Three Structural Phases of the Parkinson

DJ-1 is engaged in diverse cellular processes including cellular transformation, control of protein-RNA interaction, modulation of androgen receptor, antioxidative response, sperm fertilization, and autosomal recessive early-onset parkinsonism. Although it is not clear how DJ-1 participates in various cellular processes, structural alteration can be one of the molecular bases underlying the functional feature of DJ-1. DJ-1 forms filamentous aggregates in the presence of inorganic phosphate whereas DJ-1 normally exists as a homodimeric protein. In addition, the deletion of C-terminal fifteen residues leads to the oligomerization of DJ-1. Here, we depict the details of the three distinct structural phases of DJ-1 revealed by X-ray crystallography and electron microscopy, and investigate their functional consequences.nsonism. Although it is not clear how DJ-1 participates in various cellular processes, structural alteration can be one of the molecular bases underlying the functional feature of DJ-1. DJ-1 forms filamentous aggregates in the presence of inorganic phosphate whereas DJ-1 normally exists as a homodimeric protein. In addition, the deletion of C-terminal fifteen residues leads to the oligomerization of DJ-1. Here, we depict the details of the three distinct structural phases of DJ-1 revealed by X-ray crystallography and electron microscopy, and investigate their functional consequences.2

Structural and mechanistic characterization of an archaeal-like chaperonin from a thermophilic bacterium

The chaperonins (CPNs) are megadalton sized hollow complexes with two cavities that open and close to encapsulate non-native proteins. CPNs are assigned to two sequence-related groups that have distinct allosteric mechanisms. In Group I CPNs a detachable co-chaperone, GroES, closes the chambers whereas in Group II a built-in lid closes the chambers. Group I CPNs have a bacterial ancestry, whereas Group II CPNs are archaeal in origin. Here we describe open and closed crystal structures representing a new phylogenetic branch of CPNs. These Group III CPNs are divergent in sequence and structure from extant CPNs, but are closed by a built-in lid like Group II CPNs. A nucleotide-sensing loop, present in both Group I and Group II CPNs, is notably absent. We identified inter-ring pivot joints that articulate during ring closure. These Group III CPNs likely represent a relic from the ancestral CPN that formed distinct bacterial and archaeal branches. © 2017 The Author(s)

The crystal structure of the D-alanine-D-alanine ligase from Acinetobacter baumannii suggests a flexible conformational change in the central domain before nucleotide binding

Acinetobacter baumannii, which is emerging as a multidrugresistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 . The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays

Analysis of the FGF gene family provides insights into aquatic adaptation in cetaceans

Cetacean body structure and physiology exhibit dramatic adaptations to their aquatic environment. Fibroblast growth factors (FGFs) are a family of essential factors that regulate animal development and physiology; however, their role in cetacean evolution is not clearly understood. Here, we sequenced the fin whale genome and analysed FGFs from 8 cetaceans. FGF22, a hair follicle-enriched gene, exhibited pseudogenization, indicating that the function of this gene is no longer necessary in cetaceans that have lost most of their body hair. An evolutionary analysis revealed signatures of positive selection for FGF3 and FGF11, genes related to ear and tooth development and hypoxia, respectively. We found a D203G substitution in cetacean FGF9, which was predicted to affect FGF9 homodimerization, suggesting that this gene plays a role in the acquisition of rigid flippers for efficient manoeuvring. Cetaceans utilize low bone density as a buoyancy control mechanism, but the underlying genes are not known. We found that the expression of FGF23, a gene associated with reduced bone density, is greatly increased in the cetacean liver under hypoxic conditions, thus implicating FGF23 in low bone density in cetaceans. Altogether, our results provide novel insights into the roles of FGFs in cetacean adaptation to the aquatic environment

Genetic and Structural Characterization of a Thermo-Tolerant, Cold-Active, and Acidic Endo-β-1,4-glucanase from Antarctic Springtail, Cryptopygus antarcticus

The CaCel gene from Antarctic springtail Cryptopygus antarcticus codes for a cellulase belonging to the glycosyl hydrolase family 45 (GHF45). Phylogenetic, biochemical, and structural analyses revealed that the CaCel gene product (CaCel) is closely related to fungal GHF45 endo-β-1,4-glucanases. The organization of five introns within the open reading frame of the CaCel gene indicates its endogenous origin in the genome of the species, which suggests the horizontal transfer of the gene from fungi to the springtail. CaCel exhibited optimal activity at pH 3.5, retained 80% of its activity at 0-10 °C, and maintained a half-life of 4 h at 70 °C. Based on the structural comparison between CaCel and a fungal homologue, we deduced the structural basis for the unusual characteristics of CaCel. Under acidic conditions at 50 °C, CaCel was effective to digest the green algae (Ulva pertusa), suggesting that it could be exploited for biofuel production from seaweeds. © 2017 American Chemical Society

