scholarly journals Development of Biomolecular Interfaces Constructed on the Frameworks of Huge, Hollow Spherical Complexes

2015 ◽  
Vol 65 (0) ◽  
pp. 30-37
Author(s):  
Sota Sato
Keyword(s):  
Biomolecular Interfaces

scholarly journals Design of Biomolecular Interfaces Using Liquid Crystals Containing Oligomeric Ethylene Glycol

2010 ◽  
Vol 20 (13) ◽  
pp. 2098-2106 ◽  
Author(s):  
Zhongqiang Yang ◽  
Jugal K. Gupta ◽  
Kenji Kishimoto ◽  
Yoshiko Shoji ◽  
Takashi Kato ◽  
...  
Keyword(s):  
Liquid Crystals ◽  
Ethylene Glycol ◽  
Biomolecular Interfaces

Biomolecular interfaces based on self-assembly and self-recognition form biosensors capable of recording molecular binding and release

Nanoscale ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 4987-4998 ◽  
Author(s):  
Xiao Hu ◽  
Anthony Guiseppi-Elie ◽  
Cerasela Zoica Dinu
Keyword(s):  
Self Assembly ◽  
Molecular Binding ◽  
Self Recognition ◽  
Biomolecular Interfaces ◽  
Cellular Components

Cellular components manipulated in a synthetic environment form a biosensor capable of evaluating association and dissociation as related to molecular self-recognition and self-assembly.

Surface Chemistry for Stable and Smart Molecular and Biomolecular Interfaces via Photochemical Grafting of Alkenes

2010 ◽  
Vol 43 (9) ◽  
pp. 1205-1215 ◽  
Author(s):  
Xiaoyu Wang ◽  
Elizabeth C. Landis ◽  
Ryan Franking ◽  
Robert J. Hamers
Keyword(s):  
Surface Chemistry ◽  
Biomolecular Interfaces ◽  
Photochemical Grafting

scholarly journals Local dynamics of proteins and DNA evaluated from crystallographic B-factors

2014 ◽  
Vol 70 (a1) ◽  
pp. C1513-C1513 ◽  
Author(s):  
Bohdan Schneider ◽  
Jean-Christophe Gelly ◽  
Alexandre de Brevern ◽  
Jiří Černý
Keyword(s):  
Amino Acids ◽  
Hydration Shell ◽  
Molecular Structures ◽  
Dna Dynamics ◽  
Dna Molecules ◽  
Local Dynamics ◽  
Protein Core ◽  
Biomolecular Interfaces ◽  
Characteristic Features ◽  
Better Than

Temperature displacement factors also known as B-factors provide information about local dynamics of atoms. Because dynamic behavior of biomolecules is as important as their static molecular structures we decided to analyze B-factors in almost a thousand non-redundant crystal structures of protein-DNA complexes from a well-curated dataset described in Schneider et al. Nucleic Acids Research, 42 (2014). Biopolymer residues, amino acids and nucleotides, were classified according to their molecular neighborhood as solvent-accessible, solvent-inaccessible (buried, i. e. forming the protein core), or lying at protein-protein or protein-DNA interfaces. In addition, water molecules were labeled as solely bound to the biopolymer surface as the first hydration shell or as water bridges binding protein and DNA molecules. Distributions of scaled B-factors for these types of residues confirmed several expected features of protein and DNA dynamics but they also revealed some surprising facts. Solvent-accessible amino acids have B-factors larger than residues at both biomolecular interfaces and amino acids forming protein core are restricted in their movement the most. A really unique feature of the buried amino acids is that their side chains are restricted in their movements more than the main chains. Protein interior is therefore packed significantly better than protein-protein or protein-DNA interfaces. Low values of B-factors of the waters bridging protein and DNA molecules contrast with extremely high values of DNA phosphates. Characteristic features distinguishing different types of residues quickly vanish in structures with lower resolution and some of the observed trends are a likely consequence of improper refinement protocols that may need rectifying. Acknowledgments. This study was supported by BIOCEV CZ.1.05/1.1.00/02.0109 from the ERDF and by grant P305/12/1801 from the Czech Science Foundation.

scholarly journals Large Scale Synthesis of Native Turn and Helix Mimics Stabilized by a Generic Hydrogen Bond Surrogate

2021 ◽  
Author(s):  
Erode N Prabhakaran ◽  
Sunit Pal ◽  
Ankur Kumar ◽  
Shifali Mahajan
Keyword(s):  
Large Scale ◽  
Synthetic Approach ◽  
Size Dependent ◽  
Hydrogen Bond Surrogate ◽  
C Terminus ◽  
Postgraduate Level ◽  
Biomolecular Interfaces ◽  
Recognition Elements ◽  
High Yields ◽  
Mitsunobu Reactions

Abstract Short Turn and Helix mimics frequently represent molecular recognition surfaces perturbing bio-relevant protein-biomolecular interfaces. Generic methods that can stabilize short peptides into turns or helices by retaining all recognition elements, have tremendous applications in drug discovery. Here, a versatile modular synthetic protocol is presented for stabilizing turns and helices of different sizes by replacing their ring-closing hydrogen bonds with a generic three-carbon covalent surrogate. Two Fukuyama-Mitsunobu reactions insert the surrogate between desired residues in high yields and purity. Coupling with turn size-dependent oligopeptides containing both sterically restricted and non-coded residues, followed by macrolactamization yield a variety of stabilized turns. Short peptide extensions at the C-terminus of these turns yield stabilized 310-helices and α-helices. This solution-phase synthetic approach provides combinatorial access to libraries of stabilized turns and helices with all their native residues retained, in >100 mmole scales, in about one week per stabilized mimic, to technicians with postgraduate level training.

Biomolecular Interfaces

2015 ◽  
Author(s):  
Ariel Fernández Stigliano
Keyword(s):  
Biomolecular Interfaces

Infrared spectroscopy for characterization of biomolecular interfaces

2011 ◽  
pp. 57-82
Author(s):  
Robert J. Hamers ◽  
Xiaoyu Wang ◽  
Ryan Franking ◽  
Rose Ruther ◽  
Courtney Stavis
Keyword(s):  
Infrared Spectroscopy ◽  
Biomolecular Interfaces
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