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Modification of unprotected nucleosides has been attracting continuous interest, since these building blocks themselves and their phosphate-upgraded corresponding nucleotides have shown a plethora of uses in fields like biochemistry or pharmacy. Pd-catalyzed cross-coupling reactions, conducted in water or its mixtures with polar organic solvents, have frequently been the researchers' choice for the functionalization of the purine/pyrimidine base of the unprotected nucleosides. In this scenario, the availability of hydrophilic ligands and its water-soluble palladium complexes has markedly set the pace of the advances. The approach of our group to the synthesis of such complexes, Pd-imidates specifically, has faced critical stages, namely the jump to synthesize water soluble complexes from our experience working in conventional solvents, the preparation of phosphine free complexes and the overall goal of getting catalytic systems able to work close to room temperature. The continuous feedback with Kapdi's group, experienced in the chemistry of nucleosides, has produced over the last decade the interesting results in both fields presented here. This work has been partially supported by RTI2018-098233-B−C21 and PID2021-124695OB-C21 (MICINN) and 20790/PI/18 (Fundación SENECA CARM) grants. The Author wishes to thank the many students who have contributed to the chemistry described in this article, as well as the colleagues and supervisors from Universidad de Murcia, University of Sussex, Inorganic Chemistry Laboratory-University of Oxford, University of York, and Institute of Chemical Technology-Mumbai for his contribution to this work and his wise and continuous advice and support.

The removal of unwanted genetic material is a key aspect in many synthetic biology efforts and often requires preliminary knowledge of which genomic regions are dispensable. Typically, these efforts are guided by transposon mutagenesis studies, coupled to deepsequencing (TnSeq) to identify insertion points and gene essentiality. However, epistatic interactions can cause unforeseen changes in essentiality after the deletion of a gene, leading to the redundancy of these essentiality maps. Here, we present LoxTnSeq, a new methodology to generate and catalogue libraries of genome reduction mutants. LoxTnSeq combines random integration of lox sites by transposon mutagenesis, and the generation of mutants via Cre recombinase, catalogued via deep sequencing. When LoxTnSeq was applied to the naturally genome reduced bacterium Mycoplasma pneumoniae, we obtained a mutant pool containing 285 unique deletions. These deletions spanned from > 50 bp to 28 Kb, which represents 21% of the total genome. LoxTnSeq also highlighted large regions of non-essential genes that could be removed simultaneously, and other non-essential regions that could not, providing a guide for future genome reductions., Microbial Biotechnology, 14 (6), ISSN:1751-7915, ISSN:1751-7907

Summary Recent years have seen an increase in the number of structures available, not only for new proteins but also for the same protein crystallized with different molecules and proteins. While protein design software has proven to be successful in designing and modifying proteins, they can also be overly sensitive to small conformational differences between structures of the same protein. To cope with this, we introduce here pyFoldX, a python library that allows the integrative analysis of structures of the same protein using FoldX, an established forcefield and modelling software. The library offers new functionalities for handling different structures of the same protein, an improved molecular parametrization module and an easy integration with the data analysis ecosystem of the python programming language. Availability and implementation pyFoldX rely on the FoldX software for energy calculations and modelling, which can be downloaded upon registration in http://foldxsuite.crg.eu/ and its licence is free of charge for academics. The pyFoldX library is open-source. Full details on installation, tutorials covering the library functionality and the scripts used to generate the data and figures presented in this paper are available at https://github.com/leandroradusky/pyFoldX. Supplementary information Supplementary data are available at Bioinformatics online.

Summary Accurate 3D modelling of protein–protein interactions (PPI) is essential to compensate for the absence of experimentally determined complex structures. Here, we present a new set of commands within the ModelX toolsuite capable of generating atomic-level protein complexes suitable for interface design. Among these commands, the new tool ProteinFishing proposes known and/or putative alternative 3D PPI for a given protein complex. The algorithm exploits backbone compatibility of protein fragments to generate mutually exclusive protein interfaces that are quickly evaluated with a knowledge-based statistical force field. Using interleukin-10-R2 co-crystalized with interferon-lambda-3, and a database of X-ray structures containing interleukin-10, this algorithm was able to generate interleukin-10-R2/interleukin-10 structural models in agreement with experimental data. Availability and implementation ProteinFishing is a portable command-line tool included in the ModelX toolsuite, written in C++, that makes use of an SQL (tested for MySQL and MariaDB) relational database delivered with a template SQL dump called FishXDB. FishXDB contains the empty tables of ModelX fragments and the data used by the embedded statistical force field. ProteinFishing is compiled for Linux-64bit, MacOS-64bit and Windows-32bit operating systems. This software is a proprietary license and is distributed as an executable with its correspondent database dumps. It can be downloaded publicly at http://modelx.crg.es/. Licenses are freely available for academic users after registration on the website and are available under commercial license for for-profit organizations or companies. Contact javier.delgado@crg.eu or luis.serrano@crg.eu Supplementary information Supplementary data are available at Bioinformatics online.

14 pags. 5 figs., 2 tabs., Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease. Variants in MYBPC3, the gene encoding cardiac myosin-binding protein C (cMyBP-C), are the leading cause of HCM. However, the pathogenicity status of hundreds of MYBPC3 variants found in patients remains unknown, as a consequence of our incomplete understanding of the pathomechanisms triggered by HCM-causing variants. Here, we examined 44 nontruncating MYBPC3 variants that we classified as HCM-linked or nonpathogenic according to cosegregation and population genetics criteria. We found that around half of the HCM-linked variants showed alterations in RNA splicing or protein stability, both of which can lead to cMyBP-C haploinsufficiency. These protein haploinsufficiency drivers associated with HCM pathogenicity with 100% and 94% specificity, respectively. Furthermore, we uncovered that 11% of nontruncating MYBPC3 variants currently classified as of uncertain significance in ClinVar induced one of these molecular phenotypes. Our strategy, which can be applied to other conditions induced by protein loss of function, supports the idea that cMyBP-C haploinsufficiency is a fundamental pathomechanism in HCM., A.-C. acknowledges funding from the Ministerio de Ciencia e Innovación (MCIN) throughgrants BIO2014-54768-P; BIO2017-83640-P/MINECO/AEI/FEDER, UE; EIN2019-102966 and RYC-2014-16604, the European Research Area Network on Cardiovascular Diseases (ERA-CVD/ISCIII, Spain MINOTAUR, AC16/00045), and the Comunidad de Madrid (consortium Tec4Bio-CM, S2018/NMT-4443, FEDER). TheCNIC is supported by the ISCIII, MCIN, and the Pro CNIC Foundation and was a Severo Ochoa Center of Excellence (SEV-2015-0505). We acknowledge funding from ISCIII to the Centro de Investigación Biomédica en Red (CB16/11/00425). L. S. acknowl-edges funding from MCIN (BFU2015-63571-P). J. S. acknowledgesfunding from AEI (PID2019-107293GB-I00), Gobierno de Aragón(E45_17R), and ERDF-InterregV-A POCTEFA, Spain (PIREPRED-EFA086/15). C. S.-C. is the recipient of an FPI-SO predoctoral fellowship BES-2016-076638. M. R. P. was the recipient of a Ph D fellowship from the Italian Ministry of Education, Universities and Research, Italy. H. G.-C. is the recipient of an FPU16/04232 doctoralcontract from MCIN.

