Trimer Interaction Research Articles

Dissociation Energies via Embedding Techniques.

Due to the large number of interactions, evaluating interaction energies for large or periodic systems results in time-consuming calculations. Prime examples are liquids, adsorbates, and molecular crystals. Thus, there is a high demand for a cheap but still accurate method to determine interaction energies and gradients. One approach to counteract the computational cost is to fragment a large cluster into smaller subsystems, sometimes called many-body expansion, with the fragments being molecules or parts thereof. These subsystems can then be embedded into larger entities, representing the bigger system. In this work, we test several subsystem approaches and explore their limits and behaviors, determined by calculations of trimer interaction energies. The methods presented here encompass mechanical embedding, point charges, polarizable embedding, polarizable density embedding, and density embedding. We evaluate nonembedded fragmentation, QM/MM (quantum mechanics/molecular mechanics), and QM/QM (quantum mechanics/quantum mechanics) embedding theories. Finally, we make use of symmetry-adapted perturbation theory utilizing density functional theory for the monomers to interpret the results. Depending on the strength of the interaction, different embedding methods and schemes prove favorable to accurately describe a system. The embedding approaches presented here are able to decrease the interaction energy errors with respect to full system calculations by a factor of up to 20 in comparison to simple/unembedded approaches, leading to errors below 0.1 kJ/mol.

Accurate Prediction of Three-Body Intermolecular Interactions via Electron Deformation Density-Based Machine Learning.

This work extends the electron deformation density-based descriptor, originally developed in the electron deformation density-based interaction energy machine learning (EDDIE-ML) algorithm to predict dimer interaction energies, to the prediction of three-body interactions in trimers. Using a sequential learning process to select the training data, the resulting Gaussian process regression (GPR) model predicts the three-body interaction energy within 0.2 kcal mol-1 of the SRS-MP2/cc-pVTZ reference values for the 3B69 and S22-3 trimer data sets. A hybrid kernel function is introduced, which combines contributions from the average and individual atomic environments, allowing the total trimer interaction energy to be predicted in addition to the three-body contribution using the same descriptor. To extend the range and diversity of trimer interaction energies available in the literature, a new data set based on a protein-ligand crystal structure is introduced, consisting of 509 structures of a central ligand with two protein fragments. Benchmark calculations are provided for the new data set, which contains significantly larger molecular interactions than current databases in the literature in addition to charged fragments. Compared to density funtional theory (DFT)- and wavefunction-based methods for calculating the three-body interaction energy, our model makes predictions in a significantly shorter time frame by reducing the number of required SCF calculations from 7 to 4 performed at the PBE0 level of theory, showcasing the utility and efficiency of our Δ-ML method particularly when applied to larger systems.

In Silico Multi-Target Approach Revealed Potential Lead Compounds as Scaffold for the Synthesis of Chemical Analogues Targeting SARS-CoV-2.

Simple SummaryCOVID-19 is an infectious disease caused by SARS-CoV-2. The virus has rapidly spread to humans, causing the ongoing coronavirus pandemic. Enormous progress in finding therapies has been made, but an effective therapy is still absent. In this study, we propose a computational strategy aimed at identifying novel multi-target scaffolds against the virus. The proposed study was performed using bioinformatics methods, such as homology modeling, virtual screening and classical molecular dynamics, where 3D structures of targets were reconstructed and compounds with potential inhibitory activity against different virus targets were identified. Furthermore, a potential mechanism of action was proposed. Our study could provide new insights and approaches for the rapid identification of novel multi-target inhibitors of SARS-CoV-2.Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), an infectious disease that spreads rapidly in humans. In March 2020, the World Health Organization (WHO) declared a COVID-19 pandemic. Identifying a multi-target-directed ligand approach would open up new opportunities for drug discovery to combat COVID-19. The aim of this work was to perform a virtual screening of an exclusive chemical library of about 1700 molecules containing both pharmacologically active compounds and synthetic intermediates to propose potential protein inhibitors for use against SARS-CoV-2. In silico analysis showed that our compounds triggered an interaction network with key residues of the SARS-CoV-2 spike protein (S-protein), blocking trimer formation and interaction with the human receptor hACE2, as well as with the main 3C-like protease (3CLpro), inhibiting their biological function. Our data may represent a step forward in the search for potential new chemotherapeutic agents for the treatment of COVID-19.

