scholarly journals Influence of the H-site residue 108 on human glutathione transferase P1-1 ligand binding: Structure-thermodynamic relationships and thermal stability

2009 ◽  
Vol 18 (12) ◽  
pp. 2454-2470 ◽  
Author(s):  
Indalecio Quesada-Soriano ◽  
Lorien J. Parker ◽  
Alessandra Primavera ◽  
Juan M. Casas-Solvas ◽  
Antonio Vargas-Berenguel ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Ligand Binding ◽  
Glutathione Transferase ◽  
Thermodynamic Relationships ◽  
Binding Structure

scholarly journals Membrane Fluidity Modulates Thermal Stability and Ligand Binding of Cytochrome P4503A4 in Lipid Nanodiscs

Biochemistry ◽  
2016 ◽  
Vol 55 (45) ◽  
pp. 6258-6268 ◽  
Author(s):  
Wynton D. McClary ◽  
John P. Sumida ◽  
Michele Scian ◽  
Lorela Paço ◽  
William M. Atkins
Keyword(s):  
Thermal Stability ◽  
Ligand Binding ◽  
Membrane Fluidity ◽  
Lipid Nanodiscs

The Two-Domain NK1 Fragment of Plasminogen:  Folding, Ligand Binding, and Thermal Stability Profile†

Biochemistry ◽  
2002 ◽  
Vol 41 (10) ◽  
pp. 3302-3310 ◽  
Author(s):  
Justin T. Douglas ◽  
Priska D. von Haller ◽  
Marion Gehrmann ◽  
Miguel Llinás ◽  
Johann Schaller
Keyword(s):  
Thermal Stability ◽  
Ligand Binding

Chemical and Thermal Stability of Insulin: Effects of Zinc and Ligand Binding to the Insulin Zinc-Hexamer

2006 ◽  
Vol 23 (11) ◽  
pp. 2611-2620 ◽  
Author(s):  
Kasper Huus ◽  
Svend Havelund ◽  
Helle B. Olsen ◽  
Marco van de Weert ◽  
Sven Frokjaer
Keyword(s):  
Thermal Stability ◽  
Ligand Binding ◽  
Thermal Stability Of

scholarly journals A rush to explore protein–ligand electrostatic interaction energy with Charger

2021 ◽  
Vol 77 (10) ◽  
pp. 1292-1304 ◽  
Author(s):  
Vedran Vuković ◽  
Theo Leduc ◽  
Zoe Jelić-Matošević ◽  
Claude Didierjean ◽  
Frédérique Favier ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Interaction Energy ◽  
Electrostatic Interaction ◽  
Glutathione Transferase ◽  
Multipole Moment ◽  
Point Of View ◽  
Electrostatic Energy ◽  
Electron Densities ◽  
Acta Cryst ◽  
Ligand Interaction

The mutual penetration of electron densities between two interacting molecules complicates the computation of an accurate electrostatic interaction energy based on a pseudo-atom representation of electron densities. The numerical exact potential and multipole moment (nEP/MM) method is time-consuming since it performs a 3D integration to obtain the electrostatic energy at short interaction distances. Nguyen et al. [(2018), Acta Cryst. A74, 524–536] recently reported a fully analytical computation of the electrostatic interaction energy (aEP/MM). This method performs much faster than nEP/MM (up to two orders of magnitude) and remains highly accurate. A new program library, Charger, contains an implementation of the aEP/MM method. Charger has been incorporated into the MoProViewer software. Benchmark tests on a series of small molecules containing only C, H, N and O atoms show the efficiency of Charger in terms of execution time and accuracy. Charger is also powerful in a study of electrostatic symbiosis between a protein and a ligand. It determines reliable protein–ligand interaction energies even when both contain S atoms. It easily estimates the individual contribution of every residue to the total protein–ligand electrostatic binding energy. Glutathione transferase (GST) in complex with a benzophenone ligand was studied due to the availability of both structural and thermodynamic data. The resulting analysis highlights not only the residues that stabilize the ligand but also those that hinder ligand binding from an electrostatic point of view. This offers new perspectives in the search for mutations to improve the interaction between the two partners. A proposed mutation would improve ligand binding to GST by removing an electrostatic obstacle, rather than by the traditional increase in the number of favourable contacts.

