Synthetic Protein Surface Domains as Bioactive Stationary Phases

1993 ◽  
pp. 277-312 ◽  
Author(s):  
T. William Hutchens ◽  
Tai-Tung Yip
Keyword(s):  
Stationary Phases ◽  
Protein Surface ◽  
Synthetic Protein ◽  
Surface Domains

A Template-Assembled Synthetic Protein Surface Mimetic of the von Willebrand Factor A1 domain Inhibits Botrocetin-Induced Platelet Aggregation

ChemBioChem ◽  
2004 ◽  
Vol 5 (6) ◽  
pp. 856-864 ◽  
Author(s):  
Jacques Hauert ◽  
Jimena Fernandez-Carneado ◽  
Olivier Michielin ◽  
Stéphane Mathieu ◽  
Daniel Grell ◽  
...  
Keyword(s):  
Platelet Aggregation ◽  
Von Willebrand Factor ◽  
Protein Surface ◽  
Synthetic Protein ◽  
A1 Domain ◽  
Von Willebrand ◽  
Willebrand Factor

Synthetic metal-binding protein surface domains for metal ion-dependent interaction chromatography

1992 ◽  
Vol 604 (1) ◽  
pp. 125-132 ◽  
Author(s):  
T.William Hutchens ◽  
Randall W. Nelson ◽  
Chee Ming Li ◽  
Tai-Tung Yip
Keyword(s):  
Metal Binding ◽  
Metal Ion ◽  
Binding Protein ◽  
Protein Surface ◽  
Metal Binding Protein ◽  
Synthetic Metal ◽  
Surface Domains ◽  
Dependent Interaction

scholarly journals Protein Surface Printer for Exploring Protein Domains

2020 ◽  
Author(s):  
Yang Li ◽  
Baofu Qiao ◽  
Monica Olvera de la Cruz
Keyword(s):  
Cell Receptor ◽  
Atomistic Simulations ◽  
Protein Surface ◽  
Multiple Functions ◽  
Binding Domains ◽  
Protein Functions ◽  
Surface Domains ◽  
Positively Charged ◽  
Spike Proteins

AbstractThe surface of proteins is vital in determining protein functions. Herein, a program, Protein Surface Printer(PSP), is built that performs multiple functions in quantifying protein surface domains. Two proteins, PETase and cytochrome P450, are used to validate that the program supports atomistic simulations with different combinations of programs and force fields. A case study is conducted on the structural analysis of the spike proteins of SARS-CoV-2 and SARS-CoV, and the human cell receptor ACE2. Although the surface domains of both spike proteins are highly similar, their receptor binding domains(RBDs) and the O-linked glycan domains are structurally different. Statistically, the outer surface of ACE2 displays less correlation with the RBD of SARS-CoV-2 than that of SARS-CoV. The O-linked glycan domain of SARS-CoV-2 is highly positively charged, which may promote binding to negatively charged human cells. Our program paves the way for an accurate understanding of protein binding for aggregation and ligand recognition.

scholarly journals Water follows polar and nonpolar protein surface domains

2019 ◽  
Vol 116 (39) ◽  
pp. 19274-19281 ◽  
Author(s):  
Baofu Qiao ◽  
Felipe Jiménez-Ángeles ◽  
Trung Dac Nguyen ◽  
Monica Olvera de la Cruz
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Interactions ◽  
Protein Solubility ◽  
Protein Surface ◽  
Protein Surfaces ◽  
Charged Amino Acids ◽  
Average Water ◽  
Surface Domains ◽  
Positively Charged

The conformation of water around proteins is of paramount importance, as it determines protein interactions. Although the average water properties around the surface of proteins have been provided experimentally and computationally, protein surfaces are highly heterogeneous. Therefore, it is crucial to determine the correlations of water to the local distributions of polar and nonpolar protein surface domains to understand functions such as aggregation, mutations, and delivery. By using atomistic simulations, we investigate the orientation and dynamics of water molecules next to 4 types of protein surface domains: negatively charged, positively charged, and charge-neutral polar and nonpolar amino acids. The negatively charged amino acids orient around 98% of the neighboring water dipoles toward the protein surface, and such correlation persists up to around 16 Å from the protein surface. The positively charged amino acids orient around 94% of the nearest water dipoles against the protein surface, and the correlation persists up to around 12 Å. The charge-neutral polar and nonpolar amino acids are also orienting the water neighbors in a quantitatively weaker manner. A similar trend was observed in the residence time of the nearest water neighbors. These findings hold true for 3 technically important enzymes (PETase, cytochrome P450, and organophosphorus hydrolase). Our results demonstrate that the water−amino acid degree of correlation follows the same trend as the amino acid contribution in proteins solubility, namely, the negatively charged amino acids are the most beneficial for protein solubility, then the positively charged amino acids, and finally the charge-neutral amino acids.

Advances in profiling of natural products by triple detection techniques combined with super critical CO2 mobile phases and Sub-2 µm stationary phases

Planta Medica ◽  
2015 ◽  
Vol 81 (16) ◽  
Author(s):  
D Rodriguez Cabaleiro ◽  
P Hong ◽  
G Isaac ◽  
J Yuk ◽  
K Yu ◽  
...  
Keyword(s):  
Natural Products ◽  
Stationary Phases ◽  
Detection Techniques ◽  
Mobile Phases
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