Insights into mechanism kinematics for protein motion simulation

Background: The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein's movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost. Results: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion. Conclusions: The procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.The authors wish to acknowledge the financial support received from the Spanish Government through the Ministerio de Economia y Competitividad (Project DPI2011-22955), the Regional Government of the Basque Country through the Departamento de Educacion, Universidades e Investigacion (Project IT445-10) and UPV/EHU under program UFI 11/29 and by Grants from the Department of Education, Universities and Research of the Basque Government (PI2010-17), from the Department of Industry of the Basque Government (ETORTEK Program IE05-147 and IE07-202), from the Bizkaia Country (Exp. 7/13/08/2006/11 and 7/13/08/2005/14), and from the Spanish Ministry of Economy and Innovation (BFU2010-17857 and SICI-CONSOLIDER Program CSD2008-00005) (all to L.A.M.-C.)

Mouse Models of Human Claudin-Associated Disorders: Benefits and Limitations

In higher organisms, epithelia separate compartments in order to guarantee their proper function. Such structures are able to seal but also to allow substances to pass. Within the paracellular pathway, a supramolecular structure, the tight junction transport is largely controlled by the temporospatial regulation of its major protein family called claudins. Besides the fact that the expression of claudins has been identified in different forms of human diseases like cancer, clearly defined mutations in the corresponding claudin genes have been shown to cause distinct human disorders. Such disorders comprise the skin and its adjacent structures, liver, kidney, the inner ear, and the eye. From the phenotype analysis, it has also become clear that different claudins can cause a complex phenotype when expressed in different organs. To gain deeper insights into the physiology and pathophysiology of claudin-associated disorders, several mouse models have been generated. In order to model human disorders in detail, they have been designed either as full knockouts, knock-downs or knock-ins by a variety of techniques. Here, we review human disorders caused by CLDN mutations and their corresponding mouse models that have been generated thus far and assess their usefulness as a model for the corresponding human disorder

The CBS domain protein MJ0729 of Methanocaldococcus jannaschii binds DNA

AbstractThe cystathionine beta-synthase (CBS) domains function as regulatory motifs in several proteins. Elucidating how CBS domains exactly work is relevant because several genetic human diseases have been associated with mutations in those motifs. Here, we show, for the first time, that a CBS domain binds calf-thymus DNA and E-boxes recognized by transcription factors. We have carried out the DNA-binding characterization of the CBS domain protein MJ0729 from Methanocaldococcus jannaschii by biochemical and spectroscopic techniques. Binding induces conformational changes in the protein, and involves the sole tryptophan residue. The apparent dissociation constant for the E-boxes is ∼10μM. These results suggest that CBS domains might interact with DNA

ARL15 modulates magnesium homeostasis through N-glycosylation of CNNMs

Cyclin M (CNNM1-4) proteins maintain cellular and body magnesium (Mg2+) homeostasis. Using various biochemical approaches, we have identified members of the CNNM family as direct interacting partners of ADP-ribosylation factor-like GTPase 15 (ARL15), a small GTP-binding protein. ARL15 interacts with CNNMs at their carboxyl-terminal conserved cystathionine-β-synthase (CBS) domains. In silico modeling of the interaction between CNNM2 and ARL15 supports that the small GTPase specifically binds the CBS1 and CNBH domains. Immunocytochemical experiments demonstrate that CNNM2 and ARL15 co-localize in the kidney, with both proteins showing subcellular localization in the endoplasmic reticulum, Golgi apparatus and the plasma membrane. Most importantly, we found that ARL15 is required for forming complex N-glycosylation of CNNMs. Overexpression of ARL15 promotes complex N-glycosylation of CNNM3. Mg2+ uptake experiments with a stable isotope demonstrate that there is a significant increase of 25Mg2+ uptake upon knockdown of ARL15 in multiple kidney cancer cell lines. Altogether, our results establish ARL15 as a novel negative regulator of Mg2+ transport by promoting the complex N-glycosylation of CNNMs.European Joint Program for Rare Diseases (EJPRD2019-40)Spanish Ministry of Science and Innovation and Universities (PGC2018-096049-B-I00)Junta de Andalucía (BIO-198, US-1254317 and US-1257019

Structural and chemical reactivity modifications of a cobalt perovskite induced by Sr-substitution. An in situ XAS study

LaCoO3 and La0.5Sr0.5CoO3-δ perovskites have been studied by in situ Co K-edge XAS. Although the partial substitution of La(III) by Sr(II) species induces an important increase in the catalytic oxidation activity and modifies the electronic state of the perovskite, no changes could be detected in the oxidation state of cobalt atoms. So, maintaining the electroneutrality of the perovskite requires the generation of oxygen vacancies in the network. The presence of these vacancies explains that the substituted perovskite is now much more reducible than the original LaCoO3 perovskite. As detected by in situ XAS, after a consecutive reduction and oxidation treatment, the original crystalline structure of the LaCoO3 perovskite is maintained, although in a more disordered state, which is not the case for the Sr doped perovskite. So, the La0.5Sr0.5CoO3-δ perovskite submitted to the same hydrogen reduction treatment produces metallic cobalt, while as determined by in situ XAS spectroscopy the subsequent oxidation treatment yields a Co(III) oxide phase with spinel structure. Surprisingly, no Co(II) species are detected in this new spinel phase.Ministerio de Ciencia y Educación ENE2011-2441

Ambientes depositacionales del Plioceno y Pleistoceno en la quebrada la Cruz y alrededores, Tumbes

