Nucleotide/Protein Interaction: Energetic and Structural Features of Na,K-ATPase

Microcalorimetric titrations allow to recognize and investigate high-affinity ligand binding to Na,K-ATPase. Titrations with the cardiac glycoside Ouabain, which acts as a specific inhibitor of the enzyme, have provided not only the thermodynamic parameters of high-affinity binding with a stoichiometric coefficient of about 0.6 but also evidence for low-affinity binding to the lipid. The marked enthalpic contribution of -95 kJ mol^-1 at 298.2 K is partially compensated by a large negative entropy change, attributed to an increased interaction between water and the protein. The calorimetric ADP and ATP titrations at 298.2 K are indicative of high-affinity nucleotide binding either in 3 mM NaCl, 3 mM MgCl₂ or at high ionic strength such as 120 mM choline chloride. However, no binding is detected in the buffer solution alone at low ionic strength. The affinities for ADP and ATP are similar, around 10⁶ M^-1 and the stoichiometric coefficients are close to that of Ouabain binding. The exothermic binding of ADP is characterized by a ΔH and ΔS value of -65 kJ mol^-1 and -100 J mol^-1 K^-1, respectively. TheΔH value for ATP binding is larger than for ADP and is compensated by a larger, unfavorable ΔS value. This leads to an enthalpy/entropy compensation, which could express that H-bond formation represents the major type of interaction. As for Ouabain, the negative ΔS values that are also characteristic of nucleotide binding can indicate an increase of solvate interaction with the protein due to a conformational transition occurring subsequent to the binding process. The resulting binding constants are discussed with regard to the results of other studies employing different techniques. A molecular interaction model for nucleotide binding is suggested. This revised version was published online in July 2006 with corrections to the Cover Date.     

Ligand-protein docking using a quantum stochastic tunneling optimization method

A novel hybrid optimization method called quantum stochastic tunneling has been recently introduced. Here, we report its implementation within a new docking program called EasyDock and a validation with the CCDC/Astex data set of ligand-protein complexes using the PLP score to represent the ligand-protein potential energy surface and ScreenScore to score the ligand-protein binding energies. When taking the top energy-ranked ligand binding mode pose, we were able to predict the correct crystallographic ligand binding mode in up to 75% of the cases. By using this novel optimization method run times for typical docking simulations are significantly shortened.     

高效毛细管电泳前沿分析法研究酸性药物那格列奈与人血浆白蛋白的结合

用高效毛细管电泳前沿分析法研究了酸性药物那格列奈与人血浆白蛋白的结合常数、结合位点和结合率。使用未涂层的毛细管柱 (4 0cm× 5 0 μmi.d .;有效柱长 32cm) ,磷酸盐缓冲溶液 (pH 7.4 ,离子强度0 .17)为背景溶液 ,在紫外检测波长 2 14nm、运行电压 18kV和重力进样 10 0s的条件下 ,利用那格列奈谱峰的平台高度和游离药物浓度的良好线性关系 (r>0 .999,n =6 ) ,测定了那格列奈的游离药物浓度。固定药物浓度 (2 0 0 μmol L ,2 5 0 μmol L) ,考察不同的蛋白质浓度对结合的影响 ;固定蛋白质浓度 (10 0 μmol L) ,考察不同的药物浓度对结合的影响。实验数据采用非线性拟和程序进行处理 ,得到了那格列奈的蛋白质结合参数。高效毛细管电泳前沿分析法测定的数据重现性良好 (RSD <2 .5 % ,n =3) ,在药代动力学和药效学研究方面具有简便、准确的优点。     

Synthesis and antitumor activity of DNA binding cationic porphyrin-platinum(II) complexes

A new series of DNA binding 5,10,15-tri(N-methyl-4-pyridiniumyl)porphyrin (TrisMPyP)-platinum(II) conjugates was synthesized, in which different spacer ligands were used for appropriate coordination to platinum(II) complexes. Compound 9b exhibited in vivo antitumor activity (T/C%, 294) superior to cisplatin (T/C%, 184) against the leukemia L1210 cell line.     

用XPS研究我国一些煤中有机硫的存在形态

本文用电子能谱（xps）方法研究了我国九个不同牌号煤中有机硫的存在形态，并得到这些煤中各种不同形态硫的结合能数据。根据Lindberg等人所做模型化合物结果，给出了这些煤中硫元素结构能的化学归属。各种煤中硫的存在形态是不同的，有硫醇、硫醚、双硫醚、硫杂环、硫桥和取代基上的硫等。这一研究结果为今后研究煤的分子结构及脱硫方法提供了重要的科学依据。     

Influence of response factors on determining equilibrium association constants of non-covalent complexes by electrospray ionization mass spectrometry

