Conjugation of phosphonoacetic acid to nucleobase promotes a mechanism-based inhibition

Small molecule inhibitors have a powerful blocking action on viral polymerases. The bioavailability of the inhibitor, nevertheless, often raise a significant selectivity constraint and may substantially limit the efficacy of therapy. Phosphonoacetic acid has long been known to possess a restricted potential to block DNA biosynthesis. In order to achieve a better affinity, this compound has been linked with natural nucleotide at different positions. The structural context of the resulted conjugates has been found to be crucial for the acquisition by DNA polymerases. We show that nucleobase-conjugated phosphonoacetic acid is being accepted, but this alters the processivity of DNA polymerases. The data presented here not only provide a mechanistic rationale for a switch in the mode of DNA synthesis, but also highlight the nucleobase-targeted nucleotide functionalization as a route for enhancing the specificity of small molecule inhibitors.     

Insights into membrane translocation of the cell-penetrating peptide pVEC from molecular dynamics calculations

Discovery of cargo carrying cell-penetrating peptides has opened a new gate in the development of peptide-based drugs that can effectively target intracellular enzymes. Success in application and development of cell-penetrating peptides in drug design depends on understanding their translocation mechanisms. In this study, our aim was to examine the bacterial translocation mechanism of the cell-penetrating pVEC peptide (LLIILRRRIRKQAHAHSK) using steered molecular dynamics (SMD) simulations. The significance of specific residues or regions for translocation was studied by performing SMD simulations on the alanine mutants and other variants of pVEC. Residue-based analysis showed that positively charged residues contribute to adsorption to the lipid bilayer and to electrostatic interactions with the lipid bilayer as peptides are translocated. Translocation takes place in three main stages; the insertion of the N-terminus into the bilayer, the inclusion of the whole peptide inside the membrane and the exit of the N-terminus from the bilayer. These three stages mirror the three regions on pVEC; namely, the hydrophobic N-terminus, the cationic midsection, and the hydrophilic C-terminus. The N-terminal truncated pVEC, I3A, L5A, R7A mutants and scramble-pVEC make weaker interactions with the lipids during translocation highlighting the contribution of the N-terminal residues and the sequence of the structural regions to the translocation mechanism. This study provides atomistic detail about the mechanism of pVEC peptide translocation and can guide future peptide-based drug design efforts.     

城市扩张过程中建设用地景观格局演变特征及其驱动力

剖析城市扩张过程中建设用地景观格局演变特征及其驱动力,不仅有助于城市生态环境问题的解决,而且为城市用地结构优化、城市景观规划等工作提供科学依据。以快速城市化的中型城市—扬州市为例,利用多期(1995、2000、2005、2010年和2015年)Landsat卫星影像、乡镇水平的扬州统计年鉴等数据,运用景观格局分析、增强回归树(Boosted regression trees)等方法,研究建设用地的扩张模式、形态及景观格局,定量探究地理、社会和经济因子对景观格局的影响机制,从而明晰景观格局演变特征及其驱动力。结果表明,1995—2015年,建设用地面积持续增加,填充式(Infilling)、边缘式(Edge-expansion)和跳跃式(Leapfrog)3种扩张模式在各时段均有出现,但其优势度随着城市发展而改变。建设用地的形态在城市扩张的过程中经历着"集聚"和"扩散"的交替变化过程,景观格局则出现了同质化倾向,景观破碎化下降、聚合度增加。地理因子(海拔和到县市中心的距离)对景观格局的综合影响虽然高于社会经济,但它的影响力却随着城市发展呈现出下降趋势,社会经济的作用则逐渐增强。海拔和人口密度的增加会促进景观的破碎化、抑制景观的集聚;人口数量的增加会促进景观的集聚、降低景观的破碎化;其余因子(到县市中心的距离、人均GDP和第二产业占比)的作用则随城市的发展而发生转变,如人均GDP对景观破碎化的作用表现为"促进→抑制"的转变、第二产业则为"抑制→促进"。     

Catalysis by dienelactone hydrolase: A variation on the protease mechanism

Dienelactone hydrolase (DLH), an enzyme from the β-ketoadipate pathway, catalyzes the hydrolysis of dienelactone to maleylacetate. Our inhibitor binding studies suggest that its substrate, dienelactone, is held in the active site by hydrophobic interactions around the lactone ring and by the ion pairs between its carboxylate and Arg-81 and Arg-206. Like the cysteine/serine proteases, DLH has a catalytic triad (Cys-123, His-202, Asp-171) and its mechanism probably involves the formation of covalently bound acyl intermediate via a tetrahedral intermediate. Unlike the proteases, DLH seems to protonate the incipient leaving group only after the collapse of the first tetrahedral intermediate, rendering DLH incapable of hydrolyzing amide analogues of its ester substrate. In addition, the triad His probably does not protonate the leaving group (enolate) or deprotonate the water for deacylation; rather, the enolate anion abstracts a proton from water and, in doing so, supplies the hydroxyl for deacylation. © 1993 Wiley-Liss, Inc.