24 pags., 8 figs., 3 tabs. -- This article belongs to the Special Issue Dendrimers and Dendritic Materials against Infectious Diseases, The use of nanocarriers has been revealed as a valid strategy to facilitate drug bioavailability, and this allows for expanding the drug libraries for the treatment of certain diseases such as viral diseases. In the case of Hepatitis C, the compounds iopanoic acid and 3,3′,5-triiodothyroacetic acid (or tiratricol) were identified in a primary screening as bioactive allosteric inhibitors of viral NS3 protease, but they did not exhibit accurate activity inhibiting viral replication in cell-based assays. In this work, dendritic nanocarriers are proposed due to their unique properties as drug delivery systems to rescue the bioactivity of these two drugs. Specifically, four different amphiphilic Janus dendrimers synthesized by combining 2,2′-bis(hydroxymethyl)propionic acid (bis-MPA) and 2,2′-bis(glyciloxy)propionic acid (bis-GMPA) functionalized with either hydrophilic or lipophilic moieties at their periphery were used to entrap iopanoic acid and tiratricol. Interestingly, differences were found in the loading efficiencies depending on the dendrimer design, which also led to morphological changes of the resulting dendrimer aggregates. The most remarkable results consist of the increased water solubility of the bioactive compounds within the dendrimers and the improved antiviral activity of some of the dendrimer/drug aggregates, considerably improving antiviral activity in comparison to the free drugs. Moreover, imaging studies have been developed in order to elucidate the mechanism of cellular internalization., This research was funded by the Ministerio de Ciencia e Innovación, Spain, which included FEDER funds (PGC2018-097583-B-I00, PGC2018-093761-B-C31, MSA grant BES-2016-078774, AL grant FPU12/05210 and R.C.-G. grant FPU13/3870) Gobierno de Aragón-FSE (E47_20R); Miguel Servet Program from Instituto deSalud Carlos III (CPII13/00017 to OA); Fondo de Investigaciones Sanitarias from Instituto de Salud Carlos III and European Union (ERDF/ESF, “Investing in your future”) (PI15/00663 and PI18/00349 to O.A.); Diputación General de Aragón (Digestive Pathology Group B25_17R to O.A.); and Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd).

Aggregates of Pseudomonas aeruginosa form a protective barrier against antibiotics and the immune system. These barriers, known as biofilms, are associated with several infectious diseases. One of the main components of these biofilms is alginate, a homo- and hetero-polysaccharide that consists of β-D-mannuronate (M) and α-L-guluronate (G) units. Alginate lyases degrade this sugar and have been proposed as biotherapeutic agents to dissolve P. aeruginosa biofilms. However, there are contradictory reports in the literature regarding the efficacy of alginate lyases against biofilms and their synergistic effect with antibiotics. We found that most positive reports used a commercial crude extract from Flavobacterium multivorum as the alginate lyase source. By using anion exchange chromatography coupled to nano LC MS/MS, we identified two distinct enzymes in this extract, one has both polyM and polyG (polyM/G) degradation activities and it is similar in sequence to a broad-spectrum alginate lyase from Flavobacterium sp. S20 (Alg2A). The other enzyme has only polyG activity and it is similar in sequence to AlyA1 from Zobellia galactanivorans. By characterizing both of these enzymes together with three recombinant alginate lyases (a polyM, a polyG and a polyM/G), we showed that only enzymes with polyM/G activity such as Alg2A and A1-II' (alginate lyase from Sphingomonas sp.) are effective in dissolving biofilms. Furthermore, both activities are required to have a synergistic effect with antibiotics. We acknowledge support of the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program under agreement No 670216 (MYCOCHASSIS), the Spanish Ministry of Economy and Competitiveness and Fondo Europeo de Desarrollo Regional (MINECO-FEDER) (BIO2015-63557-R), ‘Centro de Excelencia Severo Ochoa 2013-2017’, FEDER project from Instituto Carlos III (ISCIII, Acción Estratégica en Salud 2016) (reference CP16/00094) and “Secretaria d’Universitats i Recerca del Departament d’Economia i Coneixement de la Generalitat de Catalunya / CERCA programme” (2014SGR678 and 2017SGR1079). The CRG/UPF Proteomics Unit is part of the “Plataforma de Recursos Biomoleculares y Bioinformáticos (ProteoRed)” supported by grant PT13/0001 of Instituto de Salud Carlos III from the Spanish Government.

The coronavirus disease COVID-19 constitutes the most severe pandemic of the last decades having caused more than 1 million deaths worldwide. The SARS-CoV-2 virus recognizes the angiotensin converting enzyme 2 (ACE2) on the surface of human cells through its spike protein. It has been reported that the coronavirus can mildly infect cats, and ferrets, and perhaps dogs while not pigs, mice, chicken and ducks. Differences in viral infectivity among different species or individuals could be due to amino acid differences at key positions of the host proteins that interact with the virus, the immune response, expression levels of host proteins and translation efficiency of the viral proteins among other factors. Here, first we have addressed the importance that sequence variants of different animal species, human individuals and virus isolates have on the interaction between the RBD domain of the SARS-CoV-2 spike S protein and human angiotensin converting enzyme 2 (ACE2). Second, we have looked at viral translation efficiency by using the tRNA adaptation index. We find that integration of both interaction energy with ACE2 and translational efficiency explains animal infectivity. Humans are the top species in which SARS-CoV-2 is both efficiently translated as well as optimally interacting with ACE2. We have found some viral mutations that increase affinity for hACE and some hACE2 variants affecting ACE2 stability and virus binding. These variants suggest that different sensitivities to coronavirus infection in humans could arise in some cases from allelic variability affecting ACE2 stability and virus binding., Author summary In these early stages of the COVID-19 pandemic it is urgent to understand all features determining the new virus expansion. Two significant factors conditioning infection are ACE2-mediated SARS-CoV-2 cellular entry and viral proteome translation efficiency. Genomic variability across species, including humans, results in ACE2 variants that destabilize its fold, modify ACE2/SARS-CoV-2 recognition, or both. We also point out the importance of considering waters at the interface of protein-protein interactions when performing in silico mutagenesis.

Introduction: asciminib is a first-in-class STAMP (Specifically Targeting the ABL Myristoyl Pocket) inhibitor that potently inhibits aberrant kinase activity of the BCR-ABL1 oncoprotein via allosteric binding. asciminib has shown high efficacy profile in heavily pretreated Chronic Myeloid Leukemia (CML) patients with an adequate safety profile in phase I and III clinical trials. However, data from the use of asciminib in real life setting are still scarce. Methods: We gathered real-life retrospective data from 49 patients with BCR-ABL1 positive CML treated with asciminib (mean dose: 40 mg twice daily) between October 2018 and July 2021 at 33 institutions. The indication of asciminib was made according to the criterion of the attending physician and the drug was granted by Novartis under a controlled access program. Molecular biology tests were performed according to ELN guidelines and BCR-ABL/ABL ratios were expressed as % IS in all centers. Treatment responses were calculated with the patients at risk at each specific time points. For the event free survival (EFS), the events were treatment discontinuation due to any reason, progression or death. Data collection followed the local regulations for observational studies. Results: Median time on asciminib was 11,69 months for the entire cohort. Patients' characteristics are displayed on Table 1. Most patients were heavily pretreated with at least 3 prior TKI lines in 45 patients (91,83%), 18 of them receiving prior Ponatinib. Switch to asciminib occurred due to intolerance in 32 patients and due to resistance in the remaining 17. Fifteen patients (30,61%) harbored mutations in BCR-ABL1 (3 with a T315 mutation). Regarding efficacy (Table 2), probability of reaching or maintaining previous responses were 94%, 45% and 21% for complete hematological response (CHR), complete cytogenetic response (CCyR) and major molecular response (MMR), respectively. Considering probabilities of improving previous response, rates were 40%, 42% and 33% for the same parameters. Probabilities to obtain CCyR and MMR in resistant and intolerant patients were 29% (4/14) vs 55% (6/11) and 27% (4/15) vs 52% (11/21), respectively. Amid the patients previously treated with Ponatinib, probabilities of reaching or maintaining previous response were 53% (9/17) and 35% (6/17) for CCyR and MMR respectively, and 30% (3/10), 23% (3/13) displayed improvement of response. Regarding responses in patients with mutations, 39% (5/13) achieved or maintained CCyR and 31% (4/13) MMR; whereas 20% (2/10) and 18% (2/11) improved such responses. Of the three patients with T315I mutation, one discontinued due to progression to advanced stages, and the rest maintained the previous response. With a median follow-up of 11,69 months, the estimated EFS was 80% (figure 1). In terms of safety (Table 3), the most frequent extra-hematological adverse events (AE) were: fatigue (16,2%), joint pain (13,5%) and nausea (8,1%), most of them grade 1-2. Grade 3-4 AE were observed in 10% of patient (fatigue (2), cholestasis enzyme elevation (1), hypertension (1), pancreatitis (1) and pericardial effusion (1)). Thrombocytopenia was shown as the most frequent AE (16,3%), with 6% of patients suffering from grade 3-4. Dose reduction was required in 15 patients (30,6%). After a median follow up of 51 weeks, 73,5% of the patients remained on treatment. Only fourteen patients discontinued treatment due to progression or loss of efficacy, whereas 6% of patients discontinuing treatment due to intolerance. Conclusions: The results presented are in line with the data obtained in clinical trials, positioning asciminib as a potential safe and efficacious treatment for CML patients with failure to several TKI lines. Figure 1 Figure 1. Disclosures Sanchez-Guijo: Novartis: Consultancy, Honoraria, Research Funding; Celgene/Bristol-Myers-Squibb,: Consultancy, Honoraria; Incyte: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria; Takeda: Honoraria, Research Funding; Roche: Consultancy, Honoraria; Gilead: Consultancy, Honoraria; Amgen: Consultancy, Honoraria. Garcia Gutierrez: BMS: Consultancy, Honoraria, Research Funding; Novartis: Consultancy, Honoraria, Research Funding; Pfizer: Consultancy, Honoraria, Research Funding; Incyte: Consultancy, Honoraria, Research Funding.

