Long-distance biological transport processes through the air: can nature's complexity be unfolded in silico?

<div>Human cystathionine β-synthase (hCBS) is a unique pyridoxal 5’-phosphate (PLP) dependent enzyme that catalyses the condensation reactions in the transsulfuration pathways. The specific role of Heme in the enzymatic activities has not yet been established, however, several experimental studies indicated the bi-directional communications between the Heme and PLP. Performing classical molecular dynamics (MD) simulations upon developing the necessary force field parameters for the cysteine and histidine bound hexa-coordinated Heme, we have investigated <i>In Silico</i> dynamical aspects of the bi-directional communications. Furthermore, we have investigated the comparative aspects of electron density overlap across the communicating pathways adopting the density functional theory (DFT) in conjunction with the hybrid exchange correlation functional for the CSB<sup>WT</sup> (wild-type) and CBS<sup>R266K</sup> (mutated) case. The atomistic dynamical simulations and subsequent explorations of the electronic structure not only confirm the reported observations but provide an in-depth mechanistic understating of how the non-covalent hydrogen bonding interactions with Cys52 control the such long-distance communication. Our study also provides a convincing answer to the reduced enzymatic activities in the R266K hCBS in comparison to the wild-type enzymes. We further realized that the difference in hydrogen-bonding patterns as well as salt-bridge interactions play the pivotal role in such long distant bi-directional communications.</div>

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Biological transport processes for microhydraulic actuation

Sensors and Actuators B Chemical ◽

10.1016/j.snb.2006.10.009 ◽

2007 ◽

Vol 123 (2) ◽

pp. 685-695 ◽

Cited By ~ 18

Author(s):

Vishnu Baba Sundaresan ◽

Christopher Homison ◽

Lisa M. Weiland ◽

Donald J. Leo

Keyword(s):

Transport Processes ◽

Biological Transport

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The role of roots and rhizosphere in providing tolerance to toxic metals and metalloids

10.22541/au.162409686.68663241/v1 ◽

2021 ◽

Author(s):

Dorina Podar ◽

Frans J.M. Maathuis

Keyword(s):

Negative Impact ◽

Transport Processes ◽

Long Distance ◽

Root Cells ◽

Metals And Metalloids ◽

Natural Processes ◽

Long Distance Transport ◽

Bacteria And Fungi ◽

Distance Transport

Human activity and natural processes have led to widespread dissemination of metals and metalloids, many of which are toxic and have a negative impact on agronomic production. Roots, as the first point of contact, are essential in endowing plants with tolerance to excess metal(loid) in the soil. The most important root responses include: adaptation of transport processes that affect uptake, efflux and long distance transport of metal(loid)s; metal(loid) detoxification within root cells via conjugation to thiol rich compounds and subsequent sequestration in the vacuole; plasticity in root architecture; the presence of bacteria and fungi in the rhizosphere that impact on metal(loid) bioavailability; the role of root exudates. In this review we will provide details on these processes and assess their relevance for the detoxification of arsenic, cadmium, mercury and zinc. Furthermore, we will assess if any of these methodologies has been tested in field conditions and whether they are effective in terms of improving crop metal(loid) tolerance.

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In silico identification and expression analysis of Metal-nicotianamine transporter (YSL3) and Oligopeptide transporter 3 (OPT3) under Cd stress in Brassica oleracea var. acephala

Botanical Sciences ◽

10.17129/botsci.2628 ◽

2020 ◽

Vol 98 (4) ◽

pp. 516-523

Author(s):

Jasmin Sutkovic ◽

Ajdina Karic ◽

Ahmet Yildirim

Keyword(s):

Brassica Oleracea ◽

Expression Analysis ◽

In Silico ◽

Cadmium Stress ◽

Cd Stress ◽

Long Distance ◽

Oligopeptide Transporter ◽

Metal Transporter ◽

Nitrogen Mobilization

Background: Metal-nicotianamine transporter (YSL) family protein belongs to the oligopeptide heavy metal transporter group, as characterized in Arabidopsis thaliana. Oligopeptide transporters (OPTs) are a group of membrane-localized proteins, involved in different transport mechanisms, contributing to nitrogen mobilization, glutathione transport and long-distance metal distribution. Metal-nicotianamine transporter gene 3 (YSL3) incorporates the oligopeptide transporter domain, found to transfer several heavy metals in diverse plant species, and among them cadmium transport in Brassica oleracea. Objective: To evaluate and confirm the expression of Metal-nicotianamine transporter (YSL3) under cadmium stress. Studied species: Brassica oleracea var. acephala Study site and dates: Brassica oleracea var. acephala samples were collected from Blagaj region, Bosnia and Herzegovina. Methods: Through a simple bioinformatic approach the interactome partner of Metal-nicotianamine transporter (YSL3) was discovered and annotated. Oligopeptide transporter 3 (OPT3) and Metal-nicotianamine transporter (YSL3) genes were checked for expression levels under cadmium stress. Results: We have identified a strong interacting partner of YSL3, later confirmed as Oligopeptide transporter 3 (OPT3) protein in Brassica oleracea. The in vitro expression analysis by using a qRT-PCR revealed a significant upregulation of YSL3 and OPT3, during Cd stress. Conclusions: These findings indicate that the represented in-silico approach, followed by in vitro gene expression study, successfully confirmed YSL3 and identified OPT3 as a new gene, in correlation to cadmium stress.

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Correlative Supply and Demand Functions in Lupinus havardii: A Forgotten Side of Cut Flower Physiology?

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.132.1.102 ◽

2007 ◽

Vol 132 (1) ◽

pp. 102-111 ◽

Cited By ~ 1

Author(s):

G.A. Picchioni ◽

Wayne A. Mackay ◽

Mario Valenzuela-Vázquez

Keyword(s):

Supply And Demand ◽

Balance Sheet ◽

Transport Processes ◽

Long Distance ◽

Total N ◽

Internal Resources ◽

Reproductive Tissues ◽

Long Distance Transport ◽

Mature Flower ◽

Sink Demand

Correlative control of long-distance transport processes consists of an attraction or mobilizing power of a sink organ coupled to internal degradative reactions in a target source organ and the reallocation of its resources. This phenomenon is widely recognized in the agronomic whole plant literature but poorly recognized in the floriculture literature. We calculated supply and demand balances for water, total dry matter (TDM), and minerals during a 6-day postharvest evaluation of the spatially diverse, detached, indeterminate inflorescence of Lupinus havardii Wats. ‘Texas Sapphire’ held in deionized water. The apex approximately doubled its original (harvest day) amounts of total N, P, K, Mg, and S and increased its TDM and water content by 55% and 85%, respectively, all at the expense of lower-most mature flowers. Net export from the lower mature flower fraction and, when applicable, upper mature flowers, accounted for the following apical gains: 46% of TDM, 102% of water, 100% of N, 94% of P, 99% of K, and 54% of Mg and S. Directed reallocation of resources from the senescing lower mature flowers (the main “target”) to the apical sink (the “mobilizing center”) bore a marked resemblance to the coupling of remote sink demand with vegetative decline reported in monocarpic plants (i.e., vegetative-to-reproductive exchanges), but with two distinguishing characteristics: 1) the TDM and mineral exchanges were strongly restricted to flowering units, and 2) the contributions of water, N, P, and K exports to apical sink demand were at or near 100%. This article is the first that we are aware to provide an internal supply and demand balance sheet reflecting, quantitatively, the postharvest reallocation of internal resources from mature reproductive tissues to generative reproductive tissues of a cut inflorescence.

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