scholarly journals Structural elements that modulate the substrate specificity of plant purple acid phosphatases: avenues for improved phosphorus acquisition in crops

2019 ◽  
Author(s):  
Daniel Feder ◽  
Ross P. McGeary ◽  
Natasa Mitić ◽  
Thierry Lonhienne ◽  
Agnelo Furtado ◽  
...  
Keyword(s):  
Active Sites ◽  
Crop Yields ◽  
Organic Phosphorus ◽  
Homology Modelling ◽  
Acid Phosphatases ◽  
Phosphorus Use Efficiency ◽  
Active Site Residues ◽  
Docking Simulations ◽  
Wide Range ◽  
Purple Acid Phosphatases

AbstractPhosphate acquisition by plants is an essential process that is directly implicated in the optimization of crop yields. Purple acid phosphatases (PAPs) are ubiquitous metalloenzymes, which catalyze the hydrolysis of a wide range of phosphate esters and anhydrides. While some plant PAPs display a preference for ATP as the substrate, others are efficient in hydrolyzing phytate or 2-phosphoenolpyruvate (PEP). PAP from red kidney bean (rkbPAP) is an efficient ATP- and ADPase, but has no activity towards phytate. The crystal structure of this enzyme in complex with an ATP analogue (to 2.20 Å resolution) provides insight into the amino acid residues that play an essential role in binding this substrate. Homology modelling was used to generate three-dimensional structures for the active sites of PAPs from tobacco (NtPAP) and Arabidopsis thaliana (AtPAP12 and AtPAP26) that are efficient in hydrolyzing phytate and PEP as substrates, respectively. In combination with substrate docking simulations and a phylogenetic analysis of 49 plant PAP sequences (including the first PAP sequences reported from Eucalyptus), several active site residues were identified that are important in defining the substrate specificities of plant PAPs. These results may inform bioengineering studies aimed at identifying and incorporating suitable plant PAP genes into crops to improve phosphorus use efficiency. Organic phosphorus sources increasingly supplement or replace inorganic fertilizer, and efficient phosphorus use of crops will lower the environmental footprint of agriculture while enhancing food production.

scholarly journals Identification of mammalian-like purple acid phosphatases in a wide range of plants

Gene ◽  
2000 ◽  
Vol 250 (1-2) ◽  
pp. 117-125 ◽  
Author(s):  
G. Schenk ◽  
L.W. Guddat ◽  
Y. Ge ◽  
L.E. Carrington ◽  
D.A. Hume ◽  
...  
Keyword(s):  
Acid Phosphatases ◽  
Wide Range ◽  
Purple Acid Phosphatases

Mutational Analysis of the Interaction between Active Site Residues and the Loop Region in Mammalian Purple Acid Phosphatases†

Biochemistry ◽  
2001 ◽  
Vol 40 (38) ◽  
pp. 11614-11622 ◽  
Author(s):  
Enrico G. Funhoff ◽  
Jenny Ljusberg ◽  
Yunling Wang ◽  
Goran Andersson ◽  
Bruce A. Averill
Keyword(s):  
Active Site ◽  
Mutational Analysis ◽  
Acid Phosphatases ◽  
Active Site Residues ◽  
Loop Region ◽  
Purple Acid Phosphatases

Assessment of the Role of Different Soil Properties on Crust Strength by Linear Regression Models

2019 ◽  
Vol 6 (04) ◽  
Author(s):  
MINAKSHI SERAWAT ◽  
V K PHOGAT ◽  
ANIL Abdul KAPOOR ◽  
VIJAY KANT SINGH ◽  
ASHA SERAWAT
Keyword(s):  
Hydraulic Conductivity ◽  
Soil Properties ◽  
Crop Yields ◽  
Modulus Of Rupture ◽  
Silty Clay ◽  
Linear Regression Models ◽  
Wide Range ◽  
Dispersion Ratio ◽  
Crust Strength

Soil crust strength influences seedling emergence, penetration and morphology of plant roots, and, consequently, crop yields. A study was carried out to assess the role of different soil properties on crust strength atHisar, Haryana, India. The soil samples from 0-5 and 5-15 cm depths were collected from 21 locations from farmer’s fields, having a wide range of texture.Soil propertieswere evaluated in the laboratory and theirinfluence on the modulus of rupture (MOR), which is the measure of crust strength, was evaluated.The MOR of texturally different soils was significantly correlated with saturated hydraulic conductivity at both the depths. Dispersion ratio was found to decrease with an increase in fineness of the texture of soil and the lowest value was recorded in silty clay loam soil,which decreased with depth. The modulus of rupture was significantly negatively correlative with the dispersion ratio.There was no role of calcium carbonate in influencing the values of MOR of soils. Similarly,the influence of pH, EC and SAR of soil solution on MOR was non-significant.A perusal of thevalues of the correlations between MOR and different soil properties showed that the MOR of soils of Haryana are positively correlated with silt + clay (r = 0.805) followed by water-stable aggregates (r = 0.774), organic carbon (r = 0.738), silt (r = 0.711), mean weight diameter (r = 0.608) and clay (r = 0.593) while negatively correlated with dispersion ratio (r = - 0.872), sand (r = -0.801) and hydraulic conductivity (r = -0.752) of soils.