Molecular architecture and the mechanics of Lon, a protease-chaperone machine

The ATP-dependent Lon protease, which has orthologs distributed in all kingdoms of life, is essential in bacteria and other microorganisms under stress conditions and is needed for survival of mammalian cells subjected to oxidative damage. Lon consists of a molecular chaperone belonging to the AAA+ family and a protease with a serine-lysine catalytic dyad encoded in tandem in a single polypeptide. Here, we report the 2.0 ?resolution crystal structure of Lon from Thermococcus onnurineus NA14 (TonLon). Six subunits of TonLon assemble into a cylindrical structure with a sequestered internal chamber harboring the proteolytic active sites accessible only through restricted axial channels. Alternating subunits exist in two different nucleotide states displaying different domain orientations and intersubunit contacts indicative of the ATP hydrolysis-coupled motions driving protein unfolding and translocation.1

Purification, crystallization, and preliminary X-ray crystallographic analysis of the Group III chaperonin from Carboxydothermus hydrogenoformans

Chaperonins (CPNs) are megadalton sized ATP-dependent nanomachines that facilitate protein folding through complex cycles of complex allosteric articulation. They consist of two back-to-back stacked multisubunit rings. CPNs are usually classified into Group I and Group II. Here, we report the crystallization of both the AMPPNP (an ATP analogue) and ADP bound forms of a novel CPN, classified as belonging to a third Group, recently discovered in the extreme thermophile Carboxydothermus hydrogenoformans. Crystals of the two forms were grown by the vapor batch crystallization method at 295 K. Crystals of the Ch-CPN/AMPPNP complex diffracted to 3.0 angstrom resolution and belonged to the space group P422, with unit-cell parameters a = b = 186.166, c = 160.742 angstrom. Assuming the presence of four molecules in the asymmetric unit, the solvent content was estimated to be about 60.02%. Crystals of the Ch-CPN/ADP complex diffracted to 4.0 angstrom resolution and belonged to the space group P4212, with unit-cell parameters a = b = 209.780, c = 169.813 angstrom. Assuming the presence of four molecules in the asymmetric unit, the solvent content was estimated to be about 70.19%

Crystal structures of the open and closed states of a ~1 megadalton chaperonin

Proteins mediate nearly all the biochemical reactions in cells and thus the proper protein folding is essential for the survival of cells. Accumulation of misfolded and denatured proteins is engaged in the progression of several diseases including neurodegeneration and cancer. Chaperonins (CPNs) play critical roles in proper folding of nascent proteins or in refolding of denature proteins. CPNs are multi-subunit complexes that have a folding chamber, and ATP-hydrolysis allosterically affects the conformation of CPNs to facilitate folding process. In this talk, I present the two crystal structures of a chaperonin to depict the molecular mechanism underpinning the mechanical motion of this protein machine.cluding neurodegeneration and cancer. Chaperonins (CPNs) play critical roles in proper folding of nascent proteins or in refolding of denature proteins. CPNs are multi-subunit complexes that have a folding chamber, and ATP-hydrolysis allosterically affects the conformation of CPNs to facilitate folding process. In this talk, I present the two crystal structures of a chaperonin to depict the molecular mechanism underpinning the mechanical motion of this protein machine.2

Experimental phasing using zinc anomalous scattering

Zinc is a suitable metal for anomalous dispersion phasing methods. Crystal structure determination using anomalous scattering from zinc has been limited to proteins with intrinsically bound zinc(s). Herein we report that multiple zinc ions can be charged on the surface of proteins and used for structure determination of proteins with no intrinsic zinc-binding site. The discovery of facile zinc-binding to proteins without an intrinsic zinc-binding site opens a new avenue to the usage of zinc anomalous signal for structure determination.ons can be charged on the surface of proteins and used for structure determination of proteins with no intrinsic zinc-binding site. The discovery of facile zinc-binding to proteins without an intrinsic zinc-binding site opens a new avenue to the usage of zinc anomalous signal for structure determination.2