Predicted models and CCP4.

In late 2020, the results of CASP14, the 14th event in a series of competitions to assess the latest developments in computational protein structure-prediction methodology, revealed the giant leap forward that had been made by Google's Deepmind in tackling the prediction problem. The level of accuracy in their predictions was the first instance of a competitor achieving a global distance test score of better than 90 across all categories of difficulty. This achievement represents both a challenge and an opportunity for the field of experimental structural biology. For structure determination by macromolecular X-ray crystallography, access to highly accurate structure predictions is of great benefit, particularly when it comes to solving the phase problem. Here, details of new utilities and enhanced applications in the CCP4 suite, designed to allow users to exploit predicted models in determining macromolecular structures from X-ray diffraction data, are presented. The focus is mainly on applications that can be used to solve the phase problem through molecular replacement.

The CCP4 suite: integrative software for macromolecular crystallography.

The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.

CCP4 Cloud for structure determination and project management in macromolecular crystallography.

Nowadays, progress in the determination of three-dimensional macromolecular structures from diffraction images is achieved partly at the cost of increasing data volumes. This is due to the deployment of modern high-speed, high-resolution detectors, the increased complexity and variety of crystallographic software, the use of extensive databases and high-performance computing. This limits what can be accomplished with personal, offline, computing equipment in terms of both productivity and maintainability. There is also an issue of long-term data maintenance and availability of structure-solution projects as the links between experimental observations and the final results deposited in the PDB. In this article, CCP4 Cloud, a new front-end of the CCP4 software suite, is presented which mitigates these effects by providing an online, cloud-based environment for crystallographic computation. CCP4 Cloud was developed for the efficient delivery of computing power, database services and seamless integration with web resources. It provides a rich graphical user interface that allows project sharing and long-term storage for structure-solution projects, and can be linked to data-producing facilities. The system is distributed with the CCP4 software suite version 7.1 and higher, and an online publicly available instance of CCP4 Cloud is provided by CCP4.

Differential Impact of Hexuronate Regulators ExuR and UxuR on the Escherichia coli Proteome.

ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the Escherichia coli proteome in response to a uxuR or exuR deletion. Our data clearly show that the effects are different: deletion of uxuR resulted in strongly enhanced expression of D-mannonate dehydratase UxuA and flagellar protein FliC, and in a reduced amount of outer membrane porin OmpF, while the absence of ExuR did not significantly alter the spectrum of detected proteins. Consequently, the physiological roles of proteins predicted as homologs seem to be far from identical. Effects of uxuR deletion were largely dependent on the cultivation conditions: during growth with glucose, UxuA and FliC were dramatically altered, while during growth with glucuronate, activation of both was not so prominent. During the growth with glucose, maximal activation was detected for FliC. This was further confirmed by expression analysis and physiological tests, thus suggesting the involvement of UxuR in the regulation of bacterial motility and biofilm formation.

Structure and RNA-Binding Properties of Lsm Protein from Halobacterium salinarum.

The structure and the RNA-binding properties of the Lsm protein from Halobacterium salinarum have been determined. A distinctive feature of this protein is the presence of a short L4 loop connecting the ß3 and ß4 strands. Since bacterial Lsm proteins (also called Hfq proteins) have a short L4 loop and form hexamers, whereas archaeal Lsm proteins (SmAP) have a long L4 loop and form heptamers, it has been suggested that the length of the L4 loop may affect the quaternary structure of Lsm proteins. Moreover, the L4 loop covers the region of SmAP corresponding to one of the RNA-binding sites in Hfq, and thus can affect the RNA-binding properties of the protein. Our results show that the SmAP from H. salinarum forms heptamers and possesses the same RNA-binding properties as homologous proteins with the long L4 loop. Therefore, the length of the L4 does not govern the number of monomers in the protein particles and does not affect the RNA-binding properties of Lsm proteins.

[Tobacco consumption and bladder cancer mortality in Spain]. / Consumo de tabaco y mortalidad por cáncer vesical en España.

OBJECTIVES: To establish the trend of the bladder cancer adjusted mortality and its correlation with tobacco consumption in different Spanish Autonomic Communities over a 15 year period. METHODS: We evaluate the trends of mortality rates associated with bladder cancer between January 1st 1989 and December 31st 2002 in the geographic area of Spain, as well as the tendency of tobacco consumption. Demographic and mortality data were obtained from the National Institute of Statistics, and consumption data were obtained from the Commissioner for the Tobacco Market in the Spanish Economics and Finances Ministry. We calculate the average number of cigarettes (1 package = 20 cigarettes) consumed per person; we also calculate bladder cancer adjusted mortality rates, presented as number of deaths for that cause per 100.000 persons year, and the ratio between number of packages of cigarettes consumed and adjusted mortality rate. We determine the yearly percentage increase over the whole period of study for both the mortality rate and tobacco consumption, and evaluate their correlation by the Spearman's coefficient. RESULTS: Mean adjusted bladder cancer mortality rate over the period of study was 9.4 deaths per 100.000 habitants year, and mean tobacco consumption was 109.7 packages per person year. There has been a 2.05% yearly increase of bladder cancer associated mortality, mean cigarette consumption has diminished 1.3% per year. The Spearman's test did not show any correlation between both factors (p = 0.722). CONCLUSIONS: Despite preventive measures for tobacco addiction in our country, there is an important continuous consumption. The increase in the incidence of bladder cancer does not seem to be related with higher tobacco consumption currently, therefore it may be related with other genetic or environmental factors.

[Renal cell renal carcinoma. Analysis of incidence and survival in a 90.000 citizens healthcare area]. / Carcinoma renal de células claras. Análisis de incidencia y supervivencia en un area sanitaria de 90,000 habitantes.

OBJECTIVES: To evaluate the most relevant epidemiological and survival data of the renal cell carcinoma (RCC) in a 90.000 citizens geographic area, as well as its association with risk factors such as tobacco or diuretic drugs use. METHODS: All patients with the pathologic diagnosis of renal cell carcinoma between January 1st 1987 and January 31st 2004 were included in the study. Adjusted incidence rates (standardized) per 100.000 inhabitants year, annual percentage increase, and epidemic index in the health-care area VIII in Ciudad Real (90.000 inhabitants) were calculated. For the population adjustment we used the data Published by the National Institute of Statistics. We evaluated the differences in mortality between males/females, as well as in relation to tobacco consumption, using the chi-square test or the Fisher exact test, and the overall survival by a Cox regression model. RESULTS: Thirty-eight RCC were diagnosed, with a maximum incidence of 7.21 cases per 100.000 inhabitants year. There was an annual percentage increase of 2.06% over the whole period. There were no statistically significant differences in gender-associated mortality (p = 0.1), tumor stage (p = 0.063), tobacco consumption (p = 0.13), diuretic drugs consumption (p = 0.69), or both (p = 0.5). Mortality was significantly higher during the first 5 years after surgery. CONCLUSIONS: The incidence of RCC is progressively increasing, and it is predictable that this trend will be maintained in the next years. Overall mortality (any cause) associated with RCC is higher in the first five years after diagnosis.

[Circumcision in religious art]. / La circuncisión en el arte religioso.

OBJECTIVES: The objective of this study is to perform a historical journey through the topic of circumcision from the Italian Renaissance to the Spanish Baroque. METHODS: We evaluated the paintings about circumcision between both periods, including their most representative works. RESULTS AND CONCLUSIONS: Circumcision is a frequent topic in the religious painting in both periods.