Structure Of Human Immunodeficiency Virus Research Articles

Prevalence of drug resistant HIV-1 forms in patients without any history of antiretroviral therapy in the Republic of Guinea.

To study the structure of human immunodeficiency virus(HIV)-1 drug resistance (DR) in patients with newly diagnosed infection. Residents of the Republic of Guinea (N = 2168) were tested for HIV using enzyme-linked immunosorbent assay(ELISA). Individuals with a positive result were further examined for the presence of viral loadin blood plasma. HIV was analyzed using Sanger sequencing. The obtained sequences were genotyped using REGA (version 3.0) and analyzed in MEGA 7. Analysis for the presence of DR mutations was performed using the Stanford University HIV DR Database. Serological markers of HIV were detected in 239 people, which represents 11.02% of the entire sample. HIV RNA was detected in 58 people. The following subtypes were seen: HIV CRF02_AG (41.9%); A1 (29.1%); A3 (12.9%); URF A1_G (12.9%); and G (3.2%). In 25% of patients, at least one significant mutation was encountered leading directly to HIV DR. The mutations encountered cause resistance to NRTI and NNRTI; one case of multiple resistance was identified. Major resistance to protease inhibitor was not seen. The detection of HIV-1 mutations associated with DR, in individuals who have never received antiretroviral therapy, is a cause for concern. It suggests that: new infections are occurring with strains that already have resistance; and the expansion of resistance is not always directly associated with selective drug pressure. Among the likely reasons for the high prevalence of primary HIV DR in the Republic of Guinea, drug availability is probably the key. The consequence of this is the lack of adherence of patients to treatment, the formation and transmission of resistant variants of the virus in the population. These findings suggest the need to test patients for resistant virus variants before initiating treatment.

Molecular Epidemiology Reveals Long‐Term Changes in HIV Type 1 Subtype B Transmission in Switzerland

Sequence data from resistance testing offer unique opportunities to characterize the structure of human immunodeficiency virus (HIV) infection epidemics. We analyzed a representative set of HIV type 1 (HIV-1) subtype B pol sequences from 5700 patients enrolled in the Swiss HIV Cohort Study. We pooled these sequences with the same number of sequences from foreign epidemics, inferred a phylogeny, and identified Swiss transmission clusters as clades having a minimal size of 10 and containing >or=80% Swiss sequences. More than one-half of Swiss patients were included within 60 transmission clusters. Most transmission clusters were significantly dominated by specific transmission routes, which were used to identify the following patient groups: men having sex with men (MSM) (38 transmission clusters; average cluster size, 29 patients) or patients acquiring HIV through heterosexual contact (HETs) and injection drug users (IDUs) (12 transmission clusters; average cluster size, 144 patients). Interestingly, there were no transmission clusters dominated by sequences from HETs only. Although 44% of all HETs who were infected between 1983 and 1986 clustered with injection drug users, this percentage decreased to 18% for 2003-2006 (P<.001), indicating a diminishing role of injection drug users in transmission among HETs over time. Our analysis suggests (1) the absence of a self-sustaining epidemic of HIV-1 subtype B in HETs in Switzerland and (2) a temporally decreasing clustering of HIV infections in HETs and IDUs.

Raman spectroscopic study on structure of human immunodeficiency virus (HIV) and hypericin-induced photosensitive damage of HIV

