Dual mechanisms of Bcl-2 regulation in IP3-receptor-mediated Ca2+ release: A computational study

Inositol 1,4,5-trisphosphate receptors (IP₃R)-mediated calcium ion (Ca²⁺) release plays a central role in the regulation of cell survival and death. Bcl-2 limits the Ca²⁺ release function of the IP₃R through a direct or indirect mechanism. However, the two mechanisms are overwhelmingly complex and not completely understood. Here, we convert the mechanisms into a set of ordinary differential equations. We firstly simulate the time evolution of Ca²⁺ concentration under two different levels of Bcl-2 for the direct and indirect mechanism models and compare them with experimental results available in the literature. Secondly, we employ one- and two-parameter bifurcation analysis to demonstrate that Bcl-2 can suppress Ca²⁺ signal from a global point of view both in the direct and indirect mechanism models. We then use mathematical analysis to clarify that the indirect mechanism is more efficient than the direct mechanism in repressing Ca²⁺ signal. Lastly, we predict that the two mechanisms restrict Ca²⁺ signal synergistically. Together, our study provides theoretical insights into Bcl-2 regulation in IP₃R-mediated Ca²⁺ release, which may be instrumental for the successful development of therapies to target Bcl-2 for cancer treatment.     

Bcl-2蛋白抑制钙信号的建模与全局动力学分析

钙离子(Ca~(2+))是生物体内一种"生死攸关"的信号分子,Bcl-2蛋白可以直接或间接调节IP_3R通道释放Ca~(2+)的能力,借此决定细胞命运.本文基于新近的实验成果,针对Bcl-2蛋白间接调控Ca~(2+)的信号通路建立数学模型,得到了与实验数据相符合的结果,从理论上证明了Bcl-2蛋白对钙信号有抑制作用.在对模型进行鲁棒性检验之后,本文对该信号通路中一些关键组分的作用进行了预测.以[IP_3]和[Bcl-2]为双分岔参数分析的结果表明Bcl-2对刺激强度能产生Ca~(2+)振荡的区域有重要影响.以蛋白磷酸酶1[PP1]和蛋白激酶A[PKA]为单分岔参数分析的结果揭示:PP1可以有效地抑制钙信号,而PKA对钙信号的促进作用有一定的局限性.模型结果表明,不同浓度组合的IP_3,Bcl-2和PKA会对钙信号发挥复杂的调控作用.本文不仅对相关生物学实验有一定的指导作用,而且可为治疗因钙信号失调而导致的疾病提供思路.     

Computational study on mechanisms and pathways of the atmospheric NH2 + IO reaction

ABSTRACT

The potential-energy surfaces of the amino radical (NH₂) with IO reaction have been studied at the CCSD(T)/cc-pVTZ//MP2/6-311++G(d,p) level. Two kinds of pathways are revealed, namely H-abstraction and addition/elimination. Rice–Ramsperger–Kassel–Marcus theory and transition state theory are employed to calculate the overall and individual rate constants over a wide range of temperatures and pressures. It is predicted that, at atmospheric pressure with N2 as bath gas, the formation of P1 (HI?+?HNO) is the dominant pathways at 200–700?K, while the direct H-abstraction leading to P3 (³NH?+?HOI) takes over the reaction at a temperature above 700?K. At the high-pressure limit, IM1 [IONH₂] formed by collisional stabilisation is dominant at 200–700?K; the direct H-abstraction resulting in P3 (³NH?+?HOI) plays an important role at higher temperatures. However, the total rate constants are independence on the pressure; however, the individual rate constants are sensitive to pressure. The atmospheric lifetime of NH₂ in IO is around one week. TD-DFT computations imply that IM1 [IONH₂], IM1A [IONH₂′], IM2 [IN(H₂)O], IM3 [OINH₂], IM4 [HOINH], tra-IM5 [tra-HON(H)I] and cis-IM5 [cis-HON(H)I] will photolyze under the sunlight.     

