scholarly journals How HIV-1 Integrase Associates with Human Mitochondrial Lysyl-tRNA Synthetase

Viruses ◽  
2020 ◽  
Vol 12 (10) ◽  
pp. 1202 ◽  
Author(s):  
Xaysongkhame Phongsavanh ◽  
Noha Al-Qatabi ◽  
Mohammed Samer Shaban ◽  
Fawzi Khoder-Agha ◽  
Merwan El Asri ◽  
...  
Keyword(s):  
Structural Model ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Docking Simulation ◽  
Trna Synthetase ◽  
Amino Acid Residues ◽  
3D Architecture ◽  
Polyprotein Precursor ◽  
Viral Polyprotein ◽  
Hiv 1

Replication of human immunodeficiency virus type 1 (HIV-1) requires the packaging of tRNALys,3 from the host cell into the new viral particles. The GagPol viral polyprotein precursor associates with mitochondrial lysyl-tRNA synthetase (mLysRS) in a complex with tRNALys, an essential step to initiate reverse transcription in the virions. The C-terminal integrase moiety of GagPol is essential for its association with mLysRS. We show that integrases from HIV-1 and HIV-2 bind mLysRS with the same efficiency. In this work, we have undertaken to probe the three-dimensional (3D) architecture of the complex of integrase with mLysRS. We first established that the C-terminal domain (CTD) of integrase is the major interacting domain with mLysRS. Using the pBpa-photo crosslinking approach, inter-protein cross-links were observed involving amino acid residues located at the surface of the catalytic domain of mLysRS and of the CTD of integrase. In parallel, using molecular docking simulation, a single structural model of complex was found to outscore other alternative conformations. Consistent with crosslinking experiments, this structural model was further probed experimentally. Five compensatory mutations in the two partners were successfully designed which supports the validity of the model. The complex highlights that binding of integrase could stabilize the tRNALys:mLysRS interaction.

scholarly journals Reorganization of chromosome architecture in replicative cellular senescence

2016 ◽  
Vol 2 (2) ◽  
pp. e1500882 ◽  
Author(s):  
Steven W. Criscione ◽  
Marco De Cecco ◽  
Benjamin Siranosian ◽  
Yue Zhang ◽  
Jill A. Kreiling ◽  
...  
Keyword(s):  
Cellular Senescence ◽  
Structural Model ◽  
Three Dimensional ◽  
Chromatin Accessibility ◽  
Genome Chromosome ◽  
Chromosome Conformation ◽  
Topologically Associated Domains ◽  
Chromosomal Architecture ◽  
Fundamental Biological Process ◽  
3D Architecture

Replicative cellular senescence is a fundamental biological process characterized by an irreversible arrest of proliferation. Senescent cells accumulate a variety of epigenetic changes, but the three-dimensional (3D) organization of their chromatin is not known. We applied a combination of whole-genome chromosome conformation capture (Hi-C), fluorescence in situ hybridization, and in silico modeling methods to characterize the 3D architecture of interphase chromosomes in proliferating, quiescent, and senescent cells. Although the overall organization of the chromatin into active (A) and repressive (B) compartments and topologically associated domains (TADs) is conserved between the three conditions, a subset of TADs switches between compartments. On a global level, the Hi-C interaction matrices of senescent cells are characterized by a relative loss of long-range and gain of short-range interactions within chromosomes. Direct measurements of distances between genetic loci, chromosome volumes, and chromatin accessibility suggest that the Hi-C interaction changes are caused by a significant reduction of the volumes occupied by individual chromosome arms. In contrast, centromeres oppose this overall compaction trend and increase in volume. The structural model arising from our study provides a unique high-resolution view of the complex chromosomal architecture in senescent cells.

scholarly journals Efficacy of Dideoxynucleosides against Human Foamy Virus and Relationship to Its Reverse Transcriptase Amino Acid Sequence and Structure

