In Silico Insights into HIV-1 Vpu-Tetherin Interactions and Its Mutational Counterparts

Tetherin, an interferon-induced host protein encoded by the bone marrow stromal antigen 2 (BST2/CD317/HM1.24) gene, is involved in obstructing the release of many retroviruses and other enveloped viruses by cross-linking the budding virus particles to the cell surface. This activity is antagonized in the case of human immunodeficiency virus (HIV)-1 wherein its accessory protein Viral Protein U (Vpu) interacts with tetherin, causing its downregulation from the cell surface. Vpu and tetherin connect through their transmembrane (TM) domains, culminating into events leading to tetherin degradation by recruitment of β-TrCP2. However, mutations in the TM domains of both proteins are reported to act as a resistance mechanism to Vpu countermeasure impacting tetherin’s sensitivity towards Vpu but retaining its antiviral activity. Our study illustrates the binding aspects of blood-derived, brain-derived, and consensus HIV-1 Vpu with tetherin through protein–protein docking. The analysis of the bound complexes confirms the blood-derived Vpu–tetherin complex to have the best binding affinity as compared to other two. The mutations in tetherin and Vpu are devised computationally and are subjected to protein–protein interactions. The complexes are tested for their binding affinities, residue connections, hydrophobic forces, and, finally, the effect of mutation on their interactions. The single point mutations in tetherin at positions L23Y, L24T, and P40T, and triple mutations at {L22S, F44Y, L37I} and {L23T, L37T, T45I}, while single point mutations in Vpu at positions A19H and W23Y and triplet of mutations at {V10K, A11L, A19T}, {V14T, I18T, I26S}, and {A11T, V14L, A15T} have revealed no polar contacts with minimal hydrophobic interactions between Vpu and tetherin, resulting in reduced binding affinity. Additionally, we have explored the aggregation potential of tetherin and its association with the brain-derived Vpu protein. This work is a possible step toward an understanding of Vpu–tetherin interactions.

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Changing the Antigen Binding Specificity by Single Point Mutations of an Anti-p24 (HIV-1) Antibody

The Journal of Immunology ◽

10.4049/jimmunol.165.8.4505 ◽

2000 ◽

Vol 165 (8) ◽

pp. 4505-4514 ◽

Cited By ~ 22

Author(s):

Karsten Winkler ◽

Achim Kramer ◽

Gabriele Küttner ◽

Martina Seifert ◽

Christa Scholz ◽

...

Keyword(s):

Single Point ◽

Point Mutations ◽

Binding Specificity ◽

Antigen Binding ◽

Single Point Mutations ◽

Hiv 1

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mmCSM-NA: accurately predicting effects of single and multiple mutations on protein–nucleic acid binding affinity

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab109 ◽

2021 ◽

Vol 3 (4) ◽

Author(s):

Thanh Binh Nguyen ◽

Yoochan Myung ◽

Alex G C de Sá ◽

Douglas E V Pires ◽

David B Ascher

Keyword(s):

Nucleic Acid ◽

Binding Affinity ◽

Single Point ◽

Point Mutations ◽

Multiple Point ◽

Missense Mutations ◽

Nucleic Acid Binding ◽

Single Point Mutations ◽

Protein Nucleic Acid ◽

Nucleic Acid Interactions

Abstract While protein–nucleic acid interactions are pivotal for many crucial biological processes, limited experimental data has made the development of computational approaches to characterise these interactions a challenge. Consequently, most approaches to understand the effects of missense mutations on protein-nucleic acid affinity have focused on single-point mutations and have presented a limited performance on independent data sets. To overcome this, we have curated the largest dataset of experimentally measured effects of mutations on nucleic acid binding affinity to date, encompassing 856 single-point mutations and 141 multiple-point mutations across 155 experimentally solved complexes. This was used in combination with an optimized version of our graph-based signatures to develop mmCSM-NA (http://biosig.unimelb.edu.au/mmcsm_na), the first scalable method capable of quantitatively and accurately predicting the effects of multiple-point mutations on nucleic acid binding affinities. mmCSM-NA obtained a Pearson's correlation of up to 0.67 (RMSE of 1.06 Kcal/mol) on single-point mutations under cross-validation, and up to 0.65 on independent non-redundant datasets of multiple-point mutations (RMSE of 1.12 kcal/mol), outperforming similar tools. mmCSM-NA is freely available as an easy-to-use web-server and API. We believe it will be an invaluable tool to shed light on the role of mutations affecting protein–nucleic acid interactions in diseases.

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Single-Point Mutations Causing More than 100-Fold Underestimation of Human Immunodeficiency Virus Type 1 (HIV-1) Load with the Cobas TaqMan HIV-1 Real-Time PCR Assay

Journal of Clinical Microbiology ◽

10.1128/jcm.02204-08 ◽

2009 ◽

Vol 47 (4) ◽

pp. 1238-1240 ◽

Cited By ~ 37

Author(s):

K. Korn ◽

B. Weissbrich ◽

C. Henke-Gendo ◽

A. Heim ◽

C. M. Jauer ◽

...

