scholarly journals Insights from the interfaces of HIV-1 envelope (ENV) trimer viral protein GP160 (GP120-GP41)

2021 ◽  
Vol 12 (1) ◽  
pp. 513-522
Author(s):  
Christina Nilofer ◽  
Arumugam Mohanapriya
Keyword(s):  
Hydrogen Bonds ◽  
Viral Protein ◽  
Van Der Waals ◽  
Interface Area ◽  
Protein Interfaces ◽  
Gp120 Protein ◽  
Life Threatening ◽  
Total Energies ◽  
Potential Vaccine ◽  
Hiv 1

The Human Immunodeficiency Virus (HIV-1) type 1 viral protein is a life threatening virus causing HIV/AIDS in infected humans. The HIV-1 envelope (ENV) trimer glycoprotein GP160 (GP120-GP41) is gaining attention in recent years as a potential vaccine candidate for HIV-1/AIDS. However, the sequence variation and charge polarity at the interacting sites across clades is a shortcoming faced in the development of an effective HIV-1 vaccine. We analyzed the interfaces in terms of its interface area, interface size, and interface energies (van der Waals, hydrogen bonds, and electrostatics). The interfaces were divided as dominant (≥60%) and subdominant (<60%) based on van der Waals contribution to total energies. 88% of GP120 and 74% of GP41 interfaces are highly pronounced with van der Waals energy having large interfaces with interface size (98±65 (GP120) and 73±65 (GP41)) and interface area (882±1166Å2 (GP120) and 921±1288Å2 (GP41)). Nevertheless, 12% of GP120 and 26% of GP41 interfaces have subdominant van der Waals energies having small interfaces with interface size (58±20 (GP120) and 27±9 (GP41)) and interface area (581±1605Å2 (GP120) and 483±896Å2 (GP41)). It was interesting to observe GP41 small interfaces with subdominant van der Waals are stabilized by electrostatics (r2=0.63) without hydrogen bonds (r2=0). However, GP120 small interfaces were found to have two fold more hydrogen bonds (r2=0.59) than electrostatics (r2=0.20). Therefore, our previous finding stating that small protein-protein interfaces rich in electrostatics holds true in case of GP41 whereas not with GP120 protein interfaces.

Insights from the Interfaces of Corona Viral Proteins: Homomers Versus Heteromers

2021 ◽  
Vol 14 (3) ◽  
pp. 1613-1631
Author(s):  
Christina Nilofer ◽  
Arumugam Mohanapriya
Keyword(s):  
Hydrogen Bond ◽  
Viral Proteins ◽  
Viral Disease ◽  
Electrostatic Energy ◽  
Interface Area ◽  
Hydrogen Bond Energy ◽  
Biochemical Biomarkers ◽  
Protein Interfaces ◽  
Life Threatening ◽  
Percent Contribution

The outbreak of COVID-19 and its mutant variants has become a life-threatening and fatal viral disease to mankind. Several studies have been carried out to identify an effective receptor against coronavirus using clinically driven samples distinguished as hematological, immunological and biochemical biomarkers. Simultaneously, protein interfaces are being researched to understand the structural and functional mechanism of action. Therefore, we characterized and examined the interfaces of corona viral proteins using a dataset consisting of 366 homomeric and 199 heteromeric protein interfaces. The interfaces were analyzed using six parameters including interface area, interface size, van der Waal, hydrogen bond, electrostatic and total stabilizing energies. We observed the interfaces of corona viral proteins (homomer and heteromer) to be alike. Therefore, we clustered the interfaces based on the percent contribution of vdW towards total stabilizing energy as vdW energy dominant (≥60%) and vdW energy subdominant (<60%). We found 91% of interfaces to have vdW energy in dominance with large interface size [146±29 (homomer) and 122±29 (heteromer)] and interface area [1690±683 (homomer) and 1306±355 (heteromer)]. However, we also observed 9% of interfaces to have vdW energy in sub-dominance with small interface size [60±12 (homomer) and 41±20 (heteromer)] and interface area [472±174 (homomer) and 310±199 (heteromer)]. We noticed the interface area of large interfaces to be four-fold more when compared to small interfaces in homomer and heteromer. It was interesting to observe that the small interfaces of homomers to be rich in electrostatics (r2=0.50) destitute of hydrogen bond energy (r2=0.04). However, the heteromeric interfaces were equally pronounced with hydrogen bond (r2=0.70) and electrostatic (r2=0.61) energies. Hence, our earlier findings stating that the small protein interfaces are rich in electrostatic energy remaintrue with the homomeric interfaces of corona viral proteins whereas not in heteromeric interfaces.

