scholarly journals Construction of A Preliminary Three-Dimensional Structure Simian betaretrovirus Serotype-2 (SRV-2) Reverse Transcriptase Isolated from Indonesian Cynomolgus Monkey

2020 ◽  
Vol 31 (3) ◽  
pp. 47-61
Author(s):  
Uus Saepuloh ◽  
Diah Iskandriati ◽  
Joko Pamungkas ◽  
Dedy Duryadi Solihin ◽  
Sela Septima Mariya ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Cynomolgus Monkey ◽  
Tertiary Structure ◽  
Vaccine Development ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Nucleotide Position ◽  
Structure Model ◽  
Three Dimensional Structure ◽  
Hiv 1

Simian betaretrovirus serotype-2 (SRV-2) is an important pathogenic agent in Asian macaques. It is a potential confounding variable in biomedical research. SRV-2 also provides a valuable viral model compared to other retroviruses which can be used for understanding many aspects of retroviral-host interactions and immunosuppression, infection mechanism, retroviral structure, antiretroviral and vaccine development. In this study, we isolated the gene encoding reverse transcriptase enzyme (RT) of SRV-2 that infected Indonesian cynomolgus monkey (Mf ET1006) and predicted the three dimensional structure model using the iterative threading assembly refinement (I-TASSER) computational programme. This SRV-2 RT Mf ET1006 consisted of 547 amino acids at nucleotide position 3284–4925 of whole genome SRV-2. The polymerase active site located in the finger/palm subdomain characterised by three conserved catalytic aspartates (Asp90, Asp165, Asp166), and has a highly conserved YMDD motif as Tyr163, Met164, Asp165 and Asp166. We estimated that this SRV-2 RT Mf ET1006 structure has the accuracy of template modelling score (TM-score 0.90 ± 0.06) and root mean square deviation (RMSD) 4.7 ± 3.1Å, indicating that this model can be trusted and the accuracy can be seen from the appearance of protein folding in tertiary structure. The superpositionings between SRV-2 RT Mf ET1006 and Human Immunodeficiency Virus-1 (HIV-1) RT were performed to predict the structural in details and to optimise the best fits for illustrations. This SRV-2 RT Mf ET1006 structure model has the highest homology to HIV-1 RT (2B6A.pdb) with estimated accuracy at TM-score 0.911, RMSD 1.85 Å, and coverage of 0.953. This preliminary study of SRV-2 RT Mf ET1006 structure modelling is intriguing and provide some information to explore the molecular characteristic and biochemical mechanism of this enzyme.

Three-dimensional structure of the RNase H domain of HIV-1 reverse transcriptase at 2. 4 Å resolution

Peptides ◽  
1992 ◽  
pp. 682-684
Author(s):  
David A. Matthews ◽  
Jay F. Davies ◽  
Zuzana Hostomska ◽  
Zdenek Hostomsky ◽  
Steven R. Jordan
Keyword(s):  
Reverse Transcriptase ◽  
Three Dimensional ◽  
Rnase H ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Hiv 1

Review of HIV-1 reverse transcriptase three-dimensional structure: Implications for drug design

1993 ◽  
Vol 1 (1) ◽  
pp. 129-150 ◽  
Author(s):  
Raymond G. Nanni ◽  
Jianping Ding ◽  
Alfredo Jacobo-Molina ◽  
Stephen H. Hughes ◽  
Edward Arnold
Keyword(s):  
Drug Design ◽  
Reverse Transcriptase ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Hiv 1

Locations of Anti-AIDS Drug Binding Sites and Resistance Mutations in the Three-dimensional Structure of HIV-1 Reverse Transcriptase

1994 ◽  
Vol 243 (3) ◽  
pp. 369-387 ◽  
Author(s):  
Chris Tantillo ◽  
Jianping Ding ◽  
Alfredo Jacobo-Molina ◽  
Raymond G. Nanni ◽  
Paul L. Boyer ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Binding Sites ◽  
Three Dimensional ◽  
Drug Binding ◽  
Dimensional Structure ◽  
Resistance Mutations ◽  
Three Dimensional Structure ◽  
Drug Binding Sites ◽  
Hiv 1

Three-dimensional Structure and Evolution of HIV-1 Protease

1990 ◽  
pp. 79-91
Author(s):  
Andrew Wilderspin ◽  
Duncan Gaskin ◽  
Risto Lapatto ◽  
Tom Blundell ◽  
Andrew Hemmings ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Hiv 1

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.

Three-dimensional structure of aspartyl protease from human immunodeficiency virus HIV-1

Nature ◽  
1989 ◽  
Vol 337 (6208) ◽  
pp. 615-620 ◽  
Author(s):  
Manuel A. Navia ◽  
Paula M. D. Fitzgerald ◽  
Brian M. McKeever ◽  
Chih-Tai Leu ◽  
Jill C. Heimbach ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Aspartyl Protease ◽  
Three Dimensional Structure ◽  
Immunodeficiency Virus ◽  
Hiv 1

Three-dimensional Structure of the Channel-forming Trans-membrane Domain of Virus Protein “u” (Vpu) from HIV-1

2003 ◽  
Vol 333 (2) ◽  
pp. 409-424 ◽  
Author(s):  
Sang Ho Park ◽  
Anthony A. Mrse ◽  
Alexander A. Nevzorov ◽  
Michael F. Mesleh ◽  
Myrta Oblatt-Montal ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Virus Protein ◽  
Membrane Domain ◽  
Three Dimensional Structure ◽  
Virus Protein U ◽  
Hiv 1

scholarly journals Efficient targeting to storage granules of human proinsulins with altered propeptide domain.

1988 ◽  
Vol 106 (6) ◽  
pp. 1843-1851 ◽  
Author(s):  
S K Powell ◽  
L Orci ◽  
C S Craik ◽  
H P Moore
Keyword(s):  
High Efficiency ◽  
Tertiary Structure ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Structural Domains ◽  
C Peptide ◽  
Three Dimensional Structure ◽  
Morphological Criteria ◽  
Cellular Machinery ◽  
Storage Granules

In neuronal and endocrine cells, peptide hormones are selectively segregated into storage granules, while other proteins are exported continuously without storage. Sorting of hormones by cellular machinery involves the recognition of specific structural domains on prohormone molecules. Since the propeptide of insulin is known to play an important role in its three-dimensional structure, it is reasonable to speculate that targeting of proinsulin to storage granules would require a functional connecting peptide. To test this hypothesis, we constructed two mutations in human proinsulin with different predicted structures. In one mutation, Ins delta C, the entire C peptide was deleted, resulting in an altered insulin in which the B and the A chains are joined contiguously. In the other mutation, Ins/IGF, the C peptide of proinsulin was replaced with the unrelated 12-amino acid connecting peptide of human insulin-like growth factor-I; this substitution should permit correct folding of the B and A chains to form a tertiary structure similar to that of proinsulin. By several biochemical and morphological criteria, we found that Ins/IGF is efficiently targeted to storage granules, suggesting that the C peptide of proinsulin does not contain necessary sorting information. Unexpectedly, Ins delta C, which presumably cannot fold properly, is also targeted to granules at a high efficiency. These results imply that either the targeting machinery can tolerate changes in the tertiary structure of transported proteins, or that the B and A chains of insulin can form a relatively intact three-dimensional structure even in the absence of C peptide.

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