Introduction: Asciminib is a new BCR-ABL1 inhibitor that differs from previous tyrosine kinase inhibitors (TKIs) in that it does not bind to the ATP-binding site of the kinase. Data from different clinical trials has shown an adequate safety and efficacy profile in chronic myeloid leukemia (CML) patients failing previous TKIs. However, no findings have been communicated in real life experience. The aim of our study is to present first results of asciminib in CML patients failing previous TKIs under the current compassionate use program. Methods: We retrospectively collected data from 31 patients treated with asciminib in 25 centers under compassionate use program. Data collecting was performed between October 2018 and June 2020. Patients baseline characteristics are shown in table 1. Most patients were heavily pretreated with 28 patients receiving 3 or more TKIs previous to asciminib. Eleven patients (35.5%) had been treated with ponatinib at some point throughout the disease. Twelve patients showed BCR-ABL1 mutations (only 1 case with T315I mutation). Switch to asciminib was due to intolerance in 22 patients and due to resistance in the remaining 9. Median dose of asciminib was 80mg per day (40mg every 12 hours). Treatment responses were evaluated according to European Leukemia Net recommendations. Data compilation and analysis were performed with REDCap Software and IBM SPSS (Version 25.0). Results: Median time on asciminib for the entire cohort was 35 weeks. Regarding toxicities, 13 patients (42%) experienced mild extra-hematological side effects (grade 1-2) being the most frequent fatigue (19%), joint pain (16%) and nausea (9%). Four patients (12,9%) showed severe (grade 3-4) extra-hematological events: fatigue, hepatotoxicity, hypertension and pericardial effusion (1 patient each). Three patients (9,7%) suffered from grade 4 thrombocytopenia, 2 of them associating grade 4 neutropenia. All toxicities according to previous TKIs adverse effects as well as cross-intolerance data is shown in table 2. Dose reduction had to be carried out in 9 patients (29%), 7 of those with temporary treatment interruptions; most owing to hematological adverse effects. In terms of efficacy (Graph 1), probability of reaching or at least maintaining previous response was 100%, 61.3% and 35.5% for complete hematological response (CHR), complete cytogenetic response (CCyR) and major molecular response (MMR), respectively. Regarding probabilities to improve previous responses, rates of CCyR and MMR were, respectively, 22,2% (2/9) and 22,2% (2/9) for resistant patients and 44% (4/9) and 62,5%. (10/16) for intolerant group. Amid the 11 patients previously treated with ponatinib, 3 patients (27,3%) showed improvement of response achieving at least MMR, 2 of them from the TKI-intolerant group and 1 from the TKI-resistant group. The median follow-up time was 40 weeks, after which 27 patients (87.1%) continued with asciminib. Treatment cessation happened in 2 patients due to progression to blastic phase and in 2 patients due to lack of efficacy. No patients discontinued due to side effects. Conclusion: The data presented, similar to that known from clinical trials, supports the use of asciminib in routine clinical practice in CML patients failing to previous TKIs. Disclosures Garcia-Gutiérrez: Novartis: Consultancy, Other: Travel, Accommodation, Expenses, Research Funding; Bristol-Myers Squibb: Consultancy, Other: Travel, Accommodation, Expenses, Research Funding; Pfizer: Consultancy, Other: Travel, Accommodation, Expenses, Research Funding; Incyte: Consultancy, Other: Travel, Accommodation, Expenses, Research Funding.

The C‐terminal sequence of a protein is involved in processes such as efficiency of translation termination and protein degradation. However, the general relationship between features of this C‐terminal sequence and levels of protein expression remains unknown. Here, we identified C‐terminal amino acid biases that are ubiquitous across the bacterial taxonomy (1,582 genomes). We showed that the frequency is higher for positively charged amino acids (lysine, arginine), while hydrophobic amino acids and threonine are lower. We then studied the impact of C‐terminal composition on protein levels in a library of Mycoplasma pneumoniae mutants, covering all possible combinations of the two last codons. We found that charged and polar residues, in particular lysine, led to higher expression, while hydrophobic and aromatic residues led to lower expression, with a difference in protein levels up to fourfold. We further showed that modulation of protein degradation rate could be one of the main mechanisms driving these differences. Our results demonstrate that the identity of the last amino acids has a strong influence on protein expression levels., Large‐scale genomics analyses combined with high‐throughput experimental assays reveal that the C‐terminal amino acid composition has a strong influence on protein expression levels in bacteria.

In-vehicle applications that are based on Vehicle-to-Everything (V2X) communication technologies need to be evaluated under lab-controlled conditions before performing field tests. The need for a tailored platform to perform specific research on the cooperative Advanced Driving Assistance System (ADAS) to assess the effect on driver behavior and driving performance motivated the development of a driver-centric traffic simulator that is built over a 3D graphics engine. The engine creates a driving situation as it communicates with a traffic simulator as a means to simulate real-life traffic scenarios. The TraCI as a Service (TraaS) library was implemented to perform the interaction between the driver-controlled vehicle and the Simulation of Urban MObility (SUMO). An extension of a previous version, this work improves simulation performance and realism by reducing computational demand and integrating a tailored scenario with the ADAS to be tested. The usability of the implemented simulation platform was evaluated by means of an experiment related to the efficiency of a Traffic Light Assistant (TLA), showing the analysis of the answer that 80% of the participants were satisfied with the simulator and the TLA system implemented. This research was funded by the Austrian Ministry for Transport, Innovation and Technology (BMVIT) Endowed Professorship for Sustainable Transport Logistics 4.0; the EU Erasmus + framework program and the official predoctoral mobility program for researchers from the Universidad Politécnica de Madrid within the program framework for research, development, and innovation 2017.

New dinuclear cyclometallated palladium complexes of general formula [{Pd(μ-NCO)(CˆN)} 2 ] (CˆN = 2-benzoylpyridine (bzpy) I ; NCO = saccharinate (sacc) a , Phthalimidate (phthal) b or 4,5-dichlorophthalimidate (DiClphthal) c have been synthesized by a simple acid-base reaction involving the di-μ-hydroxo-precursor [{Pd(μ-OH)(bzpy)} 2 ] recently reported. Analogous to Ic , complex IIc with CˆN = 2-phenylpyridine (phpy) II has also been prepared, meaning the first examples reported to date of complexes including 4,5-dichlorophthalimidate as ligand coordinating a metal centre. The reaction of bridged imidato precursors against triphenylphosphine to form the mononuclear N-bonded imidato derivatives of general formula [Pd(CˆN)(N-imidate)(PPh 3 )] IaP , IbP , IcP and IIcP has been achieved under mild conditions. The new complexes were characterized by partial elemental analyses and spectroscopic methods. Structural characterization by X-ray diffraction of Ib and IIcP , the first crystal structure of a complex containing 4,5-diClphthal that has been deposited to date on the Cambridge Structural Database, have confirmed the proposed formulae.