2001 ◽  
Vol 75 (15) ◽  
pp. 7184-7187 ◽  
Author(s):  
Anne Yvon-Groussin ◽  
Pierre Mugnier ◽  
Philippe Bertin ◽  
Marc Grandadam ◽  
Henri Agut ◽  
...  
Keyword(s):  
Amino Acid ◽  
Reverse Transcriptase ◽  
Foamy Virus ◽  
Three Dimensional ◽  
Retroviral Vectors ◽  
Dimensional Structure ◽  
Human Foamy Virus ◽  
Amino Acid Residues ◽  
Immunodeficiency Virus ◽  
Hiv 1

ABSTRACT Human foamy virus (HFV), a retrovirus of simian origin which occasionally infects humans, is the basis of retroviral vectors in development for gene therapy. Clinical considerations of how to treat patients developing an uncontrolled infection by either HFV or HFV-based vectors need to be raised. We determined the susceptibility of the HFV to dideoxynucleosides and found that only zidovudine was equally efficient against the replication of human immunodeficiency virus type 1 (HIV-1) and HFV. By contrast, zalcitabine (ddC), lamivudine (3TC), stavudine (d4T), and didanosine (ddI) were 3-, 3-, 30-, and 46-fold less efficient against HFV than against HIV-1, respectively. Some amino acid residues known to be involved in HIV-1 resistance to ddC, 3TC, d4T, and ddI were found at homologous positions of HFV reverse transcriptase (RT). These critical amino acids are located at the same positions in the three-dimensional structure of HIV-1 and HFV RT, suggesting that both enzymes share common patterns of inhibition.

scholarly journals Substrate (aglycone) specificity of human cytosolic beta-glucosidase

2003 ◽  
Vol 373 (1) ◽  
pp. 41-48 ◽  
Author(s):  
Jean-Guy BERRIN ◽  
Mirjam CZJZEK ◽  
Paul A. KROON ◽  
W. Russell MCLAUCHLAN ◽  
Antoine PUIGSERVER ◽  
...  
Keyword(s):  
Structural Model ◽  
Homology Modelling ◽  
Three Dimensional ◽  
Amino Acid Residues ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Mutant Proteins ◽  
Metabolizing Enzyme ◽  
Beta Glucosidase

Human cytosolic β-glucosidase (hCBG) is a xenobiotic-metabolizing enzyme that hydrolyses certain flavonoid glucosides, with specificity depending on the aglycone moiety, the type of sugar and the linkage between them. Based upon the X-ray structure of Zea mays β-glucosidase, we generated a three-dimensional model of hCBG by homology modelling. The enzyme exhibited the (β/α)8-barrel fold characteristic of family 1 β-glucosidases, with structural differences being confined mainly to loop regions. Based on the substrate specificity of the human enzymes, sequence alignment of family 1 enzymes and analysis of the hCBG structural model, we selected and mutated putative substrate (aglycone) binding site residues. Four single mutants (Val168→Tyr, Phe225→Ser, Tyr308→Ala and Tyr308→Phe) were expressed in Pichia pastoris, purified and characterized. All mutant proteins showed a decrease in activity towards a broad range of substrates. The Val168→Tyr mutation did not affect Km on p-nitrophenyl (pNP)-glycosides, but increased Km 5-fold on flavonoid glucosides, providing the first biochemical evidence supporting a role for this residue in aglycone-binding of the substrate, a finding consistent with our three-dimensional model. The Phe225→Ser and Tyr308→Ala mutations, and, to a lesser degree, the Tyr308→Phe mutation, resulted in a drastic decrease in specific activities towards all substrates tested, indicating an important role of those residues in catalysis. Taken together with the three-dimensional model, these mutation studies identified the amino-acid residues in the aglycone-binding subsite of hCBG that are essential for flavonoid glucoside binding and catalysis.

scholarly journals Peptides Derived from the Reverse Transcriptase of Human Immunodeficiency Virus Type 1 as Novel Inhibitors of the Viral Integrase

