Increased pH-sensitivity of protein binding to lipid membranes through the electrostatic-hydrogen bond switch

2013 ◽  
Vol 169 ◽  
pp. 9-18 ◽  
Author(s):  
Stephan Loew ◽  
Edgar E. Kooijman ◽  
Sylvio May
Keyword(s):  
Hydrogen Bond ◽  
Protein Binding ◽  
Lipid Membranes ◽  
Ph Sensitivity

scholarly journals Hydrogen-bond network and pH sensitivity in human transthyretin

2013 ◽  
Vol 20 (6) ◽  
pp. 834-837 ◽  
Author(s):  
Takeshi Yokoyama ◽  
Mineyuki Mizuguchi ◽  
Yuko Nabeshima ◽  
Katsuhiro Kusaka ◽  
Taro Yamada ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Ph Sensitivity ◽  
Hydrogen Bond Network ◽  
Bond Network

scholarly journals Hepatitis C virus core protein binding to lipid membranes: the role of domains 1 and 2

2008 ◽  
Vol 15 (5) ◽  
pp. 346-356 ◽  
Author(s):  
A. J. Pérez-Berná ◽  
A. S. Veiga ◽  
M. A. R. B. Castanho ◽  
J. Villalaín
Keyword(s):  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Protein Binding ◽  
Lipid Membranes ◽  
Core Protein ◽  
Virus Core

A Learning Method for Predicting the Binding Strength in RNA-Protein Complexes

2014 ◽  
Vol 644-650 ◽  
pp. 5291-5294
Author(s):  
Tong Wang ◽  
Jian Xin Xue ◽  
Tian Xia
Keyword(s):  
Hydrogen Bond ◽  
Protein Binding ◽  
Rna Binding ◽  
Protein Complexes ◽  
Van Der Waals ◽  
Van Der Waals Interactions ◽  
Protein Binding Sites ◽  
Binding Strength ◽  
Rna Protein Complexes ◽  
Score Matrix

Hydrogen bond and van der Waals interactions between protein and RNA are important. We have developed a set of algorithms for predicting RNA-Protein binding strength by analyzing hydrogen bond and van der Waals interactions between protein and RNA. Firstly, we must identify the RNA-Protein binding sites. In this study, we use features including Pseudo Position-Specific Score Matrix (PsePSSM) computed by PSI-BLAST and Dipeptide Composition (DC) as feature vectors. Then, the classifier is employed to identify the residues that interact with RNA in RNA-binding protein. Then, take into account the number of amino acids hydrogen bonding and van der Waals forces to any nucleotide, the binding strength is calculated. Finally, fuzzy sets method is adopted to predict the binding strength is strong or weak. Our experiments show that the above methods are used effectively to deal with this complicated problem of predicting RNA-protein binding strength.

Hydrogen-bond network and pH sensitivity in transthyretin: Neutron crystal structure of human transthyretin

2012 ◽  
Vol 177 (2) ◽  
pp. 283-290 ◽  
Author(s):  
Takeshi Yokoyama ◽  
Mineyuki Mizuguchi ◽  
Yuko Nabeshima ◽  
Katsuhiro Kusaka ◽  
Taro Yamada ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Ph Sensitivity ◽  
Hydrogen Bond Network ◽  
Bond Network

scholarly journals Hydrogen-bond Network and pH Sensitivity in Transthyretin

hamon ◽  
2013 ◽  
Vol 23 (2) ◽  
pp. 142-145
Author(s):  
Takeshi Yokoyama ◽  
Mineyuki Mizuguchi ◽  
Katsuhiro Kusaka ◽  
Ichiro Tanaka ◽  
Nobuo Niimura
Keyword(s):  
Hydrogen Bond ◽  
Ph Sensitivity ◽  
Hydrogen Bond Network ◽  
Bond Network

scholarly journals Exploring the strength of a hydrogen bond as a function of steric environment using 1,2-azaborine ligands and engineered T4 lysozyme receptors

2019 ◽  
Vol 17 (29) ◽  
pp. 7002-7006 ◽  
Author(s):  
Yao Liu ◽  
Shih-Yuan Liu
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Protein Binding ◽  
Bonding Strength ◽  
T4 Lysozyme ◽  
The Relationship ◽  
Hydrogen Bonding Strength

The relationship between the steric demand of the ligand and hydrogen bonding strength in the context of ligand–protein binding is revealed using engineered T4 lysozymes as the model biomacromolecules and 1,2-azaborines as ligands.

Dynamic Analysis of Backbone-Hydrogen-Bond Propensity for Protein Binding and Drug Design

2016 ◽  
pp. 317-338
Author(s):  
C Menéndez ◽  
S Accordino ◽  
J Rodriguez ◽  
D Gerbino ◽  
G Appignanesi
Keyword(s):  
Hydrogen Bond ◽  
Drug Design ◽  
Protein Binding ◽  
Dynamic Analysis ◽  
Backbone Hydrogen Bond
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