SARS-CoV-2 spike fusion peptide trans interaction with phosphatidylserine lipid triggers membrane fusion for viral entry.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike is the fusion machine for host cell entry. Still, the mechanism by which spike protein interacts with the target lipid membrane to facilitate membrane fusion during entry is not fully understood. Here, using steady-state membrane fusion and single-molecule fluorescence resonance energy transfer imaging of spike trimers on the surface of SARS-CoV-2 pseudovirion, we directly show that spike protein interacts with phosphatidylserine (PS) lipid in the target membrane for mediating fusion. We observed that the fusion peptide of the spike S2 domain interacts with the PS lipid of the target membrane. Low pH and Ca2+ trigger the spike conformational change and bring fusion peptide in close proximity to the PS lipid of the membrane. The binding of the spike with PS lipid of its viral membrane (cis interaction) impedes the fusion activation. PS on the target membrane promotes spike binding via trans interaction, prevents the cis interaction, and accelerates fusion. Sequestering or absence of PS lipid abrogates the spike-mediated fusion process and restricts SARS-CoV-2 infectivity. We found that PS-dependent interaction for fusion is conserved across all the SARS-CoV-2 spike variants of concern (D614G, Alpha, Beta, Delta, and Omicron). Our study suggests that PS lipid is indispensable for SARS-CoV-2 spike-mediated virus and target membrane fusion for entry, and restricting PS interaction with spike inhibits the SARS-CoV-2 spike-mediated entry. Therefore, PS is an important cofactor and acts as a molecular beacon in the target membrane for SARS-CoV-2 entry. IMPORTANCE: The role of lipids in the host cell target membrane for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) entry is not clear. We do not know whether SARS-CoV-2 spike protein has any specificity in terms of lipid for membrane fusion reaction. Here, using in vitro reconstitution of membrane fusion assay and single-molecule fluorescence resonance energy transfer imaging of SARS-CoV-2 spike trimers on the surface of the virion, we have demonstrated that phosphatidylserine (PS) lipid plays a key role in SARS-CoV-2 spike-mediated membrane fusion reaction for entry. Membrane-externalized PS lipid strongly promotes spike-mediated membrane fusion and COVID-19 infection. Blocking externalized PS lipid with PS-binding protein or in the absence of PS, SARS-CoV-2 spike-mediated fusion is strongly inhibited. Therefore, PS is an important target for restricting viral entry and intervening spike, and PS interaction presents new targets for COVID-19 interventions.

Proposed dual membrane contact with full-length Osh4.

Membrane contacts sites (MCSs) play important roles in lipid trafficking across cellular compartments and maintain the widespread structural diversity of organelles. We have utilized microsecond long all-atom (AA) molecular dynamics (MD) simulations and enhanced sampling techniques to unravel the MCS structure targeting by yeast oxysterol binding protein (Osh4) in an environment that mimics the interface of membranes with an increased proportion of anionic lipids using CHARMM36m forcefield with additional CUFIX parameters for lipid-protein electrostatic interactions. In a dual-membrane environment, unbiased MD simulations show that Osh4 briefly interacts with both membranes, before aligning itself with a single membrane, adopting a ß-crease-bound conformation similar to observations in a single-membrane scenario. Targeted molecular dynamics simulations followed by microsecond-long AA MD simulations have revealed a distinctive dual-membrane bound state of Osh4 at MCS, wherein the protein interacts with the lower membrane via the ß-crease surface, featuring its PHE-239 residue positioned below the phosphate plane of membrane, while concurrently establishing contact with the opposite membrane through the extended α6-α7 region. Osh4 maintains these dual membrane contacts simultaneously over the course of microsecond-long MD simulations. Moreover, binding energy calculations highlighted the essential roles played by the phenylalanine loop and the α6 helix in dynamically stabilizing dual-membrane bound state of Osh4 at MCS. Our computational findings were corroborated through frequency of contact analysis, showcasing excellent agreement with past experimental cross-linking data. Our computational study reveals a dual-membrane bound conformation of Osh4, providing insights into protein-membrane interactions at membrane contact sites and their relevance to lipid transfer processes.

Modeling the membrane binding mechanism of a lipid transport protein Osh4 to single membranes.

