scholarly journals Molecular dynamics approach for capturing calixarenes--proteins interactions: the case of cytochrome c

2020 ◽  
Author(s):  
Alessio Bartocci ◽  
florence szczepaniak ◽  
Tao Jiang ◽  
Natacha Gillet ◽  
Elise Dumont
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome C ◽  
Binding Sites ◽  
Supervised Machine Learning ◽  
Titration Calorimetry ◽  
X Ray ◽  
Poisson Boltzmann ◽  
Bond Network ◽  
Proteins Interactions ◽  
Detailed Picture

Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonatedcalix-[8]-arenes to cytochrome c. The binding sites prone to interactions with sulfonated calixarenescan be identified without prior knowledge of the X-ray structure, and the binding free energiesestimated by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) post-analysis arefound to be in neat agreement with the isothermal titration calorimetry (ITC) measurements The per-residuedecomposition reveals the detailed picture of this electrostatically-driven association and notably therole of the arginine R13 as a bridge residue between the two main anchoring sites. In addition,the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of an hydrogen bond network far from the binding sites, increasing the rigidity of theprotein.

scholarly journals Molecular dynamics approach for capturing calixarenes--proteins interactions: the case of cytochrome c

2020 ◽  
Author(s):  
Alessio Bartocci ◽  
florence szczepaniak ◽  
Tao Jiang ◽  
Natacha Gillet ◽  
Elise Dumont
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome C ◽  
Binding Sites ◽  
Supervised Machine Learning ◽  
Titration Calorimetry ◽  
X Ray ◽  
Poisson Boltzmann ◽  
Bond Network ◽  
Proteins Interactions ◽  
Detailed Picture

Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonatedcalix-[8]-arenes to cytochrome c. The binding sites prone to interactions with sulfonated calixarenescan be identified without prior knowledge of the X-ray structure, and the binding free energiesestimated by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) post-analysis arefound to be in neat agreement with the isothermal titration calorimetry (ITC) measurements The per-residuedecomposition reveals the detailed picture of this electrostatically-driven association and notably therole of the arginine R13 as a bridge residue between the two main anchoring sites. In addition,the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of an hydrogen bond network far from the binding sites, increasing the rigidity of theprotein.

scholarly journals Capturing the Supramolecular Association of Calixarenes onto Proteins Relying on Molecular Dynamics Simulations: The Case of Cytochrome C

2020 ◽  
Author(s):  
Alessio Bartocci ◽  
florence szczepaniak ◽  
Tao Jiang ◽  
Natacha Gillet ◽  
Elise Dumont
Keyword(s):  
Molecular Dynamics ◽  
Cytochrome C ◽  
Binding Sites ◽  
Supervised Machine Learning ◽  
Titration Calorimetry ◽  
X Ray ◽  
Poisson Boltzmann ◽  
Bond Network ◽  
Dynamics Simulations ◽  
Detailed Picture

Here, we propose a molecular dynamics investigation of the supramolecular association of sulfonatedcalix-[8]-arenes to cytochrome c. The binding sites prone to interactions with sulfonated calixarenescan be identified without prior knowledge of the X-ray structure, and the binding free energiesestimated by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) post-analysis arefound to be in neat agreement with the isothermal titration calorimetry (ITC) measurements The per-residuedecomposition reveals the detailed picture of this electrostatically-driven association and notably therole of the arginine R13 as a bridge residue between the two main anchoring sites. In addition,the analysis of the residue behavior by means of a supervised machine learning protocol unveils the formation of an hydrogen bond network far from the binding sites, increasing the rigidity of theprotein.

Reaction mechanism and phospholipid structures of bovine heart cytochrome c oxidase

2005 ◽  
Vol 33 (5) ◽  
pp. 934-937 ◽  
Author(s):  
S. Yoshikawa
Keyword(s):  
Hydrogen Bond ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Hydrogen Bond Network ◽  
X Ray ◽  
Bovine Heart ◽  
O2 Reduction ◽  
Bond Network ◽  
Electron Reduction ◽  
Enzyme Functions

Bovine heart cytochrome c oxidase is a large multi-component membrane protein containing several phospholipids. X-ray structures of this enzyme at high resolution, determined recently, show a trigonal planar structure of CuB site in the O2 reduction site, which could contribute critically to the four-electron reduction of O2 bound at haem a3, and a hydrogen bond network, through which the proton pump is driven by haem a. The possible roles of phospholipids in the enzyme functions are discussed.

scholarly journals Structure of a highly acidic β-lactamase from the moderate halophileChromohalobactersp. 560 and the discovery of a Cs+-selective binding site

2015 ◽  
Vol 71 (3) ◽  
pp. 541-554 ◽  
Author(s):  
Shigeki Arai ◽  
Yasushi Yonezawa ◽  
Nobuo Okazaki ◽  
Fumiko Matsumoto ◽  
Chie Shibazaki ◽  
...  
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Nuclear Power ◽  
Specific Binding ◽  
Radioactive Isotopes ◽  
Titration Calorimetry ◽  
X Ray ◽  
X Ray Crystallography ◽  
Specific Binding Sites ◽  
Enzymatic Function

