Trading in cooperativity for specificity to maintain uracil-free DNA

Members of the dUTPase superfamily play an important role in the maintenance of the pyrimidine nucleotide balance and of genome integrity. dCTP deaminases and the bifunctional dCTP deaminase-dUTPases are cooperatively regulated by dTTP. However, the manifestation of allosteric behavior within the same trimeric protein architecture of dUTPases, the third member of the superfamily, has been a question of debate for decades. Therefore, we designed hybrid dUTPase trimers to access conformational states potentially mimicking the ones observed in the cooperative relatives. We studied how the interruption of different steps of the enzyme cycle affects the active site cross talk. We found that subunits work independently in dUTPase. The experimental results combined with a comparative structural analysis of dUTPase superfamily enzymes revealed that subtile structural differences within the allosteric loop and the central channel in these enzymes give rise to their dramatically different cooperative behavior. We demonstrate that the lack of allosteric regulation in dUTPase is related to the functional adaptation to more efficient dUTP hydrolysis which is advantageous in uracil-DNA prevention

Structure and dynamics of a constitutively active neurotensin receptor

Many G protein-coupled receptors show constitutive activity, resulting in the production of a second messenger in the absence of an agonist; and naturally occurring constitutively active mutations in receptors have been implicated in diseases. To gain insight into mechanistic aspects of constitutive activity, we report here the 3.3 Å crystal structure of a constitutively active, agonist-bound neurotensin receptor (NTSR1) and molecular dynamics simulations of agonist-occupied and ligand-free receptor. Comparison with the structure of a NTSR1 variant that has little constitutive activity reveals uncoupling of the ligand-binding domain from conserved connector residues, that effect conformational changes during GPCR activation. Furthermore, molecular dynamics simulations show strong contacts between connector residue side chains and increased flexibility at the intracellular receptor face as features that coincide with robust signalling in cells. The loss of correlation between the binding pocket and conserved connector residues, combined with altered receptor dynamics, possibly explains the reduced neurotensin efficacy in the constitutively active NTSR1 and a facilitated initial engagement with G protein in the absence of agonist

Crystal structure of an HD-GYP domain cyclic-di-GMP phosphodiesterase reveals an enzyme with a novel trinuclear catalytic iron centre

Bis-(3′,5′) cyclic di-guanylate (c-di-GMP) is a key bacterial second messenger that is implicated in the regulation of many crucial processes that include biofilm formation, motility and virulence. Cellular levels of c-di-GMP are controlled through synthesis by GGDEF domain diguanylate cyclases and degradation by two classes of phosphodiesterase with EAL or HD-GYP domains. Here, we have determined the structure of an enzymatically active HD-GYP domain protein from Persephonella marina (PmGH) alone, in complex with substrate (c-di-GMP) and final reaction product (GMP). The structures reveal a novel trinuclear iron binding site, which is implicated in catalysis and identify residues involved in recognition of c-di-GMP. This structure completes the picture of all domains involved in c-di-GMP metabolism and reveals that the HD-GYP family splits into two distinct subgroups containing bi- and trinuclear metal centres.</p

Flavonoids and Related Compounds as Nucleoside Transporter Inhibitors

Mammalian nucleoside transporters can be classified into two main categories, namely, equilibrative nucleoside transporters (ENTs) and concentrative nucleoside transporters (CNTs). ENTs are ubiquitous, and mediate sodium-independent bi-directional facilitated diffusion nucleoside transport processes. CNTs on the other hand, are secondary active unidirectional transporters that are sodium-dependent. Both the equilibrative and the concentrative nucleoside transporters have several family members which are ENT1 to ENT4 and CNT1 to CNT6. Over the past two decades, important advances in the understanding of nucleoside transporter functions have been made. Identification and molecular cloning of the ENT and CNT families from mammals and protozoan parasites have provided much information about the structure, function, regulation, and tissue and cellular localization. Structure–function analyses of various nucleoside transporter chimeras and mutants have revealed important elements involved in substrate and inhibitor recognition and binding. However, the mechanisms that regulate nucleoside transporters in various tissues and cell types are just beginning to be understood. Because of the ability of these transporters to handle nucleoside analogues used in the treatment of patients with cancer and viral diseases, ongoing research should allow the design of more specifically targeted new compounds or improvements to existing drugs. New drugs are welcome not only in the treatment of cancer and viral diseases, but also in cardiovascular disorders and parasitic infections. Due to the absence of crystal structures and limited information regarding the active sites of nucleoside transporters, the designing of novel inhibitors is confined to ligand-based methods. In an effort to search for novel classes of inhibitors other than the existing ones, a series of 95 different flavone and flavone-like compounds was screened against concentrative nucleoside transporters (CNT 1, 2 and 3) and equilibrative nucleoside transporters (ENT 1 and 2). The results obtained in the form of IC50 values were further utilized to perform quantitative structure–activity relationship studies which indeed helped to understand the effects of different functionalities in the inhibition of nucleoside transporters. The validated 3D-QSAR models were used for design and activity prediction of new compounds. Pharmacophore hypotheses were also generated for hCNT3 using the PHASE pharmacophore mapping program to establish structural criteria for inhibitor design, and for database searching to find new hit molecules. Additionally, fifteen compounds were selected based on SAR and screened for equilibrative nucleoside transporter inhibition for validation of QSAR models. One novel compound, XI was designed with reduced complexity in further attempts to identify the ENT pharmacophore. But the synthetic route followed to prepare compound XI, resulted in the synthesis of compounds XII and XIII, which were evaluated as a mixture and exhibited substantial inhibitory activity against hENT1, but had no significant effect on hENT2 or hCNT3.This work has identified a novel class of CNT and ENT nucleoside transporter inhibitors and delineated structural determinants of potency and transporter subtype selectivity

