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Biology subjects

Ren, K.

Publications and source records attributed to Ren, K..

2 recordsLinked to original sources

Molecular basis for allosteric regulation of the type 2 ryanodine receptor channel gating by key modulators

The type-2 ryanodine receptor (RyR2) is responsible for releasing Ca2+ from the sarcoplasmic reticulum of cardiomyocytes, subsequently leading to muscle contraction. Here, we report four cryo-EM structures of porcine RyR2 bound to distinct modulators that collectively provide mechanistic insight into RyR2 regulation. Ca2+ alone induces a contraction of the Central domain that facilitates the dilation of S6 bundle, but is insufficient to open the pore. The small molecule agonist PCB95 helps Ca2+ to overcome the barrier for opening. FKBP12.6 induces a relaxation of the Central domain that decouples it from the S6 bundle, stabilizing RyR2 in a closed state. Caffeine locks the Central domain in a constitutively contracted state, while further addition of ATP opens the channel by strengthening the coupling between the U-motif and S6. Our study marks an important step towards mechanistic understanding of the complicated regulation of this key channel whose aberrant activity engenders life-threatening cardiac disorders.

biochemistry

A flexible simulation toolkit for designing and evaluating ChIP-sequencing experiments

A major challenge in evaluating quantitative ChIP-seq analyses, such as peak calling and differential binding, is a lack of reliable ground truth data. We present Tulip, a toolkit for rapidly simulating ChIP-seq data using statistical models of the experimental steps. Tulip may be used for a range of applications, including power analysis for experimental design, benchmarking of analysis tools, and modeling effects of processes such as replication on ChIP-seq signals.

genomics