Mutation in a valine residue induces drastic changes in 3D structure of human prion protein

Behmard, Esmaeil; Abdolmaleki, Parviz; Barzegari, Ebrahim

doi:10.1080/21553769.2013.775078

Cited by 7 publications

(4 citation statements)

References 31 publications

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“…Another example demonstrated by replacing Val 566 with Ile 566 showed the potential to interfere with hydrogen bonding and alter the solvent accessibility of 22 amino acid residues, resulting in the formation of a brief α-helix at the C-terminus of Anti-Müllerian hormone (AMH) in chickens (Dang et al 2020). While both valine and isoleucine are hydrophobic amino acids, isoleucine possesses a more substantial hydrophobic nature due to its larger side chain with additional methylene groups, resulting in a greater volume compared to valine (Behmard et al 2012). Our findings are consistent with these reports, demonstrating that the substitution of isoleucine for valine at the 403 rd position has a pronounced effect on the active site of OsNRT1.1C protein.…”

Section: Discussionmentioning

confidence: 99%

Haplo-pheno association forOsNRT1.1paralog in rice reveals superior haplogroup with high nitrate uptake efficiency

Elangovan,

Pandey,

Sharma

et al. 2023

Preprint

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Haplotype-based breeding approaches hold promise for enhancing crop improvement strategies, allowing for targeted selection of superior genetic combinations to develop high-yielding and resilient varieties. The current study aimed at identification ofNRT1.1nitrate transporter haplotype that could serve as “donors” in haplotype-based breeding. We phenotyped 272 rice accessions in hydroponics with sufficient and low nitrogen (N) for nitrate uptake efficiency. By employing principal component and hierarchical cluster analysis, the accessions were grouped into N efficient, intermediate, and inefficient clusters. Haplotype analysis unveiled the presence of two haplogroups forOsNRT1.1A, three forOsNRT1.1B, and five forOsNRT1.1C. Through haplo-pheno association, the comparison of mean trait values revealed H2 and H3 as the superior haplotypes (SH) for OsNRT1.1A and OsNRT1.1B, respectively. In the case of OsNRT1.1C, H3 and H1 emerged as SH within the N-efficient cluster. Conversely, the inferior haplotypes (IH) consisted of H1 in OsNRT1.1A, H3 in OsNRT1.1B, and H3 and H2 in OsNRT1.1C within the N-inefficient cluster. However, relative expression ofOsNRT1.1(with specific paralogs) in contrasting rice accessions revealed that a few of the inferior accession exhibited higher expression levels in the root but lower in the shoot, which might have contributed to their N-inefficiency. Furthermore, amino acid change at position 403 (Isoleucine to Valine) in inferior accessions influences the active site OsNRT1.1C protein causing N-inefficiency. Ours is the first report on haplotype analysis ofNRT1.1gene demonstrating its genetic diversity, as well as its association with phenotype will have potential implications for improving nitrate uptake efficiency.

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Section: Discussionmentioning

confidence: 99%

Haplo-pheno association forOsNRT1.1paralog in rice reveals superior haplogroup with high nitrate uptake efficiency

Elangovan,

Pandey,

Sharma

et al. 2023

Preprint

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“…The β6 connects the central β sheet to switch-I and communicates the conformational changes to the switch-II region due to ATP hydrolysis. The mutation from valine to isoleucine slightly increased hydrophobic volume due to its longer side chain, resulting in a small effect of the V220I mutation on KIF1A velocity (Behmard et al, 2012). The mutation, E233D, in the loop10 (L10) of KIF1A motor domain also did not alter the motor's processivity but drastically decreased the motor velocity compared to the WT.…”

Section: Motility Properties Of Peripheral Mutants Correlate With Mil...mentioning

confidence: 97%

KIF1A neurodegenerative disease mutations modulate motor motility and force generation

