scholarly journals Gripping stuff: Allosteric ribozymes

2006 ◽  
Vol 28 (2) ◽  
pp. 17-20
Author(s):  
Andrea Rentmeister ◽  
Michael Famulok
Keyword(s):  
Catalytic Activity ◽  
Molecular Recognition ◽  
Ligand Binding ◽  
Small Molecules ◽  
Real Time ◽  
Molecular Interactions ◽  
Rational Design ◽  
Signal Generation ◽  
Selection Strategies ◽  
Different Types

Allosteric ribozymes combine the features of ligand-binding aptamers with the catalytic activity of ribozymes and can be generated by rational design or diverse selection strategies. Their activity can be controlled by different types of effectors, ranging from small molecules to oligonucleotides and proteins. This direct coupling of molecular recognition to signal generation in real time allows the generation of versatile reporters that can be applied to report molecular interactions.

Azacyanines as Novel Topoisomerase II Alpha Inhibitors

2020 ◽  
Vol 17 (5) ◽  
pp. 666-671 ◽  
Author(s):  
Sercan Guloglu ◽  
Fahriye Nur Kirmaci ◽  
Özgül Persil Çetinkol ◽  
Mehrdad Forough ◽  
Aybuke Gulkaya
Keyword(s):  
Catalytic Activity ◽  
Small Molecules ◽  
Topoisomerase Ii ◽  
Chemotherapeutic Agents ◽  
Agarose Gel ◽  
Topoisomerase Iiα ◽  
Topoisomerase Ii Alpha ◽  
Topological Constraints ◽  
Different Types

Introduction: Topoisomerase II alpha (Topo IIα) has become one of the extensively exploited targets in chemotherapy due to its role in regulating the topological constraints of DNA during replication and transcription. Small molecules targeting Topo IIα’s activity such as etoposide (VP-16) and doxorubicin are extensively used in the treatment of many different types of cancer. Objective: Here, the effects of three small molecules, named as azacyanines, on Topo IIα have been assessed. Methods: In-vitro Topoisomerase IIα drug screening kit and agarose gel imaging were used for the assessment of Topo IIα’s activity. Results: Our results revealed that all the azacyanines investigated decreased the catalytic activity of Topo IIα dramatically. More importantly, the decrease in the catalytic activity of Topo IIα in the presence of azacyanines was higher than the presence of VP-16, which is a commercially available chemotherapy drug. Upon further investigation, it has been observed that Azamethyl’s catalytic inhibition of Topo IIα was concentration dependent and the catalytic activity of Topo IIα was almost completely abolished in the presence of 100.0 μM of Azamethyl. Conclusion: These findings reveal the potential of azacyanines as effective Topo IIα inhibitors and chemotherapeutic agents.

In the Quest for a Stable Triplet State in Small Polyaromatic Hydrocarbons : An In-Silico Tool for Rational Design and Prediction

2019 ◽  
Author(s):  
Madhumita Rano ◽  
Sumanta K Ghosh ◽  
Debashree Ghosh
Keyword(s):  
Triplet State ◽  
Small Molecules ◽  
In Silico ◽  
Qualitative Agreement ◽  
Rational Design ◽  
Polyaromatic Hydrocarbons ◽  
Spin Hamiltonian ◽  
Spin Frustration ◽  
Computationally Efficient ◽  
High Level

<div>Combining the roles of spin frustration and geometry of odd and even numbered rings in polyaromatic hydrocarbons (PAHs), we design small molecules that show exceedingly small singlet-triplet gaps and stable triplet ground states. Furthermore, a computationally efficient protocol with a model spin Hamiltonian is shown to be capable of qualitative agreement with respect to high level multireference calculations and therefore, can be used for fast molecular discovery and screening.</div>

scholarly journals Real-time observation of tetrapyrrole binding to an engineered bacterial phytochrome

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yusaku Hontani ◽  
Mikhail Baloban ◽  
Francisco Velazquez Escobar ◽  
Swetta A. Jansen ◽  
Daria M. Shcherbakova ◽  
...  
Keyword(s):  
Real Time ◽  
Rational Design ◽  
Near Infrared ◽  
Fluorescent Proteins ◽  
Covalent Bond ◽  
Binding Pocket ◽  
Tissue Imaging ◽  
Covalent Attachment ◽  
Time Resolved

