Protein target highlights in CASP15: Analysis of models by structure providers.

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the submitted predictions. While the overall ability to predict three-dimensional protein structures continues to impress, reproducing uncommon features not previously observed in experimental structures is still a challenge. Furthermore, instances with conformational flexibility and large multimeric complexes highlight the need for novel scoring strategies to better emphasize biologically relevant structural regions. Looking ahead, closer integration of computational and experimental techniques will play a key role in determining the next challenges to be unraveled in the field of structural molecular biology.

Architecture and functional dynamics of the pentafunctional AROM complex.

The AROM complex is a multifunctional metabolic machine with ten enzymatic domains catalyzing the five central steps of the shikimate pathway in fungi and protists. We determined its crystal structure and catalytic behavior, and elucidated its conformational space using a combination of experimental and computational approaches. We derived this space in an elementary approach, exploiting an abundance of conformational information from its monofunctional homologs in the Protein Data Bank. It demonstrates how AROM is optimized for spatial compactness while allowing for unrestricted conformational transitions and a decoupled functioning of its individual enzymatic entities. With this architecture, AROM poses a tractable test case for the effects of active site proximity on the efficiency of both natural metabolic systems and biotechnological pathway optimization approaches. We show that a mere colocalization of enzymes is not sufficient to yield a detectable improvement of metabolic throughput.

Development and validation of a HILIC-UV method for the determination of nucleotides in fish samples.

The aim of this work was the development of a simple, novel and accurate method for the determination of adenosine triphosphate (ATP) and its first five catabolites: adenosine diphosphate (ADP), adenosine monophosphate (AMP), inosine monophosphate (IMP), inosine (Ino) and hypoxanthine (Hx), in fish tissue, based on hydrophilic interaction liquid chromatography (HILIC). For this purpose, a stationary phase for polar and hydrophilic compounds (ZIC-pHILIC) was used. The effect of different chromatographic parameters and the molecular mechanism based on the van't Hoff plot were examined. The t-test and Dixon's Q-test were applied in order to examine statistical differences and outlier values. The recovery of the method ranged between 82.7% and 127% and the %RSD values were lower than 10% for all analytes determined. The method was applied in frozen sea bream samples stored at 0-4 °C. The Ki-, G-, H- and F values were calculated for the estimation of the level of fish freshness.

Laboratory investigation and phylogenetic analysis of enteroviruses involved in an aseptic meningitis outbreak in Greece during the summer of 2007.

BACKGROUND: Aseptic meningitis is the most commonly observed CNS infection and is mainly attributed to Non-Polio Enteroviruses (EV). OBJECTIVE: Identification and genetic analysis of the EV involved in the recent aseptic meningitis outbreak which occurred in Greece, during the summer of 2007. STUDY DESIGN: In total, 213 CSF and faecal samples were examined for EV presence by culture, while enteroviral RNA detection was performed by nucleic acid sequence-based amplification assay (NASBA). EV strains were typed by seroneutralization, as well as nested RT-PCR followed by VP1-2A gene partial sequencing. Phylogenetic analysis was carried out for the identification of the genetic relatedness among the isolated EV strains. RESULTS: EV detection rate in CSF and faecal samples was 43.9% and 70.8%, respectively. EV serotyping and VP1 region analysis revealed the predominance of echovirus 4 (ECV4) serotype and the circulation of ECV6, 9, 14, 25, Coxsackie A6, A15, A24 and Coxsackie B1 serotypes. All ECV4 isolates presented a 98.7% similarity in nucleotide sequence, with a Spanish ECV4 strain, isolated during a meningitis outbreak in 2006. CONCLUSIONS: It is the first time that ECV4 is associated with an aseptic meningitis outbreak in Greece, during which 9 different EV serotypes were co-circulating. All Greek ECV4 isolates were closely related to the Spanish ECV4 strain. Genetic analysis of the VP1 gene can significantly contribute to the revelation of the endemic EV strains circulation pattern and their phylogenetic relationship with enteroviruses involved in epidemics of distant geographical areas at different time periods.

Cocirculation of genotypes D4 and D6 in Greece during the 2005 to 2006 measles epidemic.

One of World Health Organization's proposed methods for the establishment of measles surveillance worldwide, to achieve the elimination of measles virus by 2010, is the genetic characterization of measles wild-type virus strains. In this study, 34 measles virus strains, isolated from clinical samples during the 2005 to 2006 measles outbreak in Greece, were genotyped and studied in terms of nucleotide variation and phylogeny. Interestingly, the cocirculation of 2 different genotypes, namely, D6 and D4, was revealed. In fact, the D4 genotype has never been previously reported in Greece. Finally, although the D4 Greek strains possessed identical nucleotide sequences, the D6 isolates segregated into 3 distinct subgroups, 2 of which differed genetically and phenotypically from all GenBank deposited measles sequences. It is, thus, important to continue the epidemiologic surveillance of measles in Greece to aid future studies of measles transmission, monitor the effectiveness of measles immunization, and eventually document the elimination of the virus in our country.