Structural investigation of the HIV-1 envelope glycoprotein gp160 cleavage site, 2: relevance of an N-terminal helix

Proteolytic activation of the HIV-1 envelope glycoprotein gp160 is selectively performed by the proprotein convertase furin at the C-terminus of the sequence R508-E-K-R511 (site 1), in spite of the presence of another consensus sequence, Lys500-Ala-Lys-Arg503 (site 2). On the basis of the solution structural analysis of the synthetic peptide p498, spanning the gp160 sequence Pro498-Gly516, we previously suggested a possible role of an N-terminal helix in regulating the exposure and accessibility of the gp160 physiological cleavage site, enclosed in a loop. Here we report on the activity and conformation of the 23-residue peptide h-REKR, designed to exhibit a large N-terminal helix, followed by the gp160 native sequence, Arg508-Gly516. h-REKR is digested by furin with high efficiency, comparable to the full native p498. Circular dichroism analyses, in mixtures from pure water to 98 % trifluoroethanol, outline a significant content of helical structure in the peptide conformation. The molecular model obtained from NMR data collected in trifluoroethanol/water, by means of DYANA and AMBER simulations, indeed has helical structure on a large N-terminal segment. Such a long helix does not seem to affect the loop conformation of the C-terminal site 1-containing sequence, which exhibits the same proton chemical shifts already observed for the full native p498.     

Selective inhibition of HIV-1 reverse transcriptase (HIV-1 RT) RNase H by small RNA hairpins and dumbbells

We present here the design of a novel class of RNA inhibitors of the RNase H domain of HIV-1 RT, a ribonuclease activity that is essential for viral replication in vivo. Specifically, we show that small RNA hairpins and dumbbells can selectively inhibit the RNase H activity of HIV-1 RT without affecting other cellular RNases H (e.g., E. coli and human RNase H). These results suggest that the inhibitors do not interact with the nucleic acid binding site of RT RNase H, as this region should be well conserved among the various enzymes. The most potent inhibitors displayed IC50 values in the 3-8 microM range. Remarkably, the DNA polymerase activity, an intrinsic property of HIV RT, was not inhibited by the hairpin and dumbbell aptamers, a property not previously observed for any nucleic acid aptamer directed against RT RNase H. The results described here suggest a noncompetitive binding mechanism, as outlined in the differential inhibitory characteristics of each of the nucleic acid aptamers against the bacterial, human, and viral RNase H homologues.     

MBNL1-RNA recognition: contributions of MBNL1 sequence and RNA conformation

Muscleblind-like proteins (MBNL) are RNA-binding proteins that bind to the poly(CUG) and poly(CCUG) sequences that are the causative agents of myotonic dystrophy. It has been suggested that as a result of binding to the repeating RNA sequences, MBNL1 is abnormally expressed and translocated, which leads to many of the misregulated events in myotonic dystrophy. In this work, steady-state fluorescence quenching experiments suggest that MBNL1 alters the structure of helical RNA targets upon binding, which may explain the selectivity of MBNL1 for less structured RNA sites. The removal of one pair of zinc fingers greatly impairs the binding affinity of MBNL1, which indicates that the two pairs of zinc fingers might possibly interact with RNA targets cooperatively. Alanine scanning mutagenesis results suggest that the binding energy may be distributed across the protein. Overall, the results presented here suggest that small molecules that stabilize the helical structure of poly(CUG) and poly(CCUG) RNAs will inhibit the formation of complexes with MBNL1.     

HIV-1核酸血筛试剂国家参考品的研制

目的研制HIV-1RNA血筛试剂国家参考品。方法收集HIV-1病毒培养物、我国不同地区的HIV-1感染者血浆以及正常人样品,经HIV-1病毒载量试剂检测,对HIV-1RNA阳性的样品进行env基因型分析,从中筛选参考品的候选样品。结果共筛选8份HIV-1RNA阳性的样品作为阳性参考品,病毒载量均高于5000IU/ml;8份HIV、HBV、HCV均为阴性的血浆样品作为阴性参考品;以1份病毒培养样品作为灵敏度参考品的原始样品,经WHOHIV-1RNA标准品标定,其HIV-1病毒载量为3.79×104IU/ml;反复3次冻融对参考品的病毒载量无明显影响。结论已制备HIV-1RNA血筛试剂国家参考品,为我国HIV-1核酸血筛试剂的质量控制和标准化提供了依据。     

Dendrimeric Guanidinoneomycin for Cellular Delivery of Bio‐macromolecules

We present the synthesis of polymeric amino‐ and guanidinoglycosides prepared by tethering neomycin and guanidinoneomycin to PAMAM dendrimers of generations 2 and 4. The ability of these conjugates to promote cellular uptake of high‐molecular‐weight cargo is discussed, together with their cytotoxicity and mechanisms of entry. We demonstrate that the presence of multiple guanidinoneomycin carriers on the PAMAM surface plays an important role in promoting cellular uptake of the dendrimers, maintaining the heparan sulfate specificity and negligible cytotoxicity typical of monomeric guanidinoglycoside molecular transporters.     

Structural basis of single-stranded RNA recognition

RNA is an ancient and highly versatile molecule that plays fundamental roles in all living organisms. Its molecular functions range from being a mediator of genetic information to the regulation of essential cellular processes. These functions are often accomplished in close association with RNA binding proteins. Over the past few years, a considerable number of high-resolution three-dimensional structures of important protein-RNA complexes have been determined. Here, we wish to discuss recent examples and highlight principles and distinct features of single-stranded RNA recognition by conserved RNA binding domains.     