Background: Proteins of the ubiquitously expressed core proteome are quantitatively correlated across multiple eukaryotic species. In addition, it was found that many protein paralogues exhibit expression anticorrelation, suggesting that the total level of protein with a given functionality must be kept constant. Methods: We performed Spearman’s rank correlation analyses of gene expression levels for the RAS GTPase subfamily and their regulatory GEF and GAP proteins across tissues and across individuals for each tissue. A large set of published data for normal tissues from a wide range of species, human cancer tissues and human cell lines was analysed. Results: We show that although the multidomain regulatory proteins of Ras GTPases exhibit considerable tissue and individual gene expression variability, their total amounts are balanced in normal tissues. In a given tissue, the sum of activating (GEFs) and deactivating (GAPs) domains of Ras GTPases can vary considerably, but each person has balanced GEF and GAP levels. This balance is impaired in cell lines and in cancer tissues for some individuals. Conclusions: Our results are relevant for critical considerations of knock out experiments, where functionally related homologs may compensate for the down regulation of a protein. This work was funded by the EU (PRIMES under grant agreement number FP7-HEALTH-F4- 2011-278568). This work was supported by the Spanish Ministerio de Economía y Competitividad, Plan Nacional BIO2012-39754 and Plan Estatal BFU2015-63571 and the European Fund for Regional Development. We acknowledge support of the Spanish Ministry of Economy, Industry and Competitiveness (MEIC) to the EMBL partnership, to the Spanish Ministry of Economy and Competitiveness (MEC) ‘Centro de Excelencia Severo Ochoa’ and to the CERCA Programme / Generalitat de Catalunya.

In the context of hospital management and operation, Intensive Care Units (ICU) are one of the most challenging in terms of time responsiveness and criticality, in which adequate resource management and signal processing play a key role in overall system performance. In this work, a context aware Intensive Care Unit is implemented and analyzed to provide scalable signal acquisition capabilities, as well as to provide tracking and access control. Wireless channel analysis is performed by means of hybrid optimized 3D Ray Launching deterministic simulation to assess potential interference impact as well as to provide required coverage/capacity thresholds for employed transceivers. Wireless system operation within the ICU scenario, considering conventional transceiver operation, is feasible in terms of quality of service for the complete scenario. Extensive measurements of overall interference levels have also been carried out, enabling subsequent adequate coverage/capacity estimations, for a set of Zigbee based nodes. Real system operation has been tested, with ad-hoc designed Zigbee wireless motes, employing lightweight communication protocols to minimize energy and bandwidth usage. An ICU information gathering application and software architecture for Visitor Access Control has been implemented, providing monitoring of the Boxes external doors and the identification of visitors via a RFID system. The results enable a solution to provide ICU access control and tracking capabilities previously not exploited, providing a step forward in the implementation of a Smart Health framework.

Summary A new version of FoldX, whose main new features allows running classic FoldX commands on structures containing RNA molecules and includes a module that allows parametrization of ligands or small molecules (ParamX) that were not previously recognized in old versions, has been released. An extended FoldX graphical user interface has also being developed (available as a python plugin for the YASARA molecular viewer) allowing user-friendly parametrization of new custom user molecules encoded using JSON format. Availability and implementation http://foldxsuite.crg.eu/

Nerve growth factor (NGF) is the prototypic member of the neurotrophin family and binds two receptors, TrkA and the 75 kDa neurotrophin receptor (p75NTR), through which diverse and sometimes opposing effects are mediated. Using the FoldX protein design algorithm, we generated eight NGF variants with different point mutations predicted to have altered binding to TrkA or p75NTR. Of these, the I31R NGF variant exhibited specific binding to p75NTR. The generation of this NGF variant with selective affinity for p75NTR can be used to enhance understanding of neurotrophin receptor imbalance in diseases and identifies a key targetable residue for the development of small molecules to disrupt binding of NGF to TrkA with potential uses in chronic pain. This material is based upon works supported by the Science Foundation Ireland under Grant No. 09/RFP/BMT2153, Enterprise Ireland (IP 2016 0480), the Higher Education Authority [PRTLI 5] and the Beckman Fund, School of Natural Sciences, NUI Galway, Ireland. peer-reviewed 2018-11-03

Fluorescence resonance energy transfer (FRET)-based detection of protein interactions is limited by the very narrow range of FRET-permitting distances. We show two different strategies for the rational design of weak helper interactions that co-recruit donor and acceptor fluorophores for a more robust detection of bimolecular FRET: (i) in silico design of electrostatically driven encounter complexes and (ii) fusion of tunable domain-peptide interaction modules based on WW or SH3 domains. We tested each strategy for optimization of FRET between (m)Citrine and mCherry, which do not natively interact. Both approaches yielded comparable and large increases in FRET efficiencies with little or no background. Helper-interaction modules can be fused to any pair of fluorescent proteins and could, we found, enhance FRET between mTFP1 and mCherry as well as between mTurquoise2 and mCitrine. We applied enhanced helper-interaction FRET (hiFRET) probes to study the binding between full-length H-Ras and Raf1 as well as the drug-induced interaction between Raf1 and B-Raf.

The potential of complex [Pd(PPh3)2(saccharinate)2] 1 in catalyzing Suzuki–Miyaura cross-coupling of 4-halo and 4-bromomethyl coumaryl and pyrone substrates with different aryl boronic acids has been explored. Excellent yields of the desired products are obtained in competitive reaction time and under relatively mild conditions. Negishi cross-coupling of 4-coumaryl tosylate with aryl and alkylzinc reagents has also been performed with good yields of the cross-coupled products obtained in most cases. Intra-molecular C–H bond functionalization of coumaryl ethers also furnished very high yields of synthetically attractive tetracyclic ring systems exhibiting the potential of 1 as a powerful catalyst in synthetically important reactions.

The effect of kinase, phosphatase and N-acetyltransferase deletions on proteome phosphorylation and acetylation was investigated in Mycoplasma pneumoniae. Bi-directional cross-talk between post-transcriptional modifications suggests an underlying regulatory molecular code in prokaryotes., Post-translational modifications (PTMs) change the chemical properties of proteins, conferring diversity beyond the amino-acid sequence. Proteins are often modified on multiple sites. A PTM code has been proposed, whereby modifications at specific positions influence further modifications. These regulatory circuits though have rarely been studied on a large-scale; conservation in prokaryotes remains elusive.Here, we studied two important PTMs– phosphorylation and lysine acetylation in the small bacterium Mycoplasma pneumoniae. We combined genetics and quantitative mass spectrometry to measure the effect of systematic kinase, phosphatase and N-acetyltransferase deletions on proteome abundance, phosphorylation and lysine acetylation.The data set represents a comprehensive analysis of both phosphorylation and lysine acetylation in a single prokaryote. It reveals (1) proteins often carry multiple modifications and multiple types of PTMs, reminiscent of the PTM code proposed in eukaryotes, (2) phosphorylation exerts pleiotropic effect on proteins abundances, phosphorylation, but also lysine acetylation, (3) the cross-talk between the two PTMs is bi-directional and (4) PTMs are frequently located at interaction interfaces and in multifunctional proteins, illustrating how PTMs could modulate protein functions affecting the way they interact.The study provides an unbiased and quantitative view on cross-talk between phosphorylation and lysine acetylation. It suggests that these regulatory circuits are a fundamental principle of regulation that might have evolved before the divergence of prokaryotes and eukaryotes., Protein post-translational modifications (PTMs) represent important regulatory states that when combined have been hypothesized to act as molecular codes and to generate a functional diversity beyond genome and transcriptome. We systematically investigate the interplay of protein phosphorylation with other post-transcriptional regulatory mechanisms in the genome-reduced bacterium Mycoplasma pneumoniae. Systematic perturbations by deletion of its only two protein kinases and its unique protein phosphatase identified not only the protein-specific effect on the phosphorylation network, but also a modulation of proteome abundance and lysine acetylation patterns, mostly in the absence of transcriptional changes. Reciprocally, deletion of the two putative N-acetyltransferases affects protein phosphorylation, confirming cross-talk between the two PTMs. The measured M. pneumoniae phosphoproteome and lysine acetylome revealed that both PTMs are very common, that (as in Eukaryotes) they often co-occur within the same protein and that they are frequently observed at interaction interfaces and in multifunctional proteins. The results imply previously unreported hidden layers of post-transcriptional regulation intertwining phosphorylation with lysine acetylation and other mechanisms that define the functional state of a cell.