Interaction Forces And Reaction Kinetics Of Ligand-Cell Receptor Systems Using Atomic Force Microscopy

Atomic Force Microscopy (AFM) provides superior imaging resolution and the ability to measure forces at the nanoscale. It is an important tool for studying a wide range of bio-molecular samples from proteins, DNA to living cells. We developed AFM measurement procedures to measure protein interactions on live cells at the single molecular level. These measurements can be interpreted by using proper statistical approaches and can yield important parameters about ligand-receptor interactions on live cells. However, the standard theory for analyzing rupture force data does not fit the experimental rupture force histograms. Most of the experimental measurements of rupture force data generate a probability distribution function (pdf) with a high force tail. We show that this unexpected high force tail can be attributed to multiple attachments and heterogeneous bonding by studying a model system, biotin-avidin. We have applied our methodology to the medically relevant system of discoidin domain receptors (DDR) on live cells and their interaction with their ligand, collagen. In addition, we have also used AFM to study drug-delivery particles, in particular polymer micelles containing fluorescently labeled siRNA particles. In this study, we measured interaction forces and binding probability measurements between folate receptor functionalized cantilever and different substrates, as well as combined AFM and fluorescence microscopy

Probing the Mechanism of Oxalate Decarboxylase

Oxalate decarboxylase (EC 4. 1. 1. 2 OxDC) from Bacillus subtilis is a manganese-dependent enzyme that catalyzes the cleavage of the chemically inactive C-C bond in oxalate to yield formate and carbon dioxide. A mechanism involving Mn(III) has been proposed for OxDC, however no clear spectroscopic evidence to support this mechanism has yet been obtained. In addition, a recent study has shown that N-terminal metal binding site loop variants of OxDC were able to catalyze the oxidation of oxalate to yield hydrogen peroxide and carbon dioxide, which makes OxDc function as another oxalate degradation protein in the cupin superfamily, oxalate oxidase (EC 1.2.3.4 OxOx). In this work, wild-type (WT) OxDC and a series of variants with mutations on conserved residues were characterized to further investigate the catalytic mechanism of OxDC. The application of membrane inlet mass spectrometry (MIMS), electronic paramagnetic resonance (EPR) spectroscopy and kinetic isotope effects (KIEs) provided more detailed information about the mechanism. Mn(III) was identified and characterized under acidic conditions in the presence of dioxygen. Also, mutations on the second shell residues in the N-terminal metal binding site affected the properties of the metal. In the N-terminal domain, the functional importance of the residues in the active site loop region, especially Glu162, was confirmed, and evidence for the proposed mechanism in which OxDC and OxOx share the initial steps has been found. In addition, the mono-dentate coordination of oxalate in the N-terminal metal binding site was confirmed by X-ray crystallography. A proteinase cleavable OxDC was constructed and characterized, revealing a strong interaction between the N-terminal and C-terminal domains

The human SKI complex regulates channeling of ribosome-bound RNA to the exosome via an intrinsic gatekeeping mechanism

The superkiller (SKI) complex is the cytoplasmic co-factor and regulator of the RNA-degrading exosome. In human cells, the SKI complex functions mainly in co-translational surveillance-decay pathways, and its malfunction is linked to a severe congenital disorder, the trichohepatoenteric syndrome. To obtain insights into the molecular mechanisms regulating the human SKI (hSKI) complex, we structurally characterized several of its functional states in the context of 80S ribosomes and substrate RNA. In a prehydrolytic ATP form, the hSKI complex exhibits a closed conformation with an inherent gating system that effectively traps the 80S-bound RNA into the hSKI2 helicase subunit. When active, hSKI switches to an open conformation in which the gating is released and the RNA 3′ end exits the helicase. The emerging picture is that the gatekeeping mechanism and architectural remodeling of hSKI underpin a regulated RNA channeling system that is mechanistically conserved among the cytoplasmic and nuclear helicase-exosome complexes