1H NMR study of 2-methylimidazole binding to cytochrome c: a comprehensive investigation of the role of the methyl substituent on the ligand binding affinity and heme electronic structure in imidazole–cytochrome c complexes

2001 ◽  
pp. 1841-1845 ◽  
Author(s):  
Yong Yao ◽  
Chengmin Qian ◽  
Yibing Wu ◽  
Jun Hu ◽  
Wenxia Tang
Keyword(s):  
Electronic Structure ◽  
Cytochrome C ◽  
Ligand Binding ◽  
Binding Affinity ◽  
1H Nmr ◽  
Methyl Substituent ◽  
Comprehensive Investigation ◽  
Heme Electronic Structure ◽  
Nmr Study

Experimental Studies and Computational Modeling on Cytochrome C Reduction by Quercetin: the role of oxidability and binding affinity

2021 ◽  
pp. 130995
Author(s):  
Gabriel Zazeri ◽  
Ana Paula Ribeiro Povinelli ◽  
Nathalia M. Pavan ◽  
Daniella Romano de Carvalho ◽  
Carmen Lúcia Cardoso ◽  
...  
Keyword(s):  
Cytochrome C ◽  
Computational Modeling ◽  
Binding Affinity ◽  
Experimental Studies ◽  
Cytochrome C Reduction

scholarly journals Modulation of the heme electronic structure and cystathionine β-synthase activity by second coordination sphere ligands: The role of heme ligand switching in redox regulation

2009 ◽  
Vol 103 (5) ◽  
pp. 689-697 ◽  
Author(s):  
Sangita Singh ◽  
Peter Madzelan ◽  
Jay Stasser ◽  
Colin L. Weeks ◽  
Donald Becker ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Coordination Sphere ◽  
Redox Regulation ◽  
Heme Electronic Structure ◽  
Second Coordination Sphere

1H NMR Investigation of the Role of Intrinsic Heme versus Protein-Induced Rhombic Perturbations on the Electronic Structure of Low-Spin Ferrihemoproteins:  Effect of Heme Substituents on Heme Orientation in Myoglobin

1999 ◽  
Vol 121 (4) ◽  
pp. 835-843 ◽  
Author(s):  
Urszula Kolczak ◽  
Jon B. Hauksson ◽  
Nicolette L. Davis ◽  
Usha Pande ◽  
Jeffrey S. de Ropp ◽  
...  
Keyword(s):  
Electronic Structure ◽  
1H Nmr ◽  
Versus Protein

Role of the functional group position in producing viscoelasticity in micellar solutions: A 1H NMR study

2002 ◽  
Vol 5 (2) ◽  
pp. 131-134 ◽  
Author(s):  
Kabir-ud-Din ◽  
Sanjeev Kumar ◽  
Damyanti Sharma
Keyword(s):  
1H Nmr ◽  
Functional Group ◽  
Micellar Solutions ◽  
Group Position ◽  
Nmr Study

Exploring the Role of Water Molecules in the Ligand Binding Domain of PDE4B and PDE4D: Virtual Screening Based Molecular Docking of Some Active Scaffolds

2019 ◽  
Vol 15 (4) ◽  
pp. 334-366
Author(s):  
Priya Singh ◽  
Mitali Mishra ◽  
Shivangi Agarwal ◽  
Samaresh Sau ◽  
Arun K. Iyer ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Water Molecule ◽  
Ligand Binding ◽  
Binding Affinity ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Water Molecules ◽  
Docking Experiment

Background: The phosphodiesterase (PDE) is a superfamily represented by four genes: PDE4A, B,C, and D which cause the hydrolysis of phosphodiester bond of cAMP to yield inactive AMP. c-AMP catalyzing enzyme is predominant in inflammatory and immunomodulatory cells. Therapy to treat Chronic Obstructive Pulmonary Disease (COPD) with the use of PDE4 inhibitors is highly envisaged. Objective: A molecular docking experiment with large dataset of diverse scaffolds has been performed on PDE4 inhibitors to analyze the role of amino acid responsible for binding and activation of the secondary transmitters. Apart from the general docking experiment, the main focus was to discover the role of water molecules present in the ligand-binding domain. Methods: All the compounds were docked in the PDE4B and PDE4D active cavity to produce the free binding energy scores and spatial disposition/orientation of chemical groups of inhibitors around the cavity. Under uniform condition, the experiments were carried out with and without water molecules in the LBD. The exhaustive study was carried out on the Autodock 4.2 software and explored the role of water molecules present in the binding domain. Results: In presence of water molecule, Roflumilast has more binding affinity (-8.48 Kcal/mol with PDE4B enzyme and -8.91 Kcal/mol with PDE4D enzyme) and forms two hydrogen bonds with Gln443 and Glu369 and amino acid with PDE4B and PDE4D enzymes respectively. While in absence of water molecule its binding affinity has decreased (-7.3 Kcal/mol with PDE4B enzyme and -5.17 Kcal/mol with PDE4D enzyme) as well as no H-bond interactions were observed. Similar observation was made with clinically tested molecules. Conclusion: In protein-ligand binding interactions, appropriate selection of water molecules facilitated the ligand binding, which eventually enhances the efficiency as well as the efficacy of ligand binding.

Relevant role of Leu265 in helix VI of the angiotensin AT1 receptor in agonist binding and activity

2002 ◽  
Vol 80 (5) ◽  
pp. 426-430 ◽  
Author(s):  
Silvana Aparecida Alves Correa ◽  
Lucimar Pereira França ◽  
Claudio Miguel Costa-Neto ◽  
Laerte Oliveira ◽  
Antonio Cechelli Mattos Paiva ◽  
...  
Keyword(s):  
Angiotensin Ii ◽  
Ligand Binding ◽  
Binding Affinity ◽  
Transmembrane Domain ◽  
Inositol Phosphate ◽  
Chinese Hamster ◽  
Side Chain ◽  
Maximum Effect ◽  
Agonist Binding

The finding of critical residues for angiotensin II (AII) binding and receptor signalling in helices V and VI led us to assess if, in this region of the receptor, aliphatic side chains might play a role in the agonist-mediated mechanism. Two mutations of the angiotensin AT1 receptor were designed to explore a possible role of a leucine at two positions, Leu265 and Leu268. Thus two mutants, L265D and L268D, were prepared through single substitutions of Leu265, located in the C-terminal region of transmembrane VI (TM-VI), and Leu268, in the adjoining region of the third extracellular loop (EC-3), for an aspartyl residue, and were stably transfected into Chinese hamster ovary (CHO) cells. Ligand-binding experiments and the functional assays determining inositol phosphate (IP) production were performed in these cells expressing these mutants. No significant changes were found in the binding affinity for the ligands, AII, DuP753, and [Sar1Leu8]AII in the mutant L268D. Moreover, the relative potency and the maximum effect on IP production of this mutant were similar to those of the wild-type receptor. In contrast, L265D mutant AT1 receptor, located within the transmembrane domain, markedly decreased binding affinity and ability to stimulate phosphatidylinositol turnover. Our results suggest that the hydrophobic side chain of Leu265, at the C-terminal portion of the AT1's TM-VI, but not Leu268, which belongs to the EC-3 loop, might interact with the AII molecule. On the other side, the aliphatic side chain of Leu265 may be involved in the formation of the ligand binding sites through allosteric effects, thus helping to stabilize the receptor structure around the agonist binding site for full activity.Key words: angiotensin II, AT1 receptor, site-directed mutagenesis.

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