Structure based virtual screening of natural products to disrupt the structural integrity of TRAF6 C-terminal domain homotrimer

Tumor necrosis factor receptor-associated factor 6 (TRAF6) is an E3 ligase which takes part in different cellular pathways. TRAF6 is seen to be highly expressed in various cancers and most importantly is known to drive cancer metastasis. This makes TRAF6 a potential therapeutic target. In our previous studies, we observed that the C-terminal domain of TRAF6 forms a mushroom shaped trimer structure. Lys340 and Glu345 were identified to be the most critical residues in the trimer interface. In this current work, we screened for more than 14000 small molecules derived from various natural sources and they were screened against TRAF6 C-terminal trimer interaction interface to prevent the formation of the interface. All the obtained molecules were tested for their drug-likeliness properties. The ligands which qualified the filter were considered for protein-ligand docking or structure based virtual screening in GOLD 5.2. Pose selection was carried out on the basis of GoldScore and ChemScore function of GOLD 5.2. Top 20 molecules binding the TRAF6 trimeric interface were tested for their ADME properties. From the top 20 molecules, top 3 ligands were chosen based on their abilities to pass the maximum numbers of ADME filters.

Quantum transistor with a double-cavity optomechanical system

A scheme of quantum transistor in a double-cavity optomechanical system is proposed, where the input signal of the base port is a quantum or classical signal which are discussed, respectively. In the case of quantum input signal, to treat the nonlinear trimer interaction, we propose an iterative method when the trimer interaction is weak. When the input signal is classical, we can achieve beam splitter and parametric-down-conversion interaction between collector and emitter, respectively. We calculate the output power spectrum and analyze the relations between input of the base port and output of the emitter. Our results show that the input at the base controls the on-off between the collector and emitter, and the signal imposed from the base can be amplified. For two different cases, the system both can serve as a quantum transistor.

Characterization of PC2 Cterm Calcium-Binding Interaction and its Structural Implications

Polycystin-2 (PC2) is a Ca2+-regulated Ca2+-channel from the transient receptor potential (TRP) family. Mutations in PC2 can cause autosomal dominant polycystic kidney disease (ADPKD). The C-terminal cytoplasmic tail of human PC2 (HPC2 Cterm) is crucial for channel assembly and function. We have combined biophysical and structural approaches to characterize the Ca2+-dependent molecular mechanism within the C-terminal tail that is involved in channel assembly and functional regulation. We have determined that HPC2 Cterm forms a trimer in solution with and without Ca2+-bound, even though TRP channels are generally tetrameric. We have definitively shown that there is only one Ca2+-binding site in HPC2 Cterm, located within its EF-hand domain. However, its Ca2+-binding affinity is greatly enhanced relative to its intrinsic binding affinity in the isolated EF-hand, possibly due to the positive cooperativity from the trimer interaction. We also employed sea urchin PC2 as a parallel model to study. The sea urchin C-terminal domain construct (SUPC2 Ccore) also trimerizes in solution independent of Ca2+-binding. In contrast, the SUPC2 Ccore contains two Ca2+-binding sites within its EF-hand domain, which exhibit cooperative Ca2+-binding due to internal stabilization. Consequently, trimerization does not further improve Ca2+-binding affinity in SUPC2 Ccore relative to the isolated EF-hand domain. Using both hydrogen-deuterium exchange mass spectroscopy and nuclear magnetic resonance, we have localized the Ca2+-binding sites in PC2 C-terminal tail and mapped the conformational changes induced by Ca2+-binding. We demonstrate that in addition to the direct, local stabilizing effects within the EF-hand, Ca2+-binding also causes conformational changes in the distal coiled-coil domain. This study provides a structural basis for regulation of the PC2 channel by its cytosolic C-terminal domain, with an improved understanding of the functional role of PC2 in regulating intracellular Ca2+ signaling.

