鲨鱼软骨血管形成抑制因子的分离纯化及其活性的初步研究

以广东阳江鲨鱼软骨为原料,研究了鲨鱼软骨新生血管形成抑制因子的分离纯化方法,并对其生物学活性进行了初步研究.采用盐酸胍抽提、膜超滤、丙酮分级沉淀、SephadexG-75柱层析和C₄反相高效液相色谱等步骤,分离纯化出一种新的鲨鱼软骨血管生成抑制因子-a(SharkCartilageAngiogenesisInhibitor-a,SCAI-a),分子量为12600,能显著抑制鸡胚绒毛尿囊膜血管的形成.     

17400鲨鱼软骨血管生成抑制因子的纯化及生物学活性研究

采用盐酸胍抽提、膜超滤、丙酮分级沉淀、Sephadex-75柱层析和C₄反相高效液相色谱等分离步骤,从广东阳江鲨鱼软骨中纯化获得新的鲨鱼软骨血管生成抑制因子SCAI-c(SharkCartilageAngiogenesis In-hibitor-c,SCAI-c);SDS-PAGE电泳银染显示为一条带,根据蛋白质的相对迁移率计算,分子量为17400;它对鸡胚绒毛尿囊膜血管的形成具有显著抑制效应,并有明显的浓度依赖关系.SCAI-c与SCAI-a具有类似的生物学特征.     

基因重组可溶性非融合血管生成抑制剂Kringle 5的色谱分离和纯化

Kringle 5是血纤维蛋白溶酶原中特异抑制内皮细胞增生和迁移活性最高的一种血管生成抑制剂。该实验在前期成功克隆和表达可溶性非融合血管生成抑制剂Kringle 5的基础上,建立了一种两步色谱法分离纯化Kringle 5的方法。首先用SP Sepharose Fast Flow强阳离子交换色谱柱对Kringle 5重组菌体破碎上清液进行初步分离,然后再用丙烯葡聚糖凝胶S-100 HR凝胶排阻色谱柱对其进行进一步的纯化。采用本方法得到的可溶性非融合血管生成抑制剂Kringle 5经十二烷基硫酸钠-聚丙烯酰胺凝胶电泳和高效凝胶排阻色谱检测其纯度大于98%,通过鸡胚尿囊膜法确定这种蛋白质具有抑制内皮毛细血管生长的活性。     

溶栓与抗栓双功能尿激酶原突变体的模拟、构建与表达

将抗栓肽(Decorsin)嫁接到低分子量尿激酶原(scuPA-32k)上,可以期望获得既具有抗血小板聚集活性,又具有溶栓活性的新型基因工程蛋白质分子.利用计算机辅助分子设计手段模拟了该融合蛋白的分子结构,证明其活性区可以正常发挥功能.根据大肠杆菌偏好密码子合成Decorsin的基因,与scuPA-32k基因融合在一起,构建新的嵌合体基因dscuPA,并在大肠杆菌中通过IPTG进行诱导表达,该重组蛋白在大肠杆菌中以包涵体的形式存在.对包涵体进行变性和复性并通过层析纯化得到目的蛋白质.用纤维蛋白平板法测得重组蛋白的比活为92000IU/mg.激活纤溶酶原的酶促动力学性质与天然低分子量尿激酶相似,且有较强的抑制血小板聚集的功能.重组蛋白dscuPA不但具有较强的溶栓功能,而且具有抗栓功能.     

两步柱色谱法分离纯化重组肿瘤血管生长抑制因子Kringle 5

建立了一种用Ni2+螯合的Chelating Sepharose Fast Flow亲和柱色谱和Sephadex G-75凝胶排阻柱色谱分离纯化重组肿瘤血管生长抑制因子Kringle 5的方法。采用该工艺得到的重组Kringle 5经十二烷基硫酸钠-聚丙烯酰胺凝胶电泳分析表明其纯度约为98%,且具有抑制鸡胚绒毛尿囊膜新生血管生成的生物活性。     