DFT study on abstraction reaction mechanism of oh radical with 2‐methoxyphenol

Reaction mechanism of 2‐methoxyphenol (2MP) (guaiacol) with OH radical has been performed using density functional theory methods BH&HLYP and MPW1K method with 6‐311++G(d,p) basis set. Single‐point energy calculations were done using CCSD(T)/6‐311++G(d,p). The theoretical results reveal that the hydrogen abstraction from methoxy group is found to be the dominant reaction channel with an energy barrier of 9.31 kcal/mol. Also, time‐dependent density functional theory calculations have been performed using BH&HLYP/6‐311++G(d,p) level of theory, and the results reveal that the reactions occur in ground state than the excited state. The results of reaction force profile indicate that structural rearrangements are most influential with high percentage than the relaxation process. The calculated theoretical rate constants (12.19 × 10^?11 cm³ molecule^?1 s^?1) are in good agreement with the experimental rate constant. The atmospheric lifetime of 2‐methoxyphenol with respect to OH radicals is 2.27 hours, which implies that OH radical plays an important role in the degradation of 2MP. The Wiberg bond index of the abstraction reaction reveals that the bond order is concerted, partially synchronic. The reactant‐like transition state satisfies Hammond postulate, which eventually results in an exothermic reaction, and the product‐like transition state reveals in endothermic nature.     

CH3CH2O及CH3CHOH与HO2反应机理的理论研究

采用CCSD(T)/cc-pVTZ//B3LYP/6-311++G(2df,2p)水平上对CH3CHOH + HO2和CH3CH2O + HO2反应体系的单、三重态反应机理进行了详细的理论研究.计算结果表明,CH3CHOH + HO2反应主要发生在单重态势能面上,其中四条通道均为快速自发过程;CH3CH2O + HO2反应在三重态势能面上的通道CH3CH2O + HO2 → 3IM11 → 3TS11 → P11 (CH3CH2OH + 3O2)为动力学和热力学的优势路径. 大气中CH3CHOH比CH3CH2O更容易稳定存在.     

Cu纳米粒催化CO2还原反应机理的理论研究

此文采用密度泛函理论,研究了Cu₃₈纳米粒催化剂模型,分别研究了CO₂和H₂O分子在催化剂上不同吸附位,确了稳定的吸附构型,并进一步研究了CO₂催化还原反应机理,确定催化剂的活性.本文主要研究催化CO₂还原生成CO过程,研究了两条可行的反应路径,路径I为水分子的H原子直接转移到CO₂上,路径II为H原子先迁移到Cu₃₈纳米粒上再转移到CO₂上,研究结果发现此步反应机理路径I优先.从微观角度解释了实验研究结果.     

CH3CH2O及CH3CHOH与HO2反应机理的理论研究

采用CCSD(T)/cc-pVTZ//B3LYP/6-311++G(2df,2p)水平上对CH3CHOH + HO2和CH3CH2O + HO2反应体系的单、三重态反应机理进行了详细的理论研究.计算结果表明,CH3CHOH + HO2反应主要发生在单重态势能面上,其中四条通道均为快速自发过程;CH3CH2O + HO2反应在三重态势能面上的通道CH3CH2O + HO2 → 3IM11 → 3TS11 → P11 (CH3CH2OH + 3O2)为动力学和热力学的优势路径. 大气中CH3CHOH比CH3CH2O更容易稳定存在.     

CH_3CH_2O及CH_3CHOH与HO_2反应机理的理论研究

采用CCSD(T)/cc-p VTZ//B3LYP/6-311++G(2df,2p)水平上对CH_3CHOH+HO_2和CH_3CH_2O+HO_2反应体系的单、三重态反应机理进行了详细的理论研究.计算结果表明,CH_3CHOH+HO_2反应主要发生在单重态势能面上,其中四条通道均为快速自发过程;CH_3CH_2O+HO_2反应在三重态势能面上的通道CH_3CH_2O+HO_2→~3IM11→~3TS11→P11(CH_3CH_2OH+~3O_2)为动力学和热力学的优势路径.大气中CH_3CHOH比CH_3CH_2O更容易稳定存在.     

