Molecular level picture of the interplay between pH and phosphate binding at the goethite–water interface

2020 ◽  
Vol 22 (45) ◽  
pp. 26509-26524 ◽  
Author(s):  
Ashour A. Ahmed ◽  
Stella Gypser ◽  
Dirk Freese ◽  
Peter Leinweber ◽  
Oliver Kühn
Keyword(s):  
Soil Ph ◽  
Theoretical Approach ◽  
Molecular Level ◽  
Water Interface ◽  
Phosphate Binding ◽  
Binding Motifs ◽  
Binding Process ◽  
Substantial Role

The present experimental–theoretical approach describes at a molecular level how the soil pH plays a substantial role in controlling the mechanism of the P binding process and the formed P binding motifs at the goethite/water interface.

Infrared spectroscopic characterization of phosphate binding at the goethite–water interface

2019 ◽  
Vol 21 (8) ◽  
pp. 4421-4434 ◽  
Author(s):  
Ashour A. Ahmed ◽  
Stella Gypser ◽  
Peter Leinweber ◽  
Dirk Freese ◽  
Oliver Kühn
Keyword(s):  
Theoretical Study ◽  
Spectroscopic Characterization ◽  
Water Interface ◽  
Phosphate Binding ◽  
Molecular Binding ◽  
Ft Ir ◽  
Periodic Dft Calculations ◽  
Binding Mechanisms ◽  
Ft Ir Spectroscopy

The molecular binding mechanisms for the adsorbed phosphate at the goethite–water interface have been explored via a joint experimental/theoretical study. This study involved performing sorption experiments, characterization by FT-IR spectroscopy, and performing periodic DFT calculations.

QM/MM simulations of organic phosphorus adsorption at the diaspore–water interface

2019 ◽  
Vol 21 (44) ◽  
pp. 24316-24325 ◽  
Author(s):  
Prasanth B. Ganta ◽  
Oliver Kühn ◽  
Ashour A. Ahmed
Keyword(s):  
Surface Water ◽  
Molecular Mechanisms ◽  
Organic Phosphorus ◽  
Md Simulations ◽  
Available Phosphorus ◽  
Water Interface ◽  
Mineral Surfaces ◽  
Soil Mineral ◽  
Phosphorus Adsorption ◽  
Binding Process

The available phosphorus for plants is mainly affected by the strong binding of phosphates to soil mineral surfaces. Here, we have investigated the molecular mechanisms for this binding process at the surface–water interface by QM/MM MD simulations.

scholarly journals Polyphosphate:AMP Phosphotransferase as a Polyphosphate-Dependent Nucleoside Monophosphate Kinase in Acinetobacter johnsonii 210A

2005 ◽  
Vol 187 (5) ◽  
pp. 1859-1865 ◽  
Author(s):  
Toshikazu Shiba ◽  
Hiromichi Itoh ◽  
Atsushi Kameda ◽  
Keiju Kobayashi ◽  
Yumi Kawazoe ◽  
...  
Keyword(s):  
Genomic Dna ◽  
Kinase Activity ◽  
Phosphate Binding ◽  
Binding Motifs ◽  
E Coli ◽  
Acinetobacter Johnsonii ◽  
Dna Library ◽  
Genomic Dna Library ◽  
Coupled Reactions ◽  
Coupled Reaction

ABSTRACT We have cloned the gene for polyphosphate:AMP phosphotransferase (PAP), the enzyme that catalyzes phosphorylation of AMP to ADP at the expense of polyphosphate [poly(P)] in Acinetobacter johnsonii 210A. A genomic DNA library was constructed in Escherichia coli, and crude lysates of about 6,000 clones were screened for PAP activity. PAP activity was evaluated by measuring ATP produced by the coupled reactions of PAP and purified E. coli poly(P) kinases (PPKs). In this coupled reaction, PAP produces ADP from poly(P) and AMP, and the resulting ADP is converted to ATP by PPK. The isolated pap gene (1,428 bp) encodes a protein of 475 amino acids with a molecular mass of 55.8 kDa. The C-terminal region of PAP is highly homologous with PPK2 homologs isolated from Pseudomonas aeruginosa PAO1. Two putative phosphate-binding motifs (P-loops) were also identified. The purified PAP enzyme had not only strong PAP activity but also poly(P)-dependent nucleoside monophosphate kinase activity, by which it converted ribonucleoside monophosphates and deoxyribonucleoside monophosphates to ribonucleoside diphosphates and deoxyribonucleoside diphosphates, respectively. The activity for AMP was about 10 times greater than that for GMP and 770 and about 1,100 times greater than that for UMP and CMP.

