Conformational Isomers of Calcineurin Follow Distinct Dissociation Pathways

In the gas-phase, ions of protein complexes typically follow an asymmetric dissociation pathway upon collisional activation, whereby an expelled small monomer takes a disproportionately large amount of the charges from the precursor ion. This phenomenon has been rationalized by assuming that upon activation, a single monomer becomes unfolded, thereby attracting charges to its newly exposed basic residues. Here, we report on the atypical gas-phase dissociation of the therapeutically important, heterodimeric calcium/calmodulin-dependent serine/threonine phosphatase calcineurin, using a combination of tandem mass spectrometry, ion mobility mass spectrometry, and computational modeling. Therefore, a hetero-dimeric calcineurin construct (62?kDa), composed of CNa (44?kDa, a truncation mutant missing the calmodulin binding and auto-inhibitory domains), and CNb (18?kDa), was used. Upon collisional activation, this hetero-dimer follows the commonly observed dissociation behavior, whereby the smaller CNb becomes highly charged and is expelled. Surprisingly, in addition, a second atypical dissociation pathway, whereby the charge partitioning over the two entities is more symmetric is observed. The presence of two gas-phase conformational isomers of calcineurin as revealed by ion mobility mass spectrometry (IM-MS) may explain the co-occurrence of these two dissociation pathways. We reveal the direct relationship between the conformation of the calcineurin precursor ion and its concomitant dissociation pathway and provide insights into the mechanisms underlying this co-occurrence of the typical and atypical fragmentation mechanisms.     

Pathways to Triplet or Singlet Oxygen during the Dissociation of Alkali Metal Superoxides: Insights by Multireference Calculations of Molecular Model Systems

Recent experimental investigations demonstrated the generation of singlet oxygen during charging at high potentials in lithium/oxygen batteries. To contribute to the understanding of the underlying chemical reactions a key step in the mechanism of the charging process, namely, the dissociation of the intermediate lithium superoxide to oxygen and lithium, was investigated. Therefore, the corresponding dissociation paths of the molecular model system lithium superoxide (LiO₂) were studied by CASSCF/CASPT2 calculations. The obtained results indicate the presence of different dissociation paths over crossing points of different electronic states, which lead either to the energetically preferred generation of triplet oxygen or the energetically higher lying formation of singlet oxygen. The dissociation to the corresponding superoxide anion is energetically less preferred. The understanding of the detailed reaction mechanism allows the design of strategies to avoid the formation of singlet oxygen and thus to potentially minimize the degradation of materials in alkali metal/oxygen batteries. The calculations demonstrate a qualitatively similar but energetically shifted behavior for the homologous alkali metals sodium and potassium and their superoxide species. Fundamental differences were found for the covalently bound hydroperoxyl radical.     

Transition Metal Ions: Charge Carriers that Mediate the Electron Capture Dissociation Pathways of Peptides

Electron capture dissociation (ECD) of model peptides adducted with first row divalent transition metal ions, including Mn²⁺, Fe²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺, were investigated. Model peptides with general sequence of ZGGGXGGGZ were used as probes to unveil the ECD mechanism of metalated peptides, where X is either V or W; and Z is either R or N. Peptides metalated with different divalent transition metal ions were found to generate different ECD tandem mass spectra. ECD spectra of peptides metalated by Mn²⁺ and Zn²⁺ were similar to those generated by ECD of peptides adducted with alkaline earth metal ions. Series of c-/z-type fragment ions with and without metal ions were observed. ECD of Fe²⁺, Co²⁺, and Ni²⁺ adducted peptides yielded abundant metalated a-/y-type fragment ions; whereas ECD of Cu²⁺ adducted peptides generated predominantly metalated b-/y-type fragment ions. From the present experimental results, it was postulated that electronic configuration of metal ions is an important factor in determining the ECD behavior of the metalated peptides. Due presumably to the stability of the electronic configuration, metal ions with fully-filled (i.e., Zn²⁺) and half filled (i.e., Mn²⁺) d-orbitals might not capture the incoming electron. Dissociation of the metal ions adducted peptides would proceed through the usual ECD channel(s) via “hot-hydrogen” or “superbase” intermediates, to form series of c-/z ^•- fragments. For other transition metal ions studied, reduction of the metal ions might occur preferentially. The energy liberated by the metal ion reduction would provide enough internal energy to generate the “slow-heating” type of fragment ions, i.e., metalated a-/y- fragments and metalated b-/y- fragments.     

Algorithm for Calculating the Dissociation Constants of Ampholytes in Nonbuffer Systems

An algorithm for calculating the dissociation constants of ampholytes in aqueous solutions is developed on the basis of spectrophotometric data in the UV and visible ranges without pH measurements of a medium and without buffer solutions. The proposed algorithm has been experimentally tested for five ampholytes of different strengths. The relative error of measuring dissociation constants is less than 5%.     

