A Facile Ligand-Free Route to Calcium Carbonate Superstructures

2021 ◽  
Author(s):  
Jie Wang ◽  
Yukun Zhang ◽  
Wujun Chen ◽  
Qian Li ◽  
Yudong Wu ◽  
...  
Keyword(s):  
Calcium Carbonate ◽  
Ligand Binding ◽  
Shape Control ◽  
Binding Ability ◽  
Growth Profile ◽  
Wide Range ◽  
Ligand Free

Shape control has been achievable in a wide range of mesoscale materials, while for calcium carbonate (CaCO3) which has relatively low dispersibility, limited ligand-binding ability and therefore unmanageable growth profile,...

CarR, a MarR-family regulator from Corynebacterium glutamicum, modulated antibiotic and aromatic compound resistance

2019 ◽  
Vol 476 (21) ◽  
pp. 3141-3159 ◽  
Author(s):  
Meiru Si ◽  
Can Chen ◽  
Zengfan Wei ◽  
Zhijin Gong ◽  
GuiZhi Li ◽  
...  
Keyword(s):  
Stress Response ◽  
Ligand Binding ◽  
Corynebacterium Glutamicum ◽  
Conformational Changes ◽  
Cysteine Oxidation ◽  
Transcriptional Regulatory ◽  
Ligand Free ◽  
Redox Sensing

Abstract MarR (multiple antibiotic resistance regulator) proteins are a family of transcriptional regulators that is prevalent in Corynebacterium glutamicum. Understanding the physiological and biochemical function of MarR homologs in C. glutamicum has focused on cysteine oxidation-based redox-sensing and substrate metabolism-involving regulators. In this study, we characterized the stress-related ligand-binding functions of the C. glutamicum MarR-type regulator CarR (C. glutamicum antibiotic-responding regulator). We demonstrate that CarR negatively regulates the expression of the carR (ncgl2886)–uspA (ncgl2887) operon and the adjacent, oppositely oriented gene ncgl2885, encoding the hypothetical deacylase DecE. We also show that CarR directly activates transcription of the ncgl2882–ncgl2884 operon, encoding the peptidoglycan synthesis operon (PSO) located upstream of carR in the opposite orientation. The addition of stress-associated ligands such as penicillin and streptomycin induced carR, uspA, decE, and PSO expression in vivo, as well as attenuated binding of CarR to operator DNA in vitro. Importantly, stress response-induced up-regulation of carR, uspA, and PSO gene expression correlated with cell resistance to β-lactam antibiotics and aromatic compounds. Six highly conserved residues in CarR were found to strongly influence its ligand binding and transcriptional regulatory properties. Collectively, the results indicate that the ligand binding of CarR induces its dissociation from the carR–uspA promoter to derepress carR and uspA transcription. Ligand-free CarR also activates PSO expression, which in turn contributes to C. glutamicum stress resistance. The outcomes indicate that the stress response mechanism of CarR in C. glutamicum occurs via ligand-induced conformational changes to the protein, not via cysteine oxidation-based thiol modifications.

scholarly journals Protein-ligand free energies of binding from full-protein DFT calculations: convergence and choice of exchange-correlation functional

2021 ◽  
Author(s):  
Lennart Gundelach ◽  
Christofer S Tautermann ◽  
Thomas Fox ◽  
Chris-Kriton Skylaris
Keyword(s):  
Drug Discovery ◽  
Ligand Binding ◽  
Dft Calculations ◽  
Quantum Mechanical ◽  
Free Energies ◽  
Ligand Interaction ◽  
Exchange Correlation ◽  
Ligand Free ◽  
Protein Ligand Interaction ◽  
Binding Free Energies

The accurate prediction of protein-ligand binding free energies with tractable computational methods has the potential to revolutionize drug discovery. Modeling the protein-ligand interaction at a quantum mechanical level, instead of...

