A computational study to assess the pathogenicity of single or combinations of missense variants on respiratory complex I.

Variants found in the respiratory complex I (CI) subunit genes encoded by mitochondrial DNA can cause severe genetic diseases. However, it is difficult to establish a priori whether a single or a combination of CI variants may impact oxidative phosphorylation. Here we propose a computational approach based on coarse-grained molecular dynamics simulations aimed at investigating new CI variants. One of the primary CI variants associated with the Leber hereditary optic neuropathy (m.14484T>C/MT-ND6) was used as a test case and was investigated alone or in combination with two additional rare CI variants whose role remains uncertain. We found that the primary variant positioned in the E-channel region, which is fundamental for CI function, stiffens the enzyme dynamics. Moreover, a new mechanism for the transition between π- and α-conformation in the helix carrying the primary variant is proposed. This may have implications for the E-channel opening/closing mechanism. Finally, our findings show that one of the rare variants, located next to the primary one, further worsens the stiffening, while the other rare variant does not affect CI function. This approach may be extended to other variants candidate to exert a pathogenic impact on CI dynamics, or to investigate the interaction of multiple variants.

One touch is all it takes: the supramolecular interaction between ubiquitin and lanthanide complexes revisited by paramagnetic NMR and molecular dynamics.

The supramolecular interaction between lanthanide complexes and proteins is at the heart of numerous chemical and biological studies. Some of these complexes have demonstrated remarkable interaction properties with proteins or peptides in solution and in the crystalline state. Here we have used the paramagnetism of lanthanide ions to characterize the affinity of two lanthanide complexes for ubiquitin. As the interaction process is dynamic, the acquired NMR data only reflect the time average of the different steps. We have used molecular dynamics (MD) simulations to get a deeper insight into the detailed interaction scenario at the microsecond scale. This NMR/MD approach enabled us to establish that the tris-dipicolinate complex interacts specifically with arginines and lysines, while the crystallophore explores the protein surface through weak interactions with carboxylates. These observations shed new light on the dynamic interaction properties of these complexes, which will ultimately enable us to propose a crystallization mechanism.

Situating the phosphonated calixarene-cytochrome C association by molecular dynamics simulations.

Protein-calixarenes binding plays an increasingly central role in many applications, spanning from molecular recognition to drug delivery strategies and protein inhibition. These ligands obey a specific bio-supramolecular chemistry, which can be revealed by computational approaches, such as molecular dynamics simulations. In this paper, we rely on all-atom, explicit-solvent molecular dynamics simulations to capture the electrostatically driven association of a phosphonated calix-[4]-arene with cytochome-C, which critically relies on surface-exposed paired lysines. Beyond two binding sites identified in direct agreement with the x-ray structure, the association has a larger structural impact on the protein dynamics. Then, our simulations allow a direct comparison to analogous calixarenes, namely, sulfonato, similarly reported as "molecular glue." Our work can contribute to a robust in silico predictive tool to assess binding sites for any given protein of interest for crystallization, with the specificity of a macromolecular cage whose endo/exo orientation plays a role in the binding.

Probing the dynamical interaction of the para-sulfonato-calix[4]arene with an antifungal protein.

Calixarenes are hallmark molecules in supramolecular chemistry as hosts for small ligands. They have also conversely proved their interest as ligands toward assisted co-crystallization of proteins. These functionalized macrocycles target positively-charged residues, and notably surface-exposed lysines, with a site-selectivity finely characterized experimentally, but that remains to be assessed. Relying on a tailored molecular dynamics simulations protocol, we explore the association of para-sulfonato-calix[4]arenes with an antifungal protein, as a small yet most competitive system with 13 surface-exposed lysines. Our computational approach probes de novo the electrostatically-driven interaction, ruled out by a competition with salt bridges, corroborating the presence of two main binding sites probed by X-ray. The attach-pull-release (APR) method provides a very good assessment of the overall binding free energy measured experimentally (-6.42 ± 0.5 vs. -5.45 kcal mol-1 by isothermal titration calorimetry). This work also probes dynamic modifications upon ligand binding, and our computational protocol could be generalized to situate the supramolecular forces ruling out the calixarene-assisted co-crystallization of proteins.