The first Raman spectra of HIV1-HIV2 in human sera and hypericin-induced photosensitive damage of the virus have been obtained. The prominent Raman lines in the spectra are assigned respectively to the carbohydrates of viral glycoprotein, RNA, protein and lipid. The spectra are dominated by Raman scattering of the carbohydrates. The lines of D-Mannose and N-acetylglucosamine in carbohydrates are obvious and there is a beta-configuration in the anomeric C1 position in D-Mannose. The viral RNA duplexes bound assumes an A-form geometry. The lines of backbone phosphate group, bases (involving interbase hydrogen bonding) and ribose of the RNA are complete and distinct. The secondary structure of the viral protein maintains alpha-helix, beta-sheet, beta-turn and random coil. Its side chains are rich and vary from tryptophan, phenylalanine and "buried" tyrosine; the stable conformation of the S-S bond of gauche-gauche-gauche; the two forms of C-S bonds of gauche and trans; to sulfhydrl group and ionized and unionized carboxyl groups. The viral lipid bilayer molecules are probably in the liquid ordered phase or the gel phase. It was observed that the hypericin-induced photosensitive damage of HIV1-HIV2 in human sera changed various components of HIV1-HIV2 in different degrees: The orderly A-form viral RNA would become a disordered viral RNA. There were a breakage of interbase hydrogen bonds and disruption of vertical base-base stacking interactions. In addition, the groups of ribos and four bases were damaged obviously. A decrease in ordered structure (alpha-helix and beta-sheet) of viral protein is accompanied by an increase in random coil. The Tyr buried in the three-dimensional structure of protein was damaged, but it was still "buried" and the damage of C-S bond of trans form was stronger. The groups of carbohydrates, including D-Mannos and N-acetyl glucosamine, in viral envelope glycoprotein had also been changed. The hydrophilic C-N bond of choline in viral lipid was damaged, which was the possible binding site to hypericin, whereas the viral lipids bilayers were still probably in the liquid ordered phase or the gel phase. So the space structure of HIV1-HIV2 was damaged under the experimental conditions, which might block viral infection and inhibit its growth and breeding. It is apparent that the laser Raman spectra have provided certain direct evidence at the molecular level for photosensitive damage of HIV1-HIV2.

Raman spectroscopic study on structure of human immu-nodeficiency virus (HIV) and hypericin-induced photosen-sitive damage of HIV

Raman spectroscopic study on structure of human immu-nodeficiency virus (HIV) and hypericin-induced photosen-sitive damage of HIV

Impairment by mucosal adjuvants and cross-reactivity with variant peptides of the mucosal immunity induced by injection of the fusion peptide PADRE-ELDKWA.

Secretory immunity protects against mucosal transmission of viruses, as demonstrated with the oral poliovirus vaccine. In a previous study we showed that this immunity could be induced in mice by injection of a fusion peptide consisting of an unnatural peptide-like sequence (PADRE) and a viral epitope (ELDKWASLW). PADRE is a T-helper-cell epitope able to bind most major histocompatibility complex class II molecules of different haplotypes in mice and humans and to increase antibody responses. ELDKWA is a well-known consensual sequence of gp41 involved in a key structure of human immunodeficiency virus (HIV) type 1. Here, the antibody response to the native form of ELDKWA was mainly of the immunoglobulin A isotype and selectively occurred in mucosa. Adjuvants, such as cholera toxin and cytosine polyguanine, were useless and even competed with PADRE for the response. Interestingly, these antibodies were cross-reactive with the three major variants of the epitope, as shown both by direct enzyme-linked immunosorbent assay and by inhibition. This unconventional route of mucosal immunization allows control of the administered dose. The lack of adjuvant and the cross-reactivity of the antibodies increase the safety and the spectrum of the candidate vaccine, respectively. The drug-like nature of the construct suggests further improvements by synthesis of more antigenic sequences. The reasonable cost of short peptides at the industrial level and their purity make this approach of interest for future vaccines against mucosal transmission of HIV or other pathogens.

Catalytic complex of HIV enzyme analyzed

A novel chemical cross-linking strategy devised by researchers at Harvard University has allowed them to obtain the long-sought structure of human immunodeficiency virus (HIV) reverse transcriptase (RT) bound to its natural substrates—double-stranded DNA and a deoxynucleoside triphosphate. AIDS drugs such as zidovudine (AZT) inhibit RT, short-circuiting the life cycle of HIV. But the virus has a tendency to mutate very deftly away from the drugs' range of efficacy, rendering them ineffective. The new structure helps clarify how the virus develops resistance against RT inhibitors and thus could point the way to better drugs. The Harvard team included postdoc Huifang Huang and professor Gregory L. Verdine of the department of chemistry and chemical biology and postdoc Rajiv Chopra and professor Stephen C. Harrison of Howard Hughes Medical Institute and Harvard's department of molecular and cellular biology [ Science , 282 , 1669 (1998)]. RT is a polymerase that transcribes HIV's single-stranded RNA genome i...

