Complete mutagenesis of the HIV-1 protease

Retroviruses encode a protease which needs to be active for the production of infectious virions. A disabling mutation in the protease results in the production of non-infectious virus particles and examination of proteins from these mutant virions reveals unprocessed Gag and Gag-Pol precursor proteins, the substrates of the viral protease. Each amino acid of the HIV-1 protease was individually mutated using a simple mutagenesis procedure which is capable of introducing and identifying missense mutations in each residue of a protein. Phenotypic screening of these mutants in a heterologous assay system reveals three regions within the protease where multiple consecutive amino-acid residues are sensitive to mutation. These results show that random mutagenesis can be used to identify functionally important regions within a protein. Mutants with conditional phenotypes have also been identified within this collection.     

Visualizing transient events in amino-terminal autoprocessing of HIV-1 protease

HIV-1 protease processes the Gag and Gag-Pol polyproteins into mature structural and functional proteins, including itself, and is therefore indispensable for viral maturation. The mature protease is active only as a dimer with each subunit contributing catalytic residues. The full-length transframe region protease precursor appears to be monomeric yet undergoes maturation via intramolecular cleavage of a putative precursor dimer, concomitant with the appearance of mature-like catalytic activity. How such intramolecular cleavage can occur when the amino and carboxy termini of the mature protease are part of an intersubunit beta-sheet located distal from the active site is unclear. Here we visualize the early events in N-terminal autoprocessing using an inactive mini-precursor with a four-residue N-terminal extension that mimics the transframe region protease precursor. Using paramagnetic relaxation enhancement, a technique that is exquisitely sensitive to the presence of minor species, we show that the mini-precursor forms highly transient, lowly populated (3-5%) dimeric encounter complexes that involve the mature dimer interface but occupy a wide range of subunit orientations relative to the mature dimer. Furthermore, the occupancy of the mature dimer configuration constitutes a very small fraction of the self-associated species (accounting for the very low enzymatic activity of the protease precursor), and the N-terminal extension makes transient intra- and intersubunit contacts with the substrate binding site and is therefore available for autocleavage when the correct dimer orientation is sampled within the encounter complex ensemble.     

Inhibition of furin-mediated cleavage activation of HIV-1 glycoprotein gp160.

The envelope glycoprotein of human immunodeficiency virus (HIV) initiates infection by mediating fusion of the viral envelope with the cell membrane. Fusion activity requires proteolytic cleavage of the gp160 protein into gp120 and gp41 at a site containing several arginine and lysine residues. Activation at basic cleavage sites is observed with many membrane proteins of cellular and viral origin. We have recently found that the enzyme activating the haemagglutinin of fowl plague virus (FPV), an avian influenza virus, is furin. Furin, a subtilisin-like eukaryotic endoprotease, has a substrate specificity for the consensus amino-acid sequence Arg-X-Lys/Arg-Arg at the cleavage site. We show here that the glycoprotein of HIV-1, which has the same protease recognition motif as the FPV haemagglutinin, is also activated by furin.     

艾滋病毒蛋白酶异位抑制剂体系的分子动力学研究

对艾滋病毒蛋白酶异位抑制剂体系和活性位抑制剂体系进行8 ns的分子动力学模拟,用MM-PBSA方法分别计算了抑制剂与蛋白酶的结合自由能。异位抑制剂体系中抑制剂与蛋白酶的结合自由能为-90.30 kcal/mol,活性位抑制剂体系中为-59.58 kcal/mol。在异位抑制剂体系中分子片段4DX卡在蛋白酶的exo位,使蛋白酶活性位点附近残基的活动范围减小,有利于抑制剂被束缚在活性位点附近。异位抑制剂使体系刚性更强,更稳定,抑制剂与蛋白酶的结合更为牢固。     

Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1

The crystal structure of the protease of the human immunodeficiency virus type (HIV-1), which releases structural proteins and enzymes from viral polyprotein products, has been determined to 3 A resolution. Large regions of the protease dimer, including the active site, have structural homology to the family of microbial aspartyl proteases. The structure suggests a mechanism for the autoproteolytic release of protease and a role in the control of virus maturation.     

d4T核苷酸类似物抗HIV-1活性的定量构效关系

对20个核苷酸类化合物(d4T的衍生物)进行了定量构效关系研究,建立QSAR方程。模型指出该类化合物的抗HIV-1活性与n_M、lgP、(lgP)²及分子连接性指数⁶χ^v_P具有良好的相关性,其复相关系数R为0.94。由方程可知:⁶χ^v_P在抗HIV-1过程中比电子参数σ发挥更大的作用。     

