The Journal of Physical Chemistry B最新文献

Passive and targeted delivery of peptides to cells and organelles is a fundamental biophysical process controlled by membranes surrounding biological compartments. Embedded proteins, phospholipid composition, and solution conditions contribute to targeted transport. An anticancer peptide, NAF-1^44-67, permeates to cancer cells but not to normal cells. The mechanism of this selectivity is of significant interest. However, the complexity of biomembranes makes pinpointing passive targeting mechanisms difficult. To dissect contributions to selective transport by membrane components, we constructed simplified phospholipid vesicles as plasma membrane (PM) models of cancer and normal cells and investigated NAF-1^44-67 permeation computationally and experimentally. We use atomically detailed simulations with enhanced sampling techniques to study kinetics and thermodynamics of the interaction. Experimentally, we study the interaction of the peptide with large and giant unilamellar vesicles. The large vesicles were investigated with fluorescence spectroscopy and the giant vesicles with confocal microscopy. Peptide permeation across a model of cancer PM is more efficient than permeation across a PM model of normal cells. The investigations agree on the mechanism of selectivity, which consists of three steps: (i) early electrostatic attraction of the peptide to the negatively charged membrane, (ii) the penetration of the peptide hydrophobic N-terminal segment into the lipid bilayer, and (iii) exploiting short-range electrostatic forces to create a defect in the membrane and complete the permeation process. The first step is kinetically less efficient in a normal membrane with fewer negatively charged phospholipids. The model of a normal membrane is less receptive to defect creation in the third step.

Peptides hold great promise for safe and effective treatment of viral infections. However, their use is often constrained by limited efficacy and high production costs, especially for long or complex peptide chains. Here, we used ReaxFF molecular dynamics (MD) simulations to optimize the size and activity of VIRIP (Virus Inhibitory Peptide), a naturally occurring 20-residue fragment of α1-antitrypsin that binds the HIV-1 GP41 fusion peptide (FP), thereby blocking viral fusion and entry into host cells. Specifically, we used the NMR structure of the complex between an optimized VIRIP derivative (VIR-165) and the HIV-1 gp41 FP for ReaxFF-guided in silico analysis, evaluating the contribution of each amino acid in the interaction of the inhibitor with its viral target. This approach allowed us to reduce the size of the HIV-1 FP inhibitor from 20 to 10 amino acids (2.28–1.11 kDa). HIV-1 infection assays showed that the size-optimized VIRIP derivative (soVIRIP) retains its broad-spectrum anti-HIV-1 capability and is nontoxic in the vertebrate zebrafish model. Compared to the original VIRIP, soVIRIP displayed more than 100-fold higher antiviral activity (IC₅₀ of ∼120 nM). Thus, it is more potent than a dimeric 20-residue VIRIP derivative (VIR-576) that was proven safe and effective in a phase I/II clinical trial. Our results show that ReaxFF-based MD simulations represent a suitable approach for the optimization of therapeutic peptides.

Nanopore sensing relies on associating the measured current signals with specific features of the target molecules. The diversity of amino acids presents significant challenges in detecting and sequencing peptides and proteins. The hollow and uniform tubular structure of single-walled carbon nanotubes (SWCNTs) makes them ideal candidates for nanopore sensors. Here, we demonstrate by molecular dynamics simulations the discrimination and translocation of charged proteinogenic amino acids through the nanopore sensor formed by inserting a SWCNT into lipid bilayers. Moreover, our analysis suggests that the current blockade is influenced not only by excluded atomic volume but also by noncovalent interactions between amino acids and SWCNT during similar helical translocation. The presence of noncovalent interactions enhances the understanding of current differences in nanopore translocation of molecules with similar excluded atomic volume. This finding provides new perspectives and applications for the optimal design of SWCNT nanopore sensors.