2005 ◽  
Vol 280 (23) ◽  
pp. 21987-21996 ◽  
Author(s):  
Iris Oz Gleenberg ◽  
Orna Avidan ◽  
Yehuda Goldgur ◽  
Alon Herschhorn ◽  
Amnon Hizi
Keyword(s):  
Reverse Transcriptase ◽  
Catalytic Domain ◽  
Three Dimensional ◽  
Specific Protein ◽  
Strand Transfer ◽  
Catalytic Core ◽  
Core Domain ◽  
Inhibitory Peptides ◽  
Hiv 1

Recent studies have shown that the integrase (IN) of HIV-1 is inhibited in vitro by HIV-1 reverse transcriptase (RT). We further investigated the specific protein sequences of RT that were involved in this inhibition by screening a complete library of RT-derived peptides for their inhibition of IN activities. Two 20-residue peptides, peptide 4286, derived from the RT DNA polymerase domain, and the one designated 4321, from the RT ribonuclease H domain, inhibit the enzymatic activities of IN in vitro. The former peptide inhibits all three IN-associated activities (3′-end processing, strand transfer, and disintegration), whereas the latter one inhibits primarily the first two functions. We showed the importance of the sequences and peptide length for the effective inhibition of IN activities. Binding assays of the peptides to IN (with no DNA substrate present) indicated that the two inhibitory peptides (as well as several non-inhibitory peptides) interact directly with IN. Moreover, the isolated catalytic core domain of IN also interacted directly with the two inhibitory peptides. Nevertheless, only peptide 4286 can inhibit the disintegration activity associated with the IN core domain, because this activity is the only one exhibited by this domain. This result was expected from the lack of inhibition of disintegration of full-length IN by peptide 4321. The data and the three-dimensional models presented suggested that the inhibition resulted from steric hindrance of the catalytic domain of IN. This information can substantially facilitate the development of novel drugs against HIV INs and thus contribute to the fight against AIDS.

scholarly journals Prediction and validation of the three-dimensional structure of glucokinase-1 from Phytophthora infestans

2021 ◽  
Author(s):  
Liara Villalobos-Piña ◽  
Ascanio Rojas ◽  
Héctor Acosta
Keyword(s):  
Phytophthora Infestans ◽  
Structural Model ◽  
3D Structure ◽  
Three Dimensional ◽  
Qualitative Evaluation ◽  
Dimensional Structure ◽  
Binding Motif ◽  
Amino Acid Residues ◽  
Late Blight Disease ◽  
Blight Disease

AbstractAccording to its primary structure, the [PITG_06016] gene encodes for one of the 7 glucokinases present in Phytophthora infestans (PiGlcK-1), the causal agent of late blight disease. Currently, there are no structural studies of any of its enzymes, being the determination of the three-dimensional (3D) structure of PiGlcK-1 a necessary contribution in the deduction of its functions, its interaction with ligands, and possible regulatory mechanisms. In this work we present the first structural model obtained by in silico tools for PiGlcK-1. For the prediction of this model, different algorithms were used to find the best annealing, refinement, and qualitative evaluation of them. A structural comparison of the predicted model with other structures of crystallized kinase enzymes allowed us to identify the regions of interaction with their classical substrates (glucose and ATP), as well as to identify the amino acid residues involved in the binding of other substrates such as fructose and ADP. In addition, we propose a possible recognition region of PPi, an activator of kinase activity that includes the GXGE motif, conserved in enzymes of the ribokinase (RK) family, which distinguishes this PiGlcK-1 from a classical glucokinase. Accordingly, these findings suggest PPi-binding motif as potential targets for the development of inhibitors of PiGlcK-1 activity.

Association of Mitochondrial Lysyl-tRNA Synthetase with HIV-1 GagPol Involves Catalytic Domain of the Synthetase and Transframe and Integrase Domains of Pol

2011 ◽  
Vol 410 (5) ◽  
pp. 875-886 ◽  
Author(s):  
Lydia Kobbi ◽  
Guillaume Octobre ◽  
José Dias ◽  
Martine Comisso ◽  
Marc Mirande
Keyword(s):  
Catalytic Domain ◽  
Trna Synthetase ◽  
Hiv 1

scholarly journals Association of mitochondrial lysyl-tRNA synthetase with HIV-1 GagPol involves catalytic domain of the synthetase and transframe and integrase domains of Pol