Capturing the Recognition Dynamics of para-Sulfonato-calix[4]arenes by Cytochrome c: Toward a Quantitative Free Energy Assessment.

Calix[n]arenes' selective recognition of protein surfaces covers a broad range of timely applications, from controlling protein assembly and crystallization to trapping partially disordered proteins. Here, the interaction of para-sulfonated calix-[4]-arenes with cytochrome c is investigated through all-atom, explicit water molecular dynamics simulations which allow characterization of two binding sites in quantitative agreement with experimental evidence. Free energy calculations based on the MM-PBSA and the attach-pull-release (APR) methods highlight key residues implicated in the recognition process and provide binding free energy results in quantitative agreement with isothermal titration calorimetry. Our study emphasizes the role of MD simulations to capture and describe the "walk" of sulfonated calix-[4]-arenes on the cytochrome c surface, with the arginine R13 as a pivotal interacting residue. Our MD investigation allows, through the quasi-harmonic multibasin (QHMB) method, probing an allosteric reinforcement of several per-residue interactions upon calixarene binding, which suggests a more complex mode of action of these supramolecular auxiliaries.

Towards design of drugs and delivery systems with the Martini coarse-grained model.

Coarse-grained (CG) modelling with the Martini force field has come of age. By combining a variety of bead types and sizes with a new mapping approach, the newest version of the model is able to accurately simulate large biomolecular complexes at millisecond timescales. In this perspective, we discuss possible applications of the Martini 3 model in drug discovery and development pipelines and highlight areas for future development. Owing to its high simulation efficiency and extended chemical space, Martini 3 has great potential in the area of drug design and delivery. However, several aspects of the model should be improved before Martini 3 CG simulations can be routinely employed in academic and industrial settings. These include the development of automatic parameterisation protocols for a variety of molecule types, the improvement of backmapping procedures, the description of protein flexibility and the development of methodologies enabling efficient sampling. We illustrate our view with examples on key areas where Martini could give important contributions such as drugs targeting membrane proteins, cryptic pockets and protein-protein interactions and the development of soft drug delivery systems.

Influence of Divalent Cations in the Protein Crystallization Process Assisted by Lanthanide-Based Additives.

The use of lanthanide complexes as powerful auxiliaries for biocrystallography prompted us to systematically analyze the influence of the commercial crystallization kit composition on the efficiency of two lanthanide additives: [Eu(DPA)3]3- and Tb-Xo4. This study reveals that the tris(dipicolinate) complex presents a lower chemical stability and a strong tendency toward false positives, which are detrimental for its use in a high-throughput robotized crystallization platform. In particular, the crystal structures of (Mg(H2O)6)3[Eu(DPA)3]2·7H2O (1), {(Ca(H2O)4)3[Eu(DPA)3]2}n·10nH2O (2), and {Cu(DPA)(H2O)2}n (3), resulting from spontaneous crystallization in the presence of a divalent alkaline-earth cation and transmetalation, are reported. On the other hand, Tb-Xo4 is perfectly soluble in the crystallization media, stable in the presence of alkaline-earth dications, and slowly decomposes (within days) by transmetalation with transition metals. The original structure of [Tb4L4(H2O)4]Cl4·15H2O (4) is also described, where L represents a bis(pinacolato)triazacyclononane ligand. This paper also highlights a potential synergy of interactions between Tb-Xo4 and components of the crystallization mixtures, leading to the formation of complex adducts like {AdkA/Tb-Xo4/Mg2+/glycerol} in the protein binding sites. The observation of such multicomponent adducts illustrated the complexity and versatility of the supramolecular chemistry occurring at the surface of the proteins.

Capturing the dynamic association between a tris-dipicolinate lanthanide complex and a decapeptide: a combined paramagnetic NMR and molecular dynamics exploration.

