scholarly journals Synergy and allostery in ligand binding by HIV-1 Nef

2021 ◽  
Author(s):  
Abdullah M Aldehaiman ◽  
Afaque A Momin ◽  
Audrey Restouin ◽  
Luyao Wang ◽  
Xiaoli Shi ◽  
...  
Keyword(s):  
Host Cell ◽  
Hydrophobic Core ◽  
Bioinformatics Analyses ◽  
Linear Interaction ◽  
Sh3 Domains ◽  
Core Domain ◽  
Host Cell Proteins ◽  
Human Proteins ◽  
Folded Core ◽  
Protein Ensembles

The Nef protein of human and simian immunodeficiency viruses boosts viral pathogenicity through its interactions with host cell proteins. By combining the polyvalency of its large unstructured regions with the binding selectivity and strength of its folded core domain, Nef can associate with many different host cell proteins, thereby disrupting their functions. For example, the combination of a linear proline-rich motif and hydrophobic core domain surface allows Nef to bind tightly and specifically to SH3 domains of Src family kinases. We investigated whether the interplay between Nef’s flexible regions and its core domain could allosterically influence ligand selection. We found that the flexible regions can associate with the core domain in different ways, producing distinct conformational states that alter the way in which Nef selects for SH3 domains and exposes some of its binding motifs. The ensuing crosstalk between ligands might promote functionally coherent Nef-bound protein ensembles by synergizing certain subsets of ligands while excluding others. We also combined proteomic and bioinformatics analyses to identify human proteins that select SH3 domains in the same way as Nef. We found that only 3% of clones from a whole-human fetal library displayed Nef-like SH3 selectivity. However, in most cases, this selectivity appears to be achieved by a canonical linear interaction rather than by a Nef-like “tertiary” interaction. Our analysis supports the contention that Nef’s mode of hijacking SH3 domains is a virus-specific adaptation with no or very few cellular counterparts. Thus, the Nef tertiary binding surface is a promising virus-specific drug target.

scholarly journals Synergy and allostery in ligand binding by HIV-1 Nef

2020 ◽  
Author(s):  
Abdullah Aldehaiman ◽  
Afaque A. Momin ◽  
Audrey Restouin ◽  
Luyao Wang ◽  
Xiaoli Shi ◽  
...  
Keyword(s):  
Host Cell ◽  
Hydrophobic Core ◽  
Cellular Functions ◽  
Linear Interaction ◽  
Sh3 Domains ◽  
Core Domain ◽  
Interaction Sites ◽  
Host Cell Proteins ◽  
Human Proteins ◽  
Protein Ensembles

AbstractThe Nef protein of human and simian immunodeficiency viruses (HIV and SIV, respectively) boosts viral pathogenicity through its interactions with host cell proteins. Nef has a folded core domain and large flexible regions, each carrying several protein interaction sites. By combining the polyvalency intrinsic to unstructured regions with the binding selectivity and strength of a 3D folded domain, Nef can bind to many different host cell proteins, perturbing their cellular functions. For example, the combination of a linear proline-rich motif and a hydrophobic core domain surface allows Nef to increase affinity and selectivity for particular Src family SH3 domains. Here we investigated whether the interplay between Nef’s flexible regions and its core domain can allosterically influence ligand selection. We found that the flexible regions can bind back to the core domain in different ways, producing distinct conformational states that alter the SH3 domain selectivity and availability of Nef’s functional motifs. The resulting cross-talk might help synergising certain subsets of ligands while excluding others, promoting functionally coherent Nef-bound protein ensembles. Further, we combined proteomic and bioinformatic analyses to identify human proteins that select SH3 domains in the same way as does Nef. We found that only 2–3% of clones from a whole human fetal library displayed a Nef-like SH3 selectivity. However, in most cases this selectivity appears to be achieved by a canonical linear interaction rather than a Nef-like ‘tertiary’ interaction. This analysis suggests that Nef’s SH3 recognition surface has no (or marginally few) cellular counterparts, validating the Nef tertiary binding surface as a promising unique drug target.

scholarly journals Precision analysis for the determination of steric mass action parameters using eight tobacco host cell proteins

2021 ◽  
pp. 462379
Author(s):  
C.R. Bernau ◽  
R.C. Jäpel ◽  
J.W. Hübbers ◽  
S. Nölting ◽  
P. Opdensteinen ◽  
...  
Keyword(s):  
Host Cell ◽  
Mass Action ◽  
Precision Analysis ◽  
Host Cell Proteins

Analytics of host cell proteins (HCPs): lessons from biopharmaceutical mAb analysis for Gene therapy products

