Structural conservation predominates over sequence variability in the crown of HIV type 1's V3 loop.
Ontology highlight
ABSTRACT:
SUBMITTER: Almond D
PROVIDER: S-EPMC2932551 | biostudies-literature | 2010 Jun
REPOSITORIES: biostudies-literature
Publications
Structural conservation predominates over sequence variability in the crown of HIV type 1's V3 loop.
Almond David D Kimura Tetsuya T Kong XiangPeng X Swetnam James J Zolla-Pazner Susan S Cardozo Timothy T
AIDS research and human retroviruses 20100601 6
The diversity of HIV-1 is a confounding problem for vaccine design, as the human immune response appears to favor poor or strain-specific responses to any given HIV-1 virus strain. A significant portion of this diversity is manifested as sequence variability in the loops of HIV-1's surface envelope glycoprotein. Here we show that the most variable sequence positions in the third variable (V3) loop crown cluster to a small zone on the surface of one face of the V3 loop ss-hairpin conformation. Th ...[more]
Similar Datasets
Project description:The V3 loop of the HIV-1 envelope (Env) protein elicits a vigorous, but largely non-neutralizing antibody response directed to the V3-crown, whereas rare broadly neutralizing antibodies (bnAbs) target the V3-base. Challenging this view, we present V3-crown directed broadly neutralizing Designed Ankyrin Repeat Proteins (bnDs) matching the breadth of V3-base bnAbs. While most bnAbs target prefusion Env, V3-crown bnDs bind open Env conformations triggered by CD4 engagement. BnDs achieve breadth by focusing on highly conserved residues that are accessible in two distinct V3 conformations, one of which resembles CCR5-bound V3. We further show that these V3-crown conformations can, in principle, be attacked by antibodies. Supporting this conclusion, analysis of antibody binding activity in the Swiss 4.5 K HIV-1 cohort (n = 4,281) revealed a co-evolution of V3-crown reactivities and neutralization breadth. Our results indicate a role of V3-crown responses and its conformational preferences in bnAb development to be considered in preventive and therapeutic approaches.
| S-EPMC8602657 | biostudies-literature
Project description:BACKGROUND: The net charge of the hypervariable V3 loop on the HIV-1 envelope gp120 outer domain plays a key role in modulating viral phenotype. However, the molecular mechanisms underlying the modulation remain poorly understood. METHODOLOGY/PRINCIPAL FINDINGS: By combining computational and experimental approaches, we examined how V3 net charge could influence the phenotype of the gp120 interaction surface. Molecular dynamics simulations of the identical gp120 outer domain, carrying a V3 loop with net charge of +3 or +7, showed that the V3 change alone could induce global changes in fluctuation and conformation of the loops involved in binding to CD4, coreceptor and antibodies. A neutralization study using the V3 recombinant HIV-1 infectious clones showed that the virus carrying the gp120 with +3 V3, but not with +7 V3, was resistant to neutralization by anti-CD4 binding site monoclonal antibodies. An information entropy study shows that otherwise variable surface of the gp120 outer domain, such as V3 and a region around the CD4 binding loop, are less heterogeneous in the gp120 subpopulation with +3 V3. CONCLUSIONS/SIGNIFICANCE: These results suggest that the HIV-1 gp120 V3 loop acts as an electrostatic modulator that influences the global structure and diversity of the interaction surface of the gp120 outer domain. Our findings will provide a novel structural basis to understand how HIV-1 adjusts relative replication fitness by V3 mutations.