A method for determining the equilibrium association constant of a complexation reaction A + B left harpoon over right harpoon AB by electrospray ionization mass spectrometry is described. The method consists in measuring the relative intensities of the peaks corresponding to A and to AB in equimolar A-B solutions at different concentrations C(0). The results are fitted by a non-linear least-squares procedure, with the two variable parameters being the equilibrium association constant K(a) and a factor R, defined by I(AB)/I(A) = R x [AB]/[A]. The factor R is the ratio between the response factors of AB and A, and corrects for the relative electrospray responses of the complex and the free substrate A, mass discrimination of instrumental origin and/or moderate in-source dissociation. The method is illustrated with the following two systems: complexes between a double-stranded 12-base pair oligonucleotide and minor groove binders, and cyclodextrin complexes with alpha,omega-dicarboxylic acids. For the oligonucleotide complexes, it is found that the response of the complex is not dramatically different to the response of the free oligonucleotide duplex, as the double helix conformation is disturbed by the drug only to a minor extent. In the case of cyclodextrin complexes, these complexes were found to have a much higher response than free cyclodextrin. This may be due to the fact that cyclodextrin is neutral in solution, whereas the complex is charged, but it can also stem from the fact that a significant proportion of the complex is in a non-inclusion geometry. The present method requires the exact determination of the concentrations of the reactants and is applicable to 1 : 1 complexes.     

Synthesis and DNA binding properties of pyrrole amino acid-containing peptides

Dimers of the pyrrole amino acid (Paa), 5-(aminomethyl)pyrrole-2-carboxylic acid, and its derivatives having Lys anchored on N- and C-termini bind in the minor groove of DNA with considerable apparent binding affinities. When the Lys unit is attached to the C-terminus, the resulting ligand binds to ds-DNA with twice the affinity, of the order of 10⁵, than the one carrying two positive charges at the same end.     

配体形状对多吡啶铜(Ⅱ)配合物与DNA作用的影响

合成了一系列含有平面配体的Cu(Ⅱ)多吡啶配合物[Cu(IP)₂]²⁺、[Cu(PIP)₂]²⁺、[Cu(DPPZ)₂]²⁺和[Cu(HPIP)₂]²⁺，用吸收光谱、CD光谱和粘度等方法研究了这些配合物与小牛胸腺DNA的作用。结果表明配体上的取代基及配体的平面性对这些四面体配合物与DNA的结合强弱产生一定的影响。[Cu(DPPZ)₂]²⁺与DNA的结合较强，而[Cu(HPIP)₂]²⁺与DNA的结合较弱。CD光谱显示配合物[Cu(DPPZ)₂]²⁺、[Cu(PIP)₂]²⁺和[Cu(HPIP)₂]²⁺的加入会导致DNA的CD光谱减弱。而[Cu(IP)₂]²⁺的加入则会使DNA的CD光谱增强。同时，[Cu(IP)₂]²⁺与DNA结合后，还会引起一定程度的DNA构型转换，即DNA从B型转换成Z型。     

2-(8-羟基喹啉-5-磺酸-7-偶氮)-1,8-二羟基-3,6-萘二磺酸与牛血清白蛋白的相互作用

用平衡透析法和分光光度法研究了 2 (8 羟基喹啉 5 磺酸 7 偶氮 ) 1,8 二羟基 3,6 萘二磺酸与牛血清白蛋白 (BSA)在酸性溶液中的结合反应 ,认为 8Q5SAC与BSA之间的结合力是以静电引力为主的非共键作用力 ,并探讨了其结合模型。在 2 98K下 ,测得这一反应的最大结合数为 35～ 40 ,结合常数为 6 .1× 10 5L mol。还研究了溶液基本条件如酸度和离子强度等对 8Q5SAC与牛血清白蛋白分子复合物形成的影响 ,在pH =3.34条件下 ,标准工作曲线的线性范围为 0 .2 0～ 46 .90mg L。     

Genomic variation and point mutations analysis of Indian COVID-19 patient samples submitted in GISAID database

Corona virus disease 2019 (COVID-19) endemic has havoc on the world; the causative virus of the pandemic is SARS CoV-2. Pharmaceutical companies and academic institutes are in continuous efforts to identify anti-viral therapy or vaccines, but the most significant challenge faced is the highly evolving genome of SARS CoV-2, which is imparting evolutionary selective benefits to the virus. To understand the viral mutations, we have retrieved nine hundred and thirty-four samples from different states of India via the GISAID database and analyzed the frequency of all types of point mutation in all structural, non-structural proteins, and accessory factors of SARS CoV-2. Spike glycol protein, nsp3, nsp6, nsp12, N and NS3 were the most evolving proteins. High frequency point mutations were Q496P (nsp2), A380V (nsp4), A994D (nsp3), L37F (nsp6), P323L & A97V (nsp12), Q57H (ns3), D614G (S), P13L (N), R203K (N), G204R (N) and S194L (N).