AbstractNear-infrared fluorescent proteins (NIR FPs) engineered from bacterial phytochromes are widely used for structural and functional deep-tissue imaging in vivo. To fluoresce, NIR FPs covalently bind a chromophore, such as biliverdin IXa tetrapyrrole. The efficiency of biliverdin binding directly affects the fluorescence properties, rendering understanding of its molecular mechanism of major importance. miRFP proteins constitute a family of bright monomeric NIR FPs that comprise a Per-ARNT-Sim (PAS) and cGMP-specific phosphodiesterases - Adenylyl cyclases - FhlA (GAF) domain. Here, we structurally analyze biliverdin binding to miRFPs in real time using time-resolved stimulated Raman spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations. Biliverdin undergoes isomerization, localization to its binding pocket, and pyrrolenine nitrogen protonation in <1 min, followed by hydrogen bond rearrangement in ~2 min. The covalent attachment to a cysteine in the GAF domain was detected in 4.3 min and 19 min in miRFP670 and its C20A mutant, respectively. In miRFP670, a second C–S covalent bond formation to a cysteine in the PAS domain occurred in 14 min, providing a rigid tetrapyrrole structure with high brightness. Our findings provide insights for the rational design of NIR FPs and a novel method to assess cofactor binding to light-sensitive proteins.

scholarly journals Enhancing spatial perception through sound: mapping human movements into MIDI

2021 ◽  
Author(s):  
Bernardo Breve ◽  
Stefano Cirillo ◽  
Mariano Cuofano ◽  
Domenico Desiato
Keyword(s):  
Real Time ◽  
User Study ◽  
Spatial Perception ◽  
Human Movements ◽  
Different Types ◽  
Real Time Tracking ◽  
People’S Perceptions ◽  
Novel Algorithm

AbstractGestural expressiveness plays a fundamental role in the interaction with people, environments, animals, things, and so on. Thus, several emerging application domains would exploit the interpretation of movements to support their critical designing processes. To this end, new forms to express the people’s perceptions could help their interpretation, like in the case of music. In this paper, we investigate the user’s perception associated with the interpretation of sounds by highlighting how sounds can be exploited for helping users in adapting to a specific environment. We present a novel algorithm for mapping human movements into MIDI music. The algorithm has been implemented in a system that integrates a module for real-time tracking of movements through a sample based synthesizer using different types of filters to modulate frequencies. The system has been evaluated through a user study, in which several users have participated in a room experience, yielding significant results about their perceptions with respect to the environment they were immersed.

scholarly journals Digital Twin: Origin to Future

2021 ◽  
Vol 4 (2) ◽  
pp. 36
Author(s):  
Maulshree Singh ◽  
Evert Fuenmayor ◽  
Eoin Hinchy ◽  
Yuansong Qiao ◽  
Niall Murray ◽  
...  
Keyword(s):  
Real Time ◽  
Remote Access ◽  
Physical Entity ◽  
Industrial Systems ◽  
Digital Twin ◽  
Planning Optimization ◽  
Different Types ◽  
Pros And Cons ◽  
Number Of Publications ◽  
Digital Shadow

Digital Twin (DT) refers to the virtual copy or model of any physical entity (physical twin) both of which are interconnected via exchange of data in real time. Conceptually, a DT mimics the state of its physical twin in real time and vice versa. Application of DT includes real-time monitoring, designing/planning, optimization, maintenance, remote access, etc. Its implementation is expected to grow exponentially in the coming decades. The advent of Industry 4.0 has brought complex industrial systems that are more autonomous, smart, and highly interconnected. These systems generate considerable amounts of data useful for several applications such as improving performance, predictive maintenance, training, etc. A sudden influx in the number of publications related to ‘Digital Twin’ has led to confusion between different terminologies related to the digitalization of industries. Another problem that has arisen due to the growing popularity of DT is a lack of consensus on the description of DT as well as so many different types of DT, which adds to the confusion. This paper intends to consolidate the different types of DT and different definitions of DT throughout the literature for easy identification of DT from the rest of the complimentary terms such as ‘product avatar’, ‘digital thread’, ‘digital model’, and ‘digital shadow’. The paper looks at the concept of DT since its inception to its predicted future to realize the value it can bring to certain sectors. Understanding the characteristics and types of DT while weighing its pros and cons is essential for any researcher, business, or sector before investing in the technology.

