scholarly journals Visualization of the HIV-1 Env Glycan Shield Across Scales

2019 ◽  
Author(s):  
Zachary T. Berndsen ◽  
Srirupa Chakraborty ◽  
Xiaoning Wang ◽  
Christopher A. Cottrell ◽  
Jonathan L. Torres ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Computational Modeling ◽  
Structure Function ◽  
Immune Evasion ◽  
Function Analysis ◽  
Order Structure ◽  
Immune Recognition ◽  
Typical Structure ◽  
Time Resolved ◽  
Hiv 1

AbstractThe dense array of N-linked glycans on the HIV-1 Envelope Glycoprotein (Env), known as the “glycan shield”, is a key determinant of immunogenicity, yet intrinsic heterogeneity confounds typical structure-function analysis. Here we present an integrated approach of single-particle electron cryomicroscopy (cryo-EM), computational modeling, and site-specific mass-spectrometry (MS) to probe glycan shield structure and behavior at multiple levels. We found that dynamics lead to an extensive network of inter-glycan interactions that drive the formation of higher-order structure within the glycan shield. This structure defines diffuse boundaries between buried and exposed protein surface and creates a mapping of potentially immunogenic sites on Env. Analysis of Env expressed in different cell lines revealed how cryo-EM can detect subtle changes in glycan occupancy, composition, and dynamics that impact glycan shield structure and epitope accessibility. Importantly, this identified unforeseen changes in the glycan shield of Env obtained from expression in the same CHO cell line used for GMP production. Finally, by capturing the enzymatic deglycosylation of Env in a time-resolved manner we found that highly connected glycan clusters are resistant to digestion and help stabilize the pre-fusion trimer, suggesting the glycan shield may function beyond immune evasion.Significance StatementThe HIV-1 Env “glycan shield” masks the surface of the protein from immune recognition, yet intrinsic heterogeneity defies a typical structure-function description. Using a complementary approach of cryo-EM, computational modeling, and mass-spectrometry we show how heterogeneity and dynamics affect glycan shield structure across scales. Our combined approach facilitated the development of new cryo-EM data analysis methods and allowed for validation of models against experiment. Comparison of Env across a range of glycosylation states revealed how subtle differences in composition impact glycan shield structure and affect the accessibility of epitopes on the surface. Finally, time-resolved cryo-EM experiments uncovered how highly connected glycan clusters help stabilize the pre-fusion trimer, suggesting the glycan shield may function beyond immune evasion.

scholarly journals Visualization of the HIV-1 Env glycan shield across scales

2020 ◽  
Vol 117 (45) ◽  
pp. 28014-28025 ◽  
Author(s):  
Zachary T. Berndsen ◽  
Srirupa Chakraborty ◽  
Xiaoning Wang ◽  
Christopher A. Cottrell ◽  
Jonathan L. Torres ◽  
...  
Keyword(s):  
Function Analysis ◽  
Integrated Approach ◽  
Order Structure ◽  
Vaccine Production ◽  
Specific Mass ◽  
Typical Structure ◽  
Time Resolved ◽  
Multiple Levels ◽  
And Behavior ◽  
Hiv 1

The dense array of N-linked glycans on the HIV-1 envelope glycoprotein (Env), known as the “glycan shield,” is a key determinant of immunogenicity, yet intrinsic heterogeneity confounds typical structure–function analysis. Here, we present an integrated approach of single-particle electron cryomicroscopy (cryo-EM), computational modeling, and site-specific mass spectrometry (MS) to probe glycan shield structure and behavior at multiple levels. We found that dynamics lead to an extensive network of interglycan interactions that drive the formation of higher-order structure within the glycan shield. This structure defines diffuse boundaries between buried and exposed protein surface and creates a mapping of potentially immunogenic sites on Env. Analysis of Env expressed in different cell lines revealed how cryo-EM can detect subtle changes in glycan occupancy, composition, and dynamics that impact glycan shield structure and epitope accessibility. Importantly, this identified unforeseen changes in the glycan shield of Env obtained from expression in the same cell line used for vaccine production. Finally, by capturing the enzymatic deglycosylation of Env in a time-resolved manner, we found that highly connected glycan clusters are resistant to digestion and help stabilize the prefusion trimer, suggesting the glycan shield may function beyond immune evasion.

scholarly journals Structure function analysis and intermittency in the atmospheric boundary layer

2008 ◽  
Vol 15 (6) ◽  
pp. 915-929 ◽  
Author(s):  
J. M. Vindel ◽  
C. Yagüe ◽  
J. M. Redondo
Keyword(s):  
Structure Function ◽  
Velocity Structure ◽  
Function Analysis ◽  
Inertial Range ◽  
Order Structure ◽  
Turbulence Structure ◽  
Scaling Exponent ◽  
Local Similarity ◽  
Velocity Structure Function ◽  
Velocity Increments