scholarly journals The influence of N-acetylneuraminic acid on the properties of human orosomucoid

1986 ◽  
Vol 236 (1) ◽  
pp. 149-153 ◽  
Author(s):  
M L Friedman ◽  
J R Wermeling ◽  
H B Halsall
Keyword(s):  
Thermal Stability ◽  
Biological Activity ◽  
Fluorescence Spectroscopy ◽  
Ligand Binding ◽  
Protein Conformation ◽  
Acid Content ◽  
Acetylneuraminic Acid ◽  
Water Of Hydration ◽  
Hydrophobic Binding ◽  
A Charge

Little is known of the relationships that may exist among the three principal functionalities of glycoproteins. Orosomucoids of closely defined N-acetylneuraminic acid content were examined for evidence of influence of N-acetylneuraminic acid content on the physical properties of the glycoprotein. Fluorescence spectroscopy gave no indication of conformational change in the protein core upon desialylation. Small changes in the chromatographic partition coefficient, sigma, and thermal stability, Td, are interpreted to reflect loss of water of hydration and increased glycan stem-protein interaction without a major repositioning of the chains. Ligand-binding measurements indicate no alteration in the hydrophobic binding domain and a possible interaction between chlorpromazine and N-acetylneuraminic acid. All changes seen are progressive and occur through a region where changes in biological activity are not found. It is suggested that the dependence of biological activity on N-acetylneuraminic acid content in orosomucoid reflects, not coupled changes in protein conformation, but a charge-density-related interaction such that, below a contribution of four or five N-acetylneuraminic acid residues, activity is modified.

Linking the Structure and Thermal Stability of β-Galactoside-Binding Protein Galectin-1 to Ligand Binding and Dimerization Equilibria

Biochemistry ◽  
2010 ◽  
Vol 49 (35) ◽  
pp. 7652-7658 ◽  
Author(s):  
Santiago Di Lella ◽  
Marcelo A. Martí ◽  
Diego O. Croci ◽  
Carlos M. A. Guardia ◽  
Juan C. Díaz-Ricci ◽  
...  
Keyword(s):  
Thermal Stability ◽  
Ligand Binding ◽  
Binding Protein ◽  
Thermal Stability Of

scholarly journals Thermal stability, ligand binding and allergenicity data of Mus m 1.0102 allergen and its cysteine mutants

Data in Brief ◽  
2020 ◽  
Vol 29 ◽  
pp. 105355
Author(s):  
Elena Ferrari ◽  
Romina Corsini ◽  
Samuele E. Burastero ◽  
Fabio Tanfani ◽  
Alberto Spisni
Keyword(s):  
Thermal Stability ◽  
Ligand Binding

scholarly journals MDO: A Computational Protocol for Accurate Prediction of Full Flexibility Receptor-Ligand Binding Mode Structures

2021 ◽  
Author(s):  
Amar Y. Al-Ansi ◽  
Zijing Lin
Keyword(s):  
Ligand Binding ◽  
Success Rate ◽  
Md Simulation ◽  
Binding Mode ◽  
Structure Based Drug Design ◽  
Promising Tool ◽  
Local Sampling ◽  
Binding Structure ◽  
Computational Protocol ◽  
Oniom Calculations

Abstract Predicting the binding structure of bio-complex is essential for understanding its properties, functions, and mechanisms, but is rather difficult due to the huge sampling space involved. A new computational protocol, MDO, for finding the ligand binding structure is proposed. MDO consists of global sampling via MD simulation and clustering of the receptor configurations, local sampling via molecular docking and clustering of the ligand conformations, and binding structure optimization by the ONIOM (QM/QM) method. MDO is tested on 15 protein-ligand complexes with known accurate structures. The success rate of MDO predictions, with RMSD < 2 Å, is found to be 67%, substantially higher than the 40% success rate of conventional methods. The MDO success rate can be increased to 83% if the ONIOM calculations are applied only for the starting poses with ligands inside the binding cavities. The MDO protocol is a promising tool for the structure based drug design.

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