Exploring blocker binding to a homology model of the open hERG K+ channel using docking and molecular dynamics methods

AbstractBinding of blockers to the human voltage-gated hERG potassium channel is studied using a combination of homology modelling, automated docking calculations and molecular dynamics simulations, where binding affinities are evaluated using the linear interaction energy method. A homology model was constructed based on the available crystal structure of the bacterial KvAP channel and the affinities of a series of sertindole analogues predicted using this model. The calculations reproduce the relative binding affinities of these compounds very well and indicate that both polar interactions near the intracellular opening of the selectivity filter as well as hydrophobic complementarity in the region around F656 are important for blocker binding. These results are consistent with recent alanine scanning mutation experiments on the blocking of the hERG channel by other compounds

Structure–activity relationship for extracellular block of K+ channels by tetraalkylammonium ions

AbstractExternal tetraalkylammonium ion binding to potassium channels is studied using microscopic molecular modelling methods and the experimental structure of the KcsA channel. Relative binding free energies of the KcsA complexes with Me4N+, Et4N+, and n-Pr4N+ are calculated with the molecular dynamics free energy perturbation approach together with automated ligand docking. The four-fold symmetry of the entrance cavity formed by the Tyr82 residues is found to provide stronger binding for the D2d than for the S4 conformation of the ligands. In agreement with experiment the Et4N+ blocker shows several kcal/mol better binding than the other tetraalkylammonium ions

Perhetyön kehittäminen Pohjois-Porin neuvolassa

Tämän opinnäytetyön tarkoituksena oli kehittää perhetyön toimintamalli neuvolatyöskentelyn tueksi hyödyntäen moniammatillista yhteistyötä. Opinnäytetyö toteutettiin kehittämistehtävänä Pohjois-Porin neuvolassa vuosien 2006 ja 2007 aikana. Opinnäytetyö koostui perhetyöntekijän toiminnan ennakkoarvioinnista, toiminnan tarpeen kartoituksesta sekä toiminnan mallittamisesta ja arvioinnista. Tämä opinnäytetyö on osa LAPSOS-hanketta. Opinnäytetyön teoriaosuus koostuu lapsiperheiden voimavarojen sekä yhteiskunnallisen tilanteen tarkastelusta. Teoreettisessa osuudessa tarkastellaan myös neuvolan ja perhetyöntekijän toimintaa sekä moniammatillisen yhteistyön ja ennaltaehkäisevän työn merkitystä lapsiperheiden tukemisessa. Opinnäytetyössä kehittämistehtävän empiirinen osuus toteutettiin toimintatutkimuksena. Aineistot koostuivat teksteistä, kuten kirjallisuudesta ja tutkimuksista sekä fokusryhmän haastatteluista ja kirjallisista muistiinpanoista. Osa aineistosta kerättiin kyselylomakkeella ja tehtävää varten laadittiin kyselylomake. Kerätyt aineistot analysoitiin käyttämällä apuna taulukkolaskentaohjelmaa ja sisällön analyysin menetelmää. Opinnäytetyössä tulokset esitetään kuvioiden ja taulukoiden avulla. Kyselyn keskeinen tulos oli kotikäyntien lisääminen ja sosiaalialan osaamisen tarve Pohjois-Porin neuvolassa. Kyselyn tulosten pohjalta neuvolaan suunniteltiin perhetyön toimintamalli, jota lähdettiin käytännössä kokeilemaan kuuden kuukauden kokeilujakson aikana. Kokeilujakson edetessä toimintaa arvioitiin kolme kertaa ja sitä kehitettiin paremmin neuvolatyöhön sopivaksi. Opinnäytetyön toteuttaminen perustui lapsiperheiden tuentarpeen muuttumiseen ja neuvolatoiminnan kehittämisen tarpeeseen. Opinnäytetyö tuki käytännön toiminnan kehittämistä. Neuvolan perhetyön toimintamalli muotoutuu moniammatillisen yhteistyökokemuksen karttuessa ja tulevaisuudessa toimintamallia voisi kehittää entistä paremmin lapsiperheiden tarpeita vastaavaksi.The purpose of this thesis was to develop an operating model for family work to support child health clinic services and utilize multiprofessional cooperation. The research was conducted as a development project in the Northern Pori Child Health Clinic during 2006 and 2007. The study consisted of pre-evaluation, needs analysis, modelling, and evaluation of family workers’ actions. This thesis is a part of project called LAPSOS. In the theoretical part of the study, the resources of families with children and their social situations were examined. In this same context, the services of the Child Health Clinic and actions of the family worker were studied and the importance of pre-emptive actions in supporting families was determined. In this thesis, the empirical part of the development project was implemented as action research. The study data consisted of text references, such as literature and previous research in the field, as well as focus group interviews and written notes. Some of the data was gathered with a questionnaire, which was specially designed for this task. The data was analysed by using spreadsheets and content analysis method and the results are presented as charts and tables. The key result of this survey was to increase health visits. The Northern Pori Child Health Clinic also needed more expertise in the field of social services. An operating model for family work was designed on the basis of these results. The model was implemented in practice as a pilot project for a period of six months. As the pilot project progressed, its functionality was evaluated three times. In addition, the project was further developed to meet the child health clinic needs. This thesis was based on the changing needs of families and the demand for the development of child health clinic activities. It also supported the development of practical work. The Child Health Clinic operating model for family work will find its shape as multiprofessional cooperation increases. In the future, the operating model could be further developed to better meet the families’ needs