Computational study of cycloaddition reactions on the SiC(1 0 0)-c(2 × 2) surface

Cycloaddition reactions between 1,3-butadiene and the C-terminated SiC(1 0 0)-c(2 × 2) surface have been addressed using quantum-chemical methods. The c(2 × 2) structure consists of ---CC--- bridges between underlayer Si atoms which themselves form Si---Si bonds. Of various possible reaction products, the one formed by a [2 + 4] reaction with the ---CC--- bridge (giving a species resembling 1,4-cyclohexadiene) is the lowest in energy. Density functional calculations for the bare c(2 × 2) surface, using a cluster model with mechanical embedding, gave good agreement with structural parameters obtained in previous fully ab initio studies. Similar calculations for the cycloaddition product and for the transition state gave a reaction energy of −50.3 kcal/mol and an activation energy of +6.1 kcal/mol to form a planar ring structure lying normal to the surface. Detailed results for the frequency and infrared polarization behavior of adsorbate vibrational modes have also been obtained.     

自由基OH（X^П,A^2∑^＋）的从头算研究

用分子轨道从头算方法，研究了OH分子的基态(X^П)和激发态(A^2∑^+)。结果表明，对于基态，在QCISD(T)／6—311++G(3df,3pd)理论水平上，键距是0．09704nm，与实验值0．09706nm完全吻合。对于激发态，使用完全活性空间方法(CASSCF)和大基组6—311++G(3df,3pd)，键距是0．10098nm，与实验值0．10121nm基本吻合。从激发态A^2∑^+(v＝0)到基态X^П(v＝0)的垂直跃迁能量是4．4692eV，与实验值4．3980eV也吻合较好。     

第一性原理研究O_2在CrN_4掺杂石墨烯上的氢化

掺杂是调制graphene催化特性的有效方法 .掺杂的石墨烯,因其具有对氧还原反应具有较高的活性,而作为一种新型高效质子交换膜燃料电池阴极材料.采用包含色散力校正的第一性原理的密度泛函理论方法 (DFT-D)系统的研究了O_2在CrN_4掺杂的石墨烯上的吸附和氢化特性.结果表明:(1)O_2倾向于以side-on模式吸附在Cr顶位,形成O-Cr-O三元环结构,吸附能为1.75 e V;(2)O_2在Cr N4-Gra上更倾向于直接分解成O+O,并进一步氢化为O+OH,反应的限速步为O_2的分解,相应的反应势垒为0.48 e V.     

第一性原理研究O2在CrN4掺杂石墨烯上的氢化

掺杂是调制graphene催化特性的有效方法. 掺杂的Graphene, 因其具有对氧还原反应具有较高的活性, 而作为一种新型高效质子交换膜燃料电池阴极材料. 采用包含色散力校正的第一性原理的密度泛函理论方法(DFT-D)系统的研究了O2在CrN4掺杂的Graphene上的吸附和氢化特性. 结果表明: (1) O2倾向于以side-on模式吸附在Cr顶位, 形成O-Cr-O三元环结构, 吸附能为1.75 eV; (2) O2在CrN4-Gra上更倾向于直接分解成O+O, 并进一步氢化为O+OH, 反应的限速步为O2的分解, 相应的反应势垒为0.48 eV.     

A2B模型的受迫振动模式研究的注记

讨论了A2B模型的受迫振动模式研究中的一些问题.     

A first-principles study of the catalytic mechanism of the dehydriding reaction of LiNH2 through adding Ti catalysts

Experiments on a ball milled mixture with a 1:1 molar ratio of LiNH2 and LiH with a small amount(1 mol %) of Ti nano,TiCl3 and TiO nano 2 have revealed a superior catalytic effect on Li-N-H hydrogen storage materials.In the x-ray diffraction profiles,no trace of Ti nano,TiCl3 and TiO nano 2 was found in these doped composites,by which we deduced that Ti atoms enter LiNH2 by partial element substitution.A first-principles plane-wave pseudopotential method based on density functional theory has been used to investigate the catalytic effects of Ti catalysts on the dehydrogenating properties of LiNH2 system.The results show that Ti substitution can reduce the dehydrogenation reaction activation energy of LiNH2 and improve the dehydrogenating properties of LiNH2.Based on the analysis of the density of states and overlap populations for LiNH2 before and after Ti substitution,it was found that the stability of the system of LiNH2 is reduced,which originates from the increase of the valence electrons at the Fermi level(EF) and the decrease of the highest occupied molecular orbital(HOMO)-lowest unoccupied molecular orbital(LUMO) gap(△EH-L) near E F.The catalytic effect of Ti on the dehydrogenating kinetics of LiNH2 may be attributed to the reduction of average populations between N-H per unit bond length(nm-1),which leads to the reduction of the chemical bond strength of N-H.     

