J. Appl. Cryst.の発刊に際して

https://hsrc.himmelfarb.gwu.edu/cgi/viewcontent.cgi?article=1037&context=smhs_biochem_facpubs

Histone recognition and large-scale structural analysis of the human bromodomain family.

Studies of bioactive lipids in general and sphingolipids in particular have intensified over the past several years, revealing an unprecedented and unanticipated complexity of the lipidome and its many functions, which rivals, if not exceeds, that of the genome or proteome. These results highlight critical roles for bioactive sphingolipids in most, if not all, major cell biological responses, including all major cell signalling pathways, and they link sphingolipid metabolism to key human diseases. Nevertheless, the fairly nascent field of bioactive sphingolipids still faces challenges in its biochemical and molecular underpinnings, including defining the molecular mechanisms of pathway and enzyme regulation, the study of lipid-protein interactions and the development of cellular probes, suitable biomarkers and therapeutic approaches.

/pdf/sphingolipids-and-their-metabolism-in-physiology-and-disease-e02vjx6ntt.pdf

Sphingolipids and their metabolism in physiology and disease.

Sphingolipids constitute a class of lipids defined by their eighteen carbon amino-alcohol backbones which are synthesized in the ER from nonsphingolipid precursors Modification of this basic structure is what gives rise to the vast family of sphingolipids that play significant roles in membrane biology and provide many bioactive metabolites that regulate cell function Despite the diversity of structure and function of sphingolipids, their creation and destruction are governed by common synthetic and catabolic pathways In this regard, sphingolipid metabolism can be imagined as an array of interconnected networks that diverge from a single common entry point and converge into a single common breakdown pathway In their simplest forms, sphingosine, phytosphingosine and dihydrosphingosine serve as the backbones upon which further complexity is achieved For example, phosphorylation of the C1 hydroxyl group yields the final breakdown products and/or the important signaling molecules sphingosine-1-phosphate, phytosphingosine-1-phosphate and dihydrosphingosine-1-phosphate, respectively On the other hand, acylation of sphingosine, phytosphingosine, or dihydrosphingosine with one of several possible acyl CoA molecules through the action of distinct ceramide synthases produces the molecules defined as ceramide, phytoceramide, or dihydroceramide Ceramide, due to the differing acyl CoAs that can be used to produce it, is technically a class of molecules rather than a single molecule and therefore may have different biological functions depending on the acyl chain it is composed of At the apex of complexity is the group of lipids known as glycosphingolipids (GSL) which contain dozens of different sphingolipid species differing by both the order and type of sugar residues attached to their headgroups Since these molecules are produced from ceramide precursors, they too may have differences in their acyl chain composition, revealing an additional layer of variation The glycosphingolipids are divided broadly into two categories: glucosphingolipids and galactosphingolipids The glucosphingolipids depend initially on the enzyme glucosylceramide synthase (GCS) which attaches glucose as the first residue to the C1 hydroxyl position Galactosphingolipids, on the other hand, are generated from galactosylceramide synthase (GalCerS), an evolutionarily dissimilar enzyme from GCS Glycosphingolipids are further divided based upon further modification by various glycosyltransferases which increases the potential variation in lipid species by several fold Far more abundant are the sphingomyelin species which are produced in parallel with glycosphingolipids, however they are defined by a phosphocholine headgroup rather than the addition of sugar residues Although sphingomyelin species all share a common headgroup, they too are produced from a variety of ceramide species and therefore can have differing acyl chains attached to their C-2 amino groups Whether or not the differing acyl chain lengths in SMs dictate unique functions or important biophysical distinctions has not yet been established Understanding the function of all the existing glycosphingolipids and sphingomyelin species will be a major undertaking in the future since the tools to study and measure these species are only beginning to be developed (see Fig 1 for an illustrated depiction of the various sphingolipid structures) The simple sphingolipids serve both as the precursors and the breakdown products of the more complex ones Importantly, in recent decades, these simple sphingolipids have gained attention for having significant signaling and regulatory roles within cells In addition, many tools have emerged to measure the levels of simple sphingolipids and therefore have become the focus of even more intense study in recent years With this thought in mind, this chapter will pay tribute to the complex sphingolipids, but focus on the regulation of simple sphingolipid metabolism

An overview of sphingolipid metabolism: from synthesis to breakdown.