Abstract. Data from the SABLES98 experimental campaign (Cuxart et al., 2000) have been used in order to study the relationship of the probability distribution of velocity increments (PDFs) to the scale and the degree of stability. This connection is demonstrated by means of the velocity structure functions and the PDFs of the velocity increments. Using the hypothesis of local similarity, so that the third order structure function scaling exponent is one, the inertial range in the Kolmogorov sense has been identified for different conditions, obtaining the velocity structure function scaling exponents for several orders. The degree of intermittency in the energy cascade is measured through these exponents and compared with the forcing intermittency revealed through the evolution of flatness with scale. The role of non-homogeneity in the turbulence structure is further analysed using Extended Self Similarity (ESS). A criterion to identify the inertial range and to show the scale independence of the relative exponents is described. Finally, using least-squares fits, the values of some parameters have been obtained which are able to characterize intermittency according to different models.

scholarly journals Interaction of the gp120 V1V2 loop with a neighboring gp120 unit shields the HIV envelope trimer against cross-neutralizing antibodies

2011 ◽  
Vol 208 (7) ◽  
pp. 1419-1433 ◽  
Author(s):  
Peter Rusert ◽  
Anders Krarup ◽  
Carsten Magnus ◽  
Oliver F. Brandenberg ◽  
Jacqueline Weber ◽  
...  
Keyword(s):  
Mathematical Model ◽  
Structure Function ◽  
Neutralizing Antibodies ◽  
Function Analysis ◽  
Vaccine Design ◽  
Antibody Responses ◽  
V3 Loop ◽  
Variable Loops ◽  
Hiv Envelope ◽  
Hiv 1

The HIV-1 envelope trimer adopts a quaternary conformation that effectively shields neutralization-sensitive domains and thus represents a major obstacle for natural and vaccine-elicited antibody responses. By using a structure–function analysis based on a specifically devised mathematical model, we demonstrate in this study that protection from neutralization is enforced by intersubunit contact between the variable loops 1 and 2 (V1V2) and domains of neighboring gp120 subunits in the trimer encompassing the V3 loop. Our data are consistent with an interaction of the V1V2 and V3 loop at the spike apex as proposed by cryoelectron tomography experiments. By defining the orientation of the V1V2 loop within the trimer toward the neighboring gp120 subunit’s V3 loop, our data close an important gap in the understanding of the architecture of the trimeric spike. Knowledge on how the V1V2 barrier functions in the context of the trimer to mask conserved epitopes on gp120 may aid future vaccine design.

scholarly journals Structure-Function Analysis of the HIV-1 Integrase in Complex With Two Cellular Proteins: Ledgf and INI1

2010 ◽  
Vol 98 (3) ◽  
pp. 9a
Author(s):  
Benoit Maillot ◽  
Corinne Crucifix ◽  
Florence Granger ◽  
Sylvia Eiler ◽  
Dino Moras ◽  
...  
Keyword(s):  
Structure Function ◽  
Function Analysis ◽  
Cellular Proteins ◽  
Hiv 1

scholarly journals Interaction of Upper-Tropospheric Turbulence and Gravity Waves as Obtained from Spectral and Structure Function Analyses

2008 ◽  
Vol 65 (8) ◽  
pp. 2676-2690 ◽  
Author(s):  
Chungu Lu ◽  
Steven E. Koch
Keyword(s):  
Structure Function ◽  
Gravity Waves ◽  
Function Analysis ◽  
Power Spectra ◽  
Physical Space ◽  
Energy Cascade ◽  
Small Scale ◽  
Order Structure ◽  
Scale Interactions ◽  
Inverse Energy Cascade

Abstract Spectral and structure function analyses of horizontal velocity fields observed in the upper troposphere and lower stratosphere during the Severe Clear Air Turbulence Collides with Air Traffic (SCATCAT) field program, conducted over the Pacific, were carried out in an effort to identify the scale interactions of turbulence and small-scale gravity waves. Because of the intermittent nature of turbulence, these analyses were conducted by clearly separating out the cases when turbulence did or did not occur in the data. In the presence of turbulence, transitional power spectra from k−2 to k−5/3 were found to be associated with gravity waves and turbulence, respectively. The second-order structure function analysis was able to translate these spectral slopes into r and r 2/3 scaling, consistent with the Monin and Yaglom conversion law, in physical space, which presented clearer pictures of scale interactions between turbulence and gravity waves. The third-order structure function analysis indicated the existence of a narrow region of inverse energy cascade from the scales of turbulence up to the gravity waves scales. This inverse energy cascade region was linked to the occurrence of Kelvin–Helmholtz instability and other wave-amplifying mechanisms, which were conjectured to lead to the breaking of small-scale gravity waves and the ensuing generation of turbulence. The multifractal analyses revealed further scale breaks between gravity waves and turbulence. The roughness and intermittent properties were also calculated for turbulence and gravity waves, respectively. Based on these properties, turbulence and gravity waves in a bifractal parameter space were mapped. In this way, their physical and statistical attributes were clearly manifested and understood.