Inhibition of HIV-1 by a peptide ligand of the genomic RNA packaging signal Psi

The interaction of the nucleocapsid NCp7 of the human immunodeficiency virus type 1 (HIV-1) Gag polyprotein with the RNA packaging signal Psi ensures specific encapsidation of the dimeric full length viral genome into nascent virus particles. Being an essential step in the HIV-1 replication cycle, specific genome encapsidation represents a promising target for therapeutic intervention. We previously selected peptides binding to HIV-1 Psi-RNA or stem loops (SL) thereof by phage display. Herein, we describe synthesis of peptide variants of the consensus HWWPWW motif on membrane supports to optimize Psi-RNA binding. The optimized peptide, psi-pepB, was characterized in detail with respect to its conformation and binding properties for the SL3 of the Psi packaging signal by NMR and tryptophan fluorescence quenching. Functional analysis revealed that psi-pepB caused a strong reduction of virus release by infected cells as monitored by reduced transduction efficiencies, capsid p24 antigen levels, and electron microscopy. Thus, this peptide shows antiviral activity and could serve as a lead compound to develop new drugs targeting HIV-1.     

Humanization strategies for an anti-idiotypic antibody mimicking HIV-1 gp41

Anti-idiotypic antibodies could represent an alternative vaccination approach in human therapy. The anti-idiotypic antibody Ab2/3H6 was generated in mouse and is directed against the human monoclonal antibody 2F5, which broadly and potently neutralizes primary HIV-1 isolates. Ab2/3H6 is able to mimic the antigen recognition site of 2F5 making it a putative candidate for HIV-1 vaccine purposes. In order to reduce immunogenicity of therapeutic proteins, humanization methods have been developed. The mouse variable regions of Ab2/3H6 were subjected to three different humanization approaches, namely resurfacing, complementarity determining region (CDR)-grafting and superhumanization. Four different humanized Ab2/3H6 variants were characterized for their binding affinity to 2F5 in comparison to the chimeric Ab2/3H6. The resurfaced and the 'conservative' CDR-grafted variants showed similar binding properties to 2F5 when compared to the chimeric version, while the 'aggressive' CDR-grafted antibody showed reduced affinity and the superhumanized type lost its binding ability. In this study, we developed humanized Ab2/3H6 variants that retained the same affinity as the parental antibody, and are therefore of potential interest for future clinical trails.     

TAR RNA Mediated Folding of a Single-Arginine-Mutant HIV-1 Tat Protein within HeLa Cells Experiencing Intracellular Crowding

The various effects of native protein folding on the stability and folding rate of intrinsically disordered proteins (IDPs) in crowded intracellular environments are important in biomedicine. Although most studies on protein folding have been conducted in vitro, providing valuable insights, studies on protein folding in crowded intracellular environments are scarce. This study aimed to explore the effects of intracellular molecular crowding on the folding of mutant transactivator HIV-1 Tat based on intracellular interactions, including TAR RNA, as proof of the previously reported chaperna-RNA concept. Considering that the Tat–TAR RNA motif binds RNA, we assessed the po tential function of TAR RNA as a chaperna for the refolding of R52Tat, a mutant in which the argi nine (R) residues at R52 have been replaced with alanine (A) by site-directed mutagenesis. We mon itored Tat-EGFP and Tat folding in HeLa cells via time-lapse fluorescence microscopy and biolayer interferometry using EGFP fusion as an indicator for folding status. These results show that the refolding of R52A Tat was stimulated well at a 0.3 μM TAR RNA concentration; wild-type Tat refolding was essentially abolished because of a reduction in the affinity for TAR RNA at that con centration. The folding and refolding of R52Tat were mainly promoted upon stimulation with TAR RNA. Our findings provide novel insights into the therapeutic potential of chaperna-mediated fold ing through the examination of as-yet-unexplored RNA-mediated protein folding as well as viral genetic variants that modulate viral evolutionary linkages for viral diseases inside a crowded intra cellular environment.     

RNA nucleoside recognition by phthalocyanine-based molecularly imprinted polymers

Highly selective molecularly imprinted polymers (MIPs) having a phthalocyanine-based recognition centre as receptors for RNA nucleoside were prepared. In particular, a zinc phthalocyanine peripherally substituted with methacrylic groups was synthesized and utilized as functional monomer in combination with methacrylic acid (MAA) to form polymers with the aim to obtain MIPs having improved binding capacity and selectivity for nucleosides. Tri-O-acetyladenosine (TOAA) was utilized as model template in the preparation of the MIPs. The corresponding non metallated phthalocyanine was also prepared and used as functional monomer for the preparation of the MIPs in order to understand the role of the Zinc(II) ion in the binding capacity of the polymers towards the template molecule. The MIP prepared by using both the zinc phthalocyanine and MAA showed higher binding ability towards TOAA compared to the MIPs prepared using only MAA or its combination with the non metallated phthalocyanine. The results obtained suggest that the nucleoside is specifically bound to the polymer through multi-point interactions involving both the coordination of the nucleoside to the metal of the phthalocyanine and hydrogen bonding/electrostatic interactions with MAA and the modifiers linked to the phthalocyanines. As for the selectivity, the MIPs exhibited relative high binding affinities for TOAA while they did not show any binding capacity for the other RNA nucleosides.