scholarly journals Binding Ensembles of p53-MDM2 Peptide Inhibitors by Combining Bayesian Inference and Atomistic Simulations

Molecules ◽  
2021 ◽  
Vol 26 (1) ◽  
pp. 198
Author(s):  
Lijun Lang ◽  
Alberto Perez
Keyword(s):  
Bayesian Inference ◽  
Virtual Screening ◽  
Statistical Mechanics ◽  
Small Molecules ◽  
Rational Design ◽  
Driving Forces ◽  
Peptide Inhibitors ◽  
Atomistic Simulations ◽  
Binding Mechanism ◽  
Intrinsically Disordered

Designing peptide inhibitors of the p53-MDM2 interaction against cancer is of wide interest. Computational modeling and virtual screening are a well established step in the rational design of small molecules. But they face challenges for binding flexible peptide molecules that fold upon binding. We look at the ability of five different peptides, three of which are intrinsically disordered, to bind to MDM2 with a new Bayesian inference approach (MELD × MD). The method is able to capture the folding upon binding mechanism and differentiate binding preferences between the five peptides. Processing the ensembles with statistical mechanics tools depicts the most likely bound conformations and hints at differences in the binding mechanism. Finally, the study shows the importance of capturing two driving forces to binding in this system: the ability of peptides to adopt bound conformations (ΔGconformation) and the interaction between interface residues (ΔGinteraction).

Studies on the Molecular Interactions between Plant-Derived Protein Zein and Small Molecules

2021 ◽  
Author(s):  
Yajing Wang ◽  
Fangzhi Cao ◽  
Mingchen Ge ◽  
Shiqun Lv ◽  
Jun Gao
Keyword(s):  
Small Molecules ◽  
Molecular Interactions

scholarly journals Catalytic activity of metals in heterogeneous Fenton-like oxidation of wastewater contaminants: a review

2021 ◽  
Author(s):  
Sajid Hussain ◽  
Eleonora Aneggi ◽  
Daniele Goi
Keyword(s):  
Catalytic Activity ◽  
Emerging Contaminants ◽  
Influencing Factor ◽  
Oxidation Products ◽  
Metal Oxidation ◽  
Heterogeneous Fenton ◽  
Solution Ph ◽  
Copper Manganese ◽  
Different Types ◽  
Metallic Catalyst

AbstractInnovations in water technology are needed to solve challenges of climate change, resource shortages, emerging contaminants, urbanization, sustainable development and demographic changes. In particular, conventional techniques of wastewater treatment are limited by the presence of poorly biodegradable organic matter. Alternatively, recent Fenton, Fenton-like and hybrid processes appear successful for cleaning of different types of liquid wastewaters. Here, we review the application of metallic catalyst-H2O2 systems in the heterogeneous Fenton process. Each metallic catalyst-H2O2 system has unique redox properties due to metal oxidation state. Solution pH is a major influencing factor. Catalysts made of iron and cerium form stable complexes with oxidation products and H2O2, thus resulting in reduced activities. Copper forms transitory complexes with oxidation products, but copper catalytic activity is restored during the reaction. Silver and manganese do not form complexes. The catalyst performance for degradation and mineralization decreases in the order: manganese, copper, iron, silver, cerium, yet the easiness of practical application decreases in the order: copper, manganese, iron, silver, cerium.

scholarly journals How metallylenes activate small molecules

2021 ◽  
Vol 12 (12) ◽  
pp. 4526-4535
Author(s):  
Pascal Vermeeren ◽  
Michael T. Doppert ◽  
F. Matthias Bickelhaupt ◽  
Trevor A. Hamlin
Keyword(s):  
Small Molecules ◽  
Quantum Chemical ◽  
Rational Design ◽  
Chemical Analyses

Quantum chemical analyses reveal how model metallylene catalysts activate H2. This is the first step towards the rational design of metallylenes for the activation of small molecules and subsequent reactions.

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