2018 DBC Award Winners Announced

December 17th, 2017 by pthomas2

The ACS Division of Biological Chemistry announces its 2018 Award Winners for excellence in many diverse areas of biological chemistry. Find out more here.

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Chaperone-mediated autophagy and endosomal microautophagy: joint by a chaperone [Metabolism]

December 15th, 2017 by Kumsal A Tekirdag, Ana Maria Cuervo

A variety of mechanisms deliver cytosolic materials to the lysosomal compartment for degradation through autophagy. Here, we focus on two autophagic pathways, chaperone-mediated autophagy and endosomal microautophagy that rely on the cytosolic chaperone hsc70 for substrate targeting. Although hsc70 participates in triage of proteins for degradation by different proteolytic systems, the common characteristic shared by these two forms of autophagy, is that hsc70 binds directly to a specific five amino acids motif in the cargo protein for its autophagic targeting. We summarize the current understanding of the molecular machineries behind each of these types of autophagy.

Nonhomologous DNA End Joining for Repair of DNA Double-Strand Breaks [Protein Structure and Folding]

December 14th, 2017 by Nicholas R Pannunzio, Go Watanabe, Michael R. Lieber

Nonhomologous DNA end joining (NHEJ) is the predominant DSB repair pathway throughout the cell cycle and accounts for nearly all DSB repair outside of the S and G2 phases. NHEJ relies on Ku to thread onto DNA termini and thereby improve the affinity of the NHEJ enzymatic components consisting of polymerases (Pol μ and Pol λ), a nuclease (the Artemis·DNA-PKcs complex), and a ligase (XLF·XRCC4·Lig4 complex). Each of the enzymatic components is distinctive for its versatility in acting on diverse incompatible DNA end configurations coupled with a flexibility in loading order, resulting in many possible junctional outcomes from one DSB. DNA ends can either be directly ligated or, if the ends are incompatible, processed until a ligatable configuration is achieved that is often stabilized by up to 4 bp of terminal microhomology. Processing of DNA ends results in nucleotide loss or addition, explaining why DSBs repaired by NHEJ are rarely restored to their original DNA sequence. Thus, NHEJ is a single pathway with multiple enzymes at its disposal to repair DSBs, resulting in a diversity of repair outcomes.

Subtle changes at the variable domain interface of the T-cell receptor can strongly increase affinity [Immunology]

December 14th, 2017 by Preeti Sharma, David M Kranz

Most affinity-maturation campaigns for antibodies and T cell receptors (TCRs) operate on the residues at the binding site, located within the loops known as complementarity determining regions (CDRs). Accordingly, mutations in contact residues, or so-called "second shell" residues, that increase affinity are typically identified by group at the α:β interface, at a significant distance from the TCR/pepMHC binding site, remarkably affected ligand binding. The variant retained a high degree of specificity for MART- 1/HLA-A2, indicating that our approach provides a general strategy for engineering improvements in either soluble or cell-based TCRs for therapeutic purposes.directed evolution involving combinatorial libraries. To determine the impact of residues located at a distance from the binding site, here we used single codon libraries of both CDR and non- CDR residues to generate a deep mutational scan of a human TCR against the cancer antigen MART-1/HLA-A2. Non-CDR residues included those at the interface of the TCR variable domains (α and β) and surface-exposed framework residues. Mutational analyses showed that both α:β interface and CDR residues were important in maintaining binding to MART- 1/HLA-A2, likely due to either structural requirements for proper α:β association or direct contact with the ligand. More surprisingly, many α:β interface substitutions yielded improved binding to MART-1/HLA-A2. To further explore this finding, we constructed interface libraries and selected them for improved stability or affinity. Among the variants identified, one conservative substitution (β) was most prevalent. Further analysis of β showed that it enhanced thermostability and increased affinity by 60-fold. Thus, introducing a single hydroxyl group at the α:β interface, at a significant distance from the TCR/pepMHC binding site, remarkably affected ligand binding. The variant retained a high degree of specificity for MART- 1/HLA-A2, indicating that our approach provides a general strategy for engineering improvements in either soluble or cell-based TCRs for therapeutic purposes.

