scholarly journals Structural basis for silicon uptake by higher plants

2021 ◽  
Author(s):  
Bert van den Berg ◽  
Conrado Pedebos ◽  
Jani R Bolla ◽  
Carol V Robinson ◽  
Arnaud Basle ◽  
...  
Keyword(s):  
Crop Yields ◽  
Higher Plants ◽  
Chemical Properties ◽  
Md Simulations ◽  
Structural Basis ◽  
Intracellular Loop ◽  
Biotic Stresses ◽  
Silicon Uptake ◽  
Channel Opening ◽  
Silicon Accumulation

Metalloids are elements with physical and chemical properties that are intermediate between metals and non-metals. Silicon (Si) is the most abundant metalloid in the Earth's crust and occurs at high levels in many plants, especially those belonging to the Poaceae (grasses). Most of the world's staple food crops such as rice, barley and maize accumulate silicon to high levels, resulting in resistance to abiotic and biotic stresses and consequently better plant growth and crop yields. The first step in silicon accumulation is the uptake of silicic acid (Si), the bioavailable from of silicon, by the roots, a process mediated by the structurally uncharacterised NIP subfamily of aquaporins. Here we present the X-ray crystal structure of the archetypal NIP family member from Oryza sativa (OsNIP2;1). While the OsNIP2;1 channel is closed in the crystal by intracellular loop D, unbiased molecular dynamics (MD) simulations reveal a rapid channel opening on sub-microsecond time scales. MD simulations further show how Si interacts with an extracellular five-residue selectivity filter that provides the main barrier for transmembrane diffusion. Our data provide a foundation for understanding and potential manipulation of metalloid selectivity of an important and understudied aquaporin subfamily.

Comparison study on surface and thermo-chemical properties of PFPE lubricants on DLC film through MD simulations

2021 ◽  
Vol 156 ◽  
pp. 106835
Author(s):  
Jingan Song ◽  
Sujoy Talukder ◽  
Shahriar Mufid Rahman ◽  
Yeonjin Jung ◽  
Chang-Dong Yeo
Keyword(s):  
Chemical Properties ◽  
Md Simulations ◽  
Comparison Study ◽  
Dlc Film ◽  
Pfpe Lubricants

scholarly journals Structural basis for ALK2/BMPR2 receptor complex signaling through kinase domain oligomerization

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christopher Agnew ◽  
Pelin Ayaz ◽  
Risa Kashima ◽  
Hanna S. Loving ◽  
Prajakta Ghatpande ◽  
...  
Keyword(s):  
Md Simulations ◽  
Kinase Domain ◽  
Structural Basis ◽  
Type I ◽  
Type Ii ◽  
Exchange Mass Spectrometry ◽  
Receptor Complexes ◽  
Bmp Receptors ◽  
Morphogenetic Protein ◽  
Smad Proteins

AbstractUpon ligand binding, bone morphogenetic protein (BMP) receptors form active tetrameric complexes, comprised of two type I and two type II receptors, which then transmit signals to SMAD proteins. The link between receptor tetramerization and the mechanism of kinase activation, however, has not been elucidated. Here, using hydrogen deuterium exchange mass spectrometry (HDX-MS), small angle X-ray scattering (SAXS) and molecular dynamics (MD) simulations, combined with analysis of SMAD signaling, we show that the kinase domain of the type I receptor ALK2 and type II receptor BMPR2 form a heterodimeric complex via their C-terminal lobes. Formation of this dimer is essential for ligand-induced receptor signaling and is targeted by mutations in BMPR2 in patients with pulmonary arterial hypertension (PAH). We further show that the type I/type II kinase domain heterodimer serves as the scaffold for assembly of the active tetrameric receptor complexes to enable phosphorylation of the GS domain and activation of SMADs.

scholarly journals A short-term comparison of organic v. conventional agriculture in a silty loam soil using two organic amendments

2008 ◽  
Vol 146 (6) ◽  
pp. 677-687 ◽  
Author(s):  
J. F. HERENCIA ◽  
J. C. RUIZ ◽  
S. MELERO ◽  
P. A. GARCIA GALAVÍS ◽  
C. MAQUEDA
Keyword(s):  
Organic Farming ◽  
Crop Yields ◽  
Organic Amendments ◽  
Chemical Properties ◽  
Soil Nutrient ◽  
Short Term ◽  
Organic System ◽  
Conventional Agriculture ◽  
Silty Loam ◽  
Loam Soil

SUMMARYThe transition from conventional to organic farming is accompanied by changes in soil chemical properties and processes that could affect soil fertility. The organic system is very complex and the present work carries out a short-term comparison of the effects of organic and conventional agriculture on the chemical properties of a silty loam soil (Xerofluvent) located in the Guadalquivir River Valley, Seville, Spain, through a succession of five crop cycles over a 3-year period. Crop rotation and varieties were compared in a conventional system using inorganic fertilizer and two organic systems using either plant compost or manure. At the end of the study, organic farming management resulted in higher soil organic carbon (OC), N and available P, K, Fe and Zn. The available Mn and especially Cu values did not show significant differences. In general, treatment with manure resulted in more rapid increases in soil nutrient values than did plant compost, which had an effect on several crop cycles later. The present study demonstrated that the use of organic composts results in an increase in OC and the storage of nutrients, which can provide long-term fertility benefits. Nevertheless, at least 2–3 years of organic management are necessary, depending on compost characteristics, to observe significant differences. Average crop yields were 23% lower in organic crops. Nevertheless, only two crops showed statistically significant differences.