El presente trabajo consiste en la descripción e interpretación de las facies sedimentarias de las unidades estratigráficas que corresponden al Plioceno, Pleistoceno y Holoceno de los alrededores de Zorritos en Tumbes. Estudia los procesos finales de la curva eustática hasta la actualidad. El trabajo forma parte del proyecto GR11: “Paleontología cuaternaria del noroeste de Perú” del INGEMMET. Se evalúa la sedimentología y estratigrafía del cenozoico en la Cuenca Tumbes desde el Oligoceno, representados por depósitos litorales, de shoreface y sistemas deltaicos de las formaciones Máncora y Heath durante el inicio del Oligoceno, e inicio del Mioceno. Se evalúa la sedimentación durante el plioceno y pleistoceno. Respecto al clima, se lo interpreta como húmedo, con precipitaciones frecuentes. En cuanto a los fragmentos de vertebrados fósiles, se ha identificado como correspondientes a mastodontes, perezosos, cérvidos y roedores pertenecen a la megafauna del Plio-Pleistoceno. Se considera que la edad para la Formación La Cruz es del intervalo Plioceno-Pleistoceno. El informe concluye que las sucesiones sedimentarias de la Formación La Cruz corresponden a ambientes fluviales distales con intervención marina restringido solo al finalizar las sucesiones. Así mismo, que la sedimentación desde el Mioceno se interpreta como formado durante una gran regresión marina forzada hasta los últimos tiempos, siendo comparable a las curvas de las mencionadas edades a nivel global. Los episodios de depositación progradacional del Plioceno serían similares a los sedimentos del Eoceno, Oligoceno y Mioceno de Tumbes y Talara. Se registra una ligera invasión o intervención marina al tope de la Formación La Cruz

Generation of organotypic multicellular spheres by magnetic levitation : model for the study of human hematopoietic stem cells microenvironment

Q4Q3Background and Objective: The characteristics of human hematopoietic stem cells are conditioned by the microenvironment of the bone marrow, where they interact with other cell populations, such as mesenchymal stem cells and endothelial cells; however, the study of this microenvironment is complex. The objective of this work was to develop a 3D culture system by magnetic levitation that imitates the microenvironment of human HSC. Methods and Results: Human bone marrow-mesenchymal stem cells, umbilical cord blood-hematopoietic stem cells and a non-tumoral endothelial cell line (CC2811, LonzaⓇ) were used to develop organotypic multicellular spheres by the magnetic levitation method. We obtained viable structures with an average sphericity index greater than 0.6, an average volume of 0.5 mm3 and a percentage of aggregation greater than 70%. Histological studies of the organotypic multicellular spheres used hematoxylin and eosin stains, and an evaluation of vimentin expression by means of immunohistochemistry demonstrated an organized internal structure without picnotic cells and a high expression of vimentin. The functional capacity of human hematopoietic stem cells after organotypic multicellular spheres culture was evaluated by multipotency tests, and it was demonstrated that 3D structures without exogenous Flt3L are autonomous in the maintenance of multipotency of human hematopoietic stem cells. Conclusions: We developed organotypic multicellular spheres from normal human cells that mimic the microenvironment of the human hematopoietic stem cells. These structures are the prototype for the development of complex organoids that allow the further study of the biology of normal human stem cells and their potential in regenerative medicine.https://orcid.org/0000-0002-9152-5552https://orcid.org/0000-0003-3075-9854https://orcid.org/0000-0002-0084-0339https://orcid.org/0000-0003-1881-9367N/

Randomized phase II study of fulvestrant plus palbociclib or placebo in endocrine-sensitive, hormone receptor-positive/HER2-advanced breast cancer: GEICAM/2014-12 (FLIPPER).

Este artículo ha sido publicado en la revista European Journal of Cancer. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).Background: The potential benefit of adding palbociclib to fulvestrant as first-line treatment in hormone receptor (HR)-positive, human epidermal growth factor receptor 2 (HER2)-negative endocrine-sensitive advanced breast cancer (ABC) patients remains uncharacterized. Patients and methods: In this randomized (1:1), double-blind, phase II study, postmenopausal women with HR-positive, HER2-negative ABC with de novo metastatic disease or those who relapsed after >12 months of adjuvant endocrine therapy received palbociclib/fulvestrant or placebo/fulvestrant. Stratification was based on recurrent versus de novo metastatic disease and visceral involvement. The primary objective was one-year progression-free survival (PFS-1y) rate. The sample size was 190 patients. The two-sided alpha of 0.2, 80% of power to detect a difference between the arms, assuming PFS rates of 0.695 and 0.545 for palbociclib/fulvestrant and placebo/fulvestrant, respectively. Results: In total, 189 patients were randomized to palbociclib/fulvestrant ([n = 94] or placebo/fulvestrant [n = 95]). 45.5% and 60.3% of patients had de novo metastatic disease and visceral involvement, respectively. PFS-1y rates were 83.5% and 71.9% in the palbociclib/fulvestrant and placebo/fulvestrant arms, (HR 0.55, 80% CI 0.36-0.83, P = 0.064). The median PFS were 31.8 and 22.0 months for the palbociclib/fulvestrant and placebo/fulvestrant arms (aHR 0.48, 80% CI 0.37-0.64, P = 0.001). The most frequent grade 3-4 adverse events were neutropenia (68.1% vs. 0%), leucopenia (26.6% vs. 0%), anemia (3.2% vs. 0%), and lymphopenia (14.9% vs. 2.1%) for the palbociclib/fulvestrant and placebo/fulvestrant, respectively. The most frequent non-hematologic grade 3-4 adverse event was fatigue (4.3% vs. 0%). Conclusions: Palbociclib/fulvestrant demonstrated better PFS-1y rates and median PFS than placebo/fulvestrant in HR-positive/HER2-negative endocrine-sensitive ABC patients