Predictions for water clusters from a first-principles two- and three-body force field.

A new rigid-monomer three-body potential has been developed for water by fitting it to more than 70 thousand trimer interaction energies computed ab initio using coupled-cluster methods and augmented triple-zeta-quality basis sets. This potential was used together with a modified form of a previously developed two-body potential and with a polarization model of four- and higher-body interactions to predict the energetics of the water trimer, hexamer, and 24-mer. Despite using the rigid-monomer approximation, these predictions agree better with flexible-monomer benchmarks than published results obtained with flexible-monomer force fields. An unexpected finding of our work is that simple polarization models predict four-body interactions to within a few percent, whereas for three-body interactions these models are known to have errors on the order of 50%.

Role of a Conserved Residue R780 in Escherichia coli Multidrug Transporter AcrB

Multidrug efflux pumps play important roles in bacteria drug resistance. A major multidrug efflux system in Gram-negative bacteria is composed of the inner membrane transporter AcrB, outer membrane protein channel TolC, and membrane fusion protein AcrA. These three proteins form a large complex that spans both layers of cell membranes and the periplasmic space. AcrB exists and functions as a homotrimer. To identify residues at the trimer interface that play important roles in AcrB function, we conducted site directed mutagenesis and discovered a key residue, R780. Although R780K was partially functional, all other R780 mutants tested were completely nonfunctional. Replacement of R780 by other residues disrupted trimer association. However, a decrease of trimer stability was not the lone cause for the observed loss of activity, because the activity loss could not be restored by strengthening trimer interaction. Using both heat and chemical denaturation methods, we found that the mutation decreased protein stability. Finally, we identified a repressor mutation, M774K, through random mutagenesis. It restored the activity of AcrBR780A to a level close to that of the wild-type protein. To examine the mechanism of activity restoration, we monitored denaturation of AcrBR780A/M774K and found that the repressor mutation improved protein stability. These results suggest that R780 is critical for AcrB stability. When R780 was replaced by Ala, the protein retained the overall structure, still trimerized in the cell membrane, and interacted with AcrA. However, local structural rearrangement might have occurred and lead to the decrease of protein stability and loss of substrate efflux activity.

Role of trimer–trimer interaction of bacteriorhodopsin studied by optical spectroscopy and high-speed atomic force microscopy

Bacteriorhodopsin (bR) trimers form a two-dimensional hexagonal lattice in the purple membrane of Halobacterium salinarum. However, the physiological significance of forming the lattice has long been elusive. Here, we study this issue by comparing properties of assembled and non-assembled bR trimers using directed mutagenesis, high-speed atomic force microscopy (HS-AFM), optical spectroscopy, and a proton pumping assay. First, we show that the bonds formed between W12 and F135 amino acid residues are responsible for trimer-trimer association that leads to lattice assembly; the lattice is completely disrupted in both W12I and F135I mutants. HS-AFM imaging reveals that both crystallized D96N and non-crystallized D96N/W12I mutants undergo a large conformational change (i.e., outward E-F loop displacement) upon light-activation. However, lattice disruption significantly reduces the rate of conformational change under continuous light illumination. Nevertheless, the quantum yield of M-state formation, measured by low-temperature UV-visible spectroscopy, and proton pumping efficiency are unaffected by lattice disruption. From these results, we conclude that trimer-trimer association plays essential roles in providing bound retinal with an appropriate environment to maintain its full photo-reactivity and in maintaining the natural photo-reaction pathway.