Mitochondrial neurogastrointestinal encephalopathy (MNGIE) is a rare metabolic disorder caused by missense mutations in the TYMP gene, leading to the loss of human thymidine phosphorylase (HTP) activity and subsequent mitochondrial dysfunction. Despite its well-characterized biochemical basis, the molecular mechanisms by which MNGIE-associated mutations alter HTP's structural stability, dynamics, and substrate (thymidine) binding remain unclear. In this study, we employ a multiscale computational approach, integrating AlphaFold2-based structural modeling, all-atom and coarse-grained molecular dynamics (MD) simulations, protein-ligand (HTP-thymidine) docking, HTP-thymidine complex simulations, binding free-energy landscape analysis, and systematic mutational profiling to investigate the impact of key MNGIE-associated mutations (R44Q, G145R, G153S, K222S, and E289A) on HTP function. Analyses of our long-duration multiscale simulations (comprising 9 μs coarse-grained, 1.2 μs all-atom apo HTP, and 1.2 μs HTP-thymidine complex MD simulations) and physicochemical properties reveal that while wild-type HTP maintains structural integrity and strong thymidine-binding affinity, MNGIE-associated mutations induce substantial destabilization, increased flexibility, and reduced enzymatic efficiency. Free-energy landscape analysis highlights a shift toward less stable conformational states in mutant HTPs, further supporting their functional impairment. Additionally, the G145R mutation introduces steric hindrance at the active site, preventing thymidine binding and causing off-site interactions. These findings not only provide fundamental insights into the physicochemical and dynamic alterations underlying HTP dysfunction in MNGIE but also establish a computational framework for guiding future experimental studies and the rational design of therapeutic interventions aimed at restoring HTP function.

We show that in low dielectric constant (ε_r) solvents, the prototypical cationic photoredox catalyst [Ir(III)(dFCF₃ppy)₂-(5,5′-dCF₃bpy)]⁺ is capable of oxidizing its counterion in an unexpected photoinduced electron transfer (PET) process. Photoinduced oxidation of the tetrakis[3,5-bis(trifluoromethyl)phenyl]borate (abbv. [BAr₄^F]⁻) anion leads to its irreversible decomposition and a buildup of the neutral Ir(III)(dFCF₃ppy)₃-(5,5′-dCF₃ bpy^·–) (abbv. [Ir(dCF₃^·-)]⁰) species. The rate constant of the PET reaction, k_rxn, between the two oppositely charged ions was determined by monitoring the growth of absorption features associated with the singly reduced product molecule, [Ir(dCF₃^·–)]⁰, in various solvents with a range of ε_r. The PET reaction between the ions of [Ir(dCF₃) – BAr₄^F] is predicted to be nonspontaneous (ΔG_PET ≥ 0) in high ε_r solvents, such as acetonitrile, and we observe that k_rxn ≃ 0 under these circumstances. However, k_rxn increases as ε_r decreases. We attribute this change in spontaneity to the electrostatic work described by the Born (ΔG_S) and Coulomb ($W$) correction terms to the change in Gibbs free energy of a PET (ΔG_PET). The electrostatic work associated with these often-neglected corrections can be utilized to design novel and surprising photoredox chemistry. Our facile preparation of [Ir(dCF₃^·–)]⁰ is one example of a general rule: ion-paired reactants can result in energetic neutral products that chemically store photon energy without an associated Coulomb binding between them.

Pterin (Ptr) is the model compound of aromatic pterins, which are efficient photosensitizers present in human skin and are able to oxidize biomolecules upon UVA irradiation. Photosensitization involves chemical alteration of a biomolecule as a result of the initial absorption of radiation by another chemical species, the photosensitizer. Under anaerobic conditions, Ptr reacts with thymine (T) to form photoadducts (T-Ptr). In this work, we present a method to prepare and purify T-Ptr adducts, using 2'-deoxythymidine 5'-monophosphate (dTMP) and single stranded oligonucleotide 5'-d(TTTTT)-3' (dT₅), and investigate their photosensitizing properties. Interestingly, the Ptr moiety, when attached to T, retains its photophysical properties. The adduct dTMP-Ptr, upon excitation, forms singlet and triplet excited states, the latter being capable of transferring energy to dissolved O₂ and generating singlet oxygen, with an efficiency similar to Ptr. In air-equilibrated solutions, both dTMP-Ptr and dT₅-Ptr adducts can photosensitize the oxidation of tryptophan and 2'-deoxyguanosine 5'-monophosphate, two of the main targets of photosensitization in biological systems, with efficiencies close to that of free Ptr. The mechanisms involved in the oxidation of biomolecules can be either type I (electron transfer) or type II (singlet oxygen).