Shewale

Soppina

2023

Preprint

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KIF1A is involved in fast axonal transport of synaptic vesicle precursor, neurofilament, and dense-core vesicle, essential for neuronal development and maintenance. Several point mutations in the KIF1A motor domain have been identified in patients with various motor neuron diseases. Recent studies have shown that these mutations affected the motor and cargo localization in cultured hippocampal and C.elegans neurons. However, a detailed analysis of these mutations on KIF1A motility, force generation, and cargo transport is largely unexplored. Here, we have analyzed the effect of 16 point mutations and showed that these mutations significantly decreased the motor velocity and landing rates compared to wild-type motors. Except for A255V, mutations V144F, V220I, and E233D mildly affected motor mechanical outputs. S58L, A202P, R216P, R216H, L249Q, T312M, and R316W mutants exhibited drastic impairments in the motility properties, force generation, and cargo transport. Notably, T46M, T99M, G102D, S215R, and E253K mutants showed strong microtubule binding, resulting in complete disruption of cargo transport. Our study provides the first comprehensive demonstration of KIF1A disease mutations at the molecular level. The observed changes in motility properties and cargo transport align with the severity of disease phenotype observed in KIF1A-associated neurological disorders)

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“…The most divergent variant results in an amino acid change from alanine to tryptophan at residue 284 (p.Ala284Thr), and the less divergent variant, from valine to isoleucine at residue 224 (p.Val224Ile). While all four amino acids are hydrophobic, tryptophan is more hydrophobic and larger in volume than alanine, and the equivalent occurs between isoleucine respect to valine, suggesting that these amino acid changes could potentially result in structural protein modifications (Behmard, Abdolmaleki, & Asadabadi, 2012). Therefore, it is possible that the missense mutations in opn1mw4 are causal, as they could potentially affect the structure of the photopigments and, thus, generate a shift in spectral sensitivity.…”

Section: Genomic Regions and Environmental Factors Involved In Local ...mentioning

confidence: 99%

The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus)

Fuentes‐Pardo

Farrell²,

Pettersson

et al. 2022

Preprint

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Understanding how populations adapt to local environments is increasingly important to prevent biodiversity loss due to climate change. Here we examined whole-genome variation of twelve Atlantic horse mackerel samples from the North Sea to North Africa, and the western Mediterranean Sea. This marine migratory benthopelagic fish is one of the most widely distributed and commercially important species in the eastern Atlantic. We found low population structure at neutral loci, but high differentiation at adaptive loci distinguishing the western Mediterranean and the North Sea populations from other Atlantic locations. Candidate genes distinctive of the Mediterranean include a green-sensitive-opsin harbouring two missense mutations that might fine-tune the spectral sensitivity to blue-green light conditions. Candidate genes characteristic of the North Sea could play a critical role in cold tolerance (energy metabolism and cell membrane structure) and increased sensitivity to odours, presumably to compensate reduced visibility in turbid waters. We also discovered a putative chromosomal inversion (9.9 Mb) that follows a climate-related latitudinal cline with a break near mid Portugal. Genome-environment association analysis indicated that seawater-dissolved oxygen concentration and temperature are likely the main environmental drivers of local adaptation. Our genomic data broadly supports the current stock divisions, but recommends revision of the western and southern stock boundaries. We developed a reduced SNP panel that genetically discriminate the North Sea and North Africa from neighbouring populations. Our study highlights the importance of life history and chromosomal inversions in adaptation with gene flow, and the complexity of evolutionary and ecological processes involved in local adaptation.

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Mutation in a valine residue induces drastic changes in 3D structure of human prion protein

Cited by 7 publications

References 31 publications

Haplo-pheno association forOsNRT1.1paralog in rice reveals superior haplogroup with high nitrate uptake efficiency

Haplo-pheno association forOsNRT1.1paralog in rice reveals superior haplogroup with high nitrate uptake efficiency

KIF1A neurodegenerative disease mutations modulate motor motility and force generation

The genomic basis and environmental correlates of local adaptation in the Atlantic horse mackerel (Trachurus trachurus)

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