Full-configuration-interaction calculation of three-body nonadditive contribution to helium interaction potential

The three-body nonadditive interaction energy between helium atoms was calculated at 253 trimer configurations using the full-configuration-interaction (FCI) method. The analytic potential fitted to these energies is the best current representation of the three-body nonadditive interactions between helium atoms. At the equilateral triangle configuration with R=5.6 bohr, near the minimum of the total potential, the nonadditive three-body energy calculated at the FCI level amounts to -88.5 mK, compared to -98.5 mK at the coupled cluster with single, double, and noniterative triple excitations [CCSD(T)] level. The uncertainty of the former result resulting from basis set incompleteness is estimated to be 1.5 mK. The relative uncertainty of our present complete three-body fit, including the uncertainties resulting from the fitting procedure, is estimated at 2%, a fivefold improvement over the previous best potential. Overall, the FCI contribution beyond CCSD(T) is rather important, being of the same order of magnitude as the uncertainty of the sum of two-body interactions. The inclusion of this contribution makes uncertainties of the total trimer interaction energies dominated by the uncertainties of the two-body component.

DNA Base Trimers: Empirical and Quantum Chemical Ab Initio Calculations versus Experiment in Vacuo

A complete scan of the potential-energy surfaces for selected DNA base trimers has been performed by a molecular dynamics/quenching technique using the force field of Cornell et al. implemented in the AMBER7 program. The resulting most stable/populated structures were then reoptimized at a correlated ab initio level by employing resolution of the identity, Møller-Plesset second-order perturbation theory (RI-MP2). A systematic study of these trimers at such a complete level of electronic structure theory is presented for the first time. We show that prior experimental and theoretical interpretations were incorrect in assuming that the most stable structures of the methylated trimers corresponded to planar systems characterized by cyclic intermolecular hydrogen bonding. We found that stacked structures of two bases with the third base in a T-shape arrangement are the global minima in all of the methylated systems: they are more stable than the cyclic planar structures by about 10 kcal mol(-1). The different behaviors of nonmethylated and methylated trimers is also discussed. The high-level geometries and interaction energies computed for the trimers serve also as a reference for the testing of recently developed density functional theory (DFT) functionals with respect to their ability to correctly describe the balance between the electrostatic and dispersion contributions that bind these trimers together. The recently reported M052X functional with a polarized triple-zeta basis set predicts 11 uracil trimer interaction energies with a root-mean-square error of 2.3 kcal mol(-1) relative to highly correlated ab initio theoretical calculations.

Domain III from class II fusion proteins functions as a dominant-negative inhibitor of virus membrane fusion.

Alphaviruses and flaviviruses infect cells through low pH-dependent membrane fusion reactions mediated by their structurally similar viral fusion proteins. During fusion, these class II viral fusion proteins trimerize and refold to form hairpin-like structures, with the domain III and stem regions folded back toward the target membrane-inserted fusion peptides. We demonstrate that exogenous domain III can function as a dominant-negative inhibitor of alphavirus and flavivirus membrane fusion and infection. Domain III binds stably to the fusion protein, thus preventing the foldback reaction and blocking the lipid mixing step of fusion. Our data reveal the existence of a relatively long-lived core trimer intermediate with which domain III interacts to initiate membrane fusion. These novel inhibitors of the class II fusion proteins show cross-inhibition within the virus genus and suggest that the domain III–core trimer interaction can serve as a new target for the development of antiviral reagents.

A Semiempirical Quantum Model for Hydrogen-Bonded Nucleic Acid Base Pairs.

An exploratory semiempirical Hamiltonian (PM3BP) is developed to model hydrogen bonding in nucleic acid base pairs. The PM3BP Hamiltonian is a novel reparametrization of the PM3 Hamiltonian designed to reproduce experimental base pair dimer enthalpies and high-level density-functional results. The parametrization utilized a suite of integrated nonlinear optimization algorithms interfaced with a d-orbital semiempirical program. Results are compared with experimental values and with benchmark density-functional (mPWPW91/MIDI!) calculations for hydrogen-bonded nucleic acid dimers and trimers. The PM3BP Hamiltonian is demonstrated to outperform the AM1, PM3, MNDO, and MNDO/H Hamiltonians for dimer and trimer structures and interaction enthalpies and is shown to reproduce experimental dimer interaction enthalpies that rival density-functional results for an over 3 orders of magnitude reduction in computational cost. The tradeoff between a high accuracy gain for hydrogen bonding at the expense of sacrificing some generality is discussed. These results provide insight into the limits of conventional semiempirical forms for accurate modeling of biological interactions.