2011 ◽  
Vol 27 (5) ◽  
pp. 381-382
Author(s):  
L. Kobbi ◽  
J. Dias ◽  
G. Octobre ◽  
M. Comisso ◽  
M. Kaminska ◽  
...  
Keyword(s):  
Catalytic Domain ◽  
Trna Synthetase ◽  
Hiv 1

Structure-function analysis of the EGF-CFC family member Cripto identifies residues essential for nodal signalling

Development ◽  
2001 ◽  
Vol 128 (22) ◽  
pp. 4501-4510
Author(s):  
Gabriella Minchiotti ◽  
Giuseppe Manco ◽  
Silvia Parisi ◽  
Carmine T. Lago ◽  
Frederic Rosa ◽  
...  
Keyword(s):  
Structural Model ◽  
Function Analysis ◽  
Three Dimensional ◽  
Point Mutations ◽  
Amino Acid Residues ◽  
Vertebrate Development ◽  
Loss Of Function ◽  
Protein Protein Interaction ◽  
Functional Relevance

cripto is the founding member of the family of EGF-CFC genes, a class of extracellular factors essential for early vertebrate development. In this study we show that injection of Cripto recombinant protein in mid to late zebrafish Maternal-Zygotic one-eyed pinhead (MZoep) blastulae was able to fully rescue the mutant phenotype, thus providing the first direct evidence that Cripto activity can be added extracellularly to recover oep-encoded function in zebrafish early embryos. Moreover, 15 point mutations and two deletion mutants were generated to assess in vivo their functional relevance by comparing the ability of cripto wild-type and mutant RNAs to rescue the zebrafish MZoep mutant. From this study we concluded that the EGF-CFC domain is sufficient for Cripto biological activity and identified ten point mutations with a functional defective phenotype, two of which, located in the EGF-like domain, correspond to loss-of-function mutations. Finally, we have developed a three-dimensional structural model of Cripto protein and used it as a guide to predict amino acid residues potentially implicated in protein-protein interaction.

scholarly journals 3-Dimensional architecture of the human multi-tRNA synthetase complex

2020 ◽  
Vol 48 (15) ◽  
pp. 8740-8754 ◽  
Author(s):  
Krishnendu Khan ◽  
Camelia Baleanu-Gogonea ◽  
Belinda Willard ◽  
Valentin Gogonea ◽  
Paul L Fox
Keyword(s):  
Mammalian Cells ◽  
Structural Model ◽  
Structural Information ◽  
Three Dimensional ◽  
Trna Synthetase ◽  
3 Dimensional ◽  
Trna Synthetases ◽  
Binding Domains ◽  
Cross Links ◽  
And Function

Abstract In mammalian cells, eight cytoplasmic aminoacyl-tRNA synthetases (AARS), and three non-synthetase proteins, reside in a large multi-tRNA synthetase complex (MSC). AARSs have critical roles in interpretation of the genetic code during protein synthesis, and in non-canonical functions unrelated to translation. Nonetheless, the structure and function of the MSC remain unclear. Partial or complete crystal structures of all MSC constituents have been reported; however, the structure of the holo-MSC has not been resolved. We have taken advantage of cross-linking mass spectrometry (XL-MS) and molecular docking to interrogate the three-dimensional architecture of the MSC in human HEK293T cells. The XL-MS approach uniquely provides structural information on flexibly appended domains, characteristic of nearly all MSC constituents. Using the MS-cleavable cross-linker, disuccinimidyl sulfoxide, inter-protein cross-links spanning all MSC constituents were observed, including cross-links between eight protein pairs not previously known to interact. Intra-protein cross-links defined new structural relationships between domains in several constituents. Unexpectedly, an asymmetric AARS distribution was observed featuring a clustering of tRNA anti-codon binding domains on one MSC face. Possibly, the non-uniform localization improves efficiency of delivery of charged tRNA’s to an interacting ribosome during translation. In summary, we show a highly compact, 3D structural model of the human holo-MSC.

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