scholarly journals Structures of two aptamers with differing ligand specificity reveal ruggedness in the functional landscape of RNA

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Andrew John Knappenberger ◽  
Caroline Wetherington Reiss ◽  
Scott A Strobel
Keyword(s):  
Fitness Landscape ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Ligand Specificity ◽  
Phosphoribosyl Pyrophosphate ◽  
Guanosine Tetraphosphate ◽  
Expression Platform ◽  
Rna Motif ◽  
Three Dimensional Space ◽  
Rna Fold

Two classes of riboswitches related to the ykkC guanidine-I riboswitch bind phosphoribosyl pyrophosphate (PRPP) and guanosine tetraphosphate (ppGpp). Here we report the co-crystal structure of the PRPP aptamer and its ligand. We also report the structure of the G96A point mutant that prefers ppGpp over PRPP with a dramatic 40,000-fold switch in specificity. The ends of the aptamer form a helix that is not present in the guanidine aptamer and is involved in the expression platform. In the mutant, the base of ppGpp replaces G96 in three-dimensional space. This disrupts the S-turn, which is a primary structural feature of the ykkC RNA motif. These dramatic differences in ligand specificity are achieved with minimal mutations. ykkC aptamers are therefore a prime example of an RNA fold with a rugged fitness landscape. The ease with which the ykkC aptamer acquires new specificity represents a striking case of evolvability in RNA.

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.

scholarly journals Planning model of a group UAV flight in three-dimensional space

2021 ◽  
Vol 1111 (1) ◽  
pp. 012034
Author(s):  
N A Maksimov ◽  
K Zhigalov ◽  
A V Gorban ◽  
I V Ignatev
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Planning Model ◽  
Three Dimensional Space

scholarly journals Improved Bat Algorithm for UAV Path Planning in Three-Dimensional Space

IEEE Access ◽  
2021 ◽  
Vol 9 ◽  
pp. 20100-20116
Author(s):  
Xianjin Zhou ◽  
Fei Gao ◽  
Xi Fang ◽  
Zehong Lan
Keyword(s):  
Path Planning ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Bat Algorithm ◽  
Three Dimensional Space
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