scholarly journals BODIPY- and Porphyrin-Based Sensors for Recognition of Amino Acids and Their Derivatives

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4523 ◽  
Author(s):  
Marco Farinone ◽  
Karolina Urbańska ◽  
Miłosz Pawlicki
Keyword(s):  
Amino Acids ◽  
Molecular Recognition ◽  
Biological Systems ◽  
Direct Interaction ◽  
Covalent Bonding ◽  
Molecular Probes ◽  
Chiral Discrimination ◽  
Living Matter ◽  
Diverse Range ◽  
Widespread Occurrence

Molecular recognition is a specific non-covalent and frequently reversible interaction between two or more systems based on synthetically predefined character of the receptor. This phenomenon has been extensively studied over past few decades, being of particular interest to researchers due to its widespread occurrence in biological systems. In fact, a straightforward inspiration by biological systems present in living matter and based on, e.g., hydrogen bonding is easily noticeable in construction of molecular probes. A separate aspect also incorporated into the molecular recognition relies on the direct interaction between host and guest with a covalent bonding. To date, various artificial systems exhibiting molecular recognition and based on both types of interactions have been reported. Owing to their rich optoelectronic properties, chromophores constitute a broad and powerful class of receptors for a diverse range of substrates. This review focuses on BODIPY and porphyrin chromophores as probes for molecular recognition and chiral discrimination of amino acids and their derivatives.

scholarly journals Rapid Organocatalytic Chirality Analysis of Amines, Amino Acids, Alcohols, Amino Alcohols and Diols with Achiral Iso(thio)cyanate Probes

2021 ◽  
Author(s):  
Eryn Nelson ◽  
Jeffrey S. S. K. Formen ◽  
Christian Wolf
Keyword(s):  
Amino Acids ◽  
Absolute Configuration ◽  
Rapid Determination ◽  
Amino Alcohols ◽  
Enantioselective Synthesis ◽  
Widespread Occurrence ◽  
Chiral Compounds ◽  
New Methods ◽  
The Absolute

The widespread occurrence and significance of chiral compounds does not only require new methods for their enantioselective synthesis but also efficient tools that allow rapid determination of the absolute configuration,...

scholarly journals Adventures in molecular recognition. The ins and outs of templating

2000 ◽  
Vol 72 (12) ◽  
pp. 2265-2274 ◽  
Author(s):  
Jeremy K. M. Sanders
Keyword(s):  
Molecular Recognition ◽  
Combinatorial Chemistry ◽  
Biological Systems ◽  
Design Approach ◽  
Supramolecular Systems ◽  
Disulfide Exchange ◽  
Dynamic Combinatorial Chemistry ◽  
Evolutionary Features ◽  
Selection Approach ◽  
Porphyrin Dimers

Two different approaches are described for the creation of supramolecular systems potentially capable of recognition and catalysis. Using the design approach, we have been able to accelerate and influence two different Diels­Alder reactions within the cavities of porphyrin dimers and trimers; this is templating from the outside inwards. The selection approach is a synthetic chemical attempt to capture some of the key evolutionary features of biological systems: dynamic combinatorial chemistry is used to create equilibrating mixtures of potential receptors, and then a template is used to select and amplify the desired system. Five potential reactions for such dynamic chemistry are discussed: base-catalyzed transesterification, hydrazone exchange, disulfide exchange, alkene metathesis, and Pd-catalyzed allyl exchange, and preliminary templating results (inside outwards) are presented.

