Publications by authors named "Linzhi Ye"

Type III CRISPR systems provide immunity against genetic invaders through the production of cyclic oligo-adenylate (cA) molecules that activate effector proteins that contain CRISPR-associated Rossman fold (CARF) domains. Here, we characterized the function and structure of an effector in which the CARF domain is fused to an adenosine deaminase domain, CRISPR-associated adenosine deaminase 1 (Cad1). We show that upon binding of cA or cA to its CARF domain, Cad1 converts ATP to ITP, both in vivo and in vitro.

View Article and Find Full Text PDF
Article Synopsis
  • - A new family of deubiquitylase (DUB)-resistant ubiquitin (Ub) probes, based on isopeptide-N-ethylated dimeric or polymeric Ub chains, has been developed to enhance the discovery of Ub chain-specific interactions in proteomic research.
  • - These new Ub probes can be produced efficiently through a one-step reaction involving ubiquitin-activating enzyme (E1) and recombinant Ub precursors, allowing for the creation of various Ub structures at a large scale.
  • - Label-free quantitative mass spectrometry (LFQ MS) studies suggest that these isopeptide-N-ethylated Ub probes can complement existing triazole-based probes for studying the ubiquitin interactome,
View Article and Find Full Text PDF

Native chemical ligation (NCL) has become one of the most important methods in chemical syntheses of proteins. Recently, in order to expand its scope, considerable effort has been devoted to tuning the C-terminal acyl donor thioesters used in NCL. This article reviews the recent advances in the design of C-terminal acyl donors, their precursors and surrogates, and highlights some noteworthy progress that may lead the future direction of protein chemical synthesis.

View Article and Find Full Text PDF

Solution of the three-dimensional structures of proteins is a critical step in deciphering the molecular mechanisms of their bioactivities. Among the many approaches for obtaining protein crystals, racemic protein crystallography has been developed as a unique method to solve the structures of an increasing number of proteins. Exploiting unnatural protein enantiomers in crystallization and resolution, racemic protein crystallography manifests two major advantages that are 1) to increase the success rate of protein crystallization, and 2) to obviate the phase problem in X-ray diffraction.

View Article and Find Full Text PDF