Effect of Promoters and Signal Sequences on the Production of Secreted HIV-1 gp120 Protein in the Baculovirus System

1998 ◽  
Vol 14 (1) ◽  
pp. 8-12 ◽  
Author(s):  
Alex Golden ◽  
Douglas A. Austen ◽  
M.R. van Schravendijk ◽  
Barbara J. Sullivan ◽  
Ernest S. Kawasaki ◽  
...  
Keyword(s):  
Signal Sequences ◽  
Gp120 Protein ◽  
Baculovirus System ◽  
Hiv 1

scholarly journals Effects of Gag Mutation and Processing on Retroviral Dimeric RNA Maturation

2006 ◽  
Vol 80 (3) ◽  
pp. 1242-1249 ◽  
Author(s):  
William Fu ◽  
Que Dang ◽  
Kunio Nagashima ◽  
Eric O. Freed ◽  
Vinay K. Pathak ◽  
...  
Keyword(s):  
Viral Protein ◽  
Leukemia Virus ◽  
Viral Rna ◽  
Host Cells ◽  
Protein Cleavage ◽  
Rna Packaging ◽  
Virus Rna ◽  
Rna Dimer ◽  
Rna Maturation ◽  
Hiv 1

ABSTRACT After their release from host cells, most retroviral particles undergo a maturation process, which includes viral protein cleavage, core condensation, and increased stability of the viral RNA dimer. Inactivating the viral protease prevents protein cleavage; the resulting virions lack condensed cores and contain fragile RNA dimers. Therefore, protein cleavage is linked to virion morphological change and increased stability of the RNA dimer. However, it is unclear whether protein cleavage is sufficient for mediating virus RNA maturation. We have observed a novel phenotype in a murine leukemia virus capsid mutant, which has normal virion production, viral protein cleavage, and RNA packaging. However, this mutant also has immature virion morphology and contains a fragile RNA dimer, which is reminiscent of protease-deficient mutants. To our knowledge, this mutant provides the first evidence that Gag cleavage alone is not sufficient to promote RNA dimer maturation. To extend our study further, we examined a well-defined human immunodeficiency virus type 1 (HIV-1) Gag mutant that lacks a functional PTAP motif and produces immature virions without major defects in viral protein cleavage. We found that the viral RNA dimer in the PTAP mutant is more fragile and unstable compared with those from wild-type HIV-1. Based on the results of experiments using two different Gag mutants from two distinct retroviruses, we conclude that Gag cleavage is not sufficient for promoting RNA dimer maturation, and we propose that there is a link between the maturation of virion morphology and the viral RNA dimer.

scholarly journals Modulation of NKG2D-Mediated Cytotoxic Functions of Natural Killer Cells by Viral Protein R from HIV-1 Primary Isolates

2012 ◽  
Vol 86 (3) ◽  
pp. 1902-1902
Author(s):  
T. N. Q. Pham ◽  
J. Richard ◽  
F. C. A. Gerard ◽  
C. Power ◽  
E. A. Cohen
Keyword(s):  
Natural Killer Cells ◽  
Natural Killer ◽  
Viral Protein ◽  
Killer Cells ◽  
Viral Protein R ◽  
Hiv 1

scholarly journals CH···O Hydrogen Bonds at Protein-Protein Interfaces

2002 ◽  
Vol 277 (40) ◽  
pp. 37732-37740 ◽  
Author(s):  
Lin Jiang ◽  
Luhua Lai
Keyword(s):  
Hydrogen Bonds ◽  
Protein Interfaces

Tetrakis[(1-phenyltetrazol-5-yl)sulfanylmethyl]methane

2007 ◽  
Vol 63 (3) ◽  
pp. o1145-o1147 ◽  
Author(s):  
Alexander S. Lyakhov ◽  
Marina V. Zatsepina ◽  
Tatiana V. Artamonova ◽  
Pavel N. Gaponik ◽  
Grigorii I. Koldobskii
Keyword(s):  
Hydrogen Bonds ◽  
Title Compound ◽  
Rotation Axis ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Π Interactions ◽  
Compound C

The title compound, C33H28N16S4, prepared by the divergent method, presents a core unit for further synthesis of tetrazole-containing dendrimers. The central C atom lies on a crystallographic twofold rotation axis. π–π Interactions and weak non-classical C—H...N hydrogen bonds are responsible for the formation of layers parallel to the bc plane, with van der Waals interactions between them.

scholarly journals Manganese Fluorene Phosphonates: Formation of Isolated Chains

Inorganics ◽  
2018 ◽  
Vol 6 (3) ◽  
pp. 92 ◽  
Author(s):  
Clarisse Bloyet ◽  
Jean-Michel Rueff ◽  
Vincent Caignaert ◽  
Bernard Raveau ◽  
Jean-François Lohier ◽  
...  
Keyword(s):  
Magnetic Susceptibility ◽  
Hydrogen Bonds ◽  
Phosphonic Acid ◽  
Van Der Waals ◽  
Exchange Interactions ◽  
Van Der Waals Interactions ◽  
Antiferromagnetic Exchange ◽  
Hydrothermal Conditions ◽  
Hirshfeld Surfaces ◽  
Nitrate Tetrahydrate

9,9-dimethylfluorenyl-2-phosphonic acid 1 was reacted with manganese nitrate tetrahydrate to produce under hydrothermal conditions the crystalline manganese phosphonate Mn(H2O)2[O2(OH)PC15H13]2·2H2O which crystallize in the P21/c space group. This compound is a rare example of Mn-phosphonate material featuring isolated chains. The interactions between these chains containing the 9,9-dimethylfluorenyl moieties, result from Van der Waals interactions involving the fluorene ligands and C···H–C hydrogen bonds as revealed by Hirshfeld Surfaces. This material features antiferromagnetic exchange interactions as revealed by the magnetic susceptibility as a function of the temperature.

Sign in / Sign up

Export Citation Format

Share Document