All-atom (AA) molecular dynamics simulations are used to unravel the binding mechanism of yeast oxysterol binding protein (Osh4) to model membranes with varying anionic lipid concentration using AA and the highly mobile membrane mimetic (HMMM) representations. For certain protein-lipid interactions, an improved forcefield description is used (CUFIX) to accurately describe lipid-protein electrostatic interactions. Our detailed computational studies have identified a single, ß-crease oriented, membrane-bound conformation of Osh4 for all anionic membranes. The penetration of the PHE-239 residue below the membrane phosphate plane is the characteristic signature of the membrane-bound state of Osh4. As the phenylalanine loop anchors itself deeply in the membrane; the other regions of the Osh4, namely, ALPS motif, ß6- ß7 loop, ß14- ß15 loop, and ß16- ß17 loop, maximize their contact with the membrane. Furthermore, loose lipid packing and higher mobility of HMMM enable stronger association of the ALPS motif with the membrane lipids through its hydrophobic surface. After the HMMM is converted to AA and equilibrated, the binding is two to three times stronger compared with simulations started with the AA representation, yielding the major importance of the ALPS motif to binding. Quantitative estimation of binding energy revealed that the phenylalanine loop plays a crucial role in stable membrane attachment of Osh4 and contributes significantly toward overall binding process. The CUFIX parameters provide a more balanced picture of hydrophobic and electrostatic interactions between the protein and the membrane, which differs from our past work that showed salt bridges alone stabilized Osh4-membrane contact. Our study provides a comprehensive picture of the binding mechanism of Osh4 with model single membranes and, thus, understanding of the initial interactions is important for elucidating the biological function of this protein to shuttle lipids between organelles.

External electric field control: driving the reactivity of metal-free azide-alkyne click reactions.

Recent reports have suggested that an external electric field (EEF) can assist and even control product selectivity. In this work, we have shown that the barrier for the Huisgen reaction between alkyl (aryl) azide and cyclooctyne(biflurocyclooctyne) is reduced by ∼3-4 kcal mol-1 when an oriented EEF is applied along the reaction axis. As a consequence of their inherently polar transition-states (TSs), a parallel orientation of the EEF results in enhancement of the charge transfer (CT) between the fragments and concomitant increase in the dipole moment along the reaction axes. This leads to an increase in the reaction rate for moderate EEFs in the range of 0.3-0.5 V Å-1. Since highly polar and directional environments are omnipresent in biological environments, metal-free click reactions can be further accelerated for non-invasive imaging of live-cells. Conceptually, electric field control appears to be a novel tool (catalyst) to drive, and possibly even tune, the reactivity of organic molecules.

Understanding the Reactivity of CO3·- and NO2· Radicals toward S-Containing and Aromatic Amino Acids.

The reactivity of CO3·- and NO2· radicals toward six amino acid side chains namely, cysteine (Cys), methionine (Met), phenylalanine (Phe), tyrosine (Tyr), histidine (His), and tryptophan (Trp), has been explored using state-of-art density functional theory (DFT) and transition state theory (TST). Three reaction mechanisms, namely hydrogen atom abstraction (HAT), radical adduct formation (RAF), and single electron transfer (SET), have been considered for detailed study. While CO3·- radical is highly reactive toward majority of amino acids, the reactivity of NO2· radical is limited. The CO3·- radical creates oxidative damage to amino acid residues predominantly via HAT mechanism with moderate to high rate constant. Kinetic data suggest that tryptophan and tyrosine moiety possess the highest reactivity while the phenylalanine furnishes slow reaction. On the other hand, NO2· radical cannot produce direct damage toward most of the amino acids except tryptophan and histidine. The NO2· radical reacts exclusively by SET mechanism with 6.01 × 106 M-1 s-1 and 4.69 × 102 M-1 s-1 rate constant for Trp and His, respectively. Therefore, the CO3·- radical may cause severe damage to amino acid side chains during oxidative stress conditions, whereas the NO2· radical is mostly inert. Moreover, the reaction of CO3·- and NO2· radicals with amino acid radical intermediates generate variety of oxidation and nitro products which explain the formation of different experimentally characterized biomarkers during oxidative stress.

Tunneling Control: Competition between 6π-Electrocyclization and [1,5]H-Sigmatropic Shift Reactions in Tetrahydro-1H-cyclobuta[e]indene Derivatives.

