using a straightforward procedure allowing screening in cell-free extracts. Two streptavidin isoforms were yielded with improved catalytic activity and selectivity for the reduction of cyclic imines. The evolved ATHases were stable under biphasic catalytic conditions. The X-ray structure analysis reveals that introducing bulky residues within the active site results in flexibility changes of the cofactor, thus increasing exposure of the metal to the protein surface and leading to a reversal of enantioselectivity. This hypothesis was confirmed by a multiscale approach based mostly on molecular dynamics and protein-ligand dockings.