FeIIIFeIIIand FeIIFeIIIComplexes as Synthetic Analogues for the Oxidized and Reduced Forms of Purple Acid Phosphatases

1996 ◽  
Vol 35 (8) ◽  
pp. 2360-2368 ◽  
Author(s):  
Ademir Neves ◽  
Marcos A. de Brito ◽  
Ivo Vencato ◽  
Valderes Drago ◽  
Klaus Griesar ◽  
...  
Keyword(s):  
Acid Phosphatases ◽  
Synthetic Analogues ◽  
Purple Acid Phosphatases ◽  
Reduced Forms

scholarly journals Systematic synthesis of functional unsymmetric FeZn model complexes for plant purple acid phosphatases

2010 ◽  
Vol 13 (3) ◽  
pp. 334-337 ◽  
Author(s):  
Martin Jarenmark ◽  
Håkan Carlsson ◽  
Vladimir M. Trukhan ◽  
Matti Haukka ◽  
Sophie E. Canton ◽  
...  
Keyword(s):  
Acid Phosphatases ◽  
Model Complexes ◽  
Purple Acid Phosphatases ◽  
Systematic Synthesis

scholarly journals NAD(P)H quinone oxidoreductase (NQO1): an enzyme which needs just enough mobility, in just the right places

2019 ◽  
Vol 39 (1) ◽  
Author(s):  
Angel L. Pey ◽  
Clare F. Megarity ◽  
David J. Timson
Keyword(s):  
Active Sites ◽  
Physiological Role ◽  
Polymorphic Form ◽  
Normal Function ◽  
Enzyme Mechanism ◽  
Quinone Oxidoreductase ◽  
Lower Stability ◽  
Increased Risk ◽  
Wide Range ◽  
The Right

AbstractNAD(P)H quinone oxidoreductase 1 (NQO1) catalyses the two electron reduction of quinones and a wide range of other organic compounds. Its physiological role is believed to be partly the reduction of free radical load in cells and the detoxification of xenobiotics. It also has non-enzymatic functions stabilising a number of cellular regulators including p53. Functionally, NQO1 is a homodimer with two active sites formed from residues from both polypeptide chains. Catalysis proceeds via a substituted enzyme mechanism involving a tightly bound FAD cofactor. Dicoumarol and some structurally related compounds act as competitive inhibitors of NQO1. There is some evidence for negative cooperativity in quinine oxidoreductases which is most likely to be mediated at least in part by alterations to the mobility of the protein. Human NQO1 is implicated in cancer. It is often over-expressed in cancer cells and as such is considered as a possible drug target. Interestingly, a common polymorphic form of human NQO1, p.P187S, is associated with an increased risk of several forms of cancer. This variant has much lower activity than the wild-type, primarily due to its substantially reduced affinity for FAD which results from lower stability. This lower stability results from inappropriate mobility of key parts of the protein. Thus, NQO1 relies on correct mobility for normal function, but inappropriate mobility results in dysfunction and may cause disease.

scholarly journals Computational Ion Channel Research: from the Application of Artificial Intelligence to Molecular Dynamics Simulations.

2020 ◽  
Vol 55 (S3) ◽  
pp. 14-45
Keyword(s):  
Artificial Intelligence ◽  
Molecular Dynamics ◽  
Ion Channels ◽  
Ion Channel ◽  
Computational Methods ◽  
Homology Modelling ◽  
Channel Structure ◽  
Learning Approaches ◽  
Qsar Analysis ◽  
Wide Range

Although ion channels are crucial in many physiological processes and constitute an important class of drug targets, much is still unclear about their function and possible malfunctions that lead to diseases. In recent years, computational methods have evolved into important and invaluable approaches for studying ion channels and their functions. This is mainly due to their demanding mechanism of action where a static picture of an ion channel structure is often insufficient to fully understand the underlying mechanism. Therefore, the use of computational methods is as important as chemical-biological based experimental methods for a better understanding of ion channels. This review provides an overview on a variety of computational methods and software specific to the field of ion-channels. Artificial intelligence (or more precisely machine learning) approaches are applied for the sequence-based prediction of ion channel family, or topology of the transmembrane region. In case sufficient data on ion channel modulators is available, these methods can also be applied for quantitative structureactivity relationship (QSAR) analysis. Molecular dynamics (MD) simulations combined with computational molecular design methods such as docking can be used for analysing the function of ion channels including ion conductance, different conformational states, binding sites and ligand interactions, and the influence of mutations on their function. In the absence of a three-dimensional protein structure, homology modelling can be applied to create a model of your ion channel structure of interest. Besides highlighting a wide range of successful applications, we will also provide a basic introduction to the most important computational methods and discuss best practices to get a rough idea of possible applications and risks.

