Indirect Readout in Protein-Peptide Recognition: A Different Story from Classical Biomolecular Recognition

2014 ◽  
Vol 54 (7) ◽  
pp. 2022-2032 ◽  
Author(s):  
Hua Yu ◽  
Peng Zhou ◽  
Maolin Deng ◽  
Zhicai Shang
Keyword(s):  
Biomolecular Recognition ◽  
Peptide Recognition ◽  
Indirect Readout

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 One-pot Bottom-up Synthesis of 2D Graphene Derivative: Application in Biomolecular Recognition and Nanozyme Activity

2021 ◽  
Author(s):  
Subrata Pandit ◽  
Mrinmoy De
Keyword(s):  
Growth Control ◽  
Biomolecular Recognition ◽  
Two Dimensional ◽  
One Pot ◽  
Bottom Up ◽  
2D Nanosheets

The synthesis of two-dimensional (2D) nanosheets such as graphene and their derivatives through bottom-up approach has many advantages such as growth control and functionalization, but it is always challenging to...

scholarly journals Cell penetration efficiency analysis of different atomic force microscopy nanoneedles into living cells

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Marcos Penedo ◽  
Tetsuya Shirokawa ◽  
Mohammad Shahidul Alam ◽  
Keisuke Miyazawa ◽  
Takehiko Ichikawa ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Cell Membrane ◽  
Cell Biology ◽  
Cell Damage ◽  
Efficiency Analysis ◽  
Living Cells ◽  
Biomolecular Recognition ◽  
Cell Penetration ◽  
Force Microscopy ◽  
Atomic Force

AbstractOver the last decade, nanoneedle-based systems have demonstrated to be extremely useful in cell biology. They can be used as nanotools for drug delivery, biosensing or biomolecular recognition inside cells; or they can be employed to select and sort in parallel a large number of living cells. When using these nanoprobes, the most important requirement is to minimize the cell damage, reducing the forces and indentation lengths needed to penetrate the cell membrane. This is normally achieved by reducing the diameter of the nanoneedles. However, several studies have shown that nanoneedles with a flat tip display lower penetration forces and indentation lengths. In this work, we have tested different nanoneedle shapes and diameters to reduce the force and the indentation length needed to penetrate the cell membrane, demonstrating that ultra-thin and sharp nanoprobes can further reduce them, consequently minimizing the cell damage.

Structural Perspective on Ancient Neuropeptide Y-like System reveals Hallmark Features for Peptide Recognition and Receptor Activation

2021 ◽  
Vol 433 (13) ◽  
pp. 166992
Author(s):  
Miron Mikhailowitsch Gershkovich ◽  
Victoria Elisabeth Groß ◽  
Oanh Vu ◽  
Clara Tabea Schoeder ◽  
Jens Meiler ◽  
...  
Keyword(s):  
Neuropeptide Y ◽  
Receptor Activation ◽  
Peptide Recognition ◽  
Structural Perspective

scholarly journals Enthalpy–Entropy Compensation in Biomolecular Recognition: A Computational Perspective

ACS Omega ◽  
2021 ◽  
Vol 6 (17) ◽  
pp. 11122-11130
Author(s):  
Francesca Peccati ◽  
Gonzalo Jiménez-Osés
Keyword(s):  
Biomolecular Recognition ◽  
Computational Perspective

scholarly journals Structures of designed armadillo-repeat proteins show propagation of inter-repeat interface effects

2016 ◽  
Vol 72 (1) ◽  
pp. 168-175 ◽  
Author(s):  
Christian Reichen ◽  
Chaithanya Madhurantakam ◽  
Simon Hansen ◽  
Markus G. Grütter ◽  
Andreas Plückthun ◽  
...  
Keyword(s):  
Second Generation ◽  
Body Movement ◽  
Recognition System ◽  
Third Generation ◽  
Peptide Recognition ◽  
Repeat Proteins ◽  
Peptide Binding Site ◽  
Armadillo Repeat ◽  
The Stability ◽  
Interface Effects

The armadillo repeat serves as a scaffold for the development of modular peptide-recognition modules. In order to develop such a system, three crystal structures of designed armadillo-repeat proteins with third-generation N-caps (YIII-type), four or five internal repeats (M-type) and second-generation C-caps (AII-type) were determined at 1.8 Å (His-YIIIM4AII), 2.0 Å (His-YIIIM5AII) and 1.95 Å (YIIIM5AII) resolution and compared with those of variants with third-generation C-caps. All constructs are full consensus designs in which the internal repeats have exactly the same sequence, and hence identical conformations of the internal repeats are expected. The N-cap and internal repeats M1to M3are indeed extremely similar, but the comparison reveals structural differences in internal repeats M4and M5and the C-cap. These differences are caused by long-range effects of the C-cap, contacting molecules in the crystal, and the intrinsic design of the repeat. Unfortunately, the rigid-body movement of the C-terminal part impairs the regular arrangement of internal repeats that forms the putative peptide-binding site. The second-generation C-cap improves the packing of buried residues and thereby the stability of the protein. These considerations are useful for future improvements of an armadillo-repeat-based peptide-recognition system.

scholarly journals Immunodominant-Peptide Recognition: Beta Testing TCRαβ

Immunity ◽  
2008 ◽  
Vol 28 (2) ◽  
pp. 139-141 ◽  
Author(s):  
Jia-huai Wang ◽  
Robert J. Mallis ◽  
Ellis L. Reinherz
Keyword(s):  
Peptide Recognition ◽  
Beta Testing
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