Elucidating structural basis of benzofuran pyrrolidine pyrazole derivatives for enhancing potency against both the InhA enzyme and intact M. tuberculosis cells: a combined MD simulations and 3D-QSAR study

RSC Advances ◽  
2015 ◽  
Vol 5 (65) ◽  
pp. 52926-52937 ◽  
Author(s):  
Pharit Kamsri ◽  
Auradee Punkvang ◽  
Supa Hannongbua ◽  
Patchreenart Saparpakorn ◽  
Pornpan Pungpo
Keyword(s):  
3D Qsar ◽  
Md Simulations ◽  
Structural Basis ◽  
Pyrazole Derivatives ◽  
Qsar Study ◽  
Structural Concept

The structural concept for enhancing both IC50 and MIC90 activities summarized from MD simulations and CoMSIA results.

scholarly journals Molecular insights on CALX-CBD12 inter-domain dynamics from MD simulations, RDCs and SAXS

2020 ◽  
Author(s):  
Maximilia F. de Souza Degenhardt ◽  
Phelipe A. M. Vitale ◽  
Layara A. Abiko ◽  
Martin Zacharias ◽  
Michael Sattler ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Md Simulations ◽  
Bound State ◽  
Conformational Ensemble ◽  
Regulation Mechanism ◽  
Multiple Sources ◽  
Intracellular Loop ◽  
Saxs Data ◽  
Structure Information ◽  
Apo State

ABSTRACTNa+/Ca2+ exchangers (NCX) are secondary active transporters that couple the translocation of Na+ with the transport of Ca2+ in the opposite direction. The exchanger is an essential Ca2+ extrusion mechanism in excitable cells. It consists of a transmembrane domain and a large intracellular loop that contains two Ca2+-binding domains, CBD1 and CBD2. The two CBDs are adjacent to each other and form a two-domain Ca2+-sensor called CBD12. Binding of intracellular Ca2+ to CBD12 activates the NCX but inhibits the Na+/Ca2+ exchanger of Drosophila, CALX. NMR spectroscopy and SAXS studies showed that CALX and NCX CBD12 constructs display significant inter-domain flexibility in the Apo state, but assume rigid inter-domain arrangements in the Ca2+-bound state. However, detailed structure information on CBD12 in the Apo state is missing. Structural characterization of proteins formed by two or more domains connected by flexible linkers is notoriously challenging and requires the combination of orthogonal information from multiple sources. As an attempt to characterize the conformational ensemble of CALX-CBD12 in the Apo state, we applied molecular dynamics (MD) simulations, NMR (1H-15N RDCs) and Small-Angle X-Ray Scattering (SAXS) data in a combined modelling strategy that generated atomistic information on the most representative conformations. This joint approach demonstrated that CALX-CBD12 preferentially samples closed conformations, while the wide-open inter-domain arrangement characteristic of the Ca2+-bound state is less frequently sampled. These results are consistent with the view that Ca2+ binding shifts the CBD12 conformational ensemble towards extended conformers, which could be a key step in the Na+/Ca2+ exchangers’ allosteric regulation mechanism. The present strategy, combining MD with NMR and SAXS, provides a powerful approach to select representative structures from ensembles of conformations, which could be applied to other flexible multi-domain systems.SIGNIFICANCEThe conformational ensemble of CALX-CBD12, the main Ca2+-sensor of Drosophila’s Na+/Ca2+ exchanger, was characterized by a combination of MD simulations with SAXS and NMR data using the EOM approach. This analysis showed that this two-domain construct experiences opening-closing motions, providing molecular information about CALX-CBD12 in the Apo state. Ca2+-binding shifts the conformational ensemble towards extended conformers. These findings are consistent with a model according to which Ca2+ modulation of CBD12 plasticity is a key step in the Ca2+-regulation mechanism of the full-length exchanger.

scholarly journals Structural basis for subtype-specific inhibition of the P2X7 receptor

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Akira Karasawa ◽  
Toshimitsu Kawate
Keyword(s):  
P2x7 Receptor ◽  
Hydrophobic Interactions ◽  
Binding Pocket ◽  
Drug Binding ◽  
Structural Basis ◽  
Atp Binding ◽  
Allosteric Site ◽  
Channel Opening ◽  
A Site ◽  
Novel Drug