In the realm of biomolecules, peptides can present a large diversity of structures. Our study sheds new light on the structural interplay between a tris-dipicolinate lanthanide probe and a decapeptide SASYKTLPRG. Although a rather trivial, electrostatically driven interaction was expected, the combination of paramagnetic NMR and molecular dynamics simulations reveals a highly dynamic association process and allows for providing extensive insights into the interaction sites and their occupancy. This study highlights the importance of a large conformational sampling to reconcile characteristic time in NMR with molecular dynamics simulations, where sampling in the microsecond range is needed. This study opens the door for a detailed mechanistic elucidation of the early steps of lanthanide complex-peptide or lanthanide complex-protein interaction or self-assembly processes.

Assessing the sequence dependence of pyrimidine-pyrimidone (6-4) photoproduct in a duplex double-stranded DNA: A pitfall for microsecond range simulation.

Sequence dependence of the (6-4) photoproduct conformational landscape when embedded in six 25-bp duplexes is evaluated along extensive unbiased and enhanced (replica exchange with solute tempering, REST2) molecular dynamics simulations. The structural reorganization as the central pyrimidines become covalently tethered is traced back in terms of non-covalent interactions, DNA bending, and extrusion of adenines of the opposite strands. The close sequence pattern impacts the conformational landscape around the lesion, inducing different upstream and downstream flexibilities. Moreover, REST2 simulations allow us to probe structures possibly important for damaged DNA recognition.

Molecular Dynamics Approach for Capturing Calixarene-Protein Interactions: The Case of Cytochrome C.

Functionalized supramolecular cages are of growing importance in biology and biochemistry. They have recently been proposed as efficient auxiliaries to obtain high-resolution cocrystallized proteins. Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonated calix-[8]-arenes to cytochrome c starting from initially distant proteins and ligands. We characterize two main binding sites for the sulfonated calixarene on the cytochrome c surface which are in perfect agreement with the previous experiments with regard to the structure (comparison with the X-ray structure PDB 6GD8) and the binding free energies [comparison between the molecular mechanics Poisson-Boltzmann surface area analysis and the isothermal titration calorimetry measurements]. The per-residue decomposition of the interaction energies reveals the detailed picture of this electrostatically driven association and notably the role of arginine R13 as a bridging residue between the two main anchoring sites. In addition, the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of a hydrogen bond network far from the binding sites, increasing the rigidity of the protein. This study paves the way toward an automated procedure to predict the supramolecular protein-cage association, with the possibility of a computational screening of new promising derivatives for controlled protein assembly and protein surface recognition processes.

Interaction of O2 with CH4, CF4, and CCl4 by Molecular Beam Scattering Experiments and Theoretical Calculations.

Gas phase collisions of O2 by CH4, CF4, and CCl4 have been investigated with the molecular beam technique by measuring both the integral cross section value, Q, and its dependence on the collision velocity, v. The adopted experimental conditions have been appropriate to resolve the oscillating "glory" pattern, a quantum interference effect controlled by the features of the intermolecular interaction, for all the three case studies. The analysis of the Q(v) data, performed by adopting a suitable representation of the intermolecular potential function, provided the basic features of the anisotropic potential energy surfaces at intermediate and large separation distances and information on the relative role of the physically relevant types of contributions to the global interaction. The present work demonstrates that while O2-CH4 and O2-CF4 are basically bound through the balance between size (Pauli) repulsion and dispersion attraction, an appreaciable intermolecular bond stabilization by charge transfer is operative in O2-CCl4. Ab initio calculations of the strength of the interaction, coupled with detailed analysis of electronic charge displacement promoted by the formation of the dimer, fully rationalizes the experimental findings. This investigation indicates that the interactions of O2, when averaged over its relative orientations, are similar to that of a noble gas (Ng), specifically Ar. We also show that the binding energy in the basic configurations of the prototypical Ng-CF4,CCl4 systems [ Cappelletti , D. ; Chem. Eur. J. 2015 , 21 , 6234 - 6240 ] can be reconstructed by using the interactions in Ng-F and Ng-Cl systems, previously characterized by molecular beam scattering experiments of state-selected halogen atom beams. This information is fundamental to approach the modeling of the weak intermolecular halogen bond. On the basis of the electronic polarizability, this also confirms [ Aquilanti , V. ; Angew. Chem., Int. Ed. 2005 , 44 , 2356 - 2360 ] that O2 can be taken as a proper reference partner for simulating the behavior of some basic noncovalent components of the interactions involving water. Present results are of fundamental relevance to build up the force field controlling the hydrophobic behavior of prototypical apolar CX4 (X = H, F, Cl) molecules.