scholarly journals Risk of rapid evolutionary escape from biomedical interventions targeting SARS-CoV-2 spike protein

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0250780
Author(s):  
Debra Van Egeren ◽  
Alexander Novokhodko ◽  
Madison Stoddard ◽  
Uyen Tran ◽  
Bruce Zetter ◽  
...  
Keyword(s):  
Structure Function ◽  
Immune Evasion ◽  
Immune Escape ◽  
Function Analysis ◽  
Passive Immunization ◽  
Spike Protein ◽  
Natural Immunity ◽  
Evolutionary Modeling ◽  
Modeling Framework ◽  
Biomedical Interventions

The spike protein receptor-binding domain (RBD) of SARS-CoV-2 is the molecular target for many vaccines and antibody-based prophylactics aimed at bringing COVID-19 under control. Such a narrow molecular focus raises the specter of viral immune evasion as a potential failure mode for these biomedical interventions. With the emergence of new strains of SARS-CoV-2 with altered transmissibility and immune evasion potential, a critical question is this: how easily can the virus escape neutralizing antibodies (nAbs) targeting the spike RBD? To answer this question, we combined an analysis of the RBD structure-function with an evolutionary modeling framework. Our structure-function analysis revealed that epitopes for RBD-targeting nAbs overlap one another substantially and can be evaded by escape mutants with ACE2 affinities comparable to the wild type, that are observed in sequence surveillance data and infect cells in vitro. This suggests that the fitness cost of nAb-evading mutations is low. We then used evolutionary modeling to predict the frequency of immune escape before and after the widespread presence of nAbs due to vaccines, passive immunization or natural immunity. Our modeling suggests that SARS-CoV-2 mutants with one or two mildly deleterious mutations are expected to exist in high numbers due to neutral genetic variation, and consequently resistance to vaccines or other prophylactics that rely on one or two antibodies for protection can develop quickly -and repeatedly- under positive selection. Predicted resistance timelines are comparable to those of the decay kinetics of nAbs raised against vaccinal or natural antigens, raising a second potential mechanism for loss of immunity in the population. Strategies for viral elimination should therefore be diversified across molecular targets and therapeutic modalities.

scholarly journals Structure, function, and inhibitor targeting of HIV-1 Nef-effector kinase complexes

2020 ◽  
Vol 295 (44) ◽  
pp. 15158-15171 ◽  
Author(s):  
Ryan P. Staudt ◽  
John J. Alvarado ◽  
Lori A. Emert-Sedlak ◽  
Haibin Shi ◽  
Sherry T. Shu ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Structure Function ◽  
Host Cell ◽  
Immune Escape ◽  
Cell Protein ◽  
Immune Recognition ◽  
Endosomal Trafficking ◽  
Infected Cells ◽  
Hiv 1

Antiretroviral therapy has revolutionized the treatment of AIDS, turning a deadly disease into a manageable chronic condition. Life-long treatment is required because existing drugs do not eradicate HIV-infected cells. The emergence of drug-resistant viral strains and uncertain vaccine prospects highlight the pressing need for new therapeutic approaches with the potential to clear the virus. The HIV-1 accessory protein Nef is essential for viral pathogenesis, making it a promising target for antiretroviral drug discovery. Nef enhances viral replication and promotes immune escape of HIV-infected cells but lacks intrinsic enzymatic activity. Instead, Nef works through diverse interactions with host cell proteins primarily related to kinase signaling pathways and endosomal trafficking. This review emphasizes the structure, function, and biological relevance of Nef interactions with host cell protein-tyrosine kinases in the broader context of Nef functions related to enhancement of the viral life cycle and immune escape. Drug discovery targeting Nef-mediated kinase activation has allowed identification of promising inhibitors of multiple Nef functions. Pharmacological inhibitors of Nef-induced MHC-I down-regulation restore the adaptive immune response to HIV-infected cells in vitro and have the potential to enhance immune recognition of latent viral reservoirs as part of a strategy for HIV clearance.

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