Communication in Membrane Repair

University of Minnesota M.S. thesis. June 2015. Major: Chemistry. Advisor: Dr. Anne Hinderliter. 1 computer file (PDF): x, 127 pages.

[1]  S. Takeda,et al.  Identification and characterization of a novel human dysferlin transcript: dysferlin_v1 , 2006, Human Genetics.

[2]  M. Bretscher Asymmetrical lipid bilayer structure for biological membranes. , 1972, Nature: New biology.

[3]  Vladimir N Uversky,et al.  What does it mean to be natively unfolded? , 2002, European journal of biochemistry.

[4]  K. Dill Dominant forces in protein folding. , 1990, Biochemistry.

[5]  Pieter J. de Jong,et al.  Dysferlin, a novel skeletal muscle gene, is mutated in Miyoshi myopathy and limb girdle muscular dystrophy , 1998, Nature Genetics.

[6]  Deborah A. Brown,et al.  Lipid rafts, detergent-resistant membranes, and raft targeting signals. , 2006, Physiology.

[7]  S. Takeda,et al.  Intracellular localization of dysferlin and its association with the dihydropyridine receptor. , 2005, Acta myologica : myopathies and cardiomyopathies : official journal of the Mediterranean Society of Myology.

[8]  M. Nishi,et al.  MG53 nucleates assembly of cell membrane repair machinery , 2009, Nature Cell Biology.

[9]  D. Cafiso,et al.  Membrane-bound orientation and position of the synaptotagmin I C2A domain by site-directed spin labeling. , 2003, Biochemistry.

[10]  Helmut Grubmüller,et al.  Molecular Anatomy of a Trafficking Organelle , 2006, Cell.

[11]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[12]  H. Morowitz,et al.  Energy Flow in Biology , 1969 .

[13]  Yutaka Kuroda,et al.  Structural genomics projects in Japan , 2000, Nature Structural Biology.

[14]  A. Muga,et al.  Linking new paradigms in protein chemistry to reversible membrane-protein interactions. , 2009, Current protein & peptide science.

[15]  Robert B. Gennis,et al.  Biomembranes: Molecular Structure and Function , 1988 .

[16]  Lina Baranauskienė,et al.  Measurement of Nanomolar Dissociation Constants by Titration Calorimetry and Thermal Shift Assay – Radicicol Binding to Hsp90 and Ethoxzolamide Binding to CAII , 2009, International journal of molecular sciences.

[17]  A. Rosengarth,et al.  A comparison of the energetics of annexin I and annexin V. , 1999, Journal of molecular biology.

[18]  N. Bourg,et al.  Lack of Correlation between Outcomes of Membrane Repair Assay and Correction of Dystrophic Changes in Experimental Therapeutic Strategy in Dysferlinopathy , 2012, PloS one.

[19]  N. Bresolin,et al.  Mutation finding in patients with dysferlin deficiency and role of the dysferlin interacting proteins annexin A1 and A2 in muscular dystrophies , 2005, Human mutation.

[20]  Ole G Mouritsen,et al.  Lipids do influence protein function-the hydrophobic matching hypothesis revisited. , 2004, Biochimica et biophysica acta.

[21]  A. Pokorny,et al.  Thermodynamics of membrane domains. , 2005, Biochimica et biophysica acta.

[22]  D. Davis,et al.  Calcium-sensitive Phospholipid Binding Properties of Normal and Mutant Ferlin C2 Domains* , 2002, The Journal of Biological Chemistry.

[23]  D. Cafiso,et al.  Membrane-bound orientation and position of the synaptotagmin C2B domain determined by site-directed spin labeling. , 2005, Biochemistry.

[24]  R B Sutton,et al.  Negative Coupling as a Mechanism for Signal Propagation between C2 Domains of Synaptotagmin I , 2012, PloS one.

[25]  Steven S. Vogel,et al.  Membrane wounding triggers ATP release and dysferlin-mediated intercellular calcium signaling , 2010, Journal of Cell Science.