Stereodynamics in the Collisional Autoionization of Water, Ammonia, and Hydrogen Sulfide with Metastable Rare Gas Atoms: Competition Between Intermolecular Halogen and Hydrogen Bonds.

Recent experiments on the title subject, performed with a high-resolution crossed-beam apparatus, have provided the total ionization cross sections as a function of the collision energy between noble gas atoms, electronically excited in their metastable states (Ng*), and H2 O, H2 S, and NH3 reagents, as well as the emitted electron energy spectra. This paper presents a rationalization of all the experimental findings in a unifying picture to cast light on the basic chemical properties of Ng* under conditions of great relevance both from a fundamental and from an applied point of view. The importance of this investigation is that it isolates the selective role of the intermolecular halogen and hydrogen bonds, to assess their anisotropic effects on the stereodynamics of the promoted ionization reactions, and to model energy transfer and reactivity in systems of applied interest, such as planetary atmospheres, plasmas, lasers, and flames.

The stereo-dynamics of collisional autoionization of ammonia by helium and neon metastable excited atoms through molecular beam experiments.

A combined analysis of both new (energy spectra of emitted electrons) and previously published (ionization cross sections) experimental data, measured under the same conditions and concerning electronically excited lighter noble gas -NH3 collisional autoionization processes, is carried out. Such an analysis, performed by exploiting a formulation of the full potential energy surface both in the real and imaginary parts, provides direct information on energetics, structure, and lifetime of the intermediate collision complex over all the configuration space. The marked anisotropy in the attraction of the real part, driving the approach of reagents, and the selective role of the imaginary component, associated to the charge transfer coupling between entrance and exit channels, suggests that reactive events occur almost exclusively in the molecular hemisphere containing the nitrogen lone pair. Crucial details on the stereo-dynamics of elementary collisional autoionization processes are then obtained, in which the open shell nature of the disclosed ionic core of metastable atom plays a crucial role. The same analysis also suggests that the strength of the attraction and the anisotropy of the interaction increases regularly along the series Ne*((3)P), He*((3)S), He*((1)S)-NH3. These findings can be ascribed to the strong rise of the metastable atom electronic polarizability (deformability) along the series. The obtained results can stimulate state of the art ab initio calculations focused on specific features of the transition state (energetics, structure, lifetime, etc.) which can be crucial for a further improvement of the adopted treatment and to better understand the nature of the leading interaction components which are the same responsible for the formation of the intermolecular halogen and hydrogen bond.

H2O-CH4 and H2S-CH4 complexes: a direct comparison through molecular beam experiments and ab initio calculations.

New molecular beam scattering experiments have been performed to measure the total (elastic plus inelastic) cross sections as a function of the velocity in collisions between water and hydrogen sulfide projectile molecules and the methane target. Measured data have been exploited to characterize the range and strength of the intermolecular interaction in such systems, which are of relevance as they drive the gas phase molecular dynamics and the clathrate formation. Complementary information has been obtained by rotational spectra, recorded for the hydrogen sulfide-methane complex, with a pulsed nozzle Fourier transform microwave spectrometer. Extensive ab initio calculations have been performed to rationalize all the experimental findings. The combination of experimental and theoretical information has established the ground for the understanding of the nature of the interaction and allows for its basic components to be modelled, including charge transfer, in these weakly bound systems. The intermolecular potential for H2S-CH4 is significantly less anisotropic than for H2O-CH4, although both of them have potential minima that can be characterized as 'hydrogen bonded'.

Catching the role of anisotropic electronic distribution and charge transfer in halogen bonded complexes of noble gases.