| S-EPMC3356331 | biostudies-literature
Project description:Two different states of human immunodeficiency virus type 1 are apparent in the asymptomatic and late stages of infection. Important determinants associated with these two states have been found within the V3 loop of the viral Env protein. In this study, two large data sets of published V3 sequences were analyzed to identify patterns of sequence variability that would correspond to these two states of the virus. We were especially interested in the pattern of basic amino acid substitutions, since the presence of basic amino acids in V3 has been shown to change virus tropism in cell culture. Four features of the sequence heterogeneity in V3 were observed: (i) approximately 70% of all nonconservative basic substitutions occur at four positions in V3, and V3 sequences with a basic substitution in at least one of these four positions contain approximately 95% of all nonconservative basic substitutions; (ii) substitution patterns within V3 are influenced by the identity of the amino acid at position 25; (iii) sequence polymorphisms account for a significant fraction of uncharged amino acid substitutions at several positions in V3, and sequence heterogeneity other than these polymorphisms is most significant at two positions near the tip of V3; and (iv) sequence heterogeneity in V3 (in addition to the basic amino acid substitutions) is approximately twofold greater in V3 sequences that contain basic amino acid substitutions. By using this sequence analysis, we were able to identify distinct groups of V3 sequences in infected patients that appear to correspond to these two virus states. The identification of these discrete sequence patterns in vivo demonstrates how the V3 sequence can be used as a genetic marker for studying the two states of human immunodeficiency virus type 1.
| S-EPMC237966 | biostudies-other
Project description:IntroductionMaraviroc inhibits CCR5-tropic HIV-1 across different subtypes in vitro and has demonstrated efficacy in clinical trials. V3-loop amino acid variants observed in individual maraviroc-resistant viruses have not been found to be predictive of reduced susceptibility. Sequence-database searches have demonstrated that approximately 7.3% of viruses naturally encode these variants, raising concerns regarding potential pre-existing resistance. A study from Russia reported that combinations of these same amino acids are present in the V3 loops of the Russian variant subtype A (IDU-A, now A6) with a much greater prevalence (range: 74.4%-92.3%) depending on the combination. However, these studies and database searches did not include phenotypic evaluation.MethodsSixteen Russian HIV-1 isolates (including sub-subtype A6 viruses) were assessed for V3 loop sequence and phenotypic susceptibility to maraviroc.ResultsAll 12 of the A6 viruses and 2/4 subtype B isolates encoded V3-loop variants that have previously been identified in individual virus isolates with reduced susceptibility to maraviroc. However, despite the prevalence of these V3-loop amino acid variants among the tested viruses, phenotypic sensitivity to maraviroc was observed in all instances. Similarly, reduced susceptibility to maraviroc was not found in virus from participants who experienced virologic failure in a clinical study of maraviroc in Russia (A4001101, [NCT01275625]).DiscussionAltogether, these data confirm that the presence of individual or combinations of V3-loop amino acid residues in sub-subtype A6 viruses alone does not predict natural resistance to maraviroc and that V3-loop genotype analysis of R5 virus prior to treatment is not helpful in predicting clinical outcome.
| S-EPMC8236768 | biostudies-literature
Project description:HIV-1 cell entry commonly uses, in addition to CD4, one of the chemokine receptors CCR5 or CXCR4 as coreceptor. Knowledge of coreceptor usage is critical for monitoring disease progression as well as for supporting therapy with the novel drug class of coreceptor antagonists. Predictive methods for inferring coreceptor usage based on the third hypervariable (V3) loop region of the viral gene coding for the envelope protein gp120 can provide us with these monitoring facilities while avoiding expensive phenotypic tests. All simple heuristics (such as the 11/25 rule) as well as statistical learning methods proposed to date predict coreceptor usage based on sequence features of the V3 loop exclusively. Here, we show, based on a recently resolved structure of gp120 with an untruncated V3 loop, that using structural information on the V3 loop in combination with sequence features of V3 variants improves prediction of coreceptor usage. In particular, we propose a distance-based descriptor of the spatial arrangement of physicochemical properties that increases discriminative performance. For a fixed specificity of 0.95, a sensitivity of 0.77 was achieved, improving further to 0.80 when combined with a sequence-based representation using amino acid indicators. This compares favorably with the sensitivities of 0.62 for the traditional 11/25 rule and 0.73 for a prediction based on sequence information as input to a support vector machine and constitutes a statistically significant improvement. A detailed analysis and interpretation of structural features important for classification shows the relevance of several specific hydrogen-bond donor sites and aliphatic side chains to coreceptor specificity towards CCR5 or CXCR4. Furthermore, an analysis of side chain orientation of the specificity-determining residues suggests a major role of one side of the V3 loop in the selection of the coreceptor. The proposed method constitutes the first approach to an improved prediction of coreceptor usage based on an original integration of structural bioinformatics methods with statistical learning.