机械力响应高分子体系的原理、构建与应用

具有刺激响应特性的高分子材料是目前高分子研究中的重要领域。机械力作为一种新型的刺激源,具有与传统光、热等刺激源不同的特点。机械应力刺激可以从来源上分为宏观机械力与微观机械力,宏观机械力早在人类发展初期已被广泛用于高分子材料的处理。而微观机械力对高分子作用的原理和应用近年来才逐渐成为研究重点。本文从高分子机械力响应的原理出发,分类阐述了各种机械力响应系统。其中,按照断裂的化学键将其分为共价键体系和非共价键体系。而共价键体系可以进一步按照环状结构与线型结构分为两大类。此外,本文还总结了已有应用,包括用于应力拆分外消旋体、应力活化催化剂及应力用于研究反应机理等。     

Elucidation of Binding Features and Dissociation Pathways of Inhibitors and Modulators in SARS-CoV-2 Main Protease by Multiple Molecular Dynamics Simulations

COVID-19 can cause different neurological symptoms in some people, including smell, inability to taste, dizziness, confusion, delirium, seizures, stroke, etc. Owing to the issue of vaccine effectiveness, update and coverage, we still need one or more diversified strategies as the backstop to manage illness. Characterizing the structural basis of ligand recognition in the main protease (M^pro) of SARS-CoV-2 will facilitate its rational design and development of potential drug candidates with high affinity and selectivity against COVID-19. Up to date, covalent-, non-covalent inhibitors and allosteric modulators have been reported to bind to different active sites of M^pro. In the present work, we applied the molecular dynamics (MD) simulations to systematically characterize the potential binding features of catalytic active site and allosteric binding sites in M^pro using a dataset of 163 3D structures of M^pro-inhibitor complexes, in which our results are consistent with the current studies. In addition, umbrella sampling (US) simulations were used to explore the dissociation processes of substrate pathway and allosteric pathway. All the information provided new insights into the protein features of M^pro and will facilitate its rational drug design for COVID-19.     

Interface Orientation and Chain Conformation in Simulated Symmetric Diblock Copolymer Lamellar Systems

Summary: We describe the results of Monte Carlo simulations, based on the cooperative motion algorithm, of the lamellar structure generated at finite temperature by a symmetric diblock copolymer. The (70 × 70 × 70) simulation box in which the polymer chains were embedded for each simulation was rotated, based on the interface orientation, to bring the interfacial planes of the simulated structure into parallel. We found that the interface thickness, as defined by the distribution of the junction points, became narrower at lower temperature, and that the interface plane was characterized by a waviness with a maximum peak‐to‐valley distance of 20–30 lattice bonds. Compared with the isotropic state (T/N = ∞), chains at lower temperatures were stretched in the direction perpendicular to the interface; but only modestly compressed in the direction parallel to the interface. Individual block chains within the lamellar domains still behave like random coils. The block copolymer molecules exhibit only a modest tendency to orient themselves with their end‐to‐end vector perpendicular to the plane of the lamellar interface. Considered as an ensemble average, the results we obtained are similar to those reported from small angle neutron scattering measurements for the mean conformation of the PSd blocks of symmetrical PSd‐PVP diblock copolymers.

2‐D projections onto the X‐Z plane of the end beads for the A‐ and B‐chains (gray) and the junction points J (black) at T/N = 0.2. The interface plane is oriented parallel to the Y‐Z plane by rotating the simulation box. The distribution profiles of junction points and the end beads across the system in the direction of interface normal are shown in the lower part of the figure.     

Noscapine Prevents Rotenone-Induced Neurotoxicity: Involvement of Oxidative Stress,Neuroinflammation and Autophagy Pathways

Parkinson’s disease is characterized by the loss of dopaminergic neurons in substantia nigra pars compacta (SNpc) and the resultant loss of dopamine in the striatum. Various studies have shown that oxidative stress and neuroinflammation plays a major role in PD progression. In addition, the autophagy lysosome pathway (ALP) plays an important role in the degradation of aggregated proteins, abnormal cytoplasmic organelles and proteins for intracellular homeostasis. Dysfunction of ALP results in the accumulation of α-synuclein and the loss of dopaminergic neurons in PD. Thus, modulating ALP is becoming an appealing therapeutic intervention. In our current study, we wanted to evaluate the neuroprotective potency of noscapine in a rotenone-induced PD rat model. Rats were administered rotenone injections (2.5 mg/kg, i.p.,) daily followed by noscapine (10 mg/kg, i.p.,) for four weeks. Noscapine, an iso-qinulinin alkaloid found naturally in the Papaveraceae family, has traditionally been used in the treatment of cancer, stroke and fibrosis. However, the neuroprotective potency of noscapine has not been analyzed. Our study showed that administration of noscapine decreased the upregulation of pro-inflammatory factors, oxidative stress, and α-synuclein expression with a significant increase in antioxidant enzymes. In addition, noscapine prevented rotenone-induced activation of microglia and astrocytes. These neuroprotective mechanisms resulted in a decrease in dopaminergic neuron loss in SNpc and neuronal fibers in the striatum. Further, noscapine administration enhanced the mTOR-mediated p70S6K pathway as well as inhibited apoptosis. In addition to these mechanisms, noscapine prevented a rotenone-mediated increase in lysosomal degradation, resulting in a decrease in α-synuclein aggregation. However, further studies are needed to further develop noscapine as a potential therapeutic candidate for PD treatment.     