[26]  C. Angelini,et al.  Muscular dystrophy with marked Dysferlin deficiency is consistently caused by primary dysferlin gene mutations , 2011, European Journal of Human Genetics.

[27]  R B Sutton,et al.  Mechanism for calcium ion sensing by the C2A domain of synaptotagmin I. , 2012, Biophysical journal.

[28]  Jessica W. Chen Conversation of Intrinsic Disorder in Protein Domains and Families , 2005 .

[29]  J. Pous,et al.  Structural insights into the Ca2+ and PI(4,5)P2 binding modes of the C2 domains of rabphilin 3A and synaptotagmin 1 , 2013, Proceedings of the National Academy of Sciences.

[30]  Peer Bork,et al.  SMART 7: recent updates to the protein domain annotation resource , 2011, Nucleic Acids Res..

[31]  K. Miyake,et al.  Vesicle accumulation and exocytosis at sites of plasma membrane disruption , 1995, The Journal of cell biology.

[32]  H. Brinkmeier,et al.  Calcium ion in skeletal muscle: its crucial role for muscle function, plasticity, and disease. , 2000, Physiological reviews.

[33]  M. Sinnreich,et al.  Dysferlin Interacts with Tubulin and Microtubules in Mouse Skeletal Muscle , 2010, PloS one.

[34]  Steven S. Vogel,et al.  Patching plasma membrane disruptions with cytoplasmic membrane. , 2000, Journal of cell science.

[35]  A. Hinderliter,et al.  Domain formation in a fluid mixed lipid bilayer modulated through binding of the C2 protein motif. , 2001, Biochemistry.

[36]  B. Sigurskjold,et al.  Exact analysis of competition ligand binding by displacement isothermal titration calorimetry. , 2000, Analytical biochemistry.

[37]  J. Ayala-Sanmartin,et al.  Lipid organization regulates annexin A2 Ca(2+)-sensitivity for membrane bridging and its modulator effects on membrane fluidity. , 2012, Biochimica et biophysica acta.

[38]  M. Sinnreich,et al.  Characterization of lipid binding specificities of dysferlin C2 domains reveals novel interactions with phosphoinositides. , 2009, Biochemistry.

[39]  Owen Johnson,et al.  iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM , 2011, Acta crystallographica. Section D, Biological crystallography.

[40]  A. Engel,et al.  The earliest pathologic alterations in dysferlinopathy , 2001, Neurology.

[41]  J. Beckmann,et al.  Genomic organization of the dysferlin gene and novel mutations in Miyoshi myopathy , 2001, Neurology.

[42]  K. North,et al.  Reduced Plasma Membrane Expression of Dysferlin Mutants Is Attributed to Accelerated Endocytosis via a Syntaxin-4-associated Pathway* , 2010, The Journal of Biological Chemistry.

[43]  F W McLafferty,et al.  Quantitative analysis of phospholipids in functionally important membrane domains from RBL-2H3 mast cells using tandem high-resolution mass spectrometry. , 1999, Biochemistry.

[44]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[45]  Y. Sunada,et al.  Membrane Repair Defects in Muscular Dystrophy Are Linked to Altered Interaction between MG53, Caveolin-3, and Dysferlin*◆ , 2009, The Journal of Biological Chemistry.

[46]  Wonhwa Cho,et al.  Membrane binding and subcellular targeting of C2 domains. , 2006, Biochimica et biophysica acta.

[47]  Collin M. Stultz,et al.  Protein Structure along the Order–Disorder Continuum , 2011, Journal of the American Chemical Society.

[48]  N. Verdaguer,et al.  Structure of the C2 domain from novel protein kinase Cepsilon. A membrane binding model for Ca(2+)-independent C2 domains. , 2001, Journal of molecular biology.

