scholarly journals INI1/SMARCB1 Rpt1 domain mimics TAR RNA in binding to integrase to facilitate HIV-1 replication

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Updesh Dixit ◽  
Savita Bhutoria ◽  
Xuhong Wu ◽  
Liming Qiu ◽  
Menachem Spira ◽  
...  
Keyword(s):  
Computational Modeling ◽  
Rna Binding ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Nmr Structure ◽  
Charged Surface ◽  
Tar Rna ◽  
Rna Interaction ◽  
Hiv 1 ◽  
Three Dimensional Space

AbstractINI1/SMARCB1 binds to HIV-1 integrase (IN) through its Rpt1 domain and exhibits multifaceted role in HIV-1 replication. Determining the NMR structure of INI1-Rpt1 and modeling its interaction with the IN-C-terminal domain (IN-CTD) reveal that INI1-Rpt1/IN-CTD interface residues overlap with those required for IN/RNA interaction. Mutational analyses validate our model and indicate that the same IN residues are involved in both INI1 and RNA binding. INI1-Rpt1 and TAR RNA compete with each other for IN binding with similar IC50 values. INI1-interaction-defective IN mutant viruses are impaired for incorporation of INI1 into virions and for particle morphogenesis. Computational modeling of IN-CTD/TAR complex indicates that the TAR interface phosphates overlap with negatively charged surface residues of INI1-Rpt1 in three-dimensional space, suggesting that INI1-Rpt1 domain structurally mimics TAR. This possible mimicry between INI1-Rpt1 and TAR explains the mechanism by which INI1/SMARCB1 influences HIV-1 late events and suggests additional strategies to inhibit HIV-1 replication.

Computational modeling of cracks different forms in three-dimensional space

2021 ◽  
Author(s):  
A.A. Shamina ◽  
A.V. Zvyagin ◽  
N.N. Smirnov ◽  
A.A. Luzhin ◽  
D.I. Panfilov ◽  
...  
Keyword(s):  
Computational Modeling ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Three Dimensional Space

scholarly journals Structures of microRNA-precursor apical junctions and loops reveal non-canonical base pairs important for processing

2020 ◽  
Author(s):  
Grant M. Shoffner ◽  
Zhixiang Peng ◽  
Feng Guo
Keyword(s):  
Molecular Mechanisms ◽  
Rna Binding ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Base Pairs ◽  
Canonical Base ◽  
Hairpin Loops ◽  
Heme Domain ◽  
Apical Junctions ◽  
Three Dimensional Space

AbstractMetazoan pri-miRNAs and pre-miRNAs fold into characteristic hairpins that are recognized by the processing machinery. Essential to the recognition of these miR-precursors are their apical junctions where double-stranded stems meet single-stranded hairpin loops. Little is known about how apical junctions and loops fold in three-dimensional space. Here we developed a scaffold-directed crystallography method and determined the structures of eight human miR-precursor apical junctions and loops. Six structures contain non-canonical base pairs stacking on top of the hairpin stem. U-U pair contributes to thermodynamic stability in solution and is highly enriched at human miR-precursor apical junctions. Our systematic mutagenesis shows that U-U is among the most efficiently processed variants. The RNA-binding heme domain of pri-miRNA-processing protein DGCR8 binds longer loops more tightly and non-canonical pairs at the junction appear to modulate loop length. Our study provides structural and biochemical bases for understanding miR-precursors and molecular mechanisms of microRNA maturation.

Extension of the Spatial PDI Model to Three Dimensions

1997 ◽  
Vol 84 (1) ◽  
pp. 176-178
Author(s):  
Frank O'Brien
Keyword(s):  
Population Density ◽  
Dimensional Space ◽  
Finite Lattice ◽  
Three Dimensional ◽  
Upper Bounds ◽  
Three Dimensions ◽  
Lower And Upper Bounds ◽  
Density Index ◽  
Three Dimensional Space

The author's population density index ( PDI) model is extended to three-dimensional distributions. A derived formula is presented that allows for the calculation of the lower and upper bounds of density in three-dimensional space for any finite lattice.

