scholarly journals A dynamic combinatorial library for biomimetic recognition of dipeptides in water

2020 ◽  
Vol 16 ◽  
pp. 1588-1595
Author(s):  
Florian Klepel ◽  
Bart Jan Ravoo
Keyword(s):  
Combinatorial Library ◽  
Building Blocks ◽  
Biological Processes ◽  
Powerful Method ◽  
Small Peptides ◽  
Selective Binding ◽  
Binding Motifs ◽  
Artificial Receptors ◽  
Dynamic Combinatorial Library

Small peptides are involved in countless biological processes. Hence selective binding motifs for peptides can be powerful tools for labeling or inhibition. Finding those binding motifs, especially in water which competes for intermolecular H-bonds, poses an enormous challenge. A dynamic combinatorial library can be a powerful method to overcome this issue. We previously reported artificial receptors emerging form a dynamic combinatorial library of peptide building blocks. In this study we aimed to broaden this scope towards recognition of small peptides. Employing CXC peptide building blocks, we found that cyclic dimers of oxidized CFC bind to the aromatic peptides FF and YY (K ≈ 229–702 M−1), while AA binds significantly weaker (K ≈ 65–71 M−1).

scholarly journals π-Stacking Stopper-Macrocycle Stabilized Dynamically Interlocked [2]Rotaxanes

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4704
Author(s):  
Sing-Ming Chan ◽  
Fung-Kit Tang ◽  
Ching-Yau Lam ◽  
Chak-Shing Kwan ◽  
Sam C. K. Hau ◽  
...  
Keyword(s):  
Crystal Structures ◽  
Thermodynamic Stability ◽  
Combinatorial Library ◽  
Aromatic Rings ◽  
Interlocked Molecules ◽  
X Ray ◽  
Π Stacking ◽  
Dynamic Combinatorial Library

The synthesis of mechanically interlocked molecules is valuable due to their unique topologies. With π-stacking intercomponent interaction, e.g., phenanthroline and anthracene, novel [2]rotaxanes have been synthesized by dynamic imine clipping reaction. Their X-ray crystal structures indicate the π-stackings between the anthracene moiety (stopper) on the thread and the (hetero)aromatic rings at the macrocycle of the rotaxanes. Moreover, the length of glycol chains affects the extra π-stacking intercomponent interactions between the phenyl groups and the dimethoxy phenyl groups on the thread. Dynamic combinatorial library has shown at best 84% distribution of anthracene-threaded phenanthroline-based rotaxane, coinciding with the crystallography in that the additional π-stacking intercomponent interactions could increase the thermodynamic stability and selectivity of the rotaxanes.

scholarly journals Reversed Proteolysis—Proteases as Peptide Ligases

Catalysts ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 33
Author(s):  
Peter Goettig
Keyword(s):  
Serine Proteases ◽  
Academic Research ◽  
Building Blocks ◽  
Peptide Bond ◽  
Cysteine Proteases ◽  
Small Peptides ◽  
Natural Peptide ◽  
Peptide Esters ◽  
Natural Amino Acids

Historically, ligase activity by proteases was theoretically derived due to their catalyst nature, and it was experimentally observed as early as around 1900. Initially, the digestive proteases, such as pepsin, chymotrypsin, and trypsin were employed to perform in vitro syntheses of small peptides. Protease-catalyzed ligation is more efficient than peptide bond hydrolysis in organic solvents, representing control of the thermodynamic equilibrium. Peptide esters readily form acyl intermediates with serine and cysteine proteases, followed by peptide bond synthesis at the N-terminus of another residue. This type of reaction is under kinetic control, favoring aminolysis over hydrolysis. Although only a few natural peptide ligases are known, such as ubiquitin ligases, sortases, and legumains, the principle of proteases as general catalysts could be adapted to engineer some proteases accordingly. In particular, the serine proteases subtilisin and trypsin were converted to efficient ligases, which are known as subtiligase and trypsiligase. Together with sortases and legumains, they turned out to be very useful in linking peptides and proteins with a great variety of molecules, including biomarkers, sugars or building blocks with non-natural amino acids. Thus, these engineered enzymes are a promising branch for academic research and for pharmaceutical progress.

