Molecular dynamics simulations on the conformational transitions from the GA98 (GA88) to GB98 (GB88) proteins

Song, Changcheng; Wang, Qing; Xue, Tuo; Wang, Yan; Chen, Guangju

doi:10.1002/jmr.2558

Cited by 6 publications

(6 citation statements)

References 59 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Also, the refold from 3α to 4β + α upon the mutation L20A in the sequence I25, F30, and Y45 is in agreement with our simulation results (case 14) although the effect is rather weak. To shed further light on the role of residue 45, the folding process 110,111 and the folding kinetics may have to be considered to (in)validate a pure thermodynamic analysis as carried out here. Haloalkane Dehalogenase DhaA.…”

mentioning

confidence: 99%

Exploring the Effect of Enhanced Sampling on Protein Stability Prediction

Markthaler

Fleck

Stankiewicz

et al. 2022

J. Chem. Theory Comput.

View full text Add to dashboard Cite

Changes in protein stability due to side-chain mutations are evaluated by alchemical free-energy calculations based on classical molecular dynamics (MD) simulations in explicit solvent using the GROMOS force field. Three proteins of different complexity with a total number of 93 single-point mutations are analyzed, and the relative free-energy differences are discussed with respect to configurational sampling and (dis)agreement with experimental data. For the smallest protein studied, a 34-residue WW domain, the starting structure dependence of the alchemical free-energy changes, is discussed in detail. Deviations from previous simulations for the two other proteins are shown to result from insufficient sampling in the earlier studies. Hamiltonian replica exchange in combination with multiple starting structures and sufficient sampling time of more than 100 ns per intermediate alchemical state is required in some cases to reach convergence.

show abstract

mentioning

confidence: 99%

Exploring the Effect of Enhanced Sampling on Protein Stability Prediction

Markthaler

Fleck

Stankiewicz

et al. 2022

J. Chem. Theory Comput.

View full text Add to dashboard Cite

show abstract

“…Due to the high amount of interest in the protein quality of maize, a close relative of sorghum, the sorghum syntenic orthologues of maize were extracted and compared to three studies on the maize kernel. The first, Wang et al (2016), is a proteomic analysis of intact protein bodies from maize endosperm (Wang et al, 2016). This study identified proteins that make up the composition of kernel protein bodies in maize.…”

Section: Deletions In Alpha-kafirin Genes Caused Alterations In Chrom...mentioning

confidence: 99%

“…This gene corresponds to a subtilisin protease. The syntenic orthologue was found to also be upregulated in o2 maize endosperms (Zhan et al, 2018), a component of maize protein bodies (Wang et al, 2016), as well associated with methionine to lysine ratio via GWAS (Shrestha et al, 2022). Interestingly, a second subtilisin protease was also upregulated in edited lines (SbiRTX430.06G174000).…”

Section: Deletions In Alpha-kafirin Genes Caused Alterations In Chrom...mentioning

confidence: 99%

Large and stable genome edits at the sorghum alpha kafirin locus result in changes in chromatin accessibility and globally increased expression of genes encoding lysine enrichment

Hurst

Yobi²,

Li³

et al. 2023

Front. Plant Sci.

View full text Add to dashboard Cite

IntroductionSorghum is a resilient and widely cultivated grain crop used for feed and food. However, it’s grain is deficient in lysine, an essential amino acid. This is due to the primary seed storage proteins, the alpha-kafirins, lacking lysine. It has been observed that reductions in alpha-kafirin protein results in rebalancing of the seed proteome and a corresponding increase in non-kafirin proteins which leads to an increased lysine content. However, the mechanisms underlying proteome rebalancing are unclear. This study characterizes a previously developed gene edited sorghum line, with deletions at the alpha kafirin locus.MethodsA single consensus guide RNA leads to tandem deletion of multiple members of the gene family in addition to the small target site mutations in remaining genes. RNA-seq and ATAC-seq were utilized to identify changes in gene expression and chromatin accessibility in developing kernels in the absence of most alpha-kafirin expression. ResultsSeveral differentially accessible chromatin regions and differentially expressed genes were identified. Additionally, several genes upregulated in the edited sorghum line were common with their syntenic orthologues differentially expressed in maize prolamin mutants. ATAC-seq showed enrichment of the binding motif for ZmOPAQUE 11, perhaps indicating the transcription factor’s involvement in the kernel response to reduced prolamins.DiscussionOverall, this study provides a resource of genes and chromosomal regions which may be involved in sorghum’s response to reduced seed storage proteins and the process of proteome rebalancing.

show abstract

“…The molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method was used to perform the binding free energy analysis in AMBER16 package [55,56]. The binding free energy (ΔG binding ) was calculated based on the followed equation:…”

Section: Binding Free Energy Analysismentioning

confidence: 99%

Insights into the aggregation mechanism of RNA recognition motif domains in TDP-43: a theoretical exploration

Liu

Jiang

et al. 2021

R. Soc. open sci.

Self Cite

View full text Add to dashboard Cite

The transactive response DNA-binding protein 43 (TDP-43) is associated with several diseases such as amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) due to pathogenic aggregations. In this work, we examined the dimer, tetramer and hexamer models built from the RRM domains of TDP-43 using molecular dynamics simulations in combination with the protein–protein docking. Our results showed that the formations of the dimer models are mainly achieved by the interactions of the RRM1 domains. The parallel β-sheet layers between the RRM1 domains provide most of the binding sites in these oligomer models, and thus play an important role in the aggregation process. The approaching of the parallel β-sheet layers from small oligomer models gradually expand to large ones through the allosteric communication between the α1/α2 helices of the RRM1 domains, which maintains the binding affinities and interactions in the larger oligomer models. Using the repeatable-superimposing method based on the tetramer models, we proposed a new aggregation mechanism of RRM domains in TDP-43, which could well characterize the formation of the large aggregation models with the repeated, helical and rope-like structures. These new insights help to understand the amyloid-like aggregation phenomena of TDP-43 protein in ALS and FTLD diseases.

show abstract

Molecular dynamics simulations on the conformational transitions from the G_A98 (G_A88) to G_B98 (G_B88) proteins

Cited by 6 publications

References 59 publications

Exploring the Effect of Enhanced Sampling on Protein Stability Prediction

Exploring the Effect of Enhanced Sampling on Protein Stability Prediction

Large and stable genome edits at the sorghum alpha kafirin locus result in changes in chromatin accessibility and globally increased expression of genes encoding lysine enrichment

Insights into the aggregation mechanism of RNA recognition motif domains in TDP-43: a theoretical exploration

Contact Info

Product

Resources

About