Application of Hybrid Functional Groups to Predict ATP Binding Proteins

Mbah, Andreas N.

doi:10.1155/2014/581245

Cited by 11 publications

(4 citation statements)

References 61 publications

(71 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We speculate that this change begins at the N-terminus because, during the T7 capsid I to capsid II transition, this region of gp10 undergoes (1) unraveling of an alpha helix and (2) movement from the inside to the outside of the gp10 shell [ 25 ]. Inspection of the N-terminal gp10 sequence [ 19 ] reveals no strict Walker A [GXXXXGK(T/S)] or universal stress protein [G-2X-G-9X-G(S/T)] [ 28 ] sub-sequence. The N-terminal sequence is MANIQ GGQQIGT NQGKGQSAADKLALFLKVF.…”

Section: Discussionmentioning

confidence: 99%

ATP-Driven Contraction of Phage T3 Capsids with DNA Incompletely Packaged In Vivo

Serwer

Wright

2017

Viruses

View full text Add to dashboard Cite

Adenosine triphosphate (ATP) cleavage powers packaging of a double-stranded DNA (dsDNA) molecule in a pre-assembled capsid of phages that include T3. Several observations constitute a challenge to the conventional view that the shell of the capsid is energetically inert during packaging. Here, we test this challenge by analyzing the in vitro effects of ATP on the shells of capsids generated by DNA packaging in vivo. These capsids retain incompletely packaged DNA (ipDNA) and are called ipDNA-capsids; the ipDNA-capsids are assumed to be products of premature genome maturation-cleavage. They were isolated via preparative Nycodenz buoyant density centrifugation. For some ipDNA-capsids, Nycodenz impermeability increases hydration and generates density so low that shell hyper-expansion must exist to accommodate associated water. Electron microscopy (EM) confirmed hyper-expansion and low permeability and revealed that 3.0 mM magnesium ATP (physiological concentration) causes contraction of hyper-expanded, low-permeability ipDNA-capsids to less than mature size; 5.0 mM magnesium ATP (border of supra-physiological concentration) or more disrupts them. Additionally, excess sodium ADP reverses 3.0 mM magnesium ATP-induced contraction and re-generates hyper-expansion. The Nycodenz impermeability implies assembly perfection that suggests selection for function in DNA packaging. These findings support the above challenge and can be explained via the assumption that T3 DNA packaging includes a back-up cycle of ATP-driven capsid contraction and hyper-expansion.

show abstract

Section: Discussionmentioning

confidence: 99%

ATP-Driven Contraction of Phage T3 Capsids with DNA Incompletely Packaged In Vivo

Serwer

Wright

2017

Viruses

View full text Add to dashboard Cite

show abstract

“…For the ligand ATP, the minimum limit of binding starts at 1.5 mM concentration (Figure 2d, Table 2). ATP represents a cell's source of energy and phosphate, and the ATP-binding proteins typically hydrolyze ATP to produce the energy needed for biochemical reactions in the cell (Mbah, 2014). Further studies should focus on understanding if the MRJP1 is involved in transporting substrates across cellular membranes by having ATP-binding sites.…”

Section: Resultsmentioning

confidence: 99%

Analysis of Major Royal Jelly Proteins Stability and Ligand Binding by Differential Scanning Fluorimetry

Mureșan¹,

DEZMIREAN²,

SUHAROSCHI³

et al. 2022

BUASVMCN-FST

View full text Add to dashboard Cite

Royal jelly (RJ) is produced by the hypopharingeal and mandibular glands of bees. Up to 90% of the RJ proteins are the major royal jelly proteins (MRJPs) that exhibit biological properties. Protein stability is of interest for biotechnology and can be explored by using differential scanning fluorimetry (DSF). We tested the stability by using a fluorescence dye (SYPRO® Orange,1:1000 dilution) in the presence of different ligands for MRJP1 and MRJP2 at 2 µM concentration. The fluorescence intensities (FI) were measured using the Real-Time PCR System and were fitted as a function of temperature according to the Boltzmann equation to determine the melting temperature (Tm) at which the amount of folded and unfolded protein is equal. In general, ligands stabilize the protein when binding to it and increase the Tm. Due to the increased starting fluorescence of the oligomeric MRJP1, the Tm values were only determined for monomeric MRJP1 and MRJP2. ATP, histamine, and thiamine were shown to determine an increase of Tm for the monomeric MRJP1 in 20 mM Tris-HCl, pH 7.4, 150 mM NaCl. For the ligand ATP, the minimum limit of binding starts at 1.5 mM concentration, for the ligand Histamine it starts at 0.6 mM concentration, while for the ligand Thiamine it starts at 3 mM concentration.

show abstract

“…Interaction of GUSP-2-potein with adenosine monophosphate and the presence of glycosylation, phosphorylation and ATP-binding sites (predicted by in-silico analysis) suggested its involvement in signal transduction. Previously, it was observed that rice OsUSP1 belongs to subfamily of ATP-binding USP, and plant USPs might contain ATP binding domain dimmers [25][26][27] . The functinal acitivity of GUSP-2-protein was enhanced by site directed mutations.…”

Section: Discussionmentioning

confidence: 99%

Mutant Gossypium universal stress protein-2 (GUSP-2) gene confers resistance to various abiotic stresses in E. coli BL-21 and CIM-496-Gossypium hirsutum

Hafeez

Khan

Sarwar

et al. 2021

Sci Rep

View full text Add to dashboard Cite

Gossypium arboreum is considered a rich source of stress-responsive genes and the EST database revealed that most of its genes are uncharacterized. The full-length Gossypium universal stress protein-2 (GUSP-2) gene (510 bp) was cloned in E. coli and Gossypium hirsutum, characterized and point mutated at three positions, 352–354, Lysine to proline (M1-usp-2) & 214–216, aspartic acid to serine (M2-usp-2) & 145–147, Lysine to Threonine (M3-usp-2) to study its role in abiotic stress tolerance. It was found that heterologous expression of one mutant (M1-usp-2) provided enhanced tolerance against salt and osmotic stresses, recombinant cells have higher growth up to 10-5dilution in spot assay as compared to cells expressing W-usp-2 (wild type GUSP-2), M2-usp-2 and M3-usp-2 genes. M1-usp-2 gene transcript profiling exhibited significant expression (8.7 fold) in CIM-496-Gossypium hirsutum transgenic plants and enhance drought tolerance. However, little tolerance against heat and cold stresses in bacterial cells was observed. The results from our study concluded that the activity of GUSP-2 was enhanced in M1-usp-2 but wipe out in M2-usp-2 and M3-usp-2 response remained almost parallel to W-usp-2. Further, it was predicted through in silico analysis that M1-usp-2, W-usp-2 and M3-usp-2 may be directly involved in stress tolerance or function as a signaling molecule to activate the stress adaptive mechanism. However, further investigation will be required to ascertain its role in the adaptive mechanism of stress tolerance.

show abstract

Application of Hybrid Functional Groups to Predict ATP Binding Proteins

Cited by 11 publications

References 61 publications

ATP-Driven Contraction of Phage T3 Capsids with DNA Incompletely Packaged In Vivo

ATP-Driven Contraction of Phage T3 Capsids with DNA Incompletely Packaged In Vivo

Analysis of Major Royal Jelly Proteins Stability and Ligand Binding by Differential Scanning Fluorimetry

Mutant Gossypium universal stress protein-2 (GUSP-2) gene confers resistance to various abiotic stresses in E. coli BL-21 and CIM-496-Gossypium hirsutum

Contact Info

Product

Resources

About