The synthesis of a highly efficient, water soluble [Pd(Sacc)2 (TPA)2 ] complex for C-C bond formation is described. Additionally, application of the [Pd(Sacc)2 (TPA)2 ] complex for Suzuki-Miyaura arylation of all four nucleosides (5-iodo-2'-deoxyuridine [5-IdU], 5-iodo-2'-deoxycytidine [5-IdC], 8-bromo-2'-deoxyadenosine, and 8-bromo-2'-deoxyguanosine) with various aryl/heteroaryl boronic acids in plain water under milder conditions is demonstrated. © 2016 by John Wiley & Sons, Inc.

A novel approach to ambipolar semiconductors based on hydrogen-bonded complexes between a star-shaped tris(triazolyl)triazine and triphenylene-containing benzoic acids is described. The formation of 1:3 supramolecular complexes was evidenced by different techniques. Mesogenic driving forces played a decisive role in the formation of the hydrogen-bonded complexes in the bulk. All of the complexes formed by nonmesogenic components gave rise to hexagonal columnar (Col) liquid crystal phases, which are stable at room temperature. In all cases, X-ray diffraction experiments supported by electron density distribution maps confirmed triphenylene/tris(triazolyl)triazine segregation into hexagonal sublattices and lattices, respectively, as well as remarkable intracolumnar order. These highly ordered nanostructures, obtained by the combined supramolecular H-bond/columnar liquid crystal approach, yielded donor/acceptor coaxial organization that is promising for the formation of ambipolar organic semiconductors with high mobilities, as indicated by charge transport measurements., This work was financially supported by the MINECO-FEDER funds (projects MAT2015-66208-C3-1-P, CTQ2015-70174-P, MAT2012-38538-CO3-02), the Gobierno de Aragon-FSE (E04 research group and EPIF grant to B.F.), and the Gobierno Vasco (Project IT 1130-16). A.G. acknowledges support from the ELIOTROPO project (PON03PE_00092_2). R.T. was supported by MIUR under the PRIN 2012 JHFYMC project.

A common problem encountered when performing large-scale MS proteome analysis is the loss of information due to the high percentage of unassigned spectra. To determine the causes behind this loss we have analyzed the proteome of one of the smallest living bacteria that can be grown axenically, Mycoplasma pneumoniae (729 ORFs). The proteome of M. pneumoniae cells, grown in defined media, was analyzed by MS. An initial search with both Mascot and a species-specific NCBInr database with common contaminants (NCBImpn), resulted in around 79% of the acquired spectra not having an assignment. The percentage of non-assigned spectra was reduced to 27% after re-analysis of the data with the PEAKS software, thereby increasing the proteome coverage of M. pneumoniae from the initial 60% to over 76%. Nonetheless, 33 413 spectra with assigned amino acid sequences could not be mapped to any NCBInr database protein sequence. Approximately, 1% of these unassigned peptides corresponded to PTMs and 4% to M. pneumoniae protein variants (deamidation and translation inaccuracies). The most abundant peptide sequence variants (Phe-Tyr and Ala-Ser) could be explained by alterations in the editing capacity of the corresponding tRNA synthases. About another 1% of the peptides not associated to any protein had repetitions of the same aromatic/hydrophobic amino acid at the N-terminus, or had Arg/Lys at the C-terminus. Thus, in a model system, we have maximized the number of assigned spectra to 73% (51 453 out of the 70 040 initial acquired spectra). This work was sup-ported by the European Research Council (ERC), the Fundación Marcelino Botín, the Spanish Ministerio de Economía y Com-petitividad BIO2007-61762 and the ISCIII (PI10/01702). TheCRG/UPF Proteomics Unit is part of the “Plataforma de Re-cursos Biomoleculares y Bioinform´aticos (ProteoRed)” supportedby grant PT13/0001 of Instituto de Salud Carlos III (ISCIII).We acknowledge the support of the Spanish Ministry of Economyand Competitiveness, ‘Centro de Excelencia Severo Ochoa 2013–2017’, SEV-2012-0208. This project has received funding fromthe European Union’s Horizon 2020 research and innovationprogram under grant agreement No 634942

In this work, context aware scenarios applied to e-Health and m-Health in the framework of typical households (urban and rural) by means of deploying Social Sensors will be described. Interaction with end-users and social/medical staff is achieved using a multi-signal input/output device, capable of sensing and transmitting environmental, biomedical or activity signals and information with the aid of a combined Bluetooth and Mobile system platform. The devices, which play the role of Social Sensors, are implemented and tested in order to guarantee adequate service levels in terms of multiple signal processing tasks as well as robustness in relation with the use wireless transceivers and channel variability. Initial tests within a Living Lab environment have been performed in order to validate overall system operation. The results obtained show good acceptance of the proposed system both by end users as well as by medical and social staff, increasing interaction, reducing overall response time and social inclusion levels, with a compact and moderate cost solution that can readily be largely deployed. The authors wish to acknowledge funding of project NASISTIC, from the Government of Navarra, Spain; Project TEC2013-45585-C2-1-R, funded by the Spanish Ministry of Economy and Competiveness; collaboration and support from Red Cross Navarra; and D2D, AH and ID corporations, in Spain.

Tumor Necrosis Factor Ligand (TNFL)-Tumor Necrosis Factor Receptor (TNFR) interactions control key cellular processes; however, the molecular basis of the specificity of these interactions remains poorly understood. Using the T-RMSD (tree based on root mean square deviation), a newly developed structure-based sequence clustering method, we have re-analyzed the available structural data to re-interpret the interactions between TNFLs and TNFRs. This improves the classification of both TNFLs and TNFRs, such that the new groups defined here are in much stronger agreement with structural and functional features than existing schemes. Our clustering approach also identifies traces of a convergent evolutionary process for TNFLs and TNFRs, leading us to propose the co-evolution of TNFLs and the third cysteine rich domain (CRD) of large TNFRs.

A proliferation-inducing ligand (APRIL), a member of the TNF ligand superfamily with an important role in humoral immunity, is also implicated in several cancers as a prosurvival factor. APRIL binds two different TNF receptors, B cell maturation antigen (BCMA) and transmembrane activator and cylclophilin ligand interactor (TACI), and also interacts independently with heparan sulfate proteoglycans. Because APRIL shares binding of the TNF receptors with B cell activation factor, separating the precise signaling pathways activated by either ligand in a given context has proven quite difficult. In this study, we have used the protein design algorithm FoldX to successfully generate a BCMA-specific variant of APRIL, APRIL-R206E, and two TACI-selective variants, D132F and D132Y. These APRIL variants show selective activity toward their receptors in several in vitro assays. Moreover, we have used these ligands to show that BCMA and TACI have a distinct role in APRIL-induced B cell stimulation. We conclude that these ligands are useful tools for studying APRIL biology in the context of individual receptor activation.

The supramolecular architectures of a fluorophore are controlled through the design of a conjugated polycatenar molecule, the self-assembly of which can be addressed toward a columnar liquid-crystalline phase and organogels. Thus, depending on the environmental conditions for self-assembly, compound CA9 organizes into an unprecedented hexagonal columnar mesophase in the condensed state, in which half a molecule constitutes the slice of the column, or into a rectangular mesomorphic-like organization in the presence of apolar solvents such as cyclohexane and dodecane, at a concentration in which fibers form and gelling conditions are fulfilled. In this Colr-type arrangement, the organization within the columns depends on the solvent. All of the materials prepared show luminescence, and moreover, a remarkable 3-fold increase in fluorescence intensity was observed in going from the solution to the gel state. © 2011 American Chemical Society., This work was supported by the MICINN (Projects MAT2009-14636-C03-01, CSD2006-00012, and CTQ-2007- 61048), FEDER funding (EU), the Aragon Government, and Principado Asturias (Project IB08-088).