Interaction between 2-(p-toluidino)-6-naphthalenesulfonic acid sodium salt (TNS) and β-lactoglobulin

2016 ◽  
Vol 94 (8) ◽  
pp. 680-686
Author(s):  
Huiqing Li ◽  
Jing Wei ◽  
Youming Dong ◽  
Zhiyue Yu
Keyword(s):  
Ligand Binding ◽  
Sodium Salt ◽  
Stable Complex ◽  
Sodium Dodecylbenzene Sulfonate ◽  
Ph Change ◽  
Hydrophobic Domain ◽  
Acid Sodium Salt ◽  
Wide Range ◽  
Β Lactoglobulin ◽  
Small Ligands

The major bovine milk protein β-lactoglobulin (β-LG), a member of the lipocalin superfamily, can bind a wide range of ligands and act as a transporter. In the present study, the combination of the hydrophobic molecule 2-(p-toluidino)-6-naphthalenesulfonic acid sodium salt (TNS) with β-LG was analyzed using fluorescence spectroscopy and AutoDock modeling to discern the major binding sites of the protein and to determine the capacity of other small ligands to bind with β-LG by utilizing TNS as a reference. The experimental data indicate that in a neutral pH environment, TNS is located in the hydrophobic domain of the protein, 2.5 nm away from the Trp19 residues of β-LG. The binding constant of the small molecule to β-LG is (3.30 ± 0.32) × 106 (mol L–1)−1. An interaction model between the ligand and β-LG was developed, and AutoDock modeling also demonstrates that the ligand is located in the central hydrophobic calyx of β-LG within the regions covered by the Förster radius of the Trp19–ligand pair. Although the interaction between the ligand and β-LG is affected by increasing ion strength, pH change, and heat treatment, the complex is maintained until the secondary structure of β-LG is destroyed. Additionally, the ligand binding stabilizes the folding of β-LG. The binding constants of sodium dodecyl sulfate (SDS) and sodium dodecylbenzene sulfonate (SDBS) to β-LG were obtained using competitive ligand binding measurements. With a sensitive fluorescence signal and stable complex, the ligand could be utilized as a reference to detect the binding of other small ligands to β-LG.

Free-Form Modeling in Bilateral Brep and CSG Representation Schemes

1998 ◽  
Vol 08 (05n06) ◽  
pp. 537-575 ◽  
Author(s):  
Jai Menon ◽  
Baining Guo
Keyword(s):  
Shape Control ◽  
Tangent Plane ◽  
Free Form ◽  
Unified Approach ◽  
Dual Representation ◽  
Surface Patches ◽  
Low Degree ◽  
Wide Range ◽  
Algebraic Patches ◽  
Direct Term

This paper presents a unified approach for incorporating free-form solids in bilateral Brep and CSG representation schemes, by resorting to low-degree (quadratic, cubic) algebraic surface patches. We develop a general CSG solution that represents a free-form solid as a boolean combination of a direct term and a complicated delta term. This solution gives rise to the trunctet-subshell conditions, under which the delta term computation can be obviated. We use polyhedral smoothing to construct a Brep consisting of quadratic algebraic patches that meet with tangent-plane continuity, such that the trunctet-subshell conditions are guaranteed automatically. This guarantee is not currently available for cubic patches. The general CSG solution thus applies whenever trunctet-subshell conditions are violated, e.g. sometimes for cubic patches or sometimes for patches of any degree that are subject to shape control operations. Manifold solids of arbitrary topology can be represented in our dual representation system. Ensuing CSG constructs are parallel processed on the RayCasting Engine to support a wide range of solid modeling applications, including general sweeping, Minkowski operations, NC machining, and touch-sense probing.

