▪ Abstract Hundreds of acetyltransferases exist. All use a common acetyl donor—acetyl coenzyme A—and each exhibits remarkable specificity for acetyl acceptors, which include small molecules and proteins. Analysis of the primary sequences of these enzymes indicates that they can be sorted into several superfamilies. This review covers the three-dimensional structures of members of one of these superfamilies, now referred to in the literature as the GCN5-related N-acetyltransferases (GNAT), reflecting the importance of one functional category, the histone acetyltransferases. Despite the diversity of substrate specificities, members of the GNAT superfamily demonstrate remarkable similarity in protein topology and mode of acetyl coenzyme A binding, likely reflecting a conserved catalytic mechanism.

GCN5-RELATED N-ACETYLTRANSFERASES: A Structural Overview

https://www.cell.com/molecular-cell/pdf/S1097-2765(15)00358-5.pdf

SIRT5 Regulates both Cytosolic and Mitochondrial Protein Malonylation with Glycolysis as a Major Target

Functional tools are needed to understand complex biological systems. Here we review how chemical reporters in conjunction with bioorthogonal labeling methods can be used to image and retrieve nucleic acids, proteins, glycans, lipids and other metabolites in vitro, in cells as well as in whole organisms. By tagging these biomolecules, researchers can now monitor their dynamics in living systems and discover specific substrates of cellular pathways. These advances in chemical biology are thus providing important tools to characterize biological pathways and are poised to facilitate our understanding of human diseases.

/pdf/chemical-reporters-for-biological-discovery-3wsrfbsxxs.pdf

Chemical reporters for biological discovery

The epigenetic modifications of histones are versatile marks that are intimately connected to development and disease pathogenesis including human cancers. In this review, we will discuss the many different types of histone modifications and the biological processes with which they are involved. Specifically, we review the enzymatic machineries and modifications that are involved in cancer development and progression, and how to apply currently available small molecule inhibitors for histone modifiers as tool compounds to study the functional significance of histone modifications and their clinical implications.

/pdf/epigenetic-modifications-of-histones-in-cancer-2gqxpuy10t.pdf

Epigenetic modifications of histones in cancer

Proteins constitute the majority of nature’s worker biomolecules. Designed for specific functions, complex tertiary structures make proteins ideal candidates for analysing natural systems and creating novel biological tools. Owing to both their large size and the need for proper folding, de novo synthesis of proteins has been quite a challenge, leading scientists to focus on modifying protein templates already provided by nature. Recently developed methods for protein modification fall into two broad categories: those that can modify the natural protein template directly and those that require genetic manipulation of the amino acid sequence before modification. The goal of this Review is not only to provide a window through which to view the many opportunities created by novel protein modification techniques‚ but also to act as an initial guide to help scientists find direction and form ideas in an ever-growing field. In addition to highlighting methods reported in the past 5 years, we aim to provide a broader sense of the goals and outcomes of protein modification and bioconjugation in general. While the main body of this paper comprises reactions involving the direct modification of expressed proteins, some further functionalization strategies as well as biological applications are also acknowledged. The discussion concludes by speculating which trends and discoveries will most likely come next in the field. Over the past 5 years, many novel site-selective protein modification techniques have been reported. Key features of these various strategies as well as prominent examples are discussed in this Review.

/pdf/contemporary-approaches-to-site-selective-protein-44jsa6i2gc.pdf

Contemporary approaches to site-selective protein modification

https://www.cell.com/molecular-cell/pdf/S1097-2765(19)30657-4.pdf

Glutarylation of Histone H4 Lysine 91 Regulates Chromatin Dynamics

Post-translational modifications (PTMs) have key roles in regulating protein-protein interactions in living cells. However, it remains a challenge to identify these PTM-mediated interactions. Here we develop a new lysine-based photo-reactive amino acid, termed photo-lysine. We demonstrate that photo-lysine, which is readily incorporated into proteins by native mammalian translation machinery, can be used to capture and identify proteins that recognize lysine PTMs, including 'readers' and 'erasers' of histone modifications.

Photo-lysine captures proteins that bind lysine post-translational modifications.

Dynamic combinatorial library (DCL) has emerged as an efficient tool for ligand discovery and become an important discovery modality in biomedical research. However, the applications of DCLs have been significantly hampered by low library diversity and limited analytical methods capable of processing large libraries. Here, we report a strategy that has addressed this limitation and can select cooperatively binding small-molecule pairs from large-scale dynamic libraries. Our approach is based on DNA-mediated dynamic hybridization, DNA-encoding, and a photo-cross-linking-based decoding scheme. To demonstrate the generality and performance of this approach, a 10 000-member DNA-encoded dynamic library has been prepared and selected against six protein targets. Specific binders have been identified for each target, and we have validated the biological activities of selected ligands for the targets that are implicated in important cellular functions including protein deacetylation and sumoylation. Notably, a se...

DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery

Chemical probes of epigenetic 'readers' of histone post-translational modifications (PTMs) have become powerful tools for mechanistic and functional studies of their target proteins in normal physiology and disease pathogenesis. Here we report the development of the first class of chemical probes of YEATS domains, newly identified 'readers' of histone lysine acetylation (Kac) and crotonylation (Kcr). Guided by the structural analysis of a YEATS-Kcr complex, we developed a series of peptide-based inhibitors of YEATS domains by targeting a unique π-π-π stacking interaction at the proteins' Kcr recognition site. Further structure optimization resulted in the selective inhibitors preferentially binding to individual YEATS-containing proteins including AF9 and ENL with submicromolar affinities. We demonstrate that one of the ENL YEATS-selective inhibitors, XL-13m, engages with endogenous ENL, perturbs the recruitment of ENL onto chromatin, and synergizes the BET and DOT1L inhibition-induced downregulation of oncogenes in MLL-rearranged acute leukemia.

Structure-guided development of YEATS domain inhibitors by targeting π-π-π stacking.

Protein posttranslational modifications (PTMs) play fundamental roles in regulating normal cell physiology and disease pathogenesis. Extensive studies on their cellular functions and mechanisms have advanced our understanding on some well-known PTMs such as phosphorylation, methylation, and acetylation. However, the biological roles played by many newly identified PTMs still remain poorly understood. Lysine malonylation, a covalent modification of the side chain of lysine, with a malonyl group incorporated at the eamine (Figure 1a), was recently identified as a novel PTM using two different approaches. One involved an antibody-

Xiang David Li

Papers

Glutarylation of Histone H4 Lysine 91 Regulates Chromatin Dynamics

Photo-lysine captures proteins that bind lysine post-translational modifications.

DNA-Encoded Dynamic Chemical Library and Its Applications in Ligand Discovery

Structure-guided development of YEATS domain inhibitors by targeting π-π-π stacking.

A chemical probe for lysine malonylation.