The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link.

Triple-helical collagen IV protomers associate through their N- and C-termini forming a three-dimensional network, which provides basement membranes with an anchoring scaffold and mechanical strength. The noncollagenous (NC1) domain of the C-terminal junction between two adjacent collagen IV protomers from human placenta was crystallized and its 1.9-A structure was solved by multiple anomalous diffraction (MAD) phasing. This hexameric NC1 particle is composed of two trimeric caps, which interact through a large planar interface. Each cap is formed by two alpha 1 fragments and one alpha 2 fragment with a similar previously uncharacterized fold, segmentally arranged around an axial tunnel. Each monomer chain folds into two structurally very similar subdomains, which each contain a finger-like hairpin loop that inserts into a six-stranded beta-sheet of the neighboring subdomain of the same or the adjacent chain. Thus each trimer forms a quite regular, but nonclassical, sixfold propeller. The trimer-trimer interaction is further stabilized by a previously uncharacterized type of covalent cross-link between the side chains of a Met and a Lys residue of the alpha 1 and alpha 2 chains from opposite trimers, explaining previous findings of nonreducible cross-links in NC1. This structure provides insights into NC1-related diseases such as Goodpasture and Alport syndromes.

Expression, Purification, and Characterization of Recombinant HIV gp140: THE gp41 ECTODOMAIN OF HIV OR SIMIAN IMMUNODEFICIENCY VIRUS IS SUFFICIENT TO MAINTAIN THE RETROVIRAL ENVELOPE GLYCOPROTEIN AS A TRIMER

Efforts to understand the molecular basis of human immunodeficiency virus (HIV) envelope glycoprotein function have been hampered by the inability to generate sufficient quantities of homogeneous material. We now report on the high level expression, purification, and characterization of soluble HIV gp140 ectodomain proteins in Chinese hamster ovary-Lec3.2.8.1 cells. Gel filtration and analytical ultracentrifugation show that the uncleaved ADA strain-derived gp140 proteins are trimeric without further modification required to maintain oligomers. These spike proteins are native as judged by soluble CD4 (sCD4) (K(D) = 1-2 nm) and monoclonal antibody binding studies using surface plasmon resonance. CD4 ligation induces conformational change in the trimer, exposing the chemokine receptor binding site as assessed by 17b monoclonal antibody reactivity. Lack of anti-cooperativity in sCD4-ADA trimer interaction distinct from that observed with sCD4-SIV mac32H implies quaternary structural differences in ground states of their respective spike proteins.

The L3 loop and C-terminal phosphorylation jointly define Smad protein trimerization.

Smad proteins mediate the transforming growth factor beta responses. C-terminal phosphorylation of R-Smads leads to the recruitment of Smad4 and the formation of active signaling complexes. We investigated the mechanism of phosphorylation-induced Smad complex formation with an activating pseudo-phosphorylated Smad3. Pseudo-phosphorylated Smad3 has a greater propensity to homotrimerize, and recruits Smad4 to form a heterotrimer containing two Smad3 and one Smad4. The trimeric interaction is mediated through conserved interfaces to which tumorigenic mutations map. Furthermore, a conserved Arg residue within the L3 loop, located near the C-terminal phosphorylation sites of the neighboring subunit, is essential for trimerization. We propose that the phosphorylated C-terminal residues interact with the L3 loop of the neighboring subunit to stabilize the trimer interaction.