The P2X7 receptor is a non-selective cation channel activated by extracellular adenosine triphosphate (ATP). Chronic activation of P2X7 underlies many health problems such as pathologic pain, yet we lack effective antagonists due to poorly understood mechanisms of inhibition. Here we present crystal structures of a mammalian P2X7 receptor complexed with five structurally-unrelated antagonists. Unexpectedly, these drugs all bind to an allosteric site distinct from the ATP-binding pocket in a groove formed between two neighboring subunits. This novel drug-binding pocket accommodates a diversity of small molecules mainly through hydrophobic interactions. Functional assays propose that these compounds allosterically prevent narrowing of the drug-binding pocket and the turret-like architecture during channel opening, which is consistent with a site of action distal to the ATP-binding pocket. These novel mechanistic insights will facilitate the development of P2X7-specific drugs for treating human diseases.

scholarly journals Spatial variability of soil chemical properties after coffee tree removal

2009 ◽  
Vol 33 (5) ◽  
pp. 1507-1514 ◽  
Author(s):  
Sidney Rosa Vieira ◽  
Osvaldo Guedes Filho ◽  
Márcio Koiti Chiba ◽  
Heitor Cantarella
Keyword(s):  
Spatial Variability ◽  
Spatial Dependence ◽  
Crop Yields ◽  
Management Strategies ◽  
Chemical Properties ◽  
Spherical Model ◽  
Soil Chemical Properties ◽  
Kriging Interpolation ◽  
Geostatistical Methods ◽  
Plant Removal

Assessing the spatial variability of soil chemical properties has become an important aspect of soil management strategies with a view to higher crop yields with minimal environmental degradation. This study was carried out at the Centro Experimental of the Instituto Agronomico, in Campinas, São Paulo, Brazil. The aim was to characterize the spatial variability of chemical properties of a Rhodic Hapludox on a recently bulldozer-cleaned area after over 30 years of coffee cultivation. Soil samples were collected in a 20 x 20 m grid with 36 sampling points across a 1 ha area in the layers 0.0-0.2 and 0.2-0.4 m to measure the following chemical properties: pH, organic matter, K+, P, Ca2+, Mg2+, potential acidity, NH4-N, and NO3-N. Descriptive statistics were applied to assess the central tendency and dispersion moments. Geostatistical methods were applied to evaluate and to model the spatial variability of variables by calculating semivariograms and kriging interpolation. Spatial dependence patterns defined by spherical model adjusted semivariograms were made for all cited soil properties. Moderate to strong degrees of spatial dependence were found between 31 and 60 m. It was still possible to map soil spatial variability properties in the layers 0-20 cm and 20-40 cm after plant removal with bulldozers.

scholarly journals Structural Basis of Complex Formation Between Mitochondrial Anion Channel VDAC1 and Hexokinase-II

2020 ◽  
Author(s):  
Nandan Haloi ◽  
Po-Chao Wen ◽  
Qunlii Cheng ◽  
Meiying Yang ◽  
Gayathri Natarajan ◽  
...  
Keyword(s):  
Complex Formation ◽  
Hybrid Approach ◽  
Md Simulations ◽  
Structural Basis ◽  
Stable Complex ◽  
Binary Complex ◽  
Hexokinase Ii ◽  
Insertion Depth ◽  
Form Complex ◽  
Membrane Bound

ABSTRACTComplex formation between hexokinase-II (HKII) and the mitochondrial channel VDAC1 plays a crucial role in regulating cell growth and survival; however, structural details of this complex remain elusive. We hypothesize that a conserved, hydrophobic helix (H-anchor) of HKII first inserts into the outer membrane of mitochondria (OMM) and then interacts with VDAC1 on the cytosolic leaflet of OMM to form a binary complex. To systematically investigate this process, we adopted a hybrid approach: 1) the membrane binding of HKII was first described with molecular dynamics (MD) simulations employing a membrane mimetic model with enhanced lipid diffusion, then 2) the resulting membrane-bound HKII was used to form complex with VDAC1 in millisecond-scale Brownian dynamics (BD) simulations. We show that H-anchor inserts its first 10 residues into the membrane, substantiating previous experimental findings. The insertion depth of the H-anchor was used to derive positional restraints in subsequent BD simulations to preserve the membrane-bound pose of HKII during the formation of the HKII/VDAC1 binary complex. Multiple BD-derived structural models were further refined with MD simulations, resulting in one stable complex. A major feature in the complex is the partial (not complete) blockade of VDAC1’s permeation pathway by HKII, a result supported by our comparative electrophysiological measurements of the channel in the presence and absence of HKII. Additionally, we showed how VDAC1 phosphorylation disrupts HKII binding, a feature that is verified by our electrophysiology recordings and have implications in mitochondria-mediated cell death.

scholarly journals Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when

2019 ◽  
Author(s):  
Juan J Galano-Frutos ◽  
Helena García-Cebollada ◽  
Javier Sancho
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Large Scale ◽  
Binary Classification ◽  
Chemical Properties ◽  
Md Simulations ◽  
Single Amino Acid ◽  
Medical Decision ◽  
Evolutionary Information ◽  
Protein Variants

Abstract The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical–chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80–85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore’s law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants.

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