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  • 1.
    Andersson, Alma E. V.
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Kasimova, Marina A.
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Delemotte, Lucie
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Exploring the Viral Channel Kcv(PBCV-1) Function via Computation2018Ingår i: Journal of Membrane Biology, ISSN 0022-2631, E-ISSN 1432-1424, Vol. 251, nr 3, s. 419-430Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Viral potassium channels (Kcv) are homologous to the pore module of complex -selective ion channels of cellular organisms. Due to their relative simplicity, they have attracted interest towards understanding the principles of conduction and channel gating. In this work, we construct a homology model of the open state, which we validate by studying the binding of known blockers and by monitoring ion conduction through the channel. Molecular dynamics simulations of this model reveal that the re-orientation of selectivity filter carbonyl groups coincides with the transport of potassium ions, suggesting a possible mechanism for fast gating. In addition, we show that the voltage sensitivity of this mechanism can originate from the relocation of potassium ions inside the selectivity filter. We also explore the interaction of with the surrounding bilayer and observe the binding of lipids in the area between two adjacent subunits. The model is available to the scientific community to further explore the structure/function relationship of Kcv channels.

  • 2.
    Kasimova, Marina A.
    et al.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Lindahl, Erik
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik.
    Delemotte, L.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Determining the molecular basis of voltage sensitivity in membrane proteins2018Ingår i: The Journal of General Physiology, ISSN 0022-1295, E-ISSN 1540-7748, Vol. 215, nr 10, s. 1444-1458Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Voltage-sensitive membrane proteins are united by their ability to transform changes in membrane potential into mechanical work. They are responsible for a spectrum of physiological processes in living organisms, including electrical signaling and cell-cycle progression. Although the mechanism of voltage-sensing has been well characterized for some membrane proteins, including voltage-gated ion channels, even the location of the voltage-sensing elements remains unknown for others. Moreover, the detection of these elements by using experimental techniques is challenging because of the diversity of membrane proteins. Here, we provide a computational approach to predict voltage-sensing elements in any membrane protein, independent of its structure or function. It relies on an estimation of the propensity of a protein to respond to changes in membrane potential. We first show that this property correlates well with voltage sensitivity by applying our approach to a set of voltage-sensitive and voltage-insensitive membrane proteins. We further show that it correctly identifies authentic voltage-sensitive residues in the voltage-sensor domain of voltage-gated ion channels. Finally, we investigate six membrane proteins for which the voltage-sensing elements have not yet been characterized and identify residues and ions that might be involved in the response to voltage. The suggested approach is fast and simple and enables a characterization of voltage sensitivity that goes beyond mere identification of charges. We anticipate that its application before mutagenesis experiments will significantly reduce the number of potential voltage-sensitive elements to be tested. 

  • 3.
    Kasimova, Marina A.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Lindahl, Erik
    KTH.
    Delemotte, Lucie
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Detection of Voltage-Sensing Residues in Membrane Proteins2018Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, nr 3, s. 476A-476AArtikel i tidskrift (Övrigt vetenskapligt)
  • 4.
    Kasimova, Marina A.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Tewari, Debanjan
    Univ Wisconsin, Dept Neurosci, Madison, WI 53706 USA..
    Cowgill, John B.
    Univ Wisconsin, Dept Neurosci, Madison, WI 53706 USA.;Univ Wisconsin, Grad Program Biophys, Madison, WI USA..
    Ursuleaz, Willy Carrasquel
    Univ Wisconsin, Dept Neurosci, Madison, WI 53706 USA..
    Lin, Jenna L.
    Univ Wisconsin, Dept Neurosci, Madison, WI 53706 USA.;Univ Wisconsin, Grad Program Biophys, Madison, WI USA..
    Delemotte, Lucie
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Chanda, Baron
    Univ Wisconsin, Dept Neurosci, Madison, WI 53706 USA.;Univ Wisconsin, Dept Biomol Chem, Madison, WI 53706 USA..
    Helix breaking transition in the S4 of HCN channel is critical for hyperpolarization- dependent gating2019Ingår i: eLIFE, E-ISSN 2050-084X, Vol. 8, artikel-id e53400Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    In contrast to most voltage-gated ion channels, hyperpolarization- and cAMP gated (HCN) ion channels open on hyperpolarization. Structure-function studies show that the voltagesensor of HCN channels are unique but the mechanisms that determine gating polarity remain poorly understood. All-atom molecular dynamics simulations (similar to 20 mu s) of HCN1 channel under hyperpolarization reveals an initial downward movement of the S4 voltage-sensor but following the transfer of last gating charge, the S4 breaks into two sub-helices with the lower sub-helix becoming parallel to the membrane. Functional studies on bipolar channels show that the gating polarity strongly correlates with helical turn propensity of the substituents at the breakpoint. Remarkably, in a proto-HCN background, the replacement of breakpoint serine with a bulky hydrophobic amino acid is sufficient to completely flip the gating polarity from inward to outward-rectifying. Our studies reveal an unexpected mechanism of inward rectification involving a linker sub-helix emerging from HCN S4 during hyperpolarization.

  • 5.
    Kasimova, Marina
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Yazici, Aysenur
    Granata, Daniele
    Rohacs, Tibor
    Carnevale, Vincenzo
    Dynamic Solvation of Protein Cavities Underlies TRPV1 Gating2017Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, nr 3, s. 466A-466AArtikel i tidskrift (Refereegranskat)
  • 6.
    Roose, Benjamin W.
    et al.
    Univ Penn, Dept Chem, 231 S 34th St, Philadelphia, PA 19104 USA..
    Zemerov, Serge D.
    Univ Penn, Dept Chem, 231 S 34th St, Philadelphia, PA 19104 USA..
    Wang, Yanfei
    Harvard Med Sch, 300 Longwood Ave, Boston, MA 02115 USA..
    Kasimova, Marina A.
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Carnevale, Vincenzo
    Temple Univ, Coll Sci & Technol, Inst Computat Mol Sci, 1925 N 12th St, Philadelphia, PA 19122 USA..
    Dmochowski, Ivan J.
    Univ Penn, Dept Chem, 231 S 34th St, Philadelphia, PA 19104 USA..
    A Structural Basis for Xe-129 Hyper-CEST Signal in TEM-1 beta-Lactamase2019Ingår i: ChemPhysChem, ISSN 1439-4235, E-ISSN 1439-7641, Vol. 20, nr 2, s. 260-267Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Genetically encoded (GE) contrast agents detectable by magnetic resonance imaging (MRI) enable non-invasive visualization of gene expression and cell proliferation at virtually unlimited penetration depths. Using hyperpolarized Xe-129 in combination with chemical exchange saturation transfer, an MR contrast approach known as hyper-CEST, enables ultrasensitive protein detection and biomolecular imaging. GE MRI contrast agents developed to date include nanoscale proteinaceous gas vesicles as well as the monomeric bacterial proteins TEM-1 beta-lactamase (bla) and maltose binding protein (MBP). To improve understanding of hyper-CEST NMR with proteins, structural and computational studies were performed to further characterize the Xe-bla interaction. X-ray crystallography validated the location of a high-occupancy Xe binding site predicted by MD simulations, and mutagenesis experiments confirmed this Xe site as the origin of the observed CEST contrast. Structural studies and MD simulations with representative bla mutants offered additional insight regarding the relationship between local protein structure and CEST contrast.

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