Insights into the Allosteric Effect of SENP1 Q597A Mutation on the Hydrolytic Reaction of SUMO1 via an Integrated Computational Study

Small ubiquitin-related modifier (SUMO)-specific protease 1 (SENP1) is a cysteine protease that catalyzes the cleavage of the C-terminus of SUMO1 for the processing of SUMO precursors and deSUMOylation of target proteins. SENP1 is considered to be a promising target for the treatment of hepatocellular carcinoma (HCC) and prostate cancer. SENP1 Gln597 is located at the unstructured loop connecting the helices α4 to α5. The Q597A mutation of SENP1 allosterically disrupts the hydrolytic reaction of SUMO1 through an unknown mechanism. Here, extensive multiple replicates of microsecond molecular dynamics (MD) simulations, coupled with principal component analysis, dynamic cross-correlation analysis, community network analysis, and binding free energy calculations, were performed to elucidate the detailed mechanism. Our MD simulations showed that the Q597A mutation induced marked dynamic conformational changes in SENP1, especially in the unstructured loop connecting the helices α4 to α5 which the mutation site occupies. Moreover, the Q597A mutation caused conformational changes to catalytic Cys603 and His533 at the active site, which might impair the catalytic activity of SENP1 in processing SUMO1. Moreover, binding free energy calculations revealed that the Q597A mutation had a minor effect on the binding affinity of SUMO1 to SENP1. Together, these results may broaden our understanding of the allosteric modulation of the SENP1−SUMO1 complex.     

A Reliability Analysis of Calculated Results for Odd-Even and Odd-Odd Nuclei in Relativistic Mean-Field Theory

We calculate the binding energies of Ni, Cu, Xe, Cs, Pt, Au, Np, Pu isotope chains using two interaction parameter sets NL-3 and NL-Z, and compared the relative errors of the even-even nuclei with those of odd-even nuclei and odd-odd nuclei. We find that the errors of binding energy of odd-even and odd-odd nuclei are not bigger than the one of even-even nuclei. The result shows that comparing with even-even nuclei, there is no systematic error and approximation in the calculations of the binding energy of odd-even and odd-odd nuclei with relativistic mean-field theory. In addition,the result is explained theoretically.     

Copper Binding and Oligomerization Studies of the Metal Resistance Determinant CrdA from Helicobacter pylori

Within this research, the CrdA protein from Helicobacter pylori (HpCrdA), a putative copper-binding protein important for the survival of bacterium, was biophysically characterized in a solution, and its binding affinity toward copper was experimentally determined. Incubation of HpCrdA with Cu(II) ions favors the formation of the monomeric species in the solution. The modeled HpCrdA structure shows a conserved methionine-rich region, a potential binding site for Cu(I), as in the structures of similar copper-binding proteins, CopC and PcoC, from Pseudomonas syringae and from Escherichia coli, respectively. Within the conserved amino acid motif, HpCrdA contains two additional methionines and two glutamic acid residues (MMXEMPGMXXMXEM) in comparison to CopC and PcoC but lacks the canonical Cu(II) binding site (two His) since the sequence has no His residues. The methionine-rich site is in a flexible loop and can adopt different geometries for the two copper oxidation states. It could bind copper in both oxidation states (I and II), but with different binding affinities, micromolar was found for Cu(II), and less than nanomolar is proposed for Cu(I). Considering that CrdA is a periplasmic protein involved in chaperoning copper export and delivery in the H. pylori cell and that the affinity of the interaction corresponds to a middle or strong metal–protein interaction depending on the copper oxidation state, we conclude that the interaction also occurs in vivo and is physiologically relevant for H. pylori.     

Influence of Multiple Binding Sites on the Supramolecular Assembly of N-[(3-pyridinylamino) Thioxomethyl] Carbamates

In this study, we investigated how the presence of multiple intermolecular interaction sites influences the heteromeric supramolecular assembly of N-[(3-pyridinylamino) thioxomethyl] carbamates with fluoroiodobenzenes. Three targets—R-N-[(3-pyridinylamino) thioxomethyl] carbamate (R = methyl, ethyl, and isobutyl)—were selected and crystallized, resulting in three parent structures, five co-crystals, and one co-crystal solvate. Three hydrogen-bonded parent crystal structures were stabilized by N-H···N hydrogen bonding and assembled into layers that stacked on top of one another. Molecular electrostatic potential surfaces were employed to rank binding sites (Npyr > C=S > C=O) in order to predict the dominant interactions. The N-H⋯H hydrogen bond was replaced by I⋯Npyr in 3/6 cases, I⋯C=S in 4/6 cases, and I⋯O=C in 1 case. Interestingly, the I⋯C=S halogen bond coexisted twice with I⋯Npyr and I⋯O=C. Overall, the MEPs were fairly reliable for predicting co-crystallization outcomes; however, it is crucial to also consider factors such as molecular flexibility. Finally, halogen-bond donors are capable of competing for acceptor sites, even in the presence of strong hydrogen-bond donors.     