Here, we propose a framework for the design of synthetic protein networks from modular protein-protein or protein-peptide interactions and provide a starter toolkit of protein building blocks. Our proof of concept experiments outline a general work flow for part-based protein systems engineering. We streamlined the iterative BioBrick cloning protocol and assembled 25 synthetic multidomain proteins each from seven standardized DNA fragments. A systematic screen revealed two main factors controlling protein expression in Escherichia coli: obstruction of translation initiation by mRNA secondary structure or toxicity of individual domains. Eventually, 13 proteins were purified for further characterization. Starting from well-established biotechnological tools, two general-purpose interaction input and two readout devices were built and characterized in vitro. Constitutive interaction input was achieved with a pair of synthetic leucine zippers. The second interaction was drug-controlled utilizing the rapamycin-induced binding of FRB(T2098L) to FKBP12. The interaction kinetics of both devices were analyzed by surface plasmon resonance. Readout was based on Förster resonance energy transfer between fluorescent proteins and was quantified for various combinations of input and output devices. Our results demonstrate the feasibility of parts-based protein synthetic biology. Additionally, we identify future challenges and limitations of modular design along with approaches to address them.

4 páginas, 2 figuras, 2 tablas, 1 esquema., The synthesis of a novel core based on tris(triazolyl)triazine has been accomplished by a one-pot procedure that combines a 3-fold deprotection of alkyne groups and “click chemistry” of the aromatic alkyne and azide precursors. The procedure is straightforward for the preparation of functional materials for organic electronics. Indeed, compounds with low reduction potential are obtained. These compounds also show liquid crystalline behavior, displaying columnar mesophases at room temperature, and are luminescent in the visible region both in solution and in thin films., We thank the MICINN (Spain) and FSE (UE) (projects MAT2006-13571-CO2-01 and MAT2009- 14636-CO3-01), the CSIC-I3 (project 200860I054), and the Gobierno de Aragón (Research group E04) for financial support. E.B. thanks the FPI program of MICINN (Spain) for a fellowship.

We report the formation of cylindrical micelles, sheet-like micelles, tubular micelles, as well as polymer vesicles by a new series of amphiphilic linear−dendritic block-copolymers (BCs). The BCs, noted as PEGm-AZOn, are composed of poly(ethylene glycol) (PEG) chains of different molecular weights as hydrophilic blocks and the first four generations of azobenzene-containing dendrons based on 2,2-bis(hydroxymethyl)propionic acid (bis-MPA) as hydrophobic blocks (m represents the degree of polymerization of PEG, and n is the number of azobenzene units at the periphery of dendron). The polymeric aggregates were formed by adding water to solutions of the BCs in dioxane. The micellar dispersions in water were finally obtained by removing dioxane via dialysis against water. The morphology of the micellar self-assemblies was studied by transmission electron microscopy (TEM), cryo-electron microscopy (cryo-TEM), and atomic force microscopy (AFM). A generation-dependent aggregation behavior was found for the series of BCs PEG45-AZOn. Core−shell structured nanofibers with an inner diameter of 8 nm were observed for the copolymer PEG45-AZO2 (hydrophilic/hydrophobic weight ratio equal to 67/33). Lyotropic liquid crystalline behavior was detected for the aqueous solution of the nanofibers. The coexistence of sheet-like aggregates and tubular micelles was detected for the copolymer PEG45-AZO8 in which the number of cyanoazobenzene units is increased to 8 (hydrophilic/hydrophobic weight ratio equal to 33/67). The tubular micelles could be intermediates in the sheet-like aggregate-to-vesicle transition. Polymer vesicles (polymersomes) with a diameter in the range 300−800 nm were observed for the copolymer PEG45-AZO16 (hydrophilic/hydrophobic weight ratio equal to 20/80). The membrane of the sheet-like aggregates, tubular micelles, and polymersomes was shown to have a bilayer structure, as revealed by cryo-TEM. UV illumination of the aqueous polymersome dispersion induced the formation of wrinkles in the vesicle membrane, thus showing that this type of polymeric aggregate is photoresponsive., This work was supported by the MICINN, Spain, under the project MAT2008-06522-C02, FEDER, and DGA fundings.

Protein aggregation results in beta-sheet-like assemblies that adopt either a variety of amorphous morphologies or ordered amyloid-like structures. These differences in structure also reflect biological differences; amyloid and amorphous beta-sheet aggregates have different chaperone affinities, accumulate in different cellular locations and are degraded by different mechanisms. Further, amyloid function depends entirely on a high intrinsic degree of order. Here we experimentally explored the sequence space of amyloid hexapeptides and used the derived data to build Waltz, a web-based tool that uses a position-specific scoring matrix to determine amyloid-forming sequences. Waltz allows users to identify and better distinguish between amyloid sequences and amorphous beta-sheet aggregates and allowed us to identify amyloid-forming regions in functional amyloids.

The electronic structure of a neutral, a radical anion, and a dianion carborane dimer connected via an acetylenic bridge unit (HB) 11 C C C C(BH) 11 is analyzed by quantum chemical methods. Geometries, relative stabilities, and singlet–triplet gaps are determined in the neutral and dianion species for the lowest-lying singlet and triplet states and for the doublet ground state in the radical anion. As for the recently studied biradical compounds derived from o -carborane, m -carborane and p -carborane [J. Chem. Theory Comput. 4 (2008) 1338] via double hydrogen abstraction, the neutral dimeric compound displays a biradical ground-state structure in which both singlet and triplet state are practically degenerate, with the singlet state lying slightly lower in energy (⩽0.005 eV) at both DFT broken-symmetry and ab initio CASPT2 levels of theory. The singlet–triplet splitting is therefore close to k B · T at room temperature, approaching the microwave region of the electromagnetic spectrum. The neutral dimer biradical becomes then a strong candidate to behave as a molecular magnet in molecular architectures based on carborane units. It is also shown that the system is a powerful electron acceptor with increasing stability from the neutral to the radical anion and dianion systems.

Motivation: Most of the structures and functions of proteome globular domains are yet unknown. We can use high-resolution structures from different modular domains in combination with automatic protein design algorithms to predict genome-wide potential interactions of a protein. ADAN database and related web tools are online resources for the predictive analysis of ligand–domain complexes. ADAN database is a collection of different modular protein domains (SH2, SH3, PDZ, WW, etc.). It contains 3505 entries with extensive structural and functional information available, manually integrated, curated and annotated with cross-references to other databases, biochemical and thermodynamical data, simplified coordinate files, sequence files and alignments. Prediadan, a subset of ADAN database, offers position-specific scoring matrices for protein–protein interactions, calculated by FoldX, and predictions of optimum ligands and putative binding partners. Users can also scan a query sequence against selected matrices, or improve a ligand–domain interaction. Fil: Encinar, J. A.. Universidad de Miguel Hernández; España Fil: Fernández Ballester, G.. Universidad de Miguel Hernández; España Fil: Sánchez Miguel, Ignacio Enrique. Fundación Instituto Leloir; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Hurtado Gómez, E.. Universidad de Miguel Hernández; España Fil: Stricher, F.. Universitat Pompeu Fabra; España Fil: Beltrao, P.. University of California; Estados Unidos Fil: Serrano, L.. Universitat Pompeu Fabra; España

The rational design of peptide and protein helices is not only of practical importance for protein engineering but also is a useful approach in attempts to improve our understanding of protein folding. Recent modifications of theoretical models of helix-coil transitions allow accurate predictions of the helix stability of monomeric peptides in water and provide new possibilities for protein design. We report here a new method for the design of alpha-helices in peptides and proteins using AGADIR, the statistical mechanical theory for helix-coil transitions in monomeric peptides and the tunneling algorithm of global optimization of multidimensional functions for optimization of amino acid sequences. CD measurements of helical content of peptides with optimized sequences indicate that the helical potential of protein amino acids is high enough to allow formation of stable alpha-helices in peptides as short as of 10 residues in length. The results show the maximum achievable helix content (HC) of short peptides with fully optimized sequences at 5 degrees C is expected to be approximately 70-75%. Under certain conditions the method can be a powerful practical tool for protein engineering. Unlike traditional approaches that are often used to increase protein stability by adding a few favorable interactions to the protein structure, this method deals with all possible sequences of protein helices and selects the best one from them.

