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  • 1. Ghahremanpour, Mohammad Mehdi
    et al.
    Arab, Seyed Shahriar
    Aghazadeh, Saman Biook
    Zhang, Jin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    MemBuilder: a web-based graphical interface to build heterogeneously mixed membrane bilayers for the GROMACS biomolecular simulation program2014In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 30, no 3, p. 439-441Article in journal (Refereed)
    Abstract [en]

    Motivation: Molecular dynamics (MD) simulations have had a profound impact on studies of membrane proteins during past two decades, but the accuracy of MD simulations of membranes is limited by the quality of membrane models and the applied force fields. Membrane models used in MD simulations mostly contain one kind of lipid molecule. This is far from reality, for biological membranes always contain more than one kind of lipid molecule. Moreover, the lipid composition and their distribution are functionally important. As a result, there is a necessity to prepare more realistic lipid membranes containing different types of lipids at physiological concentrations. Results: To automate and simplify the building process of heterogeneous lipid bilayers as well as providing molecular topologies for included lipids based on both united and all-atom force fields, we provided MemBuilder as a web-based graphical user interface.

  • 2.
    Manzetti, Sergio
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics. Uppsala University, Science for Life Laboratory, SciLifeLab. Fjordforsk AS, N-6896 Fresvik, Norway.
    Zhang, Jin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Zhejiang Univ, Dept Chem, Hangzhou 310027, Zhejiang, Peoples R China.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Thiamin Function, Metabolism, Uptake, and Transport2014In: Biochemistry, ISSN 0006-2960, E-ISSN 1520-4995, Vol. 53, no 5, p. 821-835Article in journal (Refereed)
    Abstract [en]

    Vitamins are crucial components in the diet of animals and many other living organisms. One of these essential nutrients, thiamin, is known to be involved in several cell functions, including energy metabolism and the degradation of sugars and carbon skeletons. Other roles that are connected to this vitamin are neuronal communication, immune system activation, signaling and maintenance processes in cells and tissues, and cell-membrane dynamics. Because of the key functions of thiamin, uptake and transport through the body are crucial. Its uptake route is relatively complex, encompassing a variety of protein families, including the solute carrier anion transporters, the alkaline phosphatase transport system, and the human extraneuronal monoamine transporter family, some of which are multispecific proteins. There are two known structures of protein (subunits) involved in thiamin uptake in prokaryotes. Binding of thiamin to these proteins is strongly guided by electrostatic interactions. The lack of structural information about thiamin binding proteins for higher organisms remains a bottleneck for understanding the uptake process of thiamin in atomic detail. This review includes recent data on thiamin metabolism, related deficiencies and pathologies, and the latest findings on thiamin binding transporters.

  • 3.
    Rask-Andersen, Mathias
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Zhang, Jin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Fabbro, Doriano
    Schiöth, Helgi B
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Functional Pharmacology.
    Advances in kinase targeting: current clinical use and clinical trials2014In: TIPS - Trends in Pharmacological Sciences, ISSN 0165-6147, E-ISSN 1873-3735, Vol. 35, no 11, p. 604-620Article, review/survey (Refereed)
    Abstract [en]

    Phosphotransferases, also known as kinases, are the most intensively studied protein drug target category in current pharmacological research, as evidenced by the vast number of kinase-targeting agents enrolled in active clinical trials. This development has emerged following the great success of small-molecule, orally available protein kinase inhibitors for the treatment of cancer, starting with the introduction of imatinib (Gleevec®) in 2003. The pharmacological utility of kinase-targeting has expanded to include treatment of inflammatory diseases, and rapid development is ongoing for kinase-targeted therapies in a broad array of indications in ophthalmology, analgesia, central nervous system (CNS) disorders, and the complications of diabetes, osteoporosis, and otology. In this review we highlight specifically the kinase drug targets and kinase-targeting agents being explored in current clinical trials. This analysis is based on a recent estimate of all established and clinical trial drug mechanisms of action, utilizing private and public databases to create an extensive dataset detailing aspects of more than 3000 approved and experimental drugs.

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