scholarly journals A Zirconium Metal-Organic Framework with SOC Topological Net for Catalytic Peptide Bond Hydrolysis

2021 ◽  
Author(s):  
Sujing Wang ◽  
Antoine Tissot ◽  
Guillaume Maurin ◽  
Tatjana Parac-Vogt ◽  
Christian Serre ◽  
...  
Keyword(s):  
Active Sites ◽  
Metal Organic Framework ◽  
Cost Effective ◽  
Peptide Bond ◽  
Catalytic Performance ◽  
Wide Range ◽  
Horse Heart Myoglobin ◽  
Metal Organic ◽  
Effective Synthesis ◽  
Organic Framework

<div>The discovery of nanozymes for selective cleavage of proteins would boost the emerging areas of modern proteomics, however, the development of efficient and reusable artificial catalysts for peptide bond hydrolysis is challenging. Here we report the detailed catalytic properties of a microporous zirconium carboxylate metal-organic framework, MIP-201, in promoting peptide bond hydrolysis in a simple dipeptide, as well as in horse-heart myoglobin (Mb) protein that consists of 153 amino acids. We demonstrate that MIP-201 features an excellent catalytic activity and selectivity, a good tolerance toward reaction conditions covering a wide range of different pH values, and importantly, an exceptional recycling ability associated with easy regeneration process. Taking into account the excellent catalytic performance of MIP-201 and its other advantages such as 6-connected Zr6 cluster active sites, the green, scalable and cost-effective synthesis, and an outstanding chemical and architectural stability, our finding suggests that MIP-201 may be a promising and practical alternative to the current commercially available catalysts for peptide bond hydrolysis.</div>

scholarly journals A Zirconium Metal-Organic Framework with SOC Topological Net for Catalytic Peptide Bond Hydrolysis

2021 ◽  
Author(s):  
Sujing Wang ◽  
Antoine Tissot ◽  
Guillaume Maurin ◽  
Tatjana Parac-Vogt ◽  
Christian Serre ◽  
...  
Keyword(s):  
Active Sites ◽  
Metal Organic Framework ◽  
Cost Effective ◽  
Peptide Bond ◽  
Catalytic Performance ◽  
Wide Range ◽  
Horse Heart Myoglobin ◽  
Metal Organic ◽  
Effective Synthesis ◽  
Organic Framework

<div>The discovery of nanozymes for selective cleavage of proteins would boost the emerging areas of modern proteomics, however, the development of efficient and reusable artificial catalysts for peptide bond hydrolysis is challenging. Here we report the detailed catalytic properties of a microporous zirconium carboxylate metal-organic framework, MIP-201, in promoting peptide bond hydrolysis in a simple dipeptide, as well as in horse-heart myoglobin (Mb) protein that consists of 153 amino acids. We demonstrate that MIP-201 features an excellent catalytic activity and selectivity, a good tolerance toward reaction conditions covering a wide range of different pH values, and importantly, an exceptional recycling ability associated with easy regeneration process. Taking into account the excellent catalytic performance of MIP-201 and its other advantages such as 6-connected Zr6 cluster active sites, the green, scalable and cost-effective synthesis, and an outstanding chemical and architectural stability, our finding suggests that MIP-201 may be a promising and practical alternative to the current commercially available catalysts for peptide bond hydrolysis.</div>

scholarly journals Proton Pumping and Non-Pumping Terminal Respiratory Oxidases: Active Sites Intermediates of These Molecular Machines and Their Derivatives

2021 ◽  
Vol 22 (19) ◽  
pp. 10852
Author(s):  
Sergey A. Siletsky ◽  
Vitaliy B. Borisov
Keyword(s):  
Active Sites ◽  
Three Dimensional ◽  
Molecular Machines ◽  
Proton Pumping ◽  
Stress Reactions ◽  
Low Oxygen ◽  
Functional Studies ◽  
Wide Range ◽  
Regulatory Cascades ◽  
Respiratory Oxidases

Terminal respiratory oxidases are highly efficient molecular machines. These most important bioenergetic membrane enzymes transform the energy of chemical bonds released during the transfer of electrons along the respiratory chains of eukaryotes and prokaryotes from cytochromes or quinols to molecular oxygen into a transmembrane proton gradient. They participate in regulatory cascades and physiological anti-stress reactions in multicellular organisms. They also allow microorganisms to adapt to low-oxygen conditions, survive in chemically aggressive environments and acquire antibiotic resistance. To date, three-dimensional structures with atomic resolution of members of all major groups of terminal respiratory oxidases, heme-copper oxidases, and bd-type cytochromes, have been obtained. These groups of enzymes have different origins and a wide range of functional significance in cells. At the same time, all of them are united by a catalytic reaction of four-electron reduction in oxygen into water which proceeds without the formation and release of potentially dangerous ROS from active sites. The review analyzes recent structural and functional studies of oxygen reduction intermediates in the active sites of terminal respiratory oxidases, the features of catalytic cycles, and the properties of the active sites of these enzymes.

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