Meningkatkan Kinerja Database Billing pada Warnet PT. Dinustech dengan Menggunakan Trigger dan Stored Procedure

Laporan Tugas Akhir dengan judul "Meningkatkan Kinerja Database Billing Pada Warnet PT. Dinustech dengan Menggunakan Trigger dan Stored Procedure" merupakan sistem yang di buat untuk memperbaiki sistem yang sudah ada dalam database billing. Sistem yang dibuat ini diharapkan dapat meningkatkan kinerja database billing sehingga mengurangi delay atau lag pada sistem sebelumnya Metodologi pengumpulan data menggunakan metode : interview yaitu cara mengumpulkan data dengan mengadakan tanya jawab langsung dengan bagian yang berhubungan dengan obyek yang diteliti. Survei yaitu pengamatan langsung mengenai sistem database yang lama pada Warnet PT. Dinustec. Studi pustaka adalah pengumpulan data dengan mempelajari buku atau literatur-literatur mengenai perancangan dan desain suatu sistem. Desain sistem dan perancangan database yang digunakan mulai dari Context Diagram, DFD Level, ERD, Normalisasi dan Kamus Data menghasilkan suatu sistem database yang lebih baik dan tertata dibandingkan dengan database sebelumnya, Peningkatan pada sistem database ini terdapat pada penataan ulang relasi-relasi tabel pada database sebelumnya. Kemudian melakukan otomatisasi pada beberapa proses dengan menggunakan trigger dan stored procedure. Dengan adanya peningkatan ini, masalah-masalah sebelumnya berupa delay atau lag pada client warnet tersebut berkurang, dan juga sistem laporan pun menjadi lebih mudah dan jelas

X‐Ray Crystallography and Free Energy Calculations Reveal the Binding Mechanism of A2A Adenosine Receptor Antagonists

We present a robust protocol based on iterations of free energy perturbation (FEP) calculations, chemical synthesis, biophysical mapping and X‐ray crystallography to reveal the binding mode of an antagonist series to the A2A adenosine receptor (AR). Eight A2AAR binding site mutations from biophysical mapping experiments were initially analyzed with sidechain FEP simulations, performed on alternate binding modes. The results distinctively supported one binding mode, which was subsequently used to design new chromone derivatives. Their affinities for the A2AAR were experimentally determined and investigated through a cycle of ligand‐FEP calculations, validating the binding orientation of the different chemical substituents proposed. Subsequent X‐ray crystallography of the A2AAR with a low and a high affinity chromone derivative confirmed the predicted binding orientation. The new molecules and structures here reported were driven by free energy calculations, and provide new insights on antagonist binding to the A2AAR, an emerging target in immuno‐oncologyThis work was financially supported by the Swedish Research Council (Grant 521‐2014‐2118); Consellería de Cultura, Educación e Ordenación Universitaria of the Galician Government (Grant ED431B2017/70); Centro Singular de Investigación de Galicia accreditation 2016–2019 (Grant ED431G/09), and the European Regional Development Fund (ERDF). Additional support from the Swedish strategic research program eSSENCE is acknowledged. The computations were performed on resources provided by the Swedish National Infrastructure for Computing (SNIC). This research program has been developed in the frame of the European COST action ERNEST (Grant CA 18133) and GLISTEN (Grant CA 1207)S

Computer Simulations Reveal an Entirely Entropic Activation Barrier for the Chemical Step in a Designer Enzyme

Despite advances in computational design of protein structures, it has proven very difficult to design efficient enzyme catalysts by such approaches. One of the challenges in the field has been to computationally design enzymes that catalyze Kemp elimination, a reaction not observed in nature. Among several such designs, there is a series for which the catalytic rate constant could be improved by several thousand-fold by laboratory evolution, although it is still modest compared to natural enzymes catalyzing similar chemistry. These evolved designer enzymes also showed unusual temperature optima that were not related to thermal unfolding. Here, we report extensive computer simulations of both the catalyzed reaction and conformational thermodynamics of one these enzymes to analyze the underlying reasons for low catalytic activity and the anomalous temperature behavior. The results reveal that there exists a lower energy state of the enzyme-substrate complex, not seen in crystal structures with transition state analogues, which explains the low activity. Computational Arrhenius and van't Hoff plots for the chemical step and the transition between the two reactant states are both linear, and the resulting reaction thermodynamics is found to render the catalytic barrier entirely entropic. Kinetic modeling based on our calculated thermodynamic parameters gives two possible quantitative explanations for the temperature optimum: a change of rate-limiting step at 308 K or a heat capacity change of -0.3 kcal/mol/K upon substrate binding, where experimental data appear most consistent with the former

Brandförlopp - Lätta stommar

This report deals with fully developed fires in compartments where the boundary structure is made of mineral wool and plasterboard. The project was initiated due to new Swedish regulations (BBR 94) that allow buildings with wood structure to be built more than two storeys high. The temperature-timecurves in this report are computed according to authorized methods used in Sweden (method I and method II). The accuracy of the first has been questioned due to simplifications in the model it is based upon and therefore the methods are thoroughly analysed. A comparison between fullscale experiments and computer simulated fires has been carried out. The results indicate that the validity of method I is good. The report also presents a comparison between light weight wall construction and concrete construction. Finally some suggestions are made concerning how further studies should be carried out