scholarly journals Towards the sequence-specific multivalent molecular recognition of cyclodextrin oligomers

2014 ◽  
Vol 10 ◽  
pp. 2428-2440 ◽  
Author(s):  
Michael Kurlemann ◽  
Bart Jan Ravoo
Keyword(s):  
Molecular Recognition ◽  
Titration Calorimetry ◽  
Biological Processes ◽  
Sequence Specificity ◽  
New Materials ◽  
Guest Molecules ◽  
Binding Motifs ◽  
Specific Recognition ◽  
Recognition Motifs ◽  
Complementary Binding

Sequence-specific multivalent molecular recognition has been recognized to play a major role in biological processes. Furthermore, sequence-specific recognition motifs have been used in various artificial systems in the last years, e.g., to emulate biological processes or to build up new materials with highly specific recognition domains. In this article, we present the preparation of cyclodextrin (CD)-based strands and complementary and non-complementary strands modified with guest molecules and the investigation of their complexation behavior towards each other by isothermal titration calorimetry (ITC). As complementary binding motifs n-butyl and α-CD and adamantane and β-CD were selected. It was found that it is possible to realize sequence-specific molecular recognition by the use of host–guest chemistry, but the recognition motifs as well as the linkages have to be chosen very carefully. In the case of trivalent systems one adamantane moiety must be included to induce preferred formation of 1:1 adducts. Due to the too weak interaction between n-butyl and α-CD these systems have a negative chelate cooperativity and open adducts are preferentially formed. As soon as two adamantane moieties are present, the complementary systems have a positive chelate cooperativity and double-stranded structures are favored over open adducts. In this system the n-butyl moiety provides insufficient discrimination towards α- and β-CD and no sequence specificity is observed. By the combination of three adamantane moieties sequence specificity can be generated. Exclusively with the complementary CD sequence double-stranded structures are formed, with non-complementary strands aggregates of higher stoichiometry are generated.

scholarly journals Systematic identification of recognition motifs for the hub protein LC8

2019 ◽  
Vol 2 (4) ◽  
pp. e201900366 ◽  
Author(s):  
Nathan Jespersen ◽  
Aidan Estelle ◽  
Nathan Waugh ◽  
Norman E Davey ◽  
Cecilia Blikstad ◽  
...  
Keyword(s):  
Phage Display Library ◽  
Titration Calorimetry ◽  
Cellular Regulation ◽  
Dynamic Binding ◽  
Binding Motifs ◽  
Dimer Interface ◽  
Binding Partners ◽  
Critical Residues ◽  
Recognition Motifs ◽  
Systematic Identification

Hub proteins participate in cellular regulation by dynamic binding of multiple proteins within interaction networks. The hub protein LC8 reversibly interacts with more than 100 partners through a flexible pocket at its dimer interface. To explore the diversity of the LC8 partner pool, we screened for LC8 binding partners using a proteomic phage display library composed of peptides from the human proteome, which had no bias toward a known LC8 motif. Of the identified hits, we validated binding of 29 peptides using isothermal titration calorimetry. Of the 29 peptides, 19 were entirely novel, and all had the canonical TQT motif anchor. A striking observation is that numerous peptides containing the TQT anchor do not bind LC8, indicating that residues outside of the anchor facilitate LC8 interactions. Using both LC8-binding and nonbinding peptides containing the motif anchor, we developed the “LC8Pred” algorithm that identifies critical residues flanking the anchor and parses random sequences to predict LC8-binding motifs with ∼78% accuracy. Our findings significantly expand the scope of the LC8 hub interactome.

Biomimetic Extracellular Vesicles Embedded with Black Phosphorus for Molecular Recognition-Guided Biomineralization

2018 ◽  
Author(s):  
Yingqian Wang ◽  
Xiaoxia Hu ◽  
Lingling Zhang ◽  
Chunli Zhu ◽  
Jie Wang ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Extracellular Vesicles ◽  
Inorganic Phosphate ◽  
Physiological Activity ◽  
Medical Engineering ◽  
Matrix Vesicles ◽  
Black Phosphorus ◽  
Photothermal Effect ◽  
Biological Processes ◽  
Extracellular Environment