FeS2(100)表面原子几何与电子结构的理论研究

采用密度泛函理论研究了FeS2(100)表面原子几何与电子结构.理论计算结果表明:FeS2(100)表面无弛豫、无重构,是体相原子几何的自然终止.与体相电子结构相比,FeS2(100)表面电子特性明显不同,禁带中央产生新的表面态,且表面态局域性强,主要由Fe原子的3d分波贡献.配位场理论定性分析表明:FeS2(100)完整晶面表面态产生机制是Fe原子的配位数减少、局部对称性下降所致 关键词： 密度泛函理论 表面电子结构 FeS2     

TiO2及金属(Cu、Ni)掺杂催化材料水解制氢反应机理的理论研究

本文研究TiO₂以及金属(Cu、Ni)掺杂TiO₂催化剂水解制氢的两种不同析氢反应机理,计算了不同反应过程催化反应活化能,同时考察了系列催化剂电子激发态的催化活性.结果表明:催化剂电子激发态的催化活性增强,说明光照有助于降低反应的活化能,提高催化剂的活性.金属(Cu、Ni)掺杂TiO₂有助于降低水解制氢反应的活化能,且Cu的掺杂催化效果更明显,这与实验报道的结果一致.     

第一性原理研究O2在TiN4掺杂石墨烯上的氢化

作为一种新型高效质子交换膜燃料电池阴极材料, 金属与N共掺杂的石墨烯因其对氧还原反应具有较高的活性而引起了人们的广泛关注. 采用包含色散力校正的密度泛函理论方法系统地研究了O₂在TiN₄掺杂的Graphene上的吸附, 氢化特性. 结果表明: 1) O₂倾向于以side-on模式吸附在Ti顶位, 形成O-Ti-O三元环结构; 2) O₂在TiN₄-Graphene上更倾向于以分子形式直接氢化, 形式OOH结构, 并进一步解离为O+OH, 反应的限速步为O₂的氢化, 对应的反应势垒为0.52 eV.     

Catalytic effect of water,water dimer,water trimer,HCOOH, H2SO4, CH3CH2COOH and HN(NO2)2 on the isomerisation of HN(NO2)2 to O2NNN(O)OH: a mechanism study

In this article, the isomerisation mechanisms of HN(NO₂)₂ to O₂NNN(O)OH without and with catalyst X (X = H₂O, (H₂O)₂, (H₂O)₃, HCOOH, H₂SO₄, CH₃CH₂COOH and HN(NO₂)₂) have been investigated theoretically at the CBS-QB3 level of theory. Our results show that the catalyst X (X = H₂O, (H₂O)₂, (H₂O)₃, HCOOH, H₂SO₄ and CH₃CH₂COOH) shows different positive catalytic effects on reducing the apparent activation energy of the isomerisation reaction processes. Such different catalytic effects are mainly related to the number of hydrogen bonds and the size of the ring structure in X (X = H₂O, (H₂O)₂ and (H₂O)₃)-assisted transition states, as well as different values of pK_a for H₂SO₄, HCOOH and CH₃CH₂COOH. Very interesting is also the fact that H₂SO₄-assisted reaction is the most favourable for the hydrogen transfer from HN(NO₂)₂ to O₂NNN(O)OH, due to the smallest pK_a (?3.0) value of H₂SO₄ than H₂O, HCOOH, H₂SO₄ and CH₃CH₂COOH, and also because of the largest ∠X???H???Y (the angle between the hydrogen bond donor and acceptor) involved in H₂SO₄-assisted transition state. Compared to the self-catalysis of the isomerisation mechanisms of HN(NO₂)₂ to O₂NNN(O)OH, the apparent activation energy of H₂SO₄-assisted channel also reduces by 9.6 kcal?mol^?1, indicating that H₂SO₄ can affect the isomerisation of HN(NO₂)₂ to O₂NNN(O)OH, most obvious among all the catalysts H₂O, (H₂O)₂, (H₂O)₃, HCOOH, H₂SO₄, CH₃CH₂COOH and HN(NO₂)₂.