scholarly journals Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies

2017 ◽  
Author(s):  
Samantha J. Ziegler ◽  
Chang Liu ◽  
Mark Landau ◽  
Olga Buzovetsky ◽  
Belete A. Desimmie ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Binding Pocket ◽  
Sequence Motif ◽  
Specific Substrate ◽  
Substrate Selection ◽  
Cytidine Deaminases ◽  
Human Apolipoprotein ◽  
Functional Studies ◽  
Dna Substrate ◽  
Hiv 1

AbstractHuman apolipoprotein B mRNA-editing enzyme-catalytic polypeptide-like 3 (A3) proteins are a family of cytidine deaminases that catalyze the conversion of cytidine to uridine in single-stranded DNA (ssDNA). A3 proteins act in the innate immune response to viral infection by mutating the viral ssDNA. One of the most well-studied human A3 family members is A3G, which is a potent inhibitor of HIV-1. Each A3 protein prefers a specific substrate sequence for catalysis - for example, A3G deaminates the third cytidine in the CCCA sequence motif. However, the interaction between A3G and ssDNA is difficult to characterize due to poor solution behavior of the full-length protein and loss of DNA affinity of the truncated protein. Here, we present a novel DNA-anchoring fusion strategy, which we have used to capture an A3G-ssDNA interaction. We characterized an A3G-DNA binding pocket that is important for the enzyme to scan the DNA for its hotspot. The results provide insights into the mechanism by which A3G selects and deaminates its preferred substrates and help define how A3 proteins are tailored to recognize specific DNA sequences. This knowledge contributes to a better understanding of the mechanism of DNA substrate selection by A3G, as well as A3G antiviral activity against HIV-1.

scholarly journals Insights into DNA substrate selection by APOBEC3G from structural, biochemical, and functional studies

PLoS ONE ◽  
2018 ◽  
Vol 13 (3) ◽  
pp. e0195048 ◽  
Author(s):  
Samantha J. Ziegler ◽  
Chang Liu ◽  
Mark Landau ◽  
Olga Buzovetsky ◽  
Belete A. Desimmie ◽  
...  
Keyword(s):  
Substrate Selection ◽  
Functional Studies ◽  
Dna Substrate

Application of Molecular Docking for the Development of Improved HIV-1 Reverse Transcriptase Inhibitors

2020 ◽  
Vol 16 ◽  
Author(s):  
Arash Soltani ◽  
Seyed Isaac Hashemy ◽  
Farnaz Zahedi Avval ◽  
Houshang Rafatpanah ◽  
Seyed Abdolrahim Rezaee ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Binding Capacity ◽  
Binding Pocket ◽  
Ligand Docking ◽  
Binding Modes ◽  
Wild Type ◽  
Parent Molecule ◽  
Discovery Studio ◽  
Approved Drugs ◽  
Hiv 1

Introoduction: Inhibition of the reverse transcriptase (RT) enzyme of human immunodeficiency virus (HIV) by low molecular weight inhibitors is still an active area of research. Here, protein-ligand interactions and possible binding modes of novel compounds with the HIV-1 RT binding pocket (the wild-type as well as Y181C and K103N mutants) were obtained and discussed. Methods: A molecular fragment-based approach using FDA-approved drugs were followed to design novel chemical derivatives using delavirdine, efavirenz, etravirine and rilpivirine as the scaffolds. The drug-likeliness of the derivatives was evaluated using Swiss-ADME. Then the parent molecule and derivatives were docked into the binding pocket of related crystal structures (PDB ID: 4G1Q, 1IKW, 1KLM and 3MEC). Genetic Optimization for Ligand Docking (GOLD) Suite 5.2.2 software was used for docking and the results analyzed in the Discovery Studio Visualizer 4. A derivative was chosen for further analysis, if it passed drug-likeliness and the docked energy was more favorable than that of its parent molecule. Out of the fifty-seven derivatives, forty-eight failed in druglikeness screening by Swiss-ADME or in docking stage. Results: The final results showed that the selected compounds had higher predicted binding affinities than their parent scaffolds in both wild-type and the mutants. Binding energy improvement was higher for the structures designed based on second-generation NNRTIs (etravirine and rilpivirine) than the first-generation NNRTIs (delavirdine and efavirenz). For example, while the docked energy for rilpivirine was -51 KJ/mol, it was improved for its derivatives RPV01 and RPV15 up to -58.3 and -54.5 KJ/mol, respectively. Conclusion: In this study, we have identified and proposed some novel molecules with improved binding capacity for HIV RT using fragment-based approach.

scholarly journals A software program combining sequence motif searches with keywords for finding repeats containing DNA sequences