| S-EPMC1848001 | biostudies-literature
Project description:The CC chemokine receptor 5 (CCR5) antagonism represents a promising pharmacological strategy for therapeutic intervention as it plays a significant role in reducing the severity and progression of a wide range of pathological conditions. Here we designed and generated peptide ligands targeting the chemokine receptor, CCR5, that were derived from the critical interaction sites of the V3 crown domain of envelope protein glycoprotein gp120 (TRKSIHIGPGRAFYTTGEI) of HIV-1 using computational biology approach and the peptide sequence corresponding to this region was taken as the template peptide, designated as TMP-1. The peptide variants were synthesized by employing Fmoc chemistry using polymer support and were labelled with rhodamine B to study their interaction with the CCR5 receptor expressed on various cells. TMP-1 and TMP-2 were selected as the high-affinity ligands from in vitro receptor-binding assays. Specific receptor-binding experiments in activated peripheral blood mononuclear cells and HOS.CCR5 cells indicated that TMP-1 and TMP-2 had significant CCR5 specificity. Further, the functional analysis of TMP peptides using chemotactic migration assay showed that both peptides did not mediate the migration of responsive cells. Thus, template TMP-1 and TMP-2 represent promising CCR5 targeting peptide candidates.
| S-EPMC9445593 | biostudies-literature
Project description:The CCR5 coreceptor amino terminus and extracellular (ECL) loops 1 and 2 have been implicated in HIV-1 infections, with species differences in these regions inhibiting zoonoses. Interactions of gp120 with CD4 and CCR5 reduce constraints on metastable envelope subunit gp41, enabling gp41 conformational changes needed for infection. We previously selected HIV-1JRCSF variants that efficiently use CCR5(?18) with a deleted amino terminus or CCR5(HHMH) with ECL2 from an NIH/Swiss mouse. Unexpectedly, the adaptive gp120 mutations were nearly identical, suggesting that they function by weakening gp120's grip on gp41 and/or by increasing interactions with ECL1. To analyze this and further wean HIV-1 from human CCR5, we selected variants using CCR5(HMMH) with murine ECL1 and 2 sequences. HIV-1JRCSF mutations adaptive for CCR5(?18) and CCR5(HHMH) were generally maladaptive for CCR5(HMMH), whereas the converse was true for CCR5(HMMH) adaptations. The HIV-1JRCSF variant adapted to CCR5(HMMH) also weakly used intact NIH/Swiss mouse CCR5. Our results strongly suggest that HIV-1JRCSF makes functionally critical contacts with human ECL1 and that adaptation to murine ECL1 requires multiple mutations in the crown of gp120's V3 loop.