尿激酶(uPA)化学合成抑制剂

胞外蛋白的水解是恶性肿瘤细胞侵袭和转移的必要条件,各种蛋白酶的水解反应降解细胞外基质,破坏细胞/细胞间的联系以适应细胞的迁移。尿激酶型纤溶酶原激活物(尿激酶,urokinase-type plasminogen activator, uPA)激活不具有丝氨酸蛋白酶活性的纤溶酶原为活性纤溶酶,在保持血流畅通与防止血栓的形成中具有重要的作用。此外,活性尿激酶降解细胞外基质,激活多种基质金属蛋白酶,以适应肿瘤细胞的侵袭、扩散和转移。抑制尿激酶的活性被公认为是抑制癌症转移的有效方法,其中合成小分子uPA抑制剂成为抗癌治疗中的新理念。本文综述了合成uPA抑制剂的研究现状。     

蜈蚣藻中一种硫酸半乳聚糖的分离纯化、结构鉴定及其抗新生血管生成活性

为了寻找多糖类血管生成抑制剂, 我们以蜈蚣藻(Grateloupia filicina)为原料, 经水提、醇沉、DEAE-Sepharose Fast Flow和Sepharose CL-6B凝胶柱层析分离纯化, 得到一个均一多糖(GFP15).采用HPGPC、糖组成分析、绝对构型测定、甲基化分析、IR和NMR等技术对GFP15进行结构鉴定.结果表明, GFP15为一琼胶和卡拉胶中间型的硫酸半乳聚糖, 主要由1,3连接的β-D-半乳糖和1,4连接的2,3位硫酸基双取代的α-D-半乳糖交替组成, 1,3连接β-D-半乳糖的4位和6位上分别有少量的硫酸基取代, 1,4连接的半乳糖有少量是α-L-半乳糖, 此外, 还有极少量的木糖、3,6-脱水半乳糖和6-甲基-半乳糖.利用鸡胚尿囊膜法(CAM)对GFP15进行抗新生血管生成活性评价, 结果显示, GFP15(100 μg/egg)能抑制尿囊膜新生血管的形成, 提示GFP15 作为一种多糖类血管生成抑制剂具有开发为抗肿瘤药物的潜在价值.     

禽流感病毒H5N1病毒颗粒中鸡胚宿主蛋白的质谱分析

在A型流感病毒等许多包膜病毒的病毒颗粒中,除包含病毒基因组编码的结构蛋白外,还包含来源于宿主细胞的多种蛋白。然而,在鸡胚内增殖的病毒颗粒所包含的宿主蛋白的种类尚不清楚。本研究采用20%～60%(w/w)蔗糖密度梯度离心法分离纯化了繁殖于鸡胚的流感病毒,并用十二烷基硫酸钠-聚丙烯酰胺凝胶电泳(Sodium dodecyl sulfate polyacrylamide gel electrophoresis,SDS-PAGE)结合质谱法对纯化的流感病毒颗粒进行了全面的蛋白质组学分析。结果表明,在病毒颗粒中,除包含9种病毒编码蛋白外,还发现了12种来源于鸡胚的蛋白,如膜联蛋白A2、肽酰脯氨酰顺反异构酶B、过氧化物酶1、磷酸甘油酸激酶、丙酮酸激酶肌组织异构酶等,以及2种细胞骨架蛋白(微管蛋白b-3和肌动蛋白)。     

重组内皮抑素的性质表征与生物活性分析

通过SDS—PAGE电泳、基质辅助激光解吸电离飞行时间质谱、高效液相色谱、地高辛方法、蛋白印迹方法、鸡胚尿囊膜血管生成抑制实验和透射电子显微镜法对重组内皮抑素进行纯度分析、鉴定和生物活性研究。重组内皮抑素纯度达到99％，能够抑制鸡胚尿囊膜新血管生成和人脐静脉内皮细胞ECV304增殖，引发内皮细胞的凋亡。     

尿激酶对纤维蛋白低亲和性的结构基础——Ⅱ.尿激酶A链149—157片段对纤维蛋白促进tPA激活纤溶酶原的抑制作用

本文从低分子量尿激酶(LUK)中分离并纯化了UK 135—157片段,用放射结合分析证明UK 135—157片段和纤维蛋白对tPA的结合呈竞争关系。用酪蛋白降解系统证明此片段可抑制纤维蛋白促进tPA对纤溶酶原的激活。化学合成了UK149—157九肽(R-肽)以及由Asp取代Arg 154和Arg 156的相应九肽(D-肽),发现R-肽对纤维蛋白促进tPA激活纤溶酶原有显著的抑制作用,而D-肽却全无作用。本文结果证明:UK 149—157片段中的正电荷残基在抑制环饼结构域的纤维蛋白结合活性中起重要作用。     