The systems studied in this work are gas-phase weakly bound adducts of the noble-gas (Ng) atoms with CCl4 and CF4. Their investigation was motivated by the widespread current interest for the intermolecular halogen bonding (XB), a structural motif recognized to play a role in fields ranging from elementary processes to biochemistry. The simulation of the static and dynamic behaviors of complex systems featuring XB requires the formulation of reliable and accurate model potentials, whose development relies on the detailed characterization of strength and nature of the interactions occurring in simple exemplary halogenated systems. We thus selected the prototypical Ng-CCl4 and Ng-CF4 and performed high-resolution molecular beam scattering experiments to measure the absolute scale of their intermolecular potentials, with high sensitivity. In general, we expected to probe typical van der Waals interactions, consisting of a combination of size (exchange) repulsion with dispersion/induction attraction. For the He/Ne-CF4, the analysis of the glory quantum interference pattern, observable in the velocity dependence of the integral cross section, confirmed indeed this expectation. On the other hand, for the He/Ne/Ar-CCl4, the scattering data unravelled much deeper potential wells, particularly for certain configurations of the interacting partners. The experimental data can be properly reproduced only including a shifting of the repulsive wall at shorter distances, accompanied by an increased role of the dispersion attraction, and an additional short-range stabilization component. To put these findings on a firmer ground, we performed, for selected geometries of the interacting complexes, accurate theoretical calculations aimed to evaluate the intermolecular interaction and the effects of the complex formation on the electron charge density of the constituting moieties. It was thus ascertained that the adjustments of the potential suggested by the analysis of the experiments actually reflect two chemically meaningful contributions, namely, a stabilizing interaction arising from the anisotropy of the charge distribution around the Cl atom in CCl4 and a stereospecific electron transfer that occurs at the intermolecular distances mainly probed by the experiments. Our model calculations suggest that the largest effect is for the vertex geometry of CCl4 while other geometries appear to play a minor to negligible role.

Experimental evidence of chemical components in the bonding of helium and neon with neutral molecules.

The complexes of helium and neon with gaseous neutral molecules are generally perceived to be van der Waals adducts held together by physical (non-covalent) forces, owing to the combination of size (exchange) repulsion with dispersion/induction attraction. Molecular beam experiments confirm that this is the case for He-CF4 , Ne-CF4 adducts, but revealed that the interaction of He and Ne with CCl4 features an appreciable contribution of chemical components that arise from the anisotropy of the electron density of CCl4 that enhances a charge transfer from Ng (Ng=He, Ne). These findings furnish a novel assay of the bonding capabilities of helium and neon, and invite to revisit the neutral complexes of these elements as systems of chemical relevance. The CCl4 -Ng are also peculiar examples of halogen bonds, a group of interactions of major current concern. Finally, this investigation is a prelude to the development of semi-empirical models for force fields aimed to the unified description of static and dynamical properties of systems of comparable or higher complexity.

Intermolecular interaction in the H2S-H2 complex: molecular beam scattering experiments and ab-inito calculations.

New molecular beam scattering experiments are reported for the H2S-H2 system recording, under high angular and velocity resolution conditions, the "glory" quantum interference in the velocity dependence of the total cross section. The analysis of the experimental data permits the determination, for the first time, of a spherically averaged intermolecular potential for this system. An evaluation of significant cuts of the potential energy surface, obtained by accurate ab initio CCSD(T) calculations using large basis sets, combined with the analysis of the electronic charge displacement accompanying the formation of H2S-H2, has been also performed in order to rationalize the experimental findings. A direct comparison with the analogous water-hydrogen complex (Belpassi, L. et al. J. Am. Chem. Soc. 2010, 132, 13046), investigated with the same experimental conditions and theoretical methodology, brings to light detailed differences in the intermolecular interaction affecting the observables. In particular, it shows the important fact that the charge transfer (CT) component of the interaction plays a minor role in H2S-H2, whereas it was found to be a crucial stabilization component of the interaction in water-H2, determining the potential energy surface anisotropy and the precise location of the energy minima.