HIV-1 蛋白酶异位抑制剂体系的长时间分子动力学模拟

采用新开发的ff12SB力场在NVIDIA CUDA GPU上对HIV-1蛋白酶的活性位抑制剂体系和异位抑制剂体系分别进行了100 ns的长时间分子动力学模拟,并用MM-PB/GBSA方法计算了活性位点抑制剂TL-3与HIV-1蛋白酶的结合自由能。异位抑制剂体系中分子片段2-甲基环己醇结合在Exo位,有利于抑制剂被束缚在活性位点附近。异位抑制剂体系中抑制剂TL-3与蛋白酶的结合自由能为-85.78 kcal/mol,活性位抑制剂体系中为-79.45 kcal/mol。这些结果有助于深入了解HIV-1 PR的动力学过程,为设计新型强效抑制剂提供了新见解。     

Inhibition of retroviral protease activity by an aspartyl proteinase inhibitor

Retrovirus protease is an enzyme that cleaves gag and gag-pol precursor polyproteins into the functional proteins of mature virus particles. The correct processing of precursor polyproteins is necessary for the infectivity of virus particles: in vitro mutagenesis which introduces deletions into the murine leukaemia virus genome produces a protease-defective virus of immature core form and lacking infectivity. A therapeutic drug effective against disease caused by retrovirus proliferation could likewise interfere with virus maturation. The primary structure has so far been determined for the protease of avian myeloblastosis virus, and of murine, feline and bovine leukaemia viruses. Amino acid sequencing of the retrovirus proteases, either after their purification or from prediction from the nucleotide sequence, shows that they possess the Asp-Thr-Gly sequence characteristic of the aspartyl proteinases. In this report we show that retrovirus proteases belong to the aspartyl proteinase group and demonstrate an inhibition by the aspartyl proteinase-specific inhibitor, pepstatin A, on the activity of bovine leukaemia, Moloney murine leukaemia and human T-cell leukaemia virus proteases.     

一类具有潜伏感染细胞的时滞HIV-1传染病模型

提出了一类具有潜伏感染细胞的时滞HIV-1传染病模型,定义了基本再生数R_0,给出了无病平衡点P_0(x_0,0,0)和慢性感染平衡点P~*(x~*,ω~*,y~*,v~*)的存在条件.首先利用线性化方法,得到了无病平衡点和慢性感染平衡点的局部渐近稳定性.进一步通过构造相应的Lyapunov函数,并结合LaSalle不变集原理,证明了当R_0≤1时,无病平衡点P_0(x_0,0,0,0)是全局渐近稳定的;当R_01时,慢性感染平衡点P~*(x~*,ω~*,y~*,v~*)是全局渐近稳定的,但无病平衡点Po (x_0,0,0,0)是不稳定的.结果表明,模型中的潜伏感染时滞和感染时滞并不影响模型的全局稳定性,并通过数值模拟验证了所得结论.     

Interaction of HIV-1 fusion peptide and its mutant with lipid membrane

HIV_WT and HIV_V2E represent the 23 amino acids fusion peptide of HIV-1 gp41 N terminus and its position 2 mutant (Val→Glu). We have studied the structure-function relationship of HIV_WT and HIV_V2E when they interact with acidic and neutral lipid membranes. The results show that HIV_WT and HIV_V2E have the same conformational characteristics and tendencies of conformational transition but definitely different functions: HIV_WT destabilizes membrane and induces fusion by adopting predominant α-helix conformation when interacting with acidic POPG membrane, its phenylalanine residues can penetrate into the hydrophobic core of POPG bilayer; HIV_V2E also adopts predominant α-helix when interacting with POPG membrane, but it cannot destabilize POPG membrane and induce fusion, the phenylalanine residues of it are located near the surface of POPG bilayer. HIV_WT and HIV_V2E both adopt predominant β-sheet conformation to interact with neutral POPC membrane, and cannot destabilize POPC membrane and induce fusion, the position of phenylalanine residues of both HIV_WT and HIV_V2E are close to the surface of POPC bilayer. These results demonstrate that the N terminal hydrophobicity of fusion peptide and the secondary structure when interacting with lipid membrane play important roles for fusion peptide exerting its function.     

尿激酶体外抑制人体免疫缺损病毒的侵染能力

人体免疫缺损病毒的包膜蛋白gp120的V3环区包含一段在人类蛋白质中很少出现的高度保守序列，但这段序列与纤溶酶原被纤溶酶原激活剂酶切位点附近序列有同源性．由于V3环区在人体免疫缺损病毒侵染细胞过程中的重要性，评估了尿激酶对人体免疫缺损病毒侵染能力的影响．通过检测逆转录酶活力，P24抗原的表达和合胞体形成情况发现尿激酶可以抑制人体免疫缺损病毒对多种淋巴瘤和白血病细胞系，如MT4、CCM、H9和外周血单核细胞的侵染能力，并且这种抑制与尿激酶浓度呈剂量依赖关系．那些能够被尿激酶抑制的人体免疫缺损病毒株其V3环区序列必须与纤溶酶原激活区亭列同源，实验事常用病毒株包括BRU和RF以及某些野生病毒株．研究结果显示尿激酶在体外实验中可以抑制人体免疫缺损病毒的侵染能力．