Environmentally friendly absorbents are needed for Sr2+and Cs+, as the removal of the radioactive Sr2+and Cs+that has leaked from the Fukushima Nuclear Power Plant is one of the most important problems in Japan. Halophilic proteins are known to have many acidic residues on their surface that can provide specific binding sites for metal ions such as Cs+or Sr2+. The crystal structure of a halophilic β-lactamase fromChromohalobactersp. 560 (HaBLA) was determined to resolutions of between 1.8 and 2.9 Å in space groupP31using X-ray crystallography. Moreover, the locations of bound Sr2+and Cs+ions were identified by anomalous X-ray diffraction. The location of one Cs+-specific binding site was identified in HaBLA even in the presence of a ninefold molar excess of Na+(90 mMNa+/10 mMCs+). From an activity assay using isothermal titration calorimetry, the bound Sr2+and Cs+ions do not significantly affect the enzymatic function of HaBLA. The observation of a selective and high-affinity Cs+-binding site provides important information that is useful for the design of artificial Cs+-binding sites that may be useful in the bioremediation of radioactive isotopes.

X-ray absorption and molecular dynamics study of cation binding sites in the purple membrane

2007 ◽  
Vol 67 (2) ◽  
pp. 360-374 ◽  
Author(s):  
Francesc Sepulcre ◽  
Arnau Cordomí ◽  
M. Grazia Proietti ◽  
Juan J. Perez ◽  
Joaquin García ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Binding Sites ◽  
Purple Membrane ◽  
Cation Binding ◽  
X Ray ◽  
X Ray Absorption

scholarly journals Hydrophobicity with atomic resolution: Steady-state and ultrafast X-ray absorption and molecular dynamics studies

2012 ◽  
Vol 85 (1) ◽  
pp. 53-60 ◽  
Author(s):  
Thomas J. Penfold ◽  
Christopher J. Milne ◽  
Ivano Tavernelli ◽  
Majed Chergui
Keyword(s):  
Molecular Dynamics ◽  
Md Simulations ◽  
Solvation Shell ◽  
Water Molecules ◽  
Time Resolved ◽  
X Ray ◽  
Bond Network ◽  
Hydrophobic Solvation ◽  
X Ray Absorption ◽  
Small Anisotropy

Static and time-resolved X-ray absorption spectroscopy (XAS) is used to probe the solvent shell structure around iodide and iodine. In particular, we characterize the changes observed upon electron abstraction of aqueous iodide, which reflects the transition from hydrophilic to hydrophobic solvation after impulsive electron abstraction from iodide. The static spectrum of aqueous iodide, which is analyzed using quantum mechanical/molecular mechanics (QM/MM) molecular dynamics (MD) simulations, indicates that the hydrogens of the closest water molecules point toward the iodide, as expected for hydrophilic solvation. In addition, these simulations demonstrate a small anisotropy in the solvent shell. Following electron abstraction, most of the water molecules move away from iodine, while one comes closer to form a complex with it that survives for 3–4 ps. This lifetime is governed by the reorganization of the main solvation shell, basically the time it takes for the water molecules to reform a hydrogen bond network in the hydrophobic solvation shell.

Real-Space X-Ray Pair Distribution Function Analysis and Molecular-Dynamics Modelling of Diflunisal Channel Hydrates

2020 ◽  
Author(s):  
Anuradha Pallipurath ◽  
Francesco Civati ◽  
Jonathan Skelton ◽  
Dean Keeble ◽  
Clare Crowley ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Structural Dynamics ◽  
First Principles ◽  
Pair Distribution Function ◽  
Function Analysis ◽  
Real Space ◽  
X Ray ◽  
Dynamics Modelling ◽  
Dynamics Simulations

X-ray pair distribution function analysis is used with first-principles molecular dynamics simulations to study the co-operative H<sub>2</sub>O binding, structural dynamics and host-guest interactions in the channel hydrate of diflunisal.

X-ray Crystallographic Study of Alkylammonium Anthracene-9-carboxylates as a Model for Fibrous Structure of Binary Anthracene Salt Gels

2004 ◽  
Vol 69 (6) ◽  
pp. 1292-1300 ◽  
Author(s):  
Tahahiro Tani ◽  
Kazuki Sada ◽  
Masatsugu Ayabe ◽  
Yuya Iwashita ◽  
Takanori Kishida ◽  
...  
Keyword(s):  
Alkyl Chain ◽  
Columnar Structure ◽  
Hydrogen Bond Network ◽  
One Dimensional ◽  
X Ray ◽  
Crystallographic Study ◽  
Alkylammonium Salts ◽  
Bond Network ◽  
Fibrous Assemblies ◽  
Long Alkyl Chain

Crystal structure of hexylammonium anthracene-9-carboxylate was investigated. The salt was arranged by a one-dimensional hydrogen bond network to form a columnar structure in the crystalline state. This columnar structure should be the model of fibrous assemblies in the organogels of anthracene-9-carboxylate alkylammonium salts having a long alkyl chain.

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