Understanding the Structure of Hydrophobic Surfactants at the Air/Water Interface from Molecular Level

Langmuir ◽  
2014 ◽  
Vol 30 (46) ◽  
pp. 13815-13822 ◽  
Author(s):  
Li Zhang ◽  
Zhipei Liu ◽  
Tao Ren ◽  
Pan Wu ◽  
Jia-Wei Shen ◽  
...  
Keyword(s):  
Molecular Level ◽  
Water Interface ◽  
Air Water Interface

scholarly journals Domains in the 1α Dynein Heavy Chain Required for Inner Arm Assembly and Flagellar Motility in Chlamydomonas

1999 ◽  
Vol 146 (4) ◽  
pp. 801-818 ◽  
Author(s):  
Steven H. Myster ◽  
Julie A. Knott ◽  
Katrina M. Wysocki ◽  
Eileen O'Toole ◽  
Mary E. Porter
Keyword(s):  
Heavy Chain ◽  
Motor Domain ◽  
Flagellar Motility ◽  
Phosphate Binding ◽  
Binding Motifs ◽  
Phototactic Behavior ◽  
Dynein Heavy Chain ◽  
Dynein Motor ◽  
Mutant Phenotypes

Flagellar motility is generated by the activity of multiple dynein motors, but the specific role of each dynein heavy chain (Dhc) is largely unknown, and the mechanism by which the different Dhcs are targeted to their unique locations is also poorly understood. We report here the complete nucleotide sequence of the Chlamydomonas Dhc1 gene and the corresponding deduced amino acid sequence of the 1α Dhc of the I1 inner dynein arm. The 1α Dhc is similar to other axonemal Dhcs, but two additional phosphate binding motifs (P-loops) have been identified in the NH2- and COOH-terminal regions. Because mutations in Dhc1 result in motility defects and loss of the I1 inner arm, a series of Dhc1 transgenes were used to rescue the mutant phenotypes. Motile cotransformants that express either full-length or truncated 1α Dhcs were recovered. The truncated 1α Dhc fragments lacked the dynein motor domain, but still assembled with the 1β Dhc and other I1 subunits into partially functional complexes at the correct axoneme location. Analysis of the transformants has identified the site of the 1α motor domain in the I1 structure and further revealed the role of the 1α Dhc in flagellar motility and phototactic behavior.

Mixing at the molecular level of two designed azobenzene-linked amphiphiles at the air-water interface

1989 ◽  
Vol 173 (2) ◽  
pp. L135-L138 ◽  
Author(s):  
Xinfei Xu ◽  
Masanao Era ◽  
Tetsuo Tsutsui ◽  
Shogo Saito
Keyword(s):  
Molecular Level ◽  
Water Interface ◽  
Air Water Interface

scholarly journals Infrared Spectroscopic Characterization of Phosphate Binding at the Goethite-Water Interface

2018 ◽  
Author(s):  
Ashour Ahmed ◽  
Stella Gypser ◽  
Peter Leinweber ◽  
Dirk Freese ◽  
Oliver Kühn
Keyword(s):  
Ir Spectra ◽  
Interaction Energy ◽  
Phosphate Adsorption ◽  
Water Molecules ◽  
Hydroxyl Groups ◽  
Water Interface ◽  
Binding Mechanism ◽  
Phosphate Binding ◽  
Covalent Bonds ◽  
Surface Plane

<div><div><div><p>The interaction between phosphates and soil mineral surfaces, such as Fe- and Al-(oxyhydr)oxides, plays a crucial role in the P immobilization and thus its availability for plants. The reactions of phosphates with Fe-hydroxides and especially goethite have been studied extensively. But a molecular-level picture about the phosphate binding mechanism at the goethite-water interface is still lacking. Therefore, in the current contribution we have explored the molecular binding mechanism for the adsorbed phosphate at the goethite–water interface by performing sorption kinetics experiments for orthophosphate and characterizing the adsorbed species by FT-IR spectroscopy. In parallel, periodic DFT calculations have been performed to explore the interaction mechanism as well as to calculate the IR spectra for monodentate (M) and bidentate (B) orthophosphate complexes at two different goethite surface planes (010 and 100) in the presence of water. In general, our interaction energy results give evidence that the mono-protonated B phosphate complex is more favored to be formed at the goethite–water interface although the M motif could exist as a minor fraction. Moreover, it was found that water plays an important role in controlling the phosphate adsorption process at the goethite surfaces. The interfacial water molecules form H-bonds (HBs) with the phosphate as well as with the goethite surface atoms. Further, some water molecules form covalent bonds with goethite Fe atoms while others dissociate at the surface to protons and hydroxyl groups. The present theoretical assignment of IR spectra introduces a benchmark for characterizing experimental IR data for the adsorbed KH2PO4 species at the goethite–water interface. In particular, IR spectra of the mono-protonated (2O+1Fe) B complex at the 010 goethite surface plane and the M complex at the 100 goethite surface plane were found to be consistent with the experimental data. In order to explore the role of different abundancies of surface planes and binding motifs, IR spectra obtained from weighted averages have been analyzed. Results confirmed the above conclusions drawn from interaction energy calculations.</p></div></div></div>

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