| S-EPMC4576943 | biostudies-literature
Project description:BackgroundHIV-1 infects the host cell by interacting with the primary receptor CD4 and a coreceptor CCR5 or CXCR4. Maraviroc, a CCR5 antagonist binds to CCR5 receptor. Thus, it is important to identify the coreceptor used by the HIV strains dominating in the patient. In past, a number of experimental assays and in-silico techniques have been developed for predicting the coreceptor tropism. The prediction accuracy of these methods is excellent when predicting CCR5(R5) tropic sequences but is relatively poor for CXCR4(X4) tropic sequences. Therefore, any new method for accurate determination of coreceptor usage would be of paramount importance to the successful management of HIV-infected individuals.ResultsThe dataset used in this study comprised 1799 R5-tropic and 598 X4-tropic third variable (V3) sequences of HIV-1. We compared the amino acid composition of both types of V3 sequences and observed that certain types of residues, e.g., Asparagine and Isoleucine, were preferred in R5-tropic sequences whereas residues like Lysine, Arginine, and Tryptophan were preferred in X4-tropic sequences. Initially, Support Vector Machine-based models were developed using amino acid composition, dipeptide composition, and split amino acid composition, which achieved accuracy up to 90%. We used BLAST to discriminate R5- and X4-tropic sequences and correctly predicted 93.16% of R5- and 75.75% of X4-tropic sequences. In order to improve the prediction accuracy, a Hybrid model was developed that achieved 91.66% sensitivity, 81.77% specificity, 89.19% accuracy and 0.72 Matthews Correlation Coefficient. The performance of our models was also evaluated on an independent dataset (256 R5- and 81 X4-tropic sequences) and achieved maximum accuracy of 84.87% with Matthews Correlation Coefficient 0.63.ConclusionThis study describes a highly efficient method for predicting HIV-1 coreceptor usage from V3 sequences. In order to provide a service to the scientific community, a webserver HIVcoPred was developed (http://www.imtech.res.in/raghava/hivcopred/) for predicting the coreceptor usage.
| S-EPMC3626595 | biostudies-literature
Project description:Identification of vulnerable sites defined by broadly neutralizing antibodies (bNAbs) on HIV-1 envelope (Env) is crucial for vaccine design, and we present here a vulnerable site defined by bNAb M4008_N1, which neutralizes about 40% of a tier-2 virus panel. A 3.2 Å resolution cryo-EM structure of M4008_N1 in complex with BG505 DS-SOSIP reveals a large, shallow protein epitope surface centered at the V3 crown of gp120 and surrounded by key glycans. M4008_N1 interacts with gp120 primarily through its hammerhead CDR H3 to form a β-sheet interaction with the V3 crown hairpin. This makes M4008_N1 compatible with the closed conformation of the prefusion Env trimer, and thus distinct from other known V3 crown mAbs. This mode of bNAb approaching the immunogenic V3 crown in the native Env trimer suggests a strategy for immunogen design targeting this site of vulnerability. Mapping of the HIV Env surface epitopes targeted by broadly neutralizing antibodies (bNAbs) is of great interest for HIV-1 vaccine design. Here, the authors present the 3.2 Å cryo-EM structure of the bNAb M4008_N1 in complex with BG505 DS-SOSIP, an engineered native-like Env trimer and observe that the bNAb epitope is centered at the V3 crown and that M4008_N1 uses its CDR H3 to form an extended β-sheet with the β-hairpin of the V3 crown in a conformation stabilized in the prefusion trimer.
| S-EPMC8578649 | biostudies-literature
Project description:gp120 is a subunit of the envelope glycoprotein of HIV-1. The third variable loop region of gp120 (V3 loop) contains multiple immunodominant epitopes and is also functionally important for deciding cell-tropism of the virus. 447-52D is a monoclonal antibody that recognizes the conserved tip of the V3 loop in a beta-turn conformation. This antibody has previously been shown to neutralize diverse strains of the virus. In an attempt to generate an immunogen competent to generate 447-52D-like antibodies, the known epitope of 447-52D was inserted at three different surface loop locations in the small, stable protein Escherichia coli Trx (thioredoxin). At one of the three locations (between residues 74 and 75), the insertion was tolerated, the resulting protein was stable and soluble, and bound 447-52D with an affinity similar to that of intact gp120. Upon immunization, the V3 peptide-inserted Trx scaffold was able to generate anti-V3 antibodies that could compete out 447-52D binding to gp120. Epitope mapping studies demonstrated that these anti-V3 antibodies recognized the same epitope as 447-52D. Although the 447-52D-type antibodies were estimated to be present at concentrations of 50-400 microg/ml of serum, these were not able to effect neutralization of strains like JRFL and BAL but could neutralize the sensitive MN strain. The data suggest that because of the low accessibility of the V3 loop on primary isolates such as JRFL, it will be difficult to elicit a V3-specific, 447-52D-like antibody response to effectively neutralize such isolates.
| S-EPMC1615908 | biostudies-literature