2004 ◽  
Vol 20 (18) ◽  
pp. 3379-3386 ◽  
Author(s):  
M. Bilgen ◽  
M. Karaca ◽  
A. N. Onus ◽  
A. G. Ince
Keyword(s):  
Dna Sequences ◽  
Sequence Motif ◽  
Software Program

Molecular Functional Studies of HIV-1 REV and NEF Proteins

1991 ◽  
pp. 189-201
Author(s):  
Sundararajan Venkatesan ◽  
Steven M. Holland ◽  
Nafees Ahmad ◽  
Paul Wingfield ◽  
Ratan K. Maitra ◽  
...  
Keyword(s):  
Functional Studies ◽  
Hiv 1

scholarly journals The Crystal Structure of Shikimate Dehydrogenase (AroE) Reveals a Unique NADPH Binding Mode

2003 ◽  
Vol 185 (14) ◽  
pp. 4144-4151 ◽  
Author(s):  
Sheng Ye ◽  
Frank von Delft ◽  
Alexei Brooun ◽  
Mark W. Knuth ◽  
Ronald V. Swanson ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Binding Pocket ◽  
Binding Mode ◽  
Sequence Motif ◽  
Binary Complex ◽  
Shikimate Dehydrogenase ◽  
Conserved Residues ◽  
Conserved Sequence ◽  
Nicotinamide Mononucleotide ◽  
Reversible Reduction

ABSTRACT Shikimate dehydrogenase catalyzes the NADPH-dependent reversible reduction of 3-dehydroshikimate to shikimate. We report the first X-ray structure of shikimate dehydrogenase from Haemophilus influenzae to 2.4-Å resolution and its complex with NADPH to 1.95-Å resolution. The molecule contains two domains, a catalytic domain with a novel open twisted α/β motif and an NADPH binding domain with a typical Rossmann fold. The enzyme contains a unique glycine-rich P-loop with a conserved sequence motif, GAGGXX, that results in NADPH adopting a nonstandard binding mode with the nicotinamide and ribose moieties disordered in the binary complex. A deep pocket with a narrow entrance between the two domains, containing strictly conserved residues primarily contributed by the catalytic domain, is identified as a potential 3-dehydroshikimate binding pocket. The flexibility of the nicotinamide mononucleotide portion of NADPH may be necessary for the substrate 3-dehydroshikimate to enter the pocket and for the release of the product shikimate.

scholarly journals Association study of RS535296987 in TEX14 gene in azoospermiamen: RFLP and DNA sequencing

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 729-737
Author(s):  
Mohammad Vahedi ◽  
Masoud Sheidai
Keyword(s):  
Dna Sequencing ◽  
Dna Sequences ◽  
Chromosome 17 ◽  
Protein Coding ◽  
Nucleotide Variability ◽  
Functional Studies ◽  
Low Degree ◽  
Different Populations ◽  
Human Chromosome 17 ◽  
And Control

Azoospermia is one of the kinds of male infertility, with clinically the most severe phenotype as the natural conception cannot occur. It has been estimated to affect 0.1 to 1% of all men and 10-15% of men in infertile couples. TEX14 (Testis expressed 14, intercellular bridge forming factor) is a protein coding gene, which is located in human chromosome 17, (17q22). Tex14 gene appears to be crucial for perfect spermatogenesis and functional studies indicate the role of TEX14 in the intercellular bridges between developing male germ cells. The gene contains 32 exons and spans 137 kb. A heterogeneousresultis available on the association TEX14 gene and azoospermia. Therefore, it is suggested to investigate this gene in different populations. We analyzed about 200 men in two categories of azoospermia and healthy persons by RFLP as well as DNA sequencing to indicate an association between rs535296987 in TEX14 and its adjacent nucleotides to azoospermia. We found no significant association based on RFLP data and also by clustering of case and control specimens based on DNA sequencing. In general, a low level of nucleotide variability was observed in DNA sequences. Therefore, both eternity in the studied samples and low degree of mutations in this genetic region, may be the reason for heterogeneous reports on association of TEX14 and azoospermia.

scholarly journals UV-induced DNA damage is an intermediate step in UV-induced expression of human immunodeficiency virus type 1, collagenase, c-fos, and metallothionein.