Theoretical study of interaction of small clusters of IrPt with H2

The study of the interaction of small clusters of IrPt with H2 is reported here through ab initio multiconfiguration self-consistent field (MC-SCF) calculations, plus extensive multireference configuration interaction (MR-CI), in its variational and perturbative modes. These calculations provide a cluster model for the activation of hydrogen by IrPt bimetallic catalysts. First, we studied the IrPt dimer interaction with H2. The five lowest states of the IrPt dimer are: 2Σ+, 2Δxy, 4Πyz, 4Σ+, and 4Δxy. For the IrPt dimer interaction with H2, we found that the IrPt dimer for both metal sides is able to capture the H2 molecule without any activation barriers, relaxing the H–H bond. The IrPt2 trimer interaction with H2 was also studied. The ground and the lowest states of the IrPt2 trimer are a 4A1 electronic state and a 4B2 electronic state, respectively. We found that for both metal sides, the IrPt2 cluster in its ground 4A1 and the low-lying 4B2 electronic states can spontaneously capture and break the hydrogen molecule. Large H–H relaxation is obtained and no activation barriers were found. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 80: 657–663, 2000

A Role for the Transmembrane Domain in the Trimerization of the MHC Class II-Associated Invariant Chain

MHC class II and invariant chain (Ii) associate early in biosynthesis to form a nonameric complex. Ii first assembles into a trimer and then associates with three class II alphabeta heterodimers. Although the membrane-proximal region of the Ii luminal domain is structurally disordered, the C-terminal segment of the luminal domain is largely alpha-helical and contains a major interaction site for the Ii trimer. In this study, we show that the Ii transmembrane domain plays an important role in the formation of Ii trimers. The Ii transmembrane domain contains an unusual patch of hydrophilic residues near the luminal interface. Substitution of these polar residues with nonpolar amino acids resulted in a decrease in the efficiency of Ii trimerization and subsequent class II association. Moreover, N-terminal fragments of Ii were found to trimerize independently of the luminal alpha-helical domain. Progressive C-terminal truncations mapped a homotypic association site to the first 80 aa of Ii. Together, these results implicate the Ii transmembrane domain as a site of trimer interaction that can play an important role in the initiation of trimer formation.

Symmetry-adapted perturbation theory of three-body nonadditivity in the Ar2HF trimer

Symmetry-adapted perturbation theory (SAPT) has been used to analyze the radial and angular dependence of the nonadditivity of the Ar2HF trimer interaction energy through fourth order. This represents the first application of the high-order SAPT to a nonadditive interaction including a polar molecule. The magnitude and anisotropy of the Hartree-Fock nonadditivity is well reproduced (to within 20%) by the sum of the first-order exchange and exchange-quenched third-order induction nonadditivities. The second-order induction effects play a smaller role. The computed SAPT corrections which contribute to the second-order supermolecular many-body perturbation theory (MBPT2) nonadditivity, Eexch-disp(2;0)[3,3] and Eind-disp(3;0)[3,3], reproduce MBPT2 values rather poorly. Using the pseudo-dimer approach it was found that the exchange quenching of the third-order induction-dispersion energy is strong. Inclusion of this quenching led to good agreement with the MBPT2 nonadditivity. The third-order MBPT nonadditivity was very well reproduced by the third-order dispersion energy. The fourth-order MBPT nonadditivity was only moderately well reproduced by the SAPT components Edisp(3;1)[3,3] and Edisp(4;0)[3,3], indicating that these terms are most likely appreciably quenched by exchange counterparts. The total nonadditivities computed using SAPT and the supermolecular method through fourth order agree remarkably well. The total SAPT nonadditivity is expressed in terms of physically interpretable components which can be easily modeled.

Structure and Stability of DNA Base Trimers: An Electrostatic Approach

Triplexes involving major groove binding of a third oligomer to the DNA duplex structure have gathered much interest in recent years. The study of base trimer interactions in the gas phase is expected to provide useful information regarding orientational preferences and inherent stabilities. A recently developed electrostatic potential for intermolecular complexation (EPIC) model has been found to be quite useful for exploring the structures and energetics in base pairs [Gadre, S. R.; Pundlik, S. S. J. Phys. Chem. 1996, 101, 3298]. This model makes use of complementary electrostatic features of the interacting species that are determined by ab initio theory. We report here the investigations on various trimers including TAT, TAG, ATG, CGG, and TCG using this model. The overall good agreement of the trimer interaction energies with the corresponding single-point SCF values made at the model-predicted geometries reveals the suitability of the EPIC model for studying DNA base complexes.