A “Dial-A-Receptor” Dynamic Combinatorial Library

2013 ◽  
Vol 125 (47) ◽  
pp. 12594-12598 ◽  
Author(s):  
Saleh Hamieh ◽  
Vittorio Saggiomo ◽  
Piotr Nowak ◽  
Elio Mattia ◽  
R. Frederick Ludlow ◽  
...  
Keyword(s):  
Combinatorial Library ◽  
Dynamic Combinatorial Library

Recent progress in transition-metal-catalyzed hydrocyanation of nonpolar alkenes and alkynes

2020 ◽  
Vol 18 (3) ◽  
pp. 391-399 ◽  
Author(s):  
Hongru Zhang ◽  
Xin Su ◽  
Kaiwu Dong
Keyword(s):  
Transition Metal ◽  
Recent Progress ◽  
Building Blocks ◽  
Powerful Method ◽  
Transition Metal Catalyzed ◽  
Metal Catalyzed

Hydrocyanation is a powerful method for the preparation of nitriles which are versatile building blocks for the synthesis of amines, acids and amides.

scholarly journals The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST)

2020 ◽  
Author(s):  
Vasundra Touré ◽  
Steven Vercruysse ◽  
Marcio Luis Acencio ◽  
Ruth C Lovering ◽  
Sandra Orchard ◽  
...  
Keyword(s):  
Molecular Interaction ◽  
Regulatory Networks ◽  
Building Blocks ◽  
Supplementary Information ◽  
Biological Processes ◽  
Causal Interaction ◽  
End User ◽  
Minimum Information ◽  
Causal Statement ◽  
In Cells

Abstract Motivation A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a so-called ‘causal interaction’ takes place. Causal interactions constitute the building blocks in our understanding of larger regulatory networks in cells. These causal interactions and the biological processes they enable (e.g. gene regulation) need to be described with a careful appreciation of the underlying molecular reactions. A proper description of this information enables archiving, sharing and reuse by humans and for automated computational processing. Various representations of causal relationships between biological components are currently used in a variety of resources. Results Here, we propose a checklist that accommodates current representations, called the Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). This checklist defines both the required core information, as well as a comprehensive set of other contextual details valuable to the end user and relevant for reusing and reproducing causal molecular interaction information. The MI2CAST checklist can be used as reporting guidelines when annotating and curating causal statements, while fostering uniformity and interoperability of the data across resources. Availability and implementation The checklist together with examples is accessible at https://github.com/MI2CAST/MI2CAST Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Single cell ecology

2019 ◽  
Vol 374 (1786) ◽  
pp. 20190076 ◽  
Author(s):  
Thomas A. Richards ◽  
Ramon Massana ◽  
Stefano Pagliara ◽  
Neil Hall
Keyword(s):  
Single Cell ◽  
Building Blocks ◽  
Biological Properties ◽  
Natural Environments ◽  
Biological Processes ◽  
Special Issue ◽  
New Approaches ◽  
New Methodologies ◽  
Biological Entities ◽  
The Way

Cells are the building blocks of life, from single-celled microbes through to multi-cellular organisms. To understand a multitude of biological processes we need to understand how cells behave, how they interact with each other and how they respond to their environment. The use of new methodologies is changing the way we study cells allowing us to study them on minute scales and in unprecedented detail. These same methods are allowing researchers to begin to sample the vast diversity of microbes that dominate natural environments. The aim of this special issue is to bring together research and perspectives on the application of new approaches to understand the biological properties of cells, including how they interact with other biological entities. This article is part of a discussion meeting issue ‘Single cell ecology’.

scholarly journals BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows

2019 ◽  
Vol 6 (1) ◽  
Author(s):  
Pau Andrio ◽  
Adam Hospital ◽  
Javier Conejero ◽  
Luis Jordá ◽  
Marc Del Pino ◽  
...  
Keyword(s):  
Building Blocks ◽  
Biological Processes ◽  
Software Management ◽  
Software Library ◽  
Management Tools ◽  
Software Packages ◽  
Biomolecular Simulations ◽  
Software And Hardware ◽  
A Chain ◽  
Workflow Orchestration

Abstract In the recent years, the improvement of software and hardware performance has made biomolecular simulations a mature tool for the study of biological processes. Simulation length and the size and complexity of the analyzed systems make simulations both complementary and compatible with other bioinformatics disciplines. However, the characteristics of the software packages used for simulation have prevented the adoption of the technologies accepted in other bioinformatics fields like automated deployment systems, workflow orchestration, or the use of software containers. We present here a comprehensive exercise to bring biomolecular simulations to the “bioinformatics way of working”. The exercise has led to the development of the BioExcel Building Blocks (BioBB) library. BioBB’s are built as Python wrappers to provide an interoperable architecture. BioBB’s have been integrated in a chain of usual software management tools to generate data ontologies, documentation, installation packages, software containers and ways of integration with workflow managers, that make them usable in most computational environments.

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