Energies and structures of different arrangements of the stacked adenine homodimer have been computed at the ab initio CASPT2 level of theory in isolation and in an aqueous environment. Adenine dimers are shown to form excimer singlet states with different degrees of stacking and interaction. A model for a 2-fold decay dynamics of adenine oligomers can be supported in which, after initial excitation in the middle UV range, unstacked or slightly stacked pairs of nucleobases will relax by an ultrafast internal conversion to the ground state, localizing the excitation in the monomer and through the corresponding conical intersection with the ground state. On the other hand, long-lifetime intrastrand stacked excimer singlet states will be formed in different conformations, including neutral and charge transfer dimers, which originate the red-shifted emission observed in the oligonucleotide chains and that will evolve toward the same monomer decay channel after surmounting an energy barrier. By computing the transient absorption spectra for the different structures considered and their relative stability in vacuo and in water, it is concluded that in the adenine homodimers the maximum-overlap face-to-face orientations are the most stable excimer conformations observed in experiment.

Tumor necrosis factor-related apoptosis-inducing ligand ( TRAIL) is a potential anticancer agent that selectively induces apoptosis in a variety of cancer cells by interacting with death receptors DR4 and DR5. TRAIL can also bind to decoy receptors ( DcR1, DcR2, and osteoprotegerin receptor) that cannot induce apoptosis. Different tumor types respond either to DR4 or to DR5 activation, and chemotherapeutic drugs can increase the expression of DR4 or DR5 in cancer cells. Thus, DR4 or DR5 receptor-specific TRAIL variants would permit new and tumor-selective therapies. Previous success in generating a DR5-selective TRAIL mutant using computer-assisted protein design prompted us to make a DR4-selective TRAIL variant. Technically, the design of DR4 receptor-selective TRAIL variants is considerably more challenging compared with DR5 receptor-selective variants, because of the lack of a crystal structure of the TRAIL-DR4 complex. A single amino acid substitution of Asp at residue position 218 of TRAIL to His or Tyr was predicted to have a favorable effect on DR4 binding specificity. Surface plasmon resonance-based receptor binding tests showed a lowered DR5 affinity in concert with increased DR4 specificity for the designed variants, D218H and D218Y. Binding to DcR1, DcR2, and osteoprotegerin was also decreased. Cell line assays confirmed that the variants could not induce apoptosis in DR5-responsive Jurkat and A2780 cells but were able to induce apoptosis in DR4-responsive EM-2 and ML-1 cells.

Based on CASPT2 results, the present contribution establishes for the first time that cytosine photodimer formation (CC) is mediated along the triplet and singlet manifold by a singlet-triplet crossing, (T1/S0)X, and by a conical intersection, (S1/S0)CI, respectively. The former can be accessed in a barrierless way from a great variety of photochemical avenues and exhibits a covalent single bond between the ethene C6-C6' carbon atoms of each monomer. The efficiency of the stepwise triplet mechanism, however, would be modulated by the effectiveness of the intersystem crossing mechanism. The results provide the grounds for the understanding of the potential photogenotoxicity of endogenous and exogenous compounds via triplet-triplet sensitization, with a lower bound for cytosine oligonucleotides predicted to be 2.70 eV, and give support to the traditional view of the primary role of triplet excited states in the photochemistry of DNA, a well-known source of photoproducts in solution under triplet photosensitization conditions. The function played by singlet excimers (excited dimers) to explain both the red-shifted fluorescence and photoreaction is highlighted. A rationale on the pronounced wavelength dependence of the observed fluorescence is offered. Geometrical arrangements at the time of light irradiation close to, but energetically above, (S1/S0)CI are suggested as reactive orientations that become prone to produce CC directly, with no energy barrier. Because of the outstanding intrinsic ability of cytosine to form stable relaxed excimers, the system located near the bound relaxed excimer has to accumulate enough vibrational energy to surmount a small barrier of 0.2 eV to reach (S1/S0)CI, making the overall process to proceed at a slower relative rate as compared to other compounds such as thymine, which is not susceptible of forming so stable excimers.

By using an amyloid sequence pattern, here we have identified putative six-residue amyloidogenic stretches in several relevant amyloid proteins. Hexapeptides synthesized on the bases of the sequence stretches matching the pattern have been shown to form amyloid fibrils in vitro. As larger pathological peptides such as A beta(1-42) do, these short amyloid peptides form heterogeneous mixtures of small aggregates that induce cell death in PC12 cells and primary hippocampal neurons. Toxic mixtures of small aggregates from these hexapeptides bind to cell membranes and can be further internalized, as also observed for natural amyloid proteins. In neurons, toxic aggregates obtained from the full length A beta(1-42) amyloid peptide or their amyloid stretch A beta(16-21) peptide preferentially localize in synapses, leading to the re-organization of the underlying actin cytoskeleton. This process does not involve stereospecific interactions between membrane and toxic species as D-sequences are as toxic as L ones, suggesting that is not receptor mediated. Based on these results, we propose here that regardless of polypeptide sequence, length and amino acid chirality, amyloid prefibrillar aggregates exert their cytotoxic effect through a common cell death mechanism related to a particular quaternary structure. The degree of toxicity of these species seems to depend, however, on cell membrane composition.

Purpose: Germline SDHB, SDHC, and/or SDHD mutations have been reported in familial and apparently sporadic paragangliomas (PGLs). There is, however, some variation in the prevalence, penetrance, and phenotypic expression of the succinate dehydrogenase (SDH) mutated gene among different populations. We sought to determine whether germline mutations in SDHB, SDHC, and/or SDHD play a role in cervical PGLs from northern Spain, where this disorder is particularly frequent, and whether there is any difference with respect to the data published in other populations. Design: Thirty-six sporadic cervical PGLs and four familial PGLs were investigated by PCR-single-strand conformation polymorphism analysis and sequencing. Computational biology was applied to address the structural-conformational changes behind missense mutations and, simultaneously, infer the possible consequences in protein function. Results: Eight sporadic cases (22.2%) carried pathogenic germline mutations, six of which were in SDHB and two in SDHD. Three families had mutations in SDHD and one in SDHB. Seven of 11 different pathogenic mutations (64%) affected SDHB. Ten mutations were novel. Missense mutations were primarily found in SDHB and frameshift mutations in SDHD. Missense SDHB mutations seemed to alter the enzymatic activity by hampering the electron transfer. SDH-linked tumors occurred mainly in males (P 0.0033), occurred at a younger age (P 0.0001), were usually multifocal (P 0.0011), and exhibited a larger size (P 0.0341). Conclusions: A significant proportion of sporadic cervical PGLs arise as a consequence of intrinsic genetic factors. At variance with previous reports, SDHB is frequently mutated in sporadic cervical PGLs and the mutations do not entail a deleterious behavior. Therefore, SDHB genetic testing may be considered in all subjects presenting with solitary cervical PGL and no family history. (J Clin Endocrinol Metab 92: 4853–4864, 2007)

11 pages, 8 figures, 4 tables, 1 scheme, 1 chart., Novel metallomesogens with luminescent properties and liquid crystalline behavior at room temperature have been achieved by the preparation of zinc complexes with polycatenar pyrazole and bis(pyrazolyl)methane ligands. Their molecular structures do not have a conventional shape in that they are far from the typical rod-like and flat disc-like geometries of common liquid crystals. They consist of a nonplanar nucleus due to the methylene spacer and/or the coordination to the tetrahedral center, as confirmed by single crystal analysis of the cores. The different numbers and positions of side chains in the pyrazole ligand enabled us to access lamellar and columnar mesophases and, of particular interest, to obtain columnar arrangements at room temperature. Supramolecular models for the organization of the molecules in the mesophases are proposed on the basis of the small-angle XRD diffractograms. The zinc complexes display luminescence in the near UV-blue region with large Stokes shifts. An interplay between non-conventional molecular shapes (due to the tetrahedral core) and the supramolecular mesomorphic order (due to the ligand design) led to materials that interestingly embody two rather opposite properties, a columnar self-organizational ability and luminescence with weak intermolecular interactions., We thank the Ministerio de Educación y Ciencia and FEDER, projects MAT2003-07806-C02-01, MAT- 2006-13571-CO2-01, the Ramón y Cajal (R.G.) and FPU (E.C.) programs, and the Gobierno de Aragón for financial support.

