Biomolecular Recognition: Nanotransduction and Nanointervention

2012 ◽  
pp. 119-146 ◽  
Author(s):  
Elizabeth Crew ◽  
Stephanie Lim ◽  
Hong Yan ◽  
Shiyao Shan ◽  
Jun Yin ◽  
...  
Keyword(s):  
Biomolecular Recognition

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.

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

Quantum Decoherence and Quantum-Holographic Information Processes: From Biomolecules to Biosystems

2006 ◽  
Vol 518 ◽  
pp. 485-490 ◽  
Author(s):  
D. Raković ◽  
M. Dugić ◽  
M.B. Plavšić ◽  
G. Keković ◽  
Irena Ćosić ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Energy State ◽  
Quantum Decoherence ◽  
Biomolecular Recognition ◽  
Control Mechanisms ◽  
Macroscopic Quantum ◽  
Resonant Recognition Model ◽  
Expression Of Genes ◽  
Quantum Approach ◽  
Quantum Ensemble

Our recently proposed quantum approach to biomolecular recognition processes is hereby additionally supported by biomolecular Resonant Recognition Model and by quantum-chemical theory of biomolecular non-radiative resonant transitions. Previously developed general quantumdecoherence framework for biopolymer conformational changes in very selective ligandproteins/ target-receptors key/lock biomolecular recognition processes (with electron-conformational coupling, giving rise to dynamical modification of many-electron energy-state hypersurface of the cellular quantum-ensemble ligand-proteins/target-receptors biomolecular macroscopic quantum system, with revealed possibility to consider cellular biomolecular recognition as a Hopfield-like quantum-holographic associative neural network) is further extended from nonlocal macroscopicquantum level of biological cell to nonlocal macroscopic-quantum level of biological organism, based on long-range coherent microwave excitations (as supported by macroscopic quantum-like microwave resonance therapy of the acupuncture system) - which might be of fundamental importance in understanding of underlying macroscopic quantum (quantum-holographic Hopfieldlike) control mechanisms of embryogenesis/ontogenesis and morphogenesis, and their backward influence on the expression of genes.

scholarly journals ssDNA-Functionalized Nanoceria: A Redox-Active Aptaswitch for Biomolecular Recognition

2016 ◽  
Vol 5 (7) ◽  
pp. 822-828 ◽  
Author(s):  
Gonca Bülbül ◽  
Akhtar Hayat ◽  
Silvana Andreescu
Keyword(s):  
Biomolecular Recognition ◽  
Redox Active

Novel Fluorescent Molecular Beacon DNA Probes for Biomolecular Recognition

2003 ◽  
Author(s):  
Kemin Wang ◽  
Jun Li ◽  
Xiaohong Fang ◽  
Sheldon Schuster ◽  
Marie Vicens ◽  
...  
Keyword(s):  
Molecular Beacon ◽  
Dna Probes ◽  
Biomolecular Recognition

High Sensitivity InSb Hall Effect Biosensor Platform for DNA Detection and Biomolecular Recognition Using Functionalized Magnetic Nanobeads

2005 ◽  
Vol 44 (No. 49) ◽  
pp. L1494-L1497 ◽  
Author(s):  
Kiyoshi Togawa ◽  
Hideaki Sanbonsugi ◽  
Adarsh Sandhu ◽  
Masanori Abe ◽  
Hiroki Narimatsu ◽  
...  
Keyword(s):  
Hall Effect ◽  
Dna Detection ◽  
High Sensitivity ◽  
Biomolecular Recognition ◽  
Magnetic Nanobeads

scholarly journals Local frustration determines loop opening during the catalytic cycle of an oxidoreductase

2019 ◽  
Author(s):  
Lukas L. Stelzl ◽  
Despoina A.I. Mavridou ◽  
Emmanuel Saridakis ◽  
Diego Gonzalez ◽  
Andrew J. Baldwin ◽  
...  
Keyword(s):  
Active Site ◽  
Binding Sites ◽  
Protein Function ◽  
Catalytic Cycle ◽  
Biomolecular Recognition ◽  
Competing Interactions ◽  
Protein Binding Sites ◽  
Loop Region ◽  
Cysteine Thiols ◽  
Small Chemical

AbstractLocal structural frustration, the existence of mutually exclusive competing interactions, may explain why some proteins are dynamic while others are rigid. Frustration is thought to underpin biomolecular recognition and the flexibility of protein binding sites. Here we show how a small chemical modification, the oxidation of two cysteine thiols to a disulfide bond, during the catalytic cycle of the N-terminal domain of the key bacterial oxidoreductase DsbD (nDsbD), introduces frustration ultimately influencing protein function. In oxidized nDsbD, local frustration disrupts the packing of the protective cap-loop region against the active site allowing loop opening. By contrast, in reduced nDsbD the cap loop is rigid, always protecting the active-site thiols from the oxidizing environment of the periplasm. Our results point towards an intricate coupling between the dynamics of the active-site cysteines and of the cap loop which modulates the association reactions of nDsbD with its partners resulting in optimized protein function.

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