Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2

BACKGROUND: The mechanisms underlying protein function and associated conformational change are dominated by a series of local entropy fluctuations affecting the global structure yet are mediated by only a few key residues. Transitional Dynamic Analysis (TDA) is a new method to detect these changes in local protein flexibility between different conformations arising from, for example, ligand binding. Additionally, Positional Impact Vertex for Entropy Transfer (PIVET) uses TDA to identify important residue contact changes that have a large impact on global fluctuation. We demonstrate the utility of these methods for Cyclin-dependent kinase 2 (CDK2), a system with crystal structures of this protein in multiple functionally relevant conformations and experimental data revealing the importance of local fluctuation changes for protein function. RESULTS: TDA and PIVET successfully identified select residues that are responsible for conformation specific regional fluctuation in the activation cycle of Cyclin Dependent Kinase 2 (CDK2). The detected local changes in protein flexibility have been experimentally confirmed to be essential for the regulation and function of the kinase. The methodologies also highlighted possible errors in previous molecular dynamic simulations that need to be resolved in order to understand this key player in cell cycle regulation. Finally, the use of entropy compensation as a possible allosteric mechanism for protein function is reported for CDK2. CONCLUSION: The methodologies embodied in TDA and PIVET provide a quick approach to identify local fluctuation change important for protein function and residue contacts that contributes to these changes. Further, these approaches can be used to check for possible errors in protein dynamic simulations and have the potential to facilitate a better understanding of the contribution of entropy to protein allostery and function

A Novel Protein Kinase-Like Domain in a Selenoprotein, Widespread in the Tree of Life

Selenoproteins serve important functions in many organisms, usually providing essential oxidoreductase enzymatic activity, often for defense against toxic xenobiotic substances. Most eukaryotic genomes possess a small number of these proteins, usually not more than 20. Selenoproteins belong to various structural classes, often related to oxidoreductase function, yet a few of them are completely uncharacterised

Ethical issues in autologous stem cell transplantation (ASCT) in advanced breast cancer: A systematic literature review

BACKGROUND: An effectiveness assessment on ASCT in locally advanced and metastatic breast cancer identified serious ethical issues associated with this intervention. Our objective was to systematically review these aspects by means of a literature analysis. METHODS: We chose the reflexive Socratic approach as the review method using Hofmann's question list, conducted a comprehensive literature search in biomedical, psychological and ethics bibliographic databases and screened the resulting hits in a 2-step selection process. Relevant arguments were assembled from the included articles, and were assessed and assigned to the question list. Hofmann's questions were addressed by synthesizing these arguments. RESULTS: Of the identified 879 documents 102 included arguments related to one or more questions from Hofmann's question list. The most important ethical issues were the implementation of ASCT in clinical practice on the basis of phase-II trials in the 1990s and the publication of falsified data in the first randomized controlled trials (Bezwoda fraud), which caused significant negative effects on recruiting patients for further clinical trials and the doctor-patient relationship. Recent meta-analyses report a marginal effect in prolonging disease-free survival, accompanied by severe harms, including death. ASCT in breast cancer remains a stigmatized technology. Reported health-related-quality-of-life data are often at high risk of bias in favor of the survivors. Furthermore little attention has been paid to those patients who were dying. CONCLUSIONS: The questions were addressed in different degrees of completeness. All arguments were assignable to the questions. The central ethical dimensions of ASCT could be discussed by reviewing the published literature

Assistência à mulher climatérica: novos paradigmas Atención a la mujer climatérica: nuevos paradigmas Assistance to the climacteric woman: new paradigms

O envelhecimento populacional é uma realidade demográfica brasileira. Como conseqüência, espera-se, nos próximos anos, um aumento progressivo na procura dos serviços de saúde por mulheres com queixas relacionadas ao climatério. Paralelamente, a assistência ao climatério tem passado por uma modificação de paradigmas, impondo aos profissionais de saúde uma mudança de atitude. Reconhece-se que o climatério é influenciado tanto por fatores biológicos, como por fatores psicossociais e culturais, cujo conhecimento é fundamental para uma assistência mais qualificada e humanizada. Este artigo propõe refletir sobre as mudanças de paradigmas na assistência ao climatério, destacando a multidisciplinaridade e interdisciplinaridade, no sentido acolher melhor essa parcela da população e proporcionar-lhe um cuidado integral e individualizado, aproximando o saber da sensibilidade, voltado a uma melhor qualidade vida.<br>Envejecimiento poblacional es una realidad demográfica brazilian. Consecuentementese espera un aumento progresivo de la búsqueda en los servicios de salud del país por mujeres con quejas relacionadas al climaterio. La asistencia al climaterio ha pasado por un cambio de paradigmas que han impuesto a los profesionales de la salud. El climaterio es influenciado por factores biológicos, factores psicosociales y culturales, cuyo conocimiento es fundamental para la planificación de una asistencia. Artículo se propone reflexionar sobre los cambios de paradigmas, el abordaje multidisciplinario e interdisciplinario, en el sentido de recibir mejor esta parcela de la población y proporcionarle un cuidado integral e individualizado, aproximando el saber de la sensibilidad, y el tener como objetivo a una mejor calidad de vida.<br>Population aging is a demographic reality for Brazil. Consequently, in the next years it is expected a progressive increase in seeking health care services in the country by women with complaints related to climacterium. Parallel to it, assistance at this part of woman's life has been going through a paradigm shift which has imposed to health professionals a change of attitude in relation to this stage of woman's life. Today it is acknowledged that the climacterium is influenced by biological, psychosocial and cultural factors, whose knowledge is fundamental for planning a more qualified and humanized care. This article proposes a reflection on the paradigm shifts in assistance at climacterium, highlighting important aspects as multidisciplinarity and interdisciplinarity, so as to serve better this portion of population, and provide it with more integrated and individualized care, bringing together knowledge and sensitivity, and always aiming at a better quality of life

Molecular cloning and expression analysis of a gene encoding KUP/HAK/KT-type potassium uptake transporter from Cryptomeria japonica

Potassium ion (K+) is an essential and the most abundant intracellular cation in plants. The roles of K+ in various aspects of plant life are closely linked to its transport across biological membranes such as the plasma membrane and the tonoplast, which is mediated by membrane-bound transport proteins known as transporters and channels. Information on the molecular basis of K+ membrane transport in trees, especially in conifers, is currently limited. In this study, we isolated one complementary DNA, CjKUP1, which is homologous to known plant K+ transporters, from Cryptomeria japonica. Complementation tests using an Escherichia coli mutant, which is deficient in K+ uptake activity, was conducted to examine the K+ uptake function of the protein encoded by CjKUP1. Transformation of the K+-uptake-deficient mutant with CjKUP1 complemented the deficiency of this mutant. This result indicates that CjKUP1 has a function of K+ uptake. The expression levels of CjKUP1 in male strobili were markedly higher from late September to early October than in other periods. The expression levels in male and female strobili were higher than those in other organs such as needles, inner bark, differentiating xylem, and roots. These results indicate that CjKUP1 is mainly involved in K+ membrane transport in the cells of reproductive organs of C. japonica trees, especially in male strobili during pollen differentiation.ArticleTrees-Struct. Funct. 28(5):1527-1537 (2014)journal articl