Motivation: One of the more challenging problems in biology is to determine the cellular protein interaction network. Progress has been made to predict protein–protein interactions based on structural information, assuming that structural similar proteins interact in a similar way. In a previous publication, we have determined a genome-wide Ras-effector interaction network based on homology models, with a high accuracy of predicting binding and non-binding domains. However, for a prediction on a genome-wide scale, homology modelling is a time-consuming process. Therefore, we here successfully developed a faster method using position energy matrices, where based on different Ras-effector X-ray template structures, all amino acids in the effector binding domain are sequentially mutated to all other amino acid residues and the effect on binding energy is calculated. Those pre-calculated matrices can then be used to score for binding any Ras or effector sequences.Results: Based on position energy matrices, the sequences of putative Ras-binding domains can be scanned quickly to calculate an energy sum value. By calibrating energy sum values using quantitative experimental binding data, thresholds can be defined and thus non-binding domains can be excluded quickly. Sequences which have energy sum values above this threshold are considered to be potential binding domains, and could be further analysed using homology modelling. This prediction method could be applied to other protein families sharing conserved interaction types, in order to determine in a fast way large scale cellular protein interaction networks. Thus, it could have an important impact on future in silico structural genomics approaches, in particular with regard to increasing structural proteomics efforts, aiming to determine all possible domain folds and interaction types.Availability: All matrices are deposited in the ADAN database (http://adan-embl.ibmc.umh.es/).Contact: christina.kiel@crg.esSupplementary information: Supplementary data are available at Bioinformatics online.

Oil and water do not normally mix, and apparently structural biology and systems biology look like two different universes. It can be argued that structural biology could play a very important role in systems biology. Although at the final stage of understanding a signal transduction pathway, a cell, an organ or a living system, structures could be obviated, we need them to be able to reach that stage. Structures of macromolecules, especially molecular machines, could provide quantitative parameters, help to elucidate functional networks or enable rational designed perturbation experiments for reverse engineering. The role of structural biology in systems biology should be to provide enough understanding so that macromolecules can be translated into dots or even into equations devoid of atoms.

Many research efforts in the last years have been directed towards understanding the factors determining protein misfolding and amyloid formation. Protein stability and amino acid composition have been identified as the two major factors in vitro. The research of our group has been focused on understanding the relationship between amino acid sequence and amyloid formation. Our approach has been the design of simple model systems that reproduce the biophysical properties of natural amyloids. An amyloid sequence pattern was extracted that can be used to detect amyloidogenic hexapeptide stretches in proteins. We have added evidence supporting that these amyloidogenic stretches can trigger amyloid formation by nonamyloidogenic proteins. Some experimental results in other amyloid proteins will be analyzed under the conclusions obtained in these studies. Our conclusions together with evidences from other groups suggest that amyloid formation is the result of the interplay between a decrease of protein stability, and the presence of highly amyloidogenic regions in proteins. As many of these results have been obtained in vitro, the challenge for the next years will be to demonstrate their validity in in vivo systems.

Environmental contamination by toxic organic compounds and antimicrobials is one of the causes for the recent surge of multidrug-resistant pathogenic bacteria. Monitoring contamination is therefore the first step in containment of antimicrobial resistance and requires the development of simple, sensitive, and quantitative tools that detect a broad spectrum of toxic compounds. In this study, we have engineered a new microbial biosensor based on the ttgR-regulated promoter that controls expression of the TtgABC extrusion efflux pump of Pseudomonas putida, coupled to a gfp reporter. The system was introduced in P. putida DOT-T1E, a strain characterized by its ability to survive in the presence of high concentrations of diverse toxic organic compounds. This whole-cell biosensor is capable to detect a wide range of structurally diverse antibiotics, as well as compounds such as toluene or flavonoids.

A good approach to test our current knowledge on formation of protein beta-sheets is de novo protein design. To obtain a three-stranded beta-sheet mini-protein, we have built a series of chimeric peptides by taking as a template a previously designed beta-sheet peptide, Betanova-LLM, and incorporating N- and/or C-terminal extensions taken from WW domains, the smallest natural beta-sheet domain that is stable in absence of disulfide bridges. Some Betanova-LLM strand residues were also substituted by those of a prototype WW domain. The designed peptides were cloned and expressed in Escherichia coli. The ability of the purified peptides to adopt beta-sheet structures was examined by circular dichroism (CD). Then, the peptide showing the highest beta-sheet population according to the CD spectra, named 3SBWW-2, was further investigated by 1H and 13C NMR. Based on NOE and chemical shift data, peptide 3SBWW-2 adopts a well defined three-stranded antiparallel beta-sheet structure with a disordered C-terminal tail. To discern between the contributions to beta-sheet stability of strand residues and the C-terminal extension, the structural behavior of a control peptide with the same strand residues as 3SBWW-2 but lacking the C-terminal extension, named Betanova-LYYL, was also investigated. beta-Sheet stability in these two peptides, in the parent Betanova-LLM and in WW-P, a prototype WW domain, decreased in the order WW-P3SBWW-2Betanova-LYYLBetanova-LLM. Conclusions about the contributions to beta-sheet stability were drawn by comparing structural properties of these four peptides.

A detailed understanding of the molecular events underlying the conversion and self-association of normally soluble proteins into amyloid fibrils is fundamental to the identification of therapeutic strategies to prevent or cure amyloid-related disorders. Recent investigations indicate that amyloid fibril formation is not just a general property of the polypeptide backbone depending on external factors, but that it is strongly modulated by amino acid side chains. Here, we propose and address the validation of the premise that the amyloidogenicity of a protein is indeed localized in short protein stretches (amyloid stretch hypothesis). We demonstrate that the conversion of a soluble nonamyloidogenic protein into an amyloidogenic prone molecule can be triggered by a nondestabilizing six-residue amyloidogenic insertion in a particular structural environment. Interestingly enough, although the inserted amyloid sequences clearly cause the process, the protease-resistant core of the fiber also includes short adjacent sequences from the otherwise soluble globular domain. Thus, short amyloid stretches accessible for intermolecular interactions trigger the self-assembly reaction and pull the rest of the protein into the fibrillar aggregate. The reliable identification of such amyloidogenic stretches in proteins opens the possibility of using them as targets for the inhibition of the amyloid fibril formation process.

The present contribution contains an overview of quantum-chemical methods and strategies to compute and interpret spectroscopic and photochemical phenomena in molecular systems. The state of the art for the quantum chemistry of the excited state is reviewed, focusing in the advantages and disadvantages of the most commonly employed computational methods, from the single configurational procedures like CI-Singles (CIS), propagator approaches, and Coupled-Cluster (CC) techniques, to the more sophisticated multiconfigurational treatments, with particular emphasis on perturbation theory, the CASPT2 approach. Also, a short summary on the performance, lights, and shadows of the popular TDDFT methods is included. The role of the differential correlation effects on quantum-chemical calculations is analyzed, especially for the location of potential energy surface crossings. The contribution finally addresses the importance that theoretical constructs as conical and non-conical intersections play in non-adiabatic photochemistry. The nice photochemistry of cytosine is used as an illustrative example of theoretical photochemistry, a continuously expanding field of research.

Taz is a chimeric receptor consisting of the periplasmic, transmembrane and most of the HAMP linker domains of the Escherichia coli aspartate receptor (Tar(Ec)) and the cytoplasmic signalling domain of the E. coli osmosensor EnvZ. Aspartate is one of several attractant ligands normally sensed by Tar and it interacts with Taz to induce OmpR-dependent transcription from the ompC promoter--albeit with reduced sensitivity relative to the chemotactic response it evokes via Tar. By combining Taz with a reporter system that expresses green fluorescent protein (GFP) from the ompC promoter, we were able to examine the interaction of Taz with all 20 natural amino acids. Some amino acids (Leu, Met, Val and Ser) reduced GFP expression, which in the case of leucine is likely attributed to a direct effect on the receptor, rather than an indirect effect through the leucine responsive protein (Lrp). Surprisingly, amino acids like Met and Ser--which are also attractants for Tar--'inhibited' Taz. Moreover, Taz exhibits a higher sensitivity to Leu compared with Asp, which is the inverse of Tar. Our results show the exquisite sensitivity of chemotactic receptors. Small conformational changes induced by making the chimera may have changed the way it responds to different amino acids.