Direct dynamics calculation using canonical variational transtition state theory (CVT) inclusive of small curvature tunneling (SCT) reveals the influential role of quantum mechanical tunneling (QMT) for 2,2a,5,7b-tetrahydro-1H-cyclobuta[e]indene derivatives (2a-2j) in governing their product selectivity. 2a-2j follow two distinct reaction channels, namely, 6π-electrocyclization (2 → 3) and [1,5]H-sigmatropic shift (2 → 4), among which the activation barrier is higher for [1,5]H-shift (2 → 4), thereby favoring the kinetically controlled product (3a-3j) as anticipated. However, SCT calculations show that a narrower barrier and smaller mass of participating atoms make QMT more pronounced for [1,5]H-shift reaction despite its higher activation energy, which results in a competition between kinetic controlled (2 → 3) and tunneling controlled (2 → 4) products. At low temperature (T ≤ 170 K), when QMT is the dominant pathway, the tunneling controlled product (4a-4j) is formed exclusively. As the reaction temperature increases, the role of QMT becomes less prominent and eventually gets kinetically controlled at room temperature. Nevertheless, QMT strongly tunes the product ratio at ambient temperatures by favoring the [1,5]H-shift reaction over 6π-electrocyclization. For 2a, k[1,5]H-shift:k6π-electrocyclization increases from 1:13 at CVT level to 1:2 at CVT+SCT level for room temperature.

Strain Control: Reversible H2 Activation and H2/D2 Exchange in Pt Complexes.

Experiments have indicated that bulky ligands are required for efficient H2 activation by Pt-Sn complexes. Herein, we unravel the mechanisms for a Pt-Sn complex, Pt(Sn(t)Bu3)2(CN(t)Bu)2 (1a), catalyzed reversible H2 activation. Among a number of Pt-Sn catalysts used to model H2 activation and H2/D2 exchange reactions, only 1a with large strain was found to be suitable because the addition of H2 to 1a requires lowest distortion energy, minimal structural changes, and smallest entropy of activation. The activity of this Pt-Sn complex was compared vis-à-vis its Pt-Ge and Pt-Si analogues, and we predicted that strained Pt-Ge complex can efficiently activate H2 reversibly. Direct dynamics calculations for the rate of reductive elimination of H2, HD, and D2 from Pt(Sn(t)Bu3)(CN(t)Bu)2H3 (4a) and Pt(Sn(t)Bu3)(CN(t)Bu)2HD2 (4a([2D])) shows that H/D atom tunneling contributes significantly, which leads to an enhanced kinetic isotope effect. Strain control is suggested as a design concept in H2 activation.

Role of Heavy Atom Tunneling in Myers-Saito Cyclization of Cyclic Enyne-Cumulene Systems.

Direct dynamics calculation using canonical variational transtition state theory (CVT) inclusive of small curvature tunneling (SCT) reveals heavy atom tunneling in Myers-Saito cyclization of 10- and 9-membered cyclic enyne-cumulene systems like 1,6-didehydro[10]annulene and derivative of neocarzinostatin, respectively. The pure density functional theory functional, BLYP at a 6-31+G (d,p) basis set reproduce the observed reaction energies and barriers within 1.0 kcal/mol. The calculated rate constants of cyclization inclusive of heavy atom tunneling (k(CVT+SCT) = 3.26 × 10(-4) s(-1) at 222 K; t1/2 = 35 min) are in excellent agreement with experiments (t1/2 ∼ 21-31 min). Both primary and secondary kinetic isotope effect (KIE) become enhanced significantly upon inclusion of quantum mechanical tunneling. An Arrhenius plot of KIE shows measurable curvature at the experimental temperature of 222 K. The translation vector for the cyclization reactions in the transition-states (TS) show significant motion of primary and secondary carbon atoms explaining the origin of large KIE.

Metal Free Azide-Alkyne Click Reaction: Role of Substituents and Heavy Atom Tunneling.