Chiral discrimination of Dns- and unmodified d,l-amino acids by copper(II) complexes of terdentate ligands in high-performance liquid chromatography

1998 ◽  
Vol 829 (1-2) ◽  
pp. 101-113 ◽  
Author(s):  
Gianni Galaverna ◽  
Roberto Corradini ◽  
Arnaldo Dossena ◽  
Emma Chiavaro ◽  
Rosangela Marchelli ◽  
...  
Keyword(s):  
Amino Acids ◽  
High Performance Liquid Chromatography ◽  
Liquid Chromatography ◽  
High Performance ◽  
Chiral Discrimination

scholarly journals Supervised Learning Model Predicts Protein Adsorption to Nanotubes

2021 ◽  
Author(s):  
Rebecca L Pinals ◽  
Nicholas Ouassil ◽  
Jackson Travis Del Bonis-O'Donnell ◽  
Jeffrey W Wang ◽  
Markita P Landry
Keyword(s):  
Amino Acids ◽  
Protein Adsorption ◽  
Biological Systems ◽  
Protein Corona ◽  
Engineered Nanoparticles ◽  
Mass Spectrometry Data ◽  
In Vitro Synthesis ◽  
Intractable Problem

Engineered nanoparticles are advantageous for numerous biotechnology applications, including biomolecular sensing and delivery. However, testing the compatibility and function of nanotechnologies in biological systems requires a heuristic approach, where unpredictable biofouling often prevents effective implementation. Such biofouling is the result of spontaneous protein adsorption to the nanoparticle surface, forming the "protein corona" and altering the physicochemical properties, and thus intended function, of the nanotechnology. To better apply engineered nanoparticles in biological systems, herein, we develop a random forest classifier (RFC) trained with proteomic mass spectrometry data that identifies which proteins adsorb to nanoparticles. We model proteins that populate the corona of a single-walled carbon nanotube (SWCNT)-based optical nanosensor. We optimize the classifier and characterize the classifier performance against other models. To evaluate the predictive power of our model, we then apply the classifier to rapidly identify and experimentally validate proteins with high binding affinity to SWCNTs. Using protein properties based solely on amino acid sequence, we further determine protein features associated with increased likelihood of SWCNT binding: proteins with high content of solvent-exposed glycine residues and non-secondary structure-associated amino acids. Furthermore, proteins with high leucine residue content and beta-sheet-associated amino acids are less likely to form the SWCNT protein corona. The classifier presented herein provides an important tool to undertake the otherwise intractable problem of predicting protein-nanoparticle interactions, which is needed for more rapid and effective translation of nanobiotechnologies from in vitro synthesis to in vivo use.

PATTERNS OF HYDROPHOBICITY FOUND IN THE FIRST AND SECOND TRANSMEMBRANE DOMAINS OF SOLUTE TRANSPORTERS SUGGEST A POSSIBLE ROLE IN NASCENT PROTEIN ANCHORING AND ORGANIZATION

2011 ◽  
Vol 09 (04) ◽  
pp. 471-488 ◽  
Author(s):  
STEVE HODGKINSON ◽  
WOLFGANG P. KASCHKA
Keyword(s):  
Amino Acids ◽  
Alpha Helix ◽  
Spatial Arrangement ◽  
Transmembrane Domains ◽  
Integral Membrane Proteins ◽  
Challenging Problem ◽  
Functional Protein ◽  
Spatial Organisation ◽  
Diverse Range ◽  
Solute Transporters

Solute transporters (STs) are an important subgroup of integral membrane proteins that facilitate the translocation of a diverse range of solutes such as sugars, amino acids, and neurotransmitters across cell membranes. Sequence analysis indicates that STs possess multiple stretches of hydrophobic-rich amino acids that are organized into the transmembrane domains (TMDs) of the functional protein, but exactly how the correct spatial arrangement of these domains is achieved remains a challenging problem. We hypothesized that perhaps differences in interdomain hydrophobicity might play some role in this process. To test this hypothesis, we generated a heptadic model of the alpha helix and mapped the average hydrophobicities (coaxial) and hydrophobic moments (radial) of 108 TMDs found in 9 different human ST proteins. Our results, taken together with earlier work from other groups, suggest that spatial patterns of hydrophobicity found in TMDs 1 and 2 are consistent with a role for these domains in the initial anchoring of the nascent ST protein to the endoplasmic reticulum (ER), as it emerges from the ribosome complex and perhaps in the subsequent spatial organisation of STs.

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