Specific Recognition of Linear Ubiquitin Chains by NEMO Is Important for NF-κB Activation

In mammalian cells, ceramide is synthesized in the endoplasmic reticulum and transferred to the Golgi apparatus for conversion to sphingomyelin. Ceramide transport occurs in a nonvesicular manner and is mediated by CERT, a cytosolic 68-kDa protein with a C-terminal steroidogenic acute regulatory protein-related lipid transfer (START) domain. The CERT START domain efficiently transfers natural d-erythro-C16-ceramide, but not lipids with longer (C20) amide-acyl chains. The molecular mechanisms of ceramide specificity, both stereo-specific recognition and length limit, are not well understood. Here we report the crystal structures of the CERT START domain in its apo-form and in complex with ceramides having different acyl chain lengths. In these complex structures, one ceramide molecule is buried in a long amphiphilic cavity. At the far end of the cavity, the amide and hydroxyl groups of ceramide form a hydrogen bond network with specific amino acid residues that play key roles in stereo-specific ceramide recognition. At the head of the ceramide molecule, there is no extra space to accommodate additional bulky groups. The two aliphatic chains of ceramide are surrounded by the hydrophobic wall of the cavity, whose size and shape dictate the length limit for cognate ceramides. Furthermore, local high-crystallographic B-factors suggest that the α-3 and the Ω1 loop might work as a gate to incorporate the ceramide into the cavity. Thus, the structures demonstrate the structural basis for the mechanism by which CERT can distinguish ceramide from other lipid types yet still recognize multiple species of ceramides.

https://www.pnas.org/content/pnas/105/2/488.full.pdf

Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide

Acylation of lysine is an important protein modification regulating diverse biological processes. It was recently demonstrated that members of the human Sirtuin family are capable of catalyzing long chain deacylation, in addition to the well-known NAD+-dependent deacetylation activity [Feldman, J. L., Baeza, J., and Denu, J. M. (2013) J. Biol. Chem. 288, 31350–31356]. Here we provide a detailed kinetic and structural analysis that describes the interdependence of NAD+-binding and acyl-group selectivity for a diverse series of human Sirtuins, SIRT1–SIRT3 and SIRT6. Steady-state and rapid-quench kinetic analyses indicated that differences in NAD+ saturation and susceptibility to nicotinamide inhibition reflect unique kinetic behavior displayed by each Sirtuin and depend on acyl substrate chain length. Though the rate of nucleophilic attack of the 2′-hydroxyl on the C1′-O-alkylimidate intermediate varies with acyl substrate chain length, this step remains rate-determining for SIRT2 and SIRT3; however, for SI...

/pdf/kinetic-and-structural-basis-for-acyl-group-selectivity-and-2jt0c9ujdd.pdf

Kinetic and Structural Basis for Acyl-Group Selectivity and NAD+ Dependence in Sirtuin-Catalyzed Deacylation

Vestibular inhibition of sympathetic nerve activities

The three-dimensional structure of oryzacystatin-I, a cysteine proteinase inhibitor of the rice, Oryza sativa L. japonica, has been determined in solution at pH 6.8 and 25 °C by 1H and 15N NMR spec...

Three-dimensional solution structure of oryzacystatin-I, a cysteine proteinase inhibitor of the rice, Oryza sativa L. japonica.

The ability of natural metalloproteins to prevent inactivation of their metal cofactors by biological metabolites, such as glutathione, is an area that has been largely ignored in the field of artificial metalloenzyme (ArM) development. Yet, for ArM research to transition into future therapeutic applications, biocompatibility remains a crucial component. The work presented here shows the creation of a human serum albumin-based ArM that can robustly protect the catalytic activity of a bound ruthenium metal, even in the presence of 20 mM glutathione under in vitro conditions. To exploit this biocompatibility, the concept of glycosylated artificial metalloenzymes (GArM) was developed, which is based on functionalizing ArMs with N-glycan targeting moieties. As a potential drug therapy, this study shows that ruthenium-bound GArM complexes could preferentially accumulate to varying cancer cell lines via glycan-based targeting for prodrug activation of the anticancer agent umbelliprenin using ring-closing metathesis. Biocompatibility plays a crucial role for the development of artificial metalloenzymes (ArMs) for therapeutic applications. This work presents an ArM with a ruthenium catalyst that is protected from physiological glutathione and accumulates in cancer cell lines for metathesis-mediated prodrug activation.

Norio Kudo

Papers

Structural basis for specific lipid recognition by CERT responsible for nonvesicular trafficking of ceramide

Kinetic and Structural Basis for Acyl-Group Selectivity and NAD+ Dependence in Sirtuin-Catalyzed Deacylation

Vestibular inhibition of sympathetic nerve activities

Three-dimensional solution structure of oryzacystatin-I, a cysteine proteinase inhibitor of the rice, Oryza sativa L. japonica.

Biocompatibility and therapeutic potential of glycosylated albumin artificial metalloenzymes