Metal free click reactions provide an excellent noninvasive tool to modify and understand the processes in biological systems. Release of ring strain in cyclooctynes on reaction with azides on the formation of triazoles results in small activation energies for various intermolecular Huisgen reactions (1-9). Substitution of difluoro groups at the α, α' position of the cyclooctyne ring enhances the rates of cycloadditions by 10 and 20 times for methyl azide and benzyl azide respectively at room temperature. The computed rate enhancement on difluoro substitution using direct dynamical calculations using the canonical variational transition state theory (CVT/CAG) with small curvature tunneling (SCT) corrections are in excellent agreement with the experimental results. For the intramolecular click reaction (10) notwithstanding its much higher activation energy, quantum mechanical tunneling (QMT) enhances the rate of cycloaddition significantly and increases the N(14)/N(15) primary kinetic isotope effect at 298 K. QMT is shown to be rather efficient in 10 due to a thin barrier of ∼2.4 Å. The present study shows that tunneling effects can be significant for intramolecular click reactions.

Understanding the mechanisms of unusually fast H-H, C-H, and C-C bond reductive eliminations from gold(III) complexes.

Carbon-carbon bond reductive elimination from gold(III) complexes are known to be very slow and require high temperatures. Recently, Toste and co-workers have demonstrated extremely rapid CC reductive elimination from cis-[AuPPh3 (4-F-C6 H4 )2 Cl] even at low temperatures. We have performed DFT calculations to understand the mechanistic pathway for these novel reductive elimination reactions. Direct dynamics calculations inclusive of quantum mechanical tunneling showed significant contribution of heavy-atom tunneling (>25 %) at the experimental reaction temperatures. In the absence of any competing side reactions, such as phosphine exchange/dissociation, the complex cis-[Au(PPh3 )2 (4-F-C6 H4 )2 ](+) was shown to undergo ultrafast reductive elimination. Calculations also revealed very facile, concerted mechanisms for HH, CH, and CC bond reductive elimination from a range of neutral and cationic gold(III) centers, except for the coupling of sp(3) carbon atoms. Metal-carbon bond strengths in the transition states that originate from attractive orbital interactions control the feasibility of a concerted reductive elimination mechanism. Calculations for the formation of methane from complex cis-[AuPPh3 (H)CH3 ](+) predict that at -52 °C, about 82 % of the reaction occurs by hydrogen-atom tunneling. Tunneling leads to subtle effects on the reaction rates, such as large primary kinetic isotope effects (KIE) and a strong violation of the rule of the geometric mean of the primary and secondary KIEs.

Tunneling assists the 1,2-hydrogen shift in N-heterocyclic carbenes.

At room temperature, 1,2-hydrogen-transfer reactions of N-heterocyclic carbenes, like the imidazol-2-ylidene to give imidazole is shown to occurr almost entirely (>90 %) by quantum mechanical tunneling (QMT). At 60 K in an Ar matrix, for the 2, 3-dihydrothiazol-2-ylidene→thiazole transformation, QMT is shown to increase the rate about 10(5)  times. Calculations including small-curvature tunneling show that the barrier for intermolecular 1,2-hydrogen-transfer reaction is small, and QMT leads to a reduced rate of the forward reaction because of nonclassical reflections even at room temperature. A small barrier also leads to smaller kinetic isotope effects because of efficient QMT by both H and D. QMT does not always lead to faster reactions or larger KIE values, particularly when the barrier is small.

Role of quantum mechanical tunneling on the γ-effect of silicon on carbenes in 3-trimethylsilylcyclobutylidene.

Quantum mechanical tunneling (QMT) is increasingly being realized as an important phenomenon that can enhance the rate of reactions even at room temperature. Recently, the ability of a trimethylsilane (TMS) group to activate 1,3-H shift to a carbene from a γ-position has been demonstrated. Direct dynamical calculations (using canonical varitational transition state theory) inclusive of small curvature tunneling (CVT-SCT) show that QMT plays a decisive role in such 1,3-hydrogen migration in both the presence and absence of TMS. The presence of a TMS group reduces the activation energy of 1,3-H shift reaction via 1,3-equatorial interaction of the TMS group with the carbene. Tunneling across the smaller barrier enhances the overall forward rate of the reaction. The Arrhenius plot for the reaction shows substantial curvature in comparison to the CVT mechanism at room temperature. Arrhenius plots for the kinetic isotope effects (KIEs) for the γ-deuterated and per deuterated 3-trimethylsilylcyclobutylidene also show strong deviations from the classical over the barrier mechanism. The magnitude of the KIE is suggestive of QMT from the vibrational excited states of the carbenes.