Application of a semi-empirical dispersion correction for modeling water clusters

The Grimme-D3 semi-empirical dispersion energy correction has been implemented for the original effective fragment potential for water (EFP1), and for systems that contain water molecules described by both correlated ab initio quantum mechanical (QM) molecules and EFP1. Binding energies obtained with these EFP1-D and QM/EFP1-D methods were tested using 27 benchmark species, including neutral, protonated, deprotonated, and auto-ionized water clusters and nine solute–water binary complexes. The EFP1-D and QM/EFP1-D binding energies are compared with those obtained using fully QM methods: second-order perturbation theory, and coupled cluster theory, CCSD(T), at the complete basis set (CBS) limit. The results show that the EFP1-D and QM/EFP1-D binding energies are in good agreement with CCSD(T)/CBS binding energies with a mean absolute error of 5.9 kcal/mol for water clusters and 0.8 kcal/mol for solute–water binary complexes. © 2018 Wiley Periodicals, Inc.     

A combined effective fragment potential-fragment molecular orbital method. II. Analytic gradient and application to the geometry optimization of solvated tetraglycine and chignolin

The gradient for the fragment molecular orbital (FMO) method interfaced with effective fragment potentials (EFP), denoted by FMO∕EFP, was developed and applied to polypeptides solvated in water. The structures of neutral and zwitterionic tetraglycine immersed in water layers of 2.0, 2.5, 3.0, 3.5, 4.0, and 4.5 A? are investigated by performing FMO∕EFP geometry optimizations at the RHF∕cc-pVDZ level of theory for the solutes. The geometries optimized with FMO-RHF∕EFP are compared to those from the conventional RHF∕EFP and are found to be in very close agreement. Using the optimized geometries, the stability of the hydrated zwitterionic and neutral structures is discussed structurally and in terms of energetics at the second-order M?ller-Plesset theory (MP2)∕cc-pVDZ level. To demonstrate the potential of the method for proteins, the geometry of hydrated chignolin (protein data bank ID: 1UAO) was optimized, and the importance of the inclusion of water was examined by comparing the solvated and gas phase structures of chignolin with the experimental NMR structure.     

Hybrid MPI/OpenMP parallelization of the effective fragment potential method in the libefp software library

A new hybrid MPI/OpenMP parallelization scheme is introduced for the Effective Fragment Potential (EFP) method implemented in the libefp software library. The new implementation employs dynamic load balancing algorithm that uses a master/slave model. The software shows excellent parallel scaling up to several hundreds of CPU‐cores across multiple nodes. The code uses functions only from the well‐established MPI‐1 standard that simplifies portability of the library. This new parallel EFP implementation greatly expands the applicability of the EFP and QM/EFP methods by extending attainable time‐ and length‐scales. © 2014 Wiley Periodicals, Inc.     

Gradients of the polarization energy in the effective fragment potential method

The effective fragment potential (EFP) method is an ab initio based polarizable classical method in which the intermolecular interaction parameters are obtained from preparative ab initio calculations on isolated molecules. The polarization energy in the EFP method is modeled with asymmetric anisotropic dipole polarizability tensors located at the centroids of localized bond and lone pair orbitals of the molecules. Analytic expressions for the translational and rotational gradients (forces and torques) of the EFP polarization energy have been derived and implemented. Periodic boundary conditions (the minimum image convention) and switching functions have also been implemented for the polarization energy, as well as for other EFP interaction terms. With these improvements, molecular dynamics simulations can be performed with the EFP method for various chemical systems.     

Accelerating quantum mechanical/molecular mechanical sampling using pure molecular mechanical potential as an importance function: the case of effective fragment potential

Acceleration of sampling from a quantum mechanical/effective fragment mechanical (QM/EFP) potential is explored with effective fragment potential (EFP) as an importance function. EFP, generated on the fly, is found to be an excellent choice for an importance function for a QM/EFP potential. This technique is used to find nine stationary points of a blocked amino acid with twelve waters in a semi-automated way.     