RATES OF CALCIUM CARBONATE REMOVAL FROM SOILS

1988 ◽  
Vol 68 (2) ◽  
pp. 449-454 ◽  
Author(s):  
N. VAN BREEMEN ◽  
R. PROTZ
Keyword(s):  
Calcium Carbonate ◽  
Calcareous Soils ◽  
Water Drainage ◽  
Carbonate Weathering ◽  
Soil Chronosequence ◽  
Drainage Rate ◽  
Wide Range ◽  
Subarctic Climate ◽  
Equilibrium Concentrations ◽  
Study Sites

Mean annual rates of calcium carbonate removal from soils in a subarctic climate estimated from data on two chronosequences of calcareous storm ridges, appeared to be relatively constant through time. Concentrations of dissolved calcium carbonate in the soil solution in the study sites calculated from the rates of weathering of CaCO3 and of water drainage are in the range expected for equilibrium with calcite. The same conclusion could be drawn from published studies elsewhere. Over a wide range of conditions, the dissolution rate of calcite appears to be high enough to maintain equilibrium concentrations in water percolating calcareous soils and rocks. Consequently, the rate of calcium carbonate weathering can be predicted from (1) the solubility of CaCO3 and (2) the water drainage rate. Key words: Calcium carbonate weathering, soil chronosequence, subarctic soils

Self-Assembly and Shape Control of Hybrid Nanocarriers Based on Calcium Carbonate and Carbon Nanodots

2016 ◽  
Vol 28 (11) ◽  
pp. 3796-3803 ◽  
Author(s):  
Victor Lauth ◽  
Brigitta Loretz ◽  
Claus-Michael Lehr ◽  
Michael Maas ◽  
Kurosch Rezwan
Keyword(s):  
Calcium Carbonate ◽  
Self Assembly ◽  
Shape Control ◽  
Carbon Nanodots

scholarly journals A class-A GPCR solubilized under high hydrostatic pressure retains its ligand binding ability

2016 ◽  
Vol 1858 (9) ◽  
pp. 2145-2151 ◽  
Author(s):  
Yukie Katayama ◽  
Tatsuya Suzuki ◽  
Tatsuki Ebisawa ◽  
Jun Ohtsuka ◽  
Shipeng Wang ◽  
...  
Keyword(s):  
Hydrostatic Pressure ◽  
Ligand Binding ◽  
High Hydrostatic Pressure ◽  
Binding Ability ◽  
Class A

scholarly journals DDR1 autophosphorylation is a result of aggregation into dense clusters

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
David S. Corcoran ◽  
Victoria Juskaite ◽  
Yuewei Xu ◽  
Frederik Görlitz ◽  
Yuriy Alexandrov ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Receptor Tyrosine Kinase ◽  
Kinase Activity ◽  
Super Resolution ◽  
Activation Kinetics ◽  
Molecular Events ◽  
Wide Range ◽  
Human Disorders ◽  
Resolution Imaging ◽  
Collagen Receptor

AbstractThe collagen receptor DDR1 is a receptor tyrosine kinase that promotes progression of a wide range of human disorders. Little is known about how ligand binding triggers DDR1 kinase activity. We previously reported that collagen induces DDR1 activation through lateral dimer association and phosphorylation between dimers, a process that requires specific transmembrane association. Here we demonstrate ligand-induced DDR1 clustering by widefield and super-resolution imaging and provide evidence for a mechanism whereby DDR1 kinase activity is determined by its molecular density. Ligand binding resulted in initial DDR1 reorganisation into morphologically distinct clusters with unphosphorylated DDR1. Further compaction over time led to clusters with highly aggregated and phosphorylated DDR1. Ligand-induced DDR1 clustering was abolished by transmembrane mutations but did not require kinase activity. Our results significantly advance our understanding of the molecular events underpinning ligand-induced DDR1 kinase activity and provide an explanation for the unusually slow DDR1 activation kinetics.

Correction to Self-Assembly and Shape Control of Hybrid Nanocarriers Based on Calcium Carbonate and Carbon Nanodots

2017 ◽  
Vol 29 (7) ◽  
pp. 3346-3346
Author(s):  
Victor Lauth ◽  
Brigitta Loretz ◽  
Claus-Michael Lehr ◽  
Michael Maas ◽  
Kurosch Rezwan
Keyword(s):  
Calcium Carbonate ◽  
Self Assembly ◽  
Shape Control ◽  
Carbon Nanodots
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