1989 ◽  
Vol 9 (11) ◽  
pp. 5169-5181 ◽  
Author(s):  
B Stein ◽  
H J Rahmsdorf ◽  
A Steffen ◽  
M Litfin ◽  
P Herrlich
Keyword(s):  
Human Immunodeficiency Virus ◽  
Dna Damage ◽  
Uv Radiation ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Sequence Motif ◽  
Nf Kappa B ◽  
Immunodeficiency Virus ◽  
Hiv 1

UV irradiation of human and murine cells enhances the transcription of several genes. Here we report on the primary target of relevant UV absorption, on pathways leading to gene activation, and on the elements receiving the UV-induced signal in the human immunodeficiency virus type 1 (HIV-1) long terminal repeat, in the gene coding for collagenase, and in the cellular oncogene fos. In order to induce the expression of genes. UV radiation needs to be absorbed by DNA and to cause DNA damage of the kind that cannot be repaired by cells from patients with xeroderma pigmentosum group A. UV-induced activation of the three genes is mediated by the major enhancer elements (located between nucleotide positions -105 and -79 of HIV-1, between positions -72 and -65 of the collagenase gene, and between positions -320 and -299 of fos). These elements share no apparent sequence motif and bind different trans-acting proteins; a member of the NF kappa B family binds to the HIV-1 enhancer, the heterodimer of Jun and Fos (AP-1) binds to the collagenase enhancer, and the serum response factors p67 and p62 bind to fos. DNA-binding activities of the factors recognizing the HIV-1 and collagenase enhancers are augmented in extracts from UV-treated cells. The increase in activity is due to posttranslational modification. While AP-1 resides in the nucleus and must be modulated there, NF kappa B is activated in the cytoplasm, indicating the existence of a cytoplasmic signal transduction pathway triggered by UV-induced DNA damage. In addition to activation, new synthesis of AP-1 is induced by UV radiation.

scholarly journals CRISPR base editors: genome editing without double-stranded breaks

2018 ◽  
Vol 475 (11) ◽  
pp. 1955-1964 ◽  
Author(s):  
Ayman Eid ◽  
Sahar Alshareef ◽  
Magdy M. Mahfouz
Keyword(s):  
Genome Editing ◽  
Dna Sequences ◽  
Genetic Diseases ◽  
Great Promise ◽  
Cytidine Deaminases ◽  
Strand Breaks ◽  
Base Editing ◽  
Potential Applications ◽  
Short Palindromic Repeat ◽  
Basic Biology

The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 adaptive immunity system has been harnessed for genome editing applications across eukaryotic species, but major drawbacks, such as the inefficiency of precise base editing and off-target activities, remain. A catalytically inactive Cas9 variant (dead Cas9, dCas9) has been fused to diverse functional domains for targeting genetic and epigenetic modifications, including base editing, to specific DNA sequences. As base editing does not require the generation of double-strand breaks, dCas9 and Cas9 nickase have been used to target deaminase domains to edit specific loci. Adenine and cytidine deaminases convert their respective nucleotides into other DNA bases, thereby offering many possibilities for DNA editing. Such base-editing enzymes hold great promise for applications in basic biology, trait development in crops, and treatment of genetic diseases. Here, we discuss recent advances in precise gene editing using different platforms as well as their potential applications in basic biology and biotechnology.

scholarly journals A VH1-69 antibody lineage from an infected Chinese donor potently neutralizes HIV-1 by targeting the V3 glycan supersite

2020 ◽  
Vol 6 (38) ◽  
pp. eabb1328 ◽  
Author(s):  
Sonu Kumar ◽  
Bin Ju ◽  
Benjamin Shapero ◽  
Xiaohe Lin ◽  
Li Ren ◽  
...  
Keyword(s):  
Cell Sorting ◽  
Neutralizing Antibodies ◽  
Critical Role ◽  
Viral Escape ◽  
Germline Gene ◽  
Broadly Neutralizing Antibodies ◽  
Functional Studies ◽  
Single Genome ◽  
Hiv 1

An oligomannose patch around the V3 base of HIV-1 envelope glycoprotein (Env) is recognized by multiple classes of broadly neutralizing antibodies (bNAbs). Here, we investigated the bNAb response to the V3 glycan supersite in an HIV-1–infected Chinese donor by Env-specific single B cell sorting, structural and functional studies, and longitudinal analysis of antibody and virus repertoires. Monoclonal antibodies 438-B11 and 438-D5 were isolated that potently neutralize HIV-1 with moderate breadth, are encoded by the VH1-69 germline gene, and have a disulfide-linked long HCDR3 loop. Crystal structures of Env-bound and unbound antibodies revealed heavy chain–mediated recognition of the glycan supersite with a unique angle of approach and a critical role of the intra-HCDR3 disulfide. The mechanism of viral escape was examined via single-genome amplification/sequencing and glycan mutations around the N332 supersite. Our findings further emphasize the V3 glycan supersite as a prominent target for Env-based vaccine design.

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