Chemical Empiricism 2.0 at Age of Big Data: Large-scale Prediction of Reaction Pathways Based on Bond Dissociation Energies

A programmable algorithm using bond dissociation energies has been proposed for the prediction of reaction pathways. It has been successfully applied to a gas-phase reaction of F₂+CH₃Cl, with the accurate revelation of the most favorable product CF₄ and its corresponding reaction pathway. This acts as an inspiring example of chemical empiricism 2.0, and may open the door for the large-scale prediction of reaction pathways at the age of big data.     

Electron Capture Dissociation and Collision Induced Dissociation of S-Dipalmitoylated Peptides

Here we investigate the effect of S-dipalmitoylation on the electron capture dissociation (ECD) behavior of peptides. The ECD and collision induced dissociation (CID) of peptides modified by covalent attachment of [(RS)-2,3-di(palmitoyloxy)-propyl] (PAM2) group to cysteine residues [C(PAM2)LEYDTGFK and RPPGC(PAM2)SPFK] were examined. The results suggest that ECD of S-dipalmitoylated peptides can provide both primary sequence information and structural information regarding the modification. The structural information provided by CID is complementary to that provided by ECD.

Direct Observation of Apatite Formation on Bioglass in Simulated Body Fluid by Atomic Force Microscopy

An in situ atomic force microscope (AFM) combined with surface potential measurement was used to observe the apatite formation on the 45S5 Bioglass-type glass in simulated body fluid (SBF). From the observation, it can be seen that small islands with 5-10 nm size are formed on the glass surface in the initial soaking period within 1 h.     

Stress distribution along a craze: Some consequences of knight's analysis

It is shown that the distribution of normal stress around a craze, found by Knight using a Fourier transform method may not be uniquely determined, and that in fact the stress field cannot be computed unless the rheological properties of the craze tip material are known.     

Reaction Kinetics and Reduced Shrinkage Stress of Thiol-Yne-Methacrylate and Thiol-Yne-Acrylate Ternary Systems

Thiol-yne-methacrylate and thiol-yne-acrylate ternary systems were investigated for polymerization kinetics and material properties and compared to the analogous pure thiol-yne and (meth)acrylate systems. Both thiol-yne-methacrylate and thiol-yne-acrylate systems were demonstrated to reduce polymerization induced shrinkage stress while simultaneously achieving high glass transition temperatures (T(g)) and modulius. Formulations with 70 wt% methacrylate increased the T(g) from 51 ± 2 to 75 ± 1 °C and the modulus from 1800 ± 100 to 3200 ± 400 MPa (44% increase) over the pure thiol-yne system. Additionally, the shrinkage stress was 1.2 ± 0.2 MPa, which is lower than that of the pure methacrylate, binary thiol-yne and thiol-ene-methacrylate control systems which are all > 2 MPa. Interestingly, with increasing methacrylate or acrylate concentration, a decrease and subsequent increase in the shrinkage stress values were observed. A minimum shrinkage stress value (1.0 ± 0.2 MPa) was observed in the 50 wt% methacrylate and 70 wt% acrylate systems. This tunable behavior results from the competitive reaction kinetics of the methacrylate or acrylate homopolymerization versus chain transfer to thiol and the accompanying thiol-yne step-growth polymerization. The crosslinking density of the networks and the amount of volumetric shrinkage that occurs prior to gelation relative to the total volumetric shrinkage were determined as two key factors that control the final shrinkage stress of the ternary systems.     

耗散粒子动力学与可极化ABEEM力场结合模拟嵌段共聚物自组装形态调控

本文采用介观尺度上的耗散粒子动力学与基于ABEEM可极化力场的全原子分子动力学相结合的方式,从理论上探究了嵌段共聚物结构、对称性、分子组成及温度等对嵌段共聚物最终自组装结构形态的影响.模拟结果表明,这些因素均会对嵌段共聚物在选择性溶剂中的最终自组装结构产生一定影响.这一理论研究为实现可控操纵自组装结构,提供了有意义的参考.     

均三溴氯磺酚离解与质子化作用的研究

本文报道测钪新试剂均三溴氯磺酚在水溶液中的离解与质子化作用，用电位法和光度法测得了它的逐级离解常数与质子化常数，以及热力学参数，并由分布函数获得试剂主要存在形式和ｐＨ值的关系。