32] Molecular modeling of ligand-gated ion channels

Publisher Summary Molecular modeling is a method for mimicking the behavior of molecules and molecular systems. Simple molecular modeling studies can be performed using mechanical models. However, molecular modeling has now become synonymous with computer modeling. Computer-based molecular models are three dimensional in nature and are interactive. In the past, molecular modeling was restricted to a small cohort of people who wrote their own programs and managed their own computer systems. Computer workstations today are much more powerful than the mainframe computers of even several years ago and are relatively inexpensive. Software can be obtained readily from commercial companies, from academic laboratories, or via the World Wide Web (WWW). Molecular modeling produces testable hypotheses. These can be extremely useful, as in successfully predicting the structure of human immunodeficiency virus (HIV) protease. They can, however, lead one astray, as in our modeling of the guanosine triphosphate (GTP) versus guanosine diphosphate (GDP) bound forms of a GTP binding protein, Cdc42Hs; nevertheless, some aspects of this modeling study proved useful. Molecular modeling is particularly powerful when used as part of a multidisciplinary study in an iterative modeling/experimental verification cycle. This chapter discusses the way such techniques can be applied to ligand-gated ion channels, using efforts to model ionotropic glutamate receptors as an example.

Crystal structure of human immunodeficiency virus (HIV) type 2 protease in complex with a reduced amide inhibitor and comparison with HIV-1 protease structures.

The crystal structure of HIV-2 protease in complex with a reduced amide inhibitor [BI-LA-398; Phe-Val-Phe-psi (CH2NH)-Leu-Glu-Ile-amide] has been determined at 2.2-A resolution and refined to a crystallographic R factor of 17.6%. The rms deviation from ideality in bond lengths is 0.018 A and in bond angles is 2.8 degrees. The largest structural differences between HIV-1 and HIV-2 proteases are located at residues 15-20, 34-40, and 65-73, away from the flap region and the substrate binding sites. The rms distance between equivalent C alpha atoms of HIV-1 and HIV-2 protease structures excluding these residues is 0.5 A. The shapes of the S1 and S2 pockets in the presence of this inhibitor are essentially unperturbed by the amino acid differences between HIV-1 and HIV-2 proteases. The interaction of the inhibitor with HIV-2 protease is similar to that observed in HIV-1 protease structures. The unprotected N terminus of the inhibitor interacts with the side chains of Asp-29 and Asp-30. The glutamate side chain of the inhibitor forms hydrogen bonds with the main-chain amido groups of residues 129 and 130.

The crystallographic structure of the protease from human immunodeficiency virus type 2 with two synthetic peptidic transition state analog inhibitors

The crystal structure of human immunodeficiency virus (HIV) type 2 protease has been determined in complexes with peptidic inhibitors Noa-His-Cha psi [CH(OH)CH(OH)]Val-Ile-Amp (U75875) and Qnc-Asn-Cha psi [CH(OH)CH2]Val-Npt(U92163) (where Noa is naphthyloxyacetyl, Cha is cyclohexylalanine, Amp is 2-aminomethylpyridine, Qnc is quinoline-2-carbonyl, and Npt is neopentylamine), which have dihydroxyethylene and hydroxyethylene moieties, respectively, in place of the normal scissile bond of the natural ligand. The complexes crystallize in space group P2(1)2(1)2(1), with one dimer-inhibitor complex per asymmetric unit and average cell dimensions of a = 33.28 A, b = 45.35 A, c = 135.84 A. Data were collected to approximately 2.5-A resolution. The model structures were refined with resulting R-factors of around 0.19. As expected, the HIV-2 protease structure is approximately C2-symmetric with a gross structure very similar to that of the HIV-1 enzyme. The inhibitors bind in an extended conformation positioned lengthwise in the binding cleft in a manner similar to that found in the HIV-1 protease-inhibitor complexes previously reported. The substitution of the bulkier Ile82 side chain in the HIV-2 protease may help explain the better ability of HIV-2 protease to bind and hydrolyze ligands with small P1 and P1' side groups. It appears that differences in specificity between the proteases of HIV-1 and HIV-2 are not merely a result of simple side chain substitutions, but may be complicated by differences in main chain flexibility as well.