Cancer-Associated Mutations of the Adenosine A2A Receptor Have Diverse Influences on Ligand Binding and Receptor Functions

The adenosine A_2A receptor (A_2AAR) is a class A G-protein-coupled receptor (GPCR). It is an immune checkpoint in the tumor micro-environment and has become an emerging target for cancer treatment. In this study, we aimed to explore the effects of cancer-patient-derived A_2AAR mutations on ligand binding and receptor functions. The wild-type A_2AAR and 15 mutants identified by Genomic Data Commons (GDC) in human cancers were expressed in HEK293T cells. Firstly, we found that the binding affinity for agonist NECA was decreased in six mutants but increased for the V275A mutant. Mutations A165V and A265V decreased the binding affinity for antagonist ZM241385. Secondly, we found that the potency of NECA (EC₅₀) in an impedance-based cell-morphology assay was mostly correlated with the binding affinity for the different mutants. Moreover, S132L and H278N were found to shift the A_2AAR towards the inactive state. Importantly, we found that ZM241385 could not inhibit the activation of V275A and P285L stimulated by NECA. Taken together, the cancer-associated mutations of A_2AAR modulated ligand binding and receptor functions. This study provides fundamental insights into the structure–activity relationship of the A_2AAR and provides insights for A_2AAR-related personalized treatment in cancer.     

四磺基酞菁钴合成及其与牛血清白蛋白结合作用的研究

以高锰酸钾降解薛氏钠盐(6-羟基-β-萘磺酸钠)合成4-磺基邻苯二甲酸,并以此为原料“固相熔融法”合成了四磺基酞菁钴(CoPcS₄)。CoPcS₄在DMSO中发生解聚,随着pH值的升高,解聚增加。CoPcS₄以二聚体形式与牛血清白蛋白(BSA)结合后具有更强的光敏活性。分别采用紫外和荧光光谱分析方法准确测定了四磺基酞菁钴与BSA的结合位置数和结合常数。两种方法的结果基本一致,数量级皆为105 L·mol-1。CoPcS₄与BSA的首要结合位置为SiteⅠ和SiteⅡ,两种结合位置的结合能力差别不大。结果表明,CoPcS₄可与牛血清白蛋白很好地结合,白蛋白起到存储与转运作用。     

金属Zn液态结构变化的研究

利用ＴＢ模型给出的原子间相互作用势详细计算了不同温度下Ｚｎ的双体分布函数ｇ（ｒ），结果发现随着温度的不断降低，液态金属Ｚｎ的ｇ（ｒ）第一峰变得高而尖，第二峰由弱变强，说明了液态金属Ｚｎ的有序度随温度降低而不断增强；利用键对分析技术统计了液态金属Ｚｎ在不同温度下的键取向序参数、键对数。键取向序参数及键对数随温度的变化，进一步证明了低温液态的有序度高于高温液态，从而充分说明液态金属在不同温度下有不同的结构形式，而不像人们想象得那样杂乱无章。     

Interaction of molecules of the neonicotinoid imidacloprid and its structural analogs with human serum albumin

We have used fluorescence spectroscopy methods to show that imidacloprid and its structural analogs form complexes with human serum albumin (HSA). The nature of the spectral changes in the ligand×protein systems and the calculated complexation parameters suggest that these low molecular weight compounds mainly bind to a specific section of the protein molecule, near the tryptophan residue in the 214 position of the polypeptide chain. We have found that the association constants are on the order of 10⁴ M⁻¹, and the affinity of the ligands for HSA varies in the series 6-chloronicotinic acid > 6-methoxynicotinic acid = imidacloprid > the keto analog of imidacloprid. The major contribution to the complexation energy probably comes from hydrophobic interaction forces with participation of the aromatic pyridine ring of the ligands, while additional enhancement of ligand-protein affinity can be provided by the nitroimine group of imidacloprid. Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 75, No. 6, pp. 859–866, November–December, 2008.     

丁酮分子内价轨道1a″的电子动量谱学研究

用高分辨率电子动量谱仪进行丁酮分子的结合能谱和内价轨道1a″电子动量谱的实验工作，以及用Hartree-Fock和密度泛函理论方法对1a″轨道电子动量谱的理论研究. 得到了各价轨道的电离能值以及理论计算的总能、偶极矩和1a″轨道的二维密度图. 并比较了内价轨道1a″的电子动量谱的实验和理论计算结果，实验结果与理论计算符合较好.