A Review of Quasi-perfect Secondary Structure Prediction Servers

Musci, Mirto; Maruccia, Gioele; Ferretti, Marco

doi:10.1007/978-3-030-27684-3_4

Cited by 1 publication

(2 citation statements)

References 26 publications

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“…The sequence lengths between the first half of the second transmembrane domain of unit 3 (U3M2a) and the beginning of the first transmembrane domain of unit 4 (U4M1) are also shorter in HKT proteins relative to those in KtrB and TrkH (except for Mar-pol-HKT1, Phy-pat-HKT1, and Pic-abi-HKT2) ( Figure 4C). .0 that was recently tested among the best performing secondary prediction programs [55,56]. Prediction is based on three classes, which correspond to helix structures represented by H in blue (DSSP classes H, G, I), to strand structures represented by E in red Figure 4.…”

Section: Structure Of the Second Transmembrane Segment In Unitmentioning

confidence: 99%

“…Unit 0 is found in bacterial Trk channels only, and the internal loop is found in Trk and Ktr channels but not in plant HKT. ( B ) The secondary structure was determined with Porter5.0 that was recently tested among the best performing secondary prediction programs [ 55 , 56 ]. Prediction is based on three classes, which correspond to helix structures represented by H in blue (DSSP classes H, G, I), to strand structures represented by E in red (DSSP classes E, B), and to coil and turn structures represented by C in yellow (DSSP classes S, T.).…”

Section: Figurementioning

confidence: 99%

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Plant HKT Channels: An Updated View on Structure, Function and Gene Regulation

Riedelsberger

Miller

Valdebenito-Maturana

et al. 2021

IJMS

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HKT channels are a plant protein family involved in sodium (Na+) and potassium (K+) uptake and Na+-K+ homeostasis. Some HKTs underlie salt tolerance responses in plants, while others provide a mechanism to cope with short-term K+ shortage by allowing increased Na+ uptake under K+ starvation conditions. HKT channels present a functionally versatile family divided into two classes, mainly based on a sequence polymorphism found in the sequences underlying the selectivity filter of the first pore loop. Physiologically, most class I members function as sodium uniporters, and class II members as Na+/K+ symporters. Nevertheless, even within these two classes, there is a high functional diversity that, to date, cannot be explained at the molecular level. The high complexity is also reflected at the regulatory level. HKT expression is modulated at the level of transcription, translation, and functionality of the protein. Here, we summarize and discuss the structure and conservation of the HKT channel family from algae to angiosperms. We also outline the latest findings on gene expression and the regulation of HKT channels.

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Section: Structure Of the Second Transmembrane Segment In Unitmentioning

confidence: 99%

Section: Figurementioning

confidence: 99%