Extracellular vesicles (EVs) are involved in the regulation of cell physiological activity and the reconstruction of extracellular environment. Matrix vesicles (MVs) are a type of EVs, and they participate in the regulation of cell mineralization. Herein, bioinspired MVs embedded with black phosphorus are functionalized with cell-specific aptamer (denoted as Apt-bioinspired MVs) for stimulating biomineralization. The aptamer can direct bioinspired MVs to targeted cells, and the increasing concentration of inorganic phosphate originated from the black phosphorus can facilitate cell biomineralization. The photothermal effect of the Apt-bioinspired MVs also positively affects mineralization. In addition, the Apt-bioinspired MVs display outstanding bone regeneration performance. Considering the excellent behavior of the Apt-bioinspired MVs for promoting biomineralization, our strategy provides a way of designing bionic tools for studying the mechanisms of biological processes and advancing the development of medical engineering.<br>

Aromatic interactions in Glycochemistry: from molecular recognition to catalysis

2021 ◽  
Vol 28 ◽  
Author(s):  
Andrés González Santana ◽  
Laura Díaz-Casado ◽  
Laura Montalvillo ◽  
Ester Jiménez-Moreno ◽  
Enrique Mann ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Transition States ◽  
Carbohydrate Binding ◽  
Potential Influence ◽  
Chemical Structures ◽  
Receptor Complexes ◽  
Binding Domains ◽  
Aromatic Interactions ◽  
Aromatic Complexes ◽  
Recognition Motifs

: Aromatic platforms are ubiquitous recognition motifs occurring in protein carbohydrate binding domains (CBDs), RNA receptors and enzymes. They stabilize the glycoside/receptor complexes by participating in stacking CH/ interactions with either the - or - face of the corresponding pyranose units. In addition, the role played by aromatic units in the stabilization of glycoside cationic transition states has started being recognized in recent years. Extensive studies carried out during the last decade have allowed to dissect the main contributing forces that stabilize the carbohydrate/aromatic complexes, while helping delineate not only the standing relationship between the glycoside/aromatic chemical structures and the strength of this interaction, but also their potential influence on glycoside reactivity.

A modular approach for molecular recognition by zinc dipicolinate complexes

2015 ◽  
Vol 44 (32) ◽  
pp. 14411-14423 ◽  
Author(s):  
Krapa Shankar ◽  
Alexander M. Kirillov ◽  
Jubaraj B. Baruah
Keyword(s):  
Molecular Recognition ◽  
Modular Approach ◽  
Guest Molecules

Recognition of 4-nitrophenol guest molecules by stacking and H-bonding interactions with a 4,4′-bipyridinium zinc dipicolinate host was found and investigated in detail.

Nanostructured sensors for molecular recognition

1995 ◽  
Vol 353 (1703) ◽  
pp. 333-354 ◽  
Keyword(s):  
Molecular Recognition ◽  
Chemical Sensors ◽  
Surface Structures ◽  
Chemical Information ◽  
New Materials ◽  
Top Down ◽  
Molecular Scale ◽  
The Common ◽  
Nanostructured Sensors ◽  
Physical And Chemical

A survey is given on typical ‘top-down’ and ‘bottom-up’ approaches to design nanostructured sensors which monitor different physical and chemical quantities. Particular emphasis is put on new materials and transducers for molecular recognition by chemical sensors. These convert chemical information into electronic signals by making use of suitable ‘key-lock’ structures. This requires the control of surface structures of chemically sensitive materials down to the molecular scale under thermodynamically or kinetically controlled conditions. This in turn requires the molecular understanding of sensor mechanisms which is deduced from comparative microscopic, spectroscopic and sensor test studies on ‘prototype materials’. Selected case studies illustrate the common mechanisms of molecular recognition with electron conductors, ion conductors, mixed conductors, molecular cages, polymers and selected biomolecular function units.

Molecular recognition between oligopeptides and nucleic acids. DNA sequence specificity and binding properties of an acridine-linked netropsin hybrid ligand

1990 ◽  
Vol 3 (1) ◽  
pp. 26-35 ◽  
Author(s):  
Christian Bailly ◽  
Nicole Helbecque ◽  
Jean-Pierre Hénichart ◽  
Pierre Colson ◽  
Claude Houssier ◽  
...  
Keyword(s):  
Molecular Recognition ◽  
Nucleic Acids ◽  
Dna Sequence ◽  
Sequence Specificity ◽  
Binding Properties ◽  
Dna Sequence Specificity
Sign in / Sign up

Export Citation Format

Share Document