Keyword(s):

Human Immunodeficiency Virus ◽

Real Time ◽

Real Time Pcr ◽

Single Point ◽

Point Mutations ◽

Pcr Assay ◽

Immunodeficiency Virus ◽

Single Point Mutations ◽

Hiv 1

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Single point mutations can potentially enhance infectivity of SARS-CoV-2 revealed by in silico affinity maturation and SPR assay

10.1101/2020.12.24.424245 ◽

2020 ◽

Author(s):

Ting Xue ◽

Weikun Wu ◽

Ning Guo ◽

Chengyong Wu ◽

Jian Huang ◽

...

Keyword(s):

Binding Affinity ◽

In Silico ◽

Cell Attachment ◽

Single Point ◽

Point Mutations ◽

Cell Receptor ◽

Affinity Maturation ◽

Promising Target ◽

Assay Result ◽

Single Point Mutations

AbstractThe RBD (receptor binding domain) of the SARS-CoV-2 virus S (spike) protein mediates the viral cell attachment and serves as a promising target for therapeutics development. Mutations on the S-RBD may alter its affinity to cell receptor and affect the potency of vaccines and antibodies. Here we used an in-silico approach to predict how mutations on RBD affect its binding affinity to hACE2 (human angiotensin-converting enzyme2). The effect of all single point mutations on the interface was predicted. SPR assay result shows that 6 out of 9 selected mutations can strengthen binding affinity. Our prediction has reasonable agreement with the previous deep mutational scan results and recently reported mutants. Our work demonstrated in silico method as a powerful tool to forecast more powerful virus mutants, which will significantly benefit for the development of broadly neutralizing vaccine and antibody.

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Cupin Variants as Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes

10.26434/chemrxiv.11481834.v1 ◽

2019 ◽

Author(s):

Nobutaka Fujieda ◽

Miho Yuasa ◽

Yosuke Nishikawa ◽

Genji Kurisu ◽

Shinobu Itoh ◽

...

Keyword(s):

Michael Addition ◽

In Silico ◽

Addition Reaction ◽

Single Point ◽

Point Mutations ◽

Unsaturated Ketone ◽

Michael Addition Reaction ◽

Beta Barrel ◽

Cupin Superfamily ◽

Single Point Mutations

Cupin superfamily proteins (TM1459) work as a macromolecular ligand framework with a double-stranded beta-barrel structure ligating to a Cu ion through histidine side chains. Variegating the first coordination sphere of TM1459 revealed that H52A and H54A/H58A mutants effectively catalyzed the diastereo- and enantio-selective Michael addition reaction of nitroalkanes to an α,β-unsaturated ketone. Moreover, in silico substrate docking signified C106N and F104W single-point mutations, which inverted the diastereoselectivity of H52A and further improved the stereoselectivity of H54A/H58A, respectively.

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Single-Point Mutations in Qβ Virus-like Particles Change Binding to Cells

Biomacromolecules ◽

10.1021/acs.biomac.1c00443 ◽

2021 ◽

Author(s):

Marisa L. Martino ◽

Stephen N. Crooke ◽

Marianne Manchester ◽

M.G. Finn

Keyword(s):

Single Point ◽

Point Mutations ◽

Virus Like Particles ◽

Single Point Mutations

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MinD directly interacting with FtsZ at the H10 helix suggests a model for robust activation of MinC to destabilize FtsZ polymers

Biochemical Journal ◽

10.1042/bcj20170357 ◽

2017 ◽

Vol 474 (18) ◽

pp. 3189-3205 ◽

Cited By ~ 6

Author(s):

Ashoka Chary Taviti ◽

Tushar Kant Beuria

Keyword(s):

Cell Division ◽

Single Point ◽

Point Mutations ◽

Direct Interaction ◽

Ring Formation ◽

Z Ring ◽

Single Point Mutations ◽

Biochemical Analyses ◽

Ftsz Assembly ◽

The Mind

Cell division in bacteria is a highly controlled and regulated process. FtsZ, a bacterial cytoskeletal protein, forms a ring-like structure known as the Z-ring and recruits more than a dozen other cell division proteins. The Min system oscillates between the poles and inhibits the Z-ring formation at the poles by perturbing FtsZ assembly. This leads to an increase in the FtsZ concentration at the mid-cell and helps in Z-ring positioning. MinC, the effector protein, interferes with Z-ring formation through two different mechanisms mediated by its two domains with the help of MinD. However, the mechanism by which MinD triggers MinC activity is not yet known. We showed that MinD directly interacts with FtsZ with an affinity stronger than the reported MinC–FtsZ interaction. We determined the MinD-binding site of FtsZ using computational, mutational and biochemical analyses. Our study showed that MinD binds to the H10 helix of FtsZ. Single-point mutations at the charged residues in the H10 helix resulted in a decrease in the FtsZ affinity towards MinD. Based on our findings, we propose a novel model for MinCD–FtsZ interaction, where MinD through its direct interaction with FtsZ would trigger MinC activity to inhibit FtsZ functions.

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