Domain communication in the dynamical structure of human immunodeficiency virus 1 protease.

A dynamical model for the structure of the human immunodeficiency virus 1 (HIV-1) protease dimer in aqueous solution has been developed on the basis of molecular dynamics simulation. The model provides an accurate account of the crystal geometry and also a prediction of the structural reorganization expected to occur in the protein in aqueous solution compared to the crystalline environment. Analysis of the results by means of dynamical cross-correlation coefficients for atomic displacements indicates that domain-domain communication is present in the protein in the form of a molecular "cantilever" and is likely to be involved in enzyme function at the molecular level. The dynamical structure also suggests information that may ultimately be useful in understanding and further development of specific inhibitors of HIV-1 protease.

Fine structure of human immunodeficiency virus (HIV), immunolocalization of structural proteins and virus-cell relation

The classification of a new agent, i.e. its grouping to a defined virus family, is facilitated by electron microscopical investigations. Depending on the method used, the different distinct features of a virus can be evaluated. Combining immunological and electron microscopical techniques we received detailed information on the morphogenesis and fine structure of the human immunodeficiency virus (HIV). Two strains of HIV-1 and HIV-2 were studied. Light microscopy and SEM of virus infected cultures allowed a rapid overview on the cell cultures and gave information on cell morphology and virus production. The more laborious surface replica preparation technique permitted, in addition to an overview, the observation of structural details on the surface of the virion. Rotational image analysis of surface knobs revealed a T = 7 laevo symmetry, indicating that icosahedral principles are governing the envelope architecture. Thin section TEM of tannic acid treated HIV- producing H9 cells proved to be the most rewarding technique for the analysis of the labile HIV. No morphological differences between HIV-1 and -2 strains were detectable. The combination of structural and immuno-electron microscopical findings led to the establishment of a structural model of HIV. Whether the submembrane p17 protein serves as a morphopoetic factor and scaffolding matrix for the envelope is discussed. The viral core is built up as a double cone with a long and a short axis. The core shell containing the major viral capsid protein p24 encloses the electron dense ribonucleoprotein complex. Structural features, including the loss of the viral surface protein gp120 and the incorporation of MHC class I and II antigents into the viral envelope are discussed as factors involved in the pathogenesis of AIDS.

Fine structure of human immunodeficiency virus (HIV) and immunolocalization of structural proteins

Ultrathin section and surface replica electron microscopy were applied in combination with immunoelectron microscopy to elucidate the fine structure of HIV. The shell of the tubular core shows p24 antigenicity, while p17 is located at the inner leaflet of the lipid membrane. The virus particle is studded with 70–80 protrusions. These knobs have a diameter of 15 nm, a height of 9 nm, and are probably arranged in a T = 7 I symmetry. The major envelope protein gpl20 is spontaneously shed from the viral surface. A possible role of released gpl20 in pathogenesis is discussed.

Fine structure of human immunodeficiency virus (HIV) and immunolocalization of structural proteins

Ultrathin section and surface replica electron microscopy were applied in combination with immunoelectron microscopy to elucidate the fine structure of HIV. The shell of the tubular core shows p24 antigenicity, while p17 is located at the inner leaflet of the lipid membrane. The virus particle is studded with 70–80 protrusions. These knobs have a diameter of 15 nm, a height of 9 nm, and are probably arranged in a T = 7 I symmetry. The major envelope protein gpl20 is spontaneously shed from the viral surface. A possible role of released gpl20 in pathogenesis is discussed.