2021 ◽  
Vol 71 ◽  
pp. 98-104
Author(s):  
Daniel G Bracewell ◽  
Victoria Smith ◽  
Mike Delahaye ◽  
C Mark Smales
Keyword(s):  
Gene Therapy ◽  
Host Cell ◽  
Host Cell Proteins

scholarly journals Host cell proteins in biologics development: Identification, quantitation and risk assessment

2009 ◽  
Vol 103 (3) ◽  
pp. 446-458 ◽  
Author(s):  
Xing Wang ◽  
Alan K. Hunter ◽  
Ned M. Mozier
Keyword(s):  
Risk Assessment ◽  
Host Cell ◽  
Host Cell Proteins

Antibody capture by mixed-mode chromatography: A comprehensive study from determination of optimal purification conditions to identification of contaminating host cell proteins

2011 ◽  
Vol 1218 (45) ◽  
pp. 8197-8208 ◽  
Author(s):  
Jerome Pezzini ◽  
Gilles Joucla ◽  
René Gantier ◽  
Magali Toueille ◽  
Anne-Marie Lomenech ◽  
...  
Keyword(s):  
Host Cell ◽  
Mixed Mode ◽  
Host Cell Proteins ◽  
Antibody Capture ◽  
Comprehensive Study

scholarly journals Novel compound inhibitors of HIV-1NL4-3 Vpu

2021 ◽  
Author(s):  
Carolyn A Robinson ◽  
Terri D Lyddon ◽  
Hwi Min Gil ◽  
David T. Evans ◽  
Yury V Kuzmichev ◽  
...  
Keyword(s):  
Host Cell ◽  
Particle Production ◽  
Viral Glycoprotein ◽  
New Class ◽  
Host Cell Proteins ◽  
Viral Particles ◽  
Dependent Cell ◽  
A Cell ◽  
Hiv 1

HIV-1 Vpu targets the host cell proteins CD4 and BST-2/Tetherin for degradation, ultimately resulting in enhanced virus spread and host immune evasion. The discovery and characterization of small molecules that antagonize Vpu would further elucidate the contribution of Vpu to pathogenesis and lay the foundation for the study of a new class of novel HIV-1 therapeutics. To identify novel compounds that block Vpu activity, we developed a cell-based 'gain of function' assay that produces a positive signal in response to Vpu inhibition. To develop this assay, we took advantage of the viral glycoprotein, GaLV Env. In the presence of Vpu, GaLV Env is not incorporated into viral particles, resulting in non-infectious virions. Vpu inhibition restores infectious particle production. Using this assay, a high throughput screen of >650,000 compounds was performed to identify inhibitors that block the biological activity of Vpu. From this screen, we identified several positive hits but focused on two compounds from one structural family, SRI-41897 and SRI-42371. It was conceivable that the compounds inhibited the formation of infectious virions by targeting host cell proteins instead of Vpu directly, so we developed independent counter-screens for off target interactions of the compounds and found no off target interactions. Additionally, these compounds block Vpu-mediated modulation of CD4, BST-2/Tetherin and antibody dependent cell-mediated toxicity (ADCC). Unfortunately, both SRI-41897 and SRI-42371 were shown to be specific to the N-terminal region of NL4-3 Vpu and did not function against other, more clinically relevant, strains of Vpu.

scholarly journals Characterisation of the Semliki Forest Virus-host cell interactome reveals the viral capsid protein as an inhibitor of nonsense-mediated mRNA decay

2020 ◽  
Author(s):  
Lara Contu ◽  
Giuseppe Balistreri ◽  
Michal Domanski ◽  
Anne-Christine Uldry ◽  
Oliver Mühlemann
Keyword(s):  
Host Cell ◽  
Capsid Protein ◽  
Mrna Decay ◽  
Semliki Forest Virus ◽  
Protein Protein Interaction ◽  
Host Cell Proteins ◽  
Complex Interactions ◽  
Nonsense Mediated Mrna Decay ◽  
Interaction Map ◽  
The Many

AbstractThe positive-sense, single-stranded RNA alphaviruses pose a potential epidemic threat. Understanding the complex interactions between the viral and the host cell proteins is crucial for elucidating the mechanisms underlying successful virus replication strategies and for developing specific antiviral interventions. Here we present the first comprehensive protein-protein interaction map between the proteins of Semliki Forest Virus (SFV), a mosquito-borne member of the alphaviruses, and host cell proteins. Among the many identified cellular interactors of SFV proteins, the enrichment of factors involved in translation and nonsense-mediated mRNA decay (NMD) was striking, reflecting the virus’ hijacking of the translation machinery and indicating viral countermeasures for escaping NMD by inhibiting NMD at later time points during the infectious cycle. In addition to observing a general inhibition of NMD about 4 hours post infection, we also demonstrate that transient expression of the SFV capsid protein is sufficient to inhibit NMD in cells, suggesting that the massive production of capsid protein during the SFV reproduction cycle is responsible for NMD inhibition.

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