A Peptoid with Extended Shape in Water

2019 ◽  
Author(s):  
Jumpei Morimoto ◽  
Yasuhiro Fukuda ◽  
Takumu Watanabe ◽  
Daisuke Kuroda ◽  
Kouhei Tsumoto ◽  
...  
Keyword(s):  
Spectroscopic Analysis ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Biomolecular Recognition ◽  
Biological Application ◽  
New Class ◽  
Proteolytic Resistance ◽  
Pharmacokinetic Properties ◽  
Optically Pure ◽  
Three Dimensional Space

<div> <div> <div> <p>“Peptoids” was proposed, over decades ago, as a term describing analogs of peptides that exhibit better physicochemical and pharmacokinetic properties than peptides. Oligo-(N-substituted glycines) (oligo-NSG) was previously proposed as a peptoid due to its high proteolytic resistance and membrane permeability. However, oligo-NSG is conformationally flexible and is difficult to achieve a defined shape in water. This conformational flexibility is severely limiting biological application of oligo-NSG. Here, we propose oligo-(N-substituted alanines) (oligo-NSA) as a new peptoid that forms a defined shape in water. A synthetic method established in this study enabled the first isolation and conformational study of optically pure oligo-NSA. Computational simulations, crystallographic studies and spectroscopic analysis demonstrated the well-defined extended shape of oligo-NSA realized by backbone steric effects. The new class of peptoid achieves the constrained conformation without any assistance of N-substituents and serves as an ideal scaffold for displaying functional groups in well-defined three-dimensional space, which leads to effective biomolecular recognition. </p> </div> </div> </div>

scholarly journals Quantitative image analysis of microbial communities with BiofilmQ

2021 ◽  
Author(s):  
Raimo Hartmann ◽  
Hannah Jeckel ◽  
Eric Jelli ◽  
Praveen K. Singh ◽  
Sanika Vaidya ◽  
...  
Keyword(s):  
Image Analysis ◽  
Microbial Communities ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Software Tool ◽  
Image Cytometry ◽  
Quantitative Image Analysis ◽  
Space And Time ◽  
Quantitative Image ◽  
Three Dimensional Space

AbstractBiofilms are microbial communities that represent a highly abundant form of microbial life on Earth. Inside biofilms, phenotypic and genotypic variations occur in three-dimensional space and time; microscopy and quantitative image analysis are therefore crucial for elucidating their functions. Here, we present BiofilmQ—a comprehensive image cytometry software tool for the automated and high-throughput quantification, analysis and visualization of numerous biofilm-internal and whole-biofilm properties in three-dimensional space and time.

scholarly journals How Can I Grab That?

i-com ◽  
2020 ◽  
Vol 19 (2) ◽  
pp. 67-85
Author(s):  
Matthias Weise ◽  
Raphael Zender ◽  
Ulrike Lucke
Keyword(s):  
Virtual Reality ◽  
User Experience ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Advantages And Disadvantages ◽  
Multiple Dimensions ◽  
Application Developers ◽  
Three Dimensional Space

AbstractThe selection and manipulation of objects in Virtual Reality face application developers with a substantial challenge as they need to ensure a seamless interaction in three-dimensional space. Assessing the advantages and disadvantages of selection and manipulation techniques in specific scenarios and regarding usability and user experience is a mandatory task to find suitable forms of interaction. In this article, we take a look at the most common issues arising in the interaction with objects in VR. We present a taxonomy allowing the classification of techniques regarding multiple dimensions. The issues are then associated with these dimensions. Furthermore, we analyze the results of a study comparing multiple selection techniques and present a tool allowing developers of VR applications to search for appropriate selection and manipulation techniques and to get scenario dependent suggestions based on the data of the executed study.

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