Solvent effects on the S(N)2 reaction: Application of the density functional theory-based effective fragment potential method

The performance of the density functional theory (DFT)-based effective fragment potential (EFP) method is assessed using the S(N)2 reaction: Cl- + nH2O + CH3Br = CH3Cl + Br- + nH2O. The effect of the systematic addition of water molecules on the structures and relative energies of all species involved in the reaction has been studied. The EFP1 method is compared with second-order perturbation theory (MP2) and DFT results for n = 1, 2, and 3, and EFP1 results are also presented for four water molecules. The incremental hydration effects on the barrier height are the same for all methods. However, only full MP2 or MP2 with EFP1 solvent molecules are able to provide an accurate treatment of the transition state (TS) and hence the central barriers. Full DFT and DFT with EFP1 solvent molecules both predict central barriers that are too small. The results illustrate that the EFP1-based DFT method gives reliable results when combined with an accurate quantum mechanical (QM) method, so it may be used as an efficient alternative to fully QM methods in the treatment of larger microsolvated systems.     

Solvent effects on the electronic transitions of p-nitroaniline: a QM/EFP study

Solvatochromic shifts of the electronic states of a chromophore can be used as a measure of solute-solvent interactions. The shifts of the electronic states of a model organic chromophore, p-nitroaniline (pNA), embedded in solvents with different polarities (water, 1,4-dioxane, and cyclohexane) are studied using a hybrid quantum mechanics/molecular-mechanics-type technique in which the chromophore is described by the configuration interaction singles with perturbative doubles (CIS(D)) method while the solvent is treated by the effective fragment potential (EFP) method. This newly developed CIS(D)/EFP scheme includes the quantum-mechanical coupling of the Coulomb and polarization terms; however, short-range dispersion and exchange-repulsion terms of EFP are not included in the quantum Hamiltonian. The CIS(D)/EFP model is benchmarked against the more accurate equation of motion coupled cluster with singles and doubles (EOM-CCSD)/EFP method on a set of small pNA-water clusters. CIS(D)/EFP accurately predicts the red solvatochromic shift of the charge-transfer π → π* state of pNA in polar water. The shift is underestimated in less polar dioxane and cyclohexane probably because of the omission of the explicit quantum-mechanical treatment of the short-range terms. Different solvation of singlet and triplet states of pNA results in different probabilities of intersystem crossing (ISC) and internal conversion (IC) pathways of energy relaxation in solvents of different polarity. Computed singlet-triplet splittings in water and dioxane qualitatively explain the active ISC channel in dioxane and predict almost no conversion to the triplet manifold in water, in agreement with experimental findings.     

The effective fragment potential: small clusters and radial distribution functions

The effective fragment potential (EFP) method for treating solvent effects provides relative energies and structures that are in excellent agreement with the analogous fully quantum [i.e., Hartree-Fock (HF), density functional theory (DFT), and second order perturbation theory (MP2)] results for small water clusters. The ability of the method to predict bulk water properties with a comparable accuracy is assessed by performing EFP molecular dynamics simulations. The resulting radial distribution functions (RDF) suggest that as the underlying quantum method is improved from HF to DFT to MP2, the agreement with the experimental RDF also improves. The MP2-based EFP method yields a RDF that is in excellent agreement with experiment.     

Optimizing conical intersections of solvated molecules: the combined spin-flip density functional theory/effective fragment potential method

Solvent effects on a potential energy surface crossing are investigated by optimizing a conical intersection (CI) in solution. To this end, the analytic energy gradient has been derived and implemented for the collinear spin-flip density functional theory (SFDFT) combined with the effective fragment potential (EFP) solvent model. The new method is applied to the azomethane-water cluster and the chromophore of green fluorescent protein in aqueous solution. These applications illustrate not only dramatic changes in the CI geometries but also strong stabilization of the CI in a polar solvent. Furthermore, the CI geometries obtained by the hybrid SFDFT/EFP scheme reproduce those by the full SFDFT, indicating that the SFDFT/EFP method is an efficient and promising approach for understanding nonadiabatic processes in solution.