The initial light-induced electron transfer (ET) steps in the bacterial photosynthetic reaction center (RC) have been extensively studied and provide a paradigm for connecting structure and function. Although RCs have local pseudo-C₂ symmetry, ET only occurs along the A branch of chromophores. Tyrosine M210 is a key symmetry-breaking residue adjacent to bacteriochlorophyll B_A that bridges the primary electron donor P and the bacteriopheophytin acceptor H_A. We used amber suppression to incorporate phenylalanine variants with different electron-withdrawing/-donating capabilities at the position M210. X-ray data generally reveal no appreciable structural changes due to the mutations. P* decay and P⁺H_A^- formation are multiexponential (∼2 to 9, ∼10 to 60, and ∼100 to 300 ps) and temperature dependent. The 1020 nm transient-absorption band of P⁺B_A^- is barely resolved for a few variants at 295 K and for none at 77 K. The results indicate a change from two-step ET for wild-type RCs to the dominance of one-step superexchange ET for the mutants. Resonance Stark spectroscopy reveals that the free energy of P⁺B_A^- changes by -57 to +66 meV among the phenylalanine variants. Because P⁺B_A^- apparently lies above P* in all phenylalanine variants, the perturbations primarily affect the energy denominator for superexchange mixing. The findings deepen insight into primary ET in the bacterial RC.

We compute the potential of mean force (PMF) between semicrystalline polyethylene (PE) nanoplastics (NPLs) and model POPC and DPPC bilayers, which approximate in vivo membranes, using atomistic simulations. Our work shows that atomistic resolution is required to characterize the NPL and lipid interactions. By analyzing the PMF, we demonstrate that the mechanical properties of membranes, rather than NPL semicrystalline morphologies, govern NPL-membrane interactions. Resistance to NPL penetration arises from the elastic energy of the membrane deformation. The flexible POPC membranes resist NPL translocation, and the brittle DPPC membranes fracture under stress. Using an elastic free energy model, we approximate effective repulsions between lipid membranes and NPLs of various sizes. Our mean first-passage time analysis shows that even small, bare NPLs cannot easily penetrate brittle lipid membranes via passive diffusion, even at high concentrations. However, eco-coronas or other mechanisms, such as endocytosis, may still facilitate the cellular uptake of NPLs and MPLs. While semicrystalline morphologies do not directly impact NPL translocation, they do influence NPL behavior within lipid membranes upon translocation. Semicrystalline NPLs remain intact within lipid membranes, whereas amorphous NPLs can dissolve into the hydrophobic core and alter the elastic properties of the membrane.

Conjugated polymers are indispensable building blocks in a variety of organic electronics applications such as solar cells, light-emitting diodes, and field-effect transistors. Poly[N-9'-heptadecanyl-2,7-carbazole-alt-5,5-(4',7'-di-2-thienyl-2',1',3'-benzothiadiazole)] (PCDTBT) is a carbazole-benzothiadiazole-based copolymer with a donor-acceptor structure, consisting of electron-donating and electron-withdrawing subunits and featuring a low band gap. In this work, the General Amber Force Field is extended in two ways, specifically for modeling PCDTBT. First, a set of partial atomic charges is derived that mimic a long chain and adequately describe different conformations that may be encountered in a bulk environment. Second, torsional terms are reparametrized for all dihedral angles in the backbone via ab initio computations. Subsequently, a series of large-scale Molecular Dynamics simulations are employed to construct and equilibrate bulk ensembles of three PCDTBT oligomers using different starting conformations of the oligomer chains. Several structural properties are computed, namely mass density, chain stiffness (through persistence length and Kuhn segment length), and glass transition temperature. Our results are in good agreement with available literature data, demonstrating the suitability of the new parametrization.

A retinylidene photoreceptor from the cyanobacterium Mastigocladopsis repens (MrHR) is a novel type of light-driven Cl^– pump that has a structural similarity to the archaeal H⁺ pumps but transports Cl^–. An open question regarding the photocycle of this photoreceptor involves the role of a late red-shifted photoproduct, the O intermediate, which is reportedly present at high Cl^– concentrations. In this study, we used cryo-Raman spectroscopy to examine the chromophore structures of the photointermediates at a high Cl^– concentration. When compared to the photointermediates formed as MrHR + hv → K → L → N1 → N2 → MrHR′ at a low Cl^– concentration, we found that N2 kinetically disappears at a high Cl^– concentration. This indicated that N2 is the transient Cl^–-unbound state of MrHR. In addition, we found that no Raman signal of the O intermediate is observed at the high Cl^– concentration, while the signal from N1 is exclusively observed in the later stages of the photocycle. After confirming that N1’s absorption spectrum displays an extending red edge, we concluded that the O intermediate is attributable to the red edge of the absorption band of N1. Here, we report a revised understanding of the photocycle for Cl^– transport of MrHR.