The ubiquitin E3 ligase CHIP promotes proteasomal degradation of the serine/threonine protein kinase PINK1 during staurosporine-induced cell death [Cell Biology]

December 14th, 2017 by Lang Yoo, Kwang Chul Chung

Mutations in the gene for the serine/threonine protein kinase PTEN-induced putative kinase 1 (PINK1) are the second most frequent cause of autosomal recessive Parkinson disease (PD). Via its kinase activity, PINK1 regulates neuronal cell survival and mitochondrial quality control. Numerous reports have revealed that PINK1 has diverse and physiologically significant functions, and, therefore, its activity should be tightly regulated. However, the molecular mechanisms regulating PINK1 stability and the modulator(s) involved have not been elucidated. In this study, we demonstrate that the ubiquitin E3 ligase CHIP promotes PINK1 ubiquitination and decreases its steady-state levels. Moreover, PINK1 levels were strongly reduced in HEK293 and SH-SY5Y cells exposed to the apoptosis-inducer staurosporine. Of note, we found that this reduction resulted from CHIP-mediated PINK1 ubiquitination. Accordingly, siRNA-mediated CHIP knockdown reduced susceptibility to staurosporine-induced cell death. Taken together, these findings suggest that CHIP plays a role in negative regulation of PINK1 stability and may suppress PINK1 cytoprotective effect during staurosporine-induced mammalian cell death. We propose that this PINK1 regulatory pathway might contribute to PD pathogenesis.
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The inducible microRNA-203 in fish represses the inflammatory responses to Gram-negative bacteria by targeting IL-1 receptor-associated kinase 4 [Gene Regulation]

December 14th, 2017 by Tianjun Xu, Qing Chu, Junxia Cui, Xueyan Zhao

Innate immune responses are the first defense against pathogenic invaders. Activation and termination of these immune responses are regulated by several mechanisms. MicroRNAs (miRNAs), a group of small non-coding RNAs, have been implicated in the regulation of a spectrum of both physiological and pathological conditions, including immune responses. Although immune regulatory miRNAs networks in higher vertebrates have been well described, regulation of these responses in fish species is poorly understood in fish species. In the present study, we investigated the role of the miRNA miR-203 involved in inflammatory responses in miiuy croaker (Miichthys miiuy). We found that the Gram-negative bacterium, Vibrio anguillarum and LPS significantly upregulated host miR-203 expression. The increased miR-203 expression suppressed the production of inflammatory cytokines and thereby prevented mounting of a full immune response. Mechanistically, we identified and validated IL-1 receptor-associated kinase 4 (IRAK4) as a target of miR-203. We observed that miR-203 could post-transcriptionally controls IRAK4 expression and thereby inhibits the activation of nuclear factor kappa B (NF-κB) signaling. In summary, our findings reveal that miR-203 in fish is a critical suppressor of innate immune responses to bacterial infection by suppressing a feedback to IRAK4-NF-κB-mediated signaling in fish.
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Neurobiology: Defining your territory

December 12th, 2017 by Grant Miura

Neurobiology: Defining your territory

Neurobiology: Defining your territory, Published online: 12 December 2017; doi:10.1038/nchembio.2544

Neurobiology: Defining your territory

Protein engineering: Finding the best ligase

December 12th, 2017 by Christian F W Becker

Protein engineering: Finding the best ligase

Protein engineering: Finding the best ligase, Published online: 12 December 2017; doi:10.1038/nchembio.2533

Modification of folded proteins at will, within any sequence context, remains an elusive goal. A proteome-wide screening approach has now identified a set of protein ligases that enables conjugation of peptides to almost any protein N terminus, overcoming longstanding limitations in protein engineering.

Resistance mechanisms: Watering down a warhead

December 12th, 2017 by Caitlin Deane

Resistance mechanisms: Watering down a warhead

Resistance mechanisms: Watering down a warhead, Published online: 12 December 2017; doi:10.1038/nchembio.2542

Resistance mechanisms: Watering down a warhead

Microbiology: Trapping Rac1

December 12th, 2017 by Karin Kuehnel

Microbiology: Trapping Rac1

Microbiology: Trapping Rac1, Published online: 12 December 2017; doi:10.1038/nchembio.2541

Microbiology: Trapping Rac1