[49]  R. Jahn,et al.  The Ca2+ Affinity of Synaptotagmin 1 Is Markedly Increased by a Specific Interaction of Its C2B Domain with Phosphatidylinositol 4,5-Bisphosphate , 2009, The Journal of Biological Chemistry.

[50]  M. Lek,et al.  Phylogenetic analysis of ferlin genes reveals ancient eukaryotic origins , 2010, BMC Evolutionary Biology.

[51]  M. Baiget,et al.  Distal anterior compartment myopathy: A dysferlin mutation causing a new muscular dystrophy phenotype , 2001, Annals of neurology.

[52]  V. Hilser,et al.  Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins , 2007, Proceedings of the National Academy of Sciences.

[53]  A. Hinderliter,et al.  Allostery and instability in the functional plasticity of synaptotagmin I , 2013, Communicative & integrative biology.

[54]  J. O. D. Kamp,et al.  LIPID ASYMMETRY IN MEMBRANES , 1979 .

[55]  P. Lai,et al.  Identification and characterisation of human dysferlin transcript variants: implications for dysferlin mutational screening and isoforms , 2009, Human Genetics.

[56]  B. Lentz,et al.  Membrane modulates affinity for calcium ion to create an apparent cooperative binding response by annexin a5. , 2013, Biophysical journal.

[57]  P. Mcneil,et al.  Repairing a torn cell surface: make way, lysosomes to the rescue. , 2002, Journal of Cell Science.

[58]  Ralf Kühnemuth,et al.  Supertertiary structure of the synaptic MAGuK scaffold proteins is conserved , 2012, Proceedings of the National Academy of Sciences.

[59]  G. Phillips,et al.  Molecular mechanisms of calcium and magnesium binding to parvalbumin. , 2002, Biophysical journal.

[60]  I. Bahar,et al.  Sequence Evolution Correlates with Structural Dynamics , 2012, Molecular biology and evolution.

[61]  T. Südhof,et al.  C2-domains, Structure and Function of a Universal Ca2+-binding Domain* , 1998, The Journal of Biological Chemistry.

[62]  I. Bahar,et al.  The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding , 2009, Proceedings of the National Academy of Sciences.

[63]  E. Freire,et al.  Direct measurement of protein binding energetics by isothermal titration calorimetry. , 2001, Current opinion in structural biology.

[64]  M. Menéndez,et al.  Calorimetric study of the interaction of the C2 domains of classical protein kinase C isoenzymes with Ca2+ and phospholipids. , 2004, Biochemistry.

[65]  H. Galla,et al.  Lipid Segregation and Membrane Budding Induced by the Peripheral Membrane Binding Protein Annexin A2* , 2013, The Journal of Biological Chemistry.

[66]  G. Lamb,et al.  Isolation of Sarcolemmal Plasma Membranes by Mechanically Skinning Rat Skeletal Muscle Fibers for Phospholipid Analysis , 2013, Lipids.

[67]  K. Bushby,et al.  Dysferlin associates with the developing T‐tubule system in rodent and human skeletal muscle , 2010, Muscle & nerve.

[68]  G. Feigenson,et al.  1H-NMR study of the location and motion of ubiquinones in perdeuterated phosphatidylcholine bilayers. , 1981, Biochimica et biophysica acta.

[69]  T. Moser,et al.  The crystal structure of the C₂A domain of otoferlin reveals an unconventional top loop region. , 2011, Journal of molecular biology.

[70]  Ramu Anandakrishnan,et al.  H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations , 2012, Nucleic Acids Res..

[71]  A. Meyer,et al.  Alternate splicing of dysferlin C2A confers Ca²⁺-dependent and Ca²⁺-independent binding for membrane repair. , 2014, Structure.

[72]  Barry Honig,et al.  Electrostatic control of the membrane targeting of C2 domains. , 2002, Molecular cell.

[73]  Chien-Chang Chen,et al.  Defective membrane repair in dysferlin-deficient muscular dystrophy , 2003, Nature.