HIV-1 gp41 Tertiary Structure Studied by EPR Spectroscopy†

Biochemistry ◽  
1996 ◽  
Vol 35 (44) ◽  
pp. 13922-13928 ◽  
Author(s):  
Mark David Rabenstein ◽  
Yeon-Kyun Shin
Keyword(s):  
Epr Spectroscopy ◽  
Tertiary Structure ◽  
Hiv 1

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.

scholarly journals Contribution of MxB Oligomerization to HIV-1 Capsid Binding and Restriction

2015 ◽  
Vol 89 (6) ◽  
pp. 3285-3294 ◽  
Author(s):  
Cindy Buffone ◽  
Bianca Schulte ◽  
Silvana Opp ◽  
Felipe Diaz-Griffero
Keyword(s):  
T Cells ◽  
Structure Function ◽  
Capsid Protein ◽  
Reverse Transcription ◽  
Tertiary Structure ◽  
Alpha Interferon ◽  
Restriction Factor ◽  
Current Structure ◽  
Modeled Structure ◽  
Hiv 1

ABSTRACTThe alpha interferon (IFN-α)-inducible restriction factor myxovirus B (MxB) blocks HIV-1 infection after reverse transcription but prior to integration. MxB binds to the HIV-1 core, which is composed of capsid protein, and this interaction leads to inhibition of the uncoating process of HIV-1. Previous studies suggested that HIV-1 restriction by MxB requires binding to capsid. This work tests the hypothesis that MxB oligomerization is important for the ability of MxB to bind to the HIV-1 core. For this purpose, we modeled the structure of MxB using the published tertiary structure of MxA. The modeled structure of MxB guided our mutagenic studies and led to the discovery of several MxB variants that lose the capacity to oligomerize. In agreement with our hypothesis, MxB variants that lost the oligomerization capacity also lost the ability to bind to the HIV-1 core. MxB variants deficient for oligomerization were not able to block HIV-1 infection. Overall, our work showed that oligomerization is required for the ability of MxB to bind to the HIV-1 core and block HIV-1 infection.IMPORTANCEMxB is a novel restriction factor that blocks infection of HIV-1. MxB is inducible by IFN-α, particularly in T cells. The current work studies the oligomerization determinants of MxB and carefully explores the contribution of oligomerization to capsid binding and restriction. This work takes advantage of the current structure of MxA and models the structure of MxB, which is used to guide structure-function studies. This work leads to the conclusion that MxB oligomerization is important for HIV-1 capsid binding and restriction.

scholarly journals The Molten Globule State of Maltose-Binding Protein: Structural and Thermodynamic Characterization by EPR Spectroscopy and Isothermal Titration Calorimetry

2020 ◽  
Vol 51 (9-10) ◽  
pp. 877-886
Author(s):  
Chen Nickolaus ◽  
Carolyn Vargas ◽  
Jörg Reichenwallner ◽  
Mohammed Chakour ◽  
Benjamin Selmke ◽  
...  
Keyword(s):  
Epr Spectroscopy ◽  
Tertiary Structure ◽  
Binding Protein ◽  
Molten Globule ◽  
Spin Labeling ◽  
Maltose Binding Protein ◽  
Titration Calorimetry ◽  
Native State ◽  
Paramagnetic Resonance ◽  
Distance Information

Abstract Employing site-directed spin labeling (SDSL), the structure of maltose-binding protein (MBP) had previously been studied in the native state by electron paramagnetic resonance (EPR) spectroscopy. Several spin-labeled double cysteine mutants were distributed all over the structure of this cysteine-free protein and revealed distance information between the nitroxide residues from double electron–electron resonance (DEER). The results were in good agreement with the known X-ray structure. We have now extended these studies to the molten globule (MG) state, a folding intermediate, which can be stabilized around pH 3 and that is characterized by secondary but hardly any tertiary structure. Instead of clearly defined distance features as found in the native state, several additional characteristics indicate that the MG structure of MBP contains different polypeptide chain and domain orientations. MBP is also known to bind its substrate maltose even in MG state although with lower affinity. Additionally, we have now created new mutants allowing for spin labeling at or near the active site. Our data confirm an already preformed ligand site structure in the MG explaining its substrate binding capability and thus most probably serving as a nucleation center for the final native structure.

scholarly journals The leader of the HIV-1 RNA genome forms a compactly folded tertiary structure

RNA ◽  
2000 ◽  
Vol 6 (2) ◽  
pp. 282-295 ◽  
Author(s):  
BEN BERKHOUT ◽  
JEROEN L.B. VAN WAMEL
Keyword(s):  
Tertiary Structure ◽  
Rna Genome ◽  
Hiv 1

scholarly journals A novel strategy for site selective spin-labeling to investigate bioactive entities by DNP and EPR spectroscopy

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kevin Herr ◽  
Max Fleckenstein ◽  
Martin Brodrecht ◽  
Mark V. Höfler ◽  
Henrike Heise ◽  
...  
Keyword(s):  
Solid State ◽  
Epr Spectroscopy ◽  
Spin Label ◽  
Tertiary Structure ◽  
Spin Labeling ◽  
Disulfide Bridge ◽  
Bioactive Molecules ◽  
Spin Labels ◽  
Time Saving ◽  
Site Selective

AbstractA novel specific spin-labeling strategy for bioactive molecules is presented for eptifibatide (integrilin) an antiplatelet aggregation inhibitor, which derives from the venom of certain rattlesnakes. By specifically labeling the disulfide bridge this molecule becomes accessible for analytical techniques such as Electron Paramagnetic Resonance (EPR) and solid state Dynamic Nuclear Polarization (DNP). The necessary spin-label was synthesized and inserted into the disulfide bridge of eptifibatide via reductive followed by insertion by a double Michael addition under physiological conditions. This procedure is universally applicable for disulfide containing biomolecules and is expected to preserve their tertiary structure with minimal change due to the small size of the label and restoring of the previous disulfide connection. HPLC and MS analysis show the successful introduction of the spin label and EPR spectroscopy confirms its activity. DNP-enhanced solid state NMR experiments show signal enhancement factors of up to 19 in 13C CP MAS experiments which corresponds to time saving factors of up to 361. This clearly shows the high potential of our new spin labeling strategy for the introduction of site selective radical spin labels into biomolecules and biosolids without compromising its conformational integrity for structural investigations employing solid-state DNP or advanced EPR techniques.

Monitoring Inhibitor-Induced Conformational Population Shifts in HIV-1 Protease by Pulsed EPR Spectroscopy

Biochemistry ◽  
2009 ◽  
Vol 48 (37) ◽  
pp. 8765-8767 ◽  
Author(s):  
Mandy E. Blackburn ◽  
Angelo M. Veloro ◽  
Gail E. Fanucci
Keyword(s):  
Epr Spectroscopy ◽  
Pulsed Epr ◽  
Conformational Population ◽  
Hiv 1

Dynamics of “Flap” Structures in Three HIV-1 Protease/Inhibitor Complexes Probed by Total Chemical Synthesis and Pulse-EPR Spectroscopy

2009 ◽  
Vol 131 (3) ◽  
pp. 884-885 ◽  
Author(s):  
Vladimir Yu. Torbeev ◽  
H. Raghuraman ◽  
Kalyaneswar Mandal ◽  
Sanjib Senapati ◽  
Eduardo Perozo ◽  
...  
Keyword(s):  
Chemical Synthesis ◽  
Protease Inhibitor ◽  
Epr Spectroscopy ◽  
Pulse Epr ◽  
Hiv 1
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