Crystal structure of nucleotide-free dynamin

Dynamin is a mechanochemical GTPase that oligomerizes around the neck of clathrin-coated pits and catalyses vesicle scission in a GTP-hydrolysis-dependent manner. The molecular details of oligomerization and the mechanism of the mechanochemical coupling are currently unknown. Here we present the crystal structure of human dynamin 1 in the nucleotide-free state with a four-domain architecture comprising the GTPase domain, the bundle signalling element, the stalk and the pleckstrin homology domain. Dynamin 1 oligomerized in the crystals via the stalks, which assemble in a criss-cross fashion. The stalks further interact via conserved surfaces with the pleckstrin homology domain and the bundle signalling element of the neighbouring dynamin molecule. This intricate domain interaction rationalizes a number of disease-related mutations in dynamin 2 and suggests a structural model for the mechanochemical coupling that reconciles previous models of dynamin function.

[1]  G. Kochs,et al.  Structural basis of oligomerization in the stalk region of dynamin-like MxA , 2010, Nature.

[2]  J. Thompson,et al.  CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. , 1994, Nucleic acids research.

[3]  G. Murshudov,et al.  Refinement of macromolecular structures by the maximum-likelihood method. , 1997, Acta crystallographica. Section D, Biological crystallography.

[4]  J. Zheng,et al.  Identification of the binding site for acidic phospholipids on the pH domain of dynamin: implications for stimulation of GTPase activity. , 1996, Journal of molecular biology.

[5]  M. Bitoun,et al.  Dynamin 2 and human diseases , 2010, Journal of Molecular Medicine.

[6]  M. McNiven,et al.  Identification of dynamin 2, an isoform ubiquitously expressed in rat tissues. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[7]  S. Schmid,et al.  G domain dimerization controls dynamin's assembly-stimulated GTPase activity , 2010, Nature.

[8]  T. Darden,et al.  A smooth particle mesh Ewald method , 1995 .

[9]  Wolfgang Kabsch,et al.  Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants , 1993 .

[10]  I. Mills,et al.  GTPase activity of dynamin and resulting conformation change are essential for endocytosis , 2001, Nature.

[11]  T. Rapoport,et al.  Structures of the atlastin GTPase provide insight into homotypic fusion of endoplasmic reticulum membranes , 2011, Proceedings of the National Academy of Sciences.

[12]  Harvey T. McMahon,et al.  The dynamin superfamily: universal membrane tubulation and fission molecules? , 2004, Nature Reviews Molecular Cell Biology.

[13]  S. Schmid,et al.  Real-Time Visualization of Dynamin-Catalyzed Membrane Fission and Vesicle Release , 2008, Cell.

[14]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[15]  P. De Camilli,et al.  A Selective Activity-Dependent Requirement for Dynamin 1 in Synaptic Vesicle Endocytosis , 2007, Science.

[16]  S. Schmid,et al.  Crystal structure of the GTPase domain of rat dynamin 1. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[17]  Collaborative Computational,et al.  The CCP4 suite: programs for protein crystallography. , 1994, Acta crystallographica. Section D, Biological crystallography.

[18]  J. Thornton,et al.  PROCHECK: a program to check the stereochemical quality of protein structures , 1993 .

[19]  Alexander M. van der Bliek,et al.  Dynamin-like protein encoded by the Drosophila shibire gene associated with vesicular traffic , 1991, Nature.

[20]  Peijun Zhang,et al.  Three-dimensional reconstruction of dynamin in the constricted state , 2001, Nature Cell Biology.

[21]  P. Camilli,et al.  GTP-dependent twisting of dynamin implicates constriction and tension in membrane fission , 2006, Nature.

[22]  S. Schmid,et al.  Dynamin self-assembles into rings suggesting a mechanism for coated vesicle budding , 1995, Nature.

[23]  S. Schmid,et al.  GTPase Cycle of Dynamin Is Coupled to Membrane Squeeze and Release, Leading to Spontaneous Fission , 2008, Cell.

[24]  J. Joanny,et al.  Deformation of dynamin helices damped by membrane friction. , 2010, Biophysical journal.

[25]  S. Schmid,et al.  An intramolecular signaling element that modulates dynamin function in vitro and in vivo. , 2009, Molecular biology of the cell.

[26]  Michael Levitt,et al.  Super-resolution biomolecular crystallography with low-resolution data , 2010, Nature.

[27]  K. Hirose,et al.  The dynamin A ring complex: molecular organization and nucleotide‐dependent conformational changes , 2002, The EMBO journal.

[28]  E. Querfurth,et al.  Distinct specificity in the recognition of phosphoinositides by the pleckstrin homology domains of dynamin and Bruton's tyrosine kinase. , 1996, The EMBO journal.

[29]  W. Delano.  The PyMOL Molecular Graphics System , 2002 .

[30]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[31]  M. Ehlers,et al.  Postsynaptic Positioning of Endocytic Zones and AMPA Receptor Cycling by Physical Coupling of Dynamin-3 to Homer , 2007, Neuron.

[32]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[33]  J. Mears,et al.  A corkscrew model for dynamin constriction. , 2007, Structure.

[34]  Frank Noé,et al.  Markov models of molecular kinetics: generation and validation. , 2011, The Journal of chemical physics.

[35]  C. Sachse,et al.  Structure of a Bacterial Dynamin-like Protein Lipid Tube Provides a Mechanism For Assembly and Membrane Curving , 2009, Cell.

[36]  M. Lemmon,et al.  Dynamin GTPase regulation is altered by PH domain mutations found in centronuclear myopathy patients , 2010, The EMBO journal.

[37]  J. Löwe,et al.  Dynamin architecture--from monomer to polymer. , 2010, Current opinion in structural biology.

[38]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[39]  G. Kochs,et al.  Assay and functional analysis of dynamin-like Mx proteins. , 2005, Methods in enzymology.

[40]  T. Südhof,et al.  Dynamin GTPase regulated by protein kinase C phosphorylation in nerve terminals , 1993, Nature.

[41]  H. Sondermann,et al.  Structural basis for the nucleotide-dependent dimerization of the large G protein atlastin-1/SPG3A , 2011, Proceedings of the National Academy of Sciences.

[42]  M. Stowell,et al.  Nucleotide-dependent conformational changes in dynamin: evidence for a mechanochemical molecular spring , 1999, Nature Cell Biology.

[43]  A. Sali,et al.  Modeling of loops in protein structures , 2000, Protein science : a publication of the Protein Society.

[44]  J. McCaffery,et al.  Dnm1 forms spirals that are structurally tailored to fit mitochondria , 2005, The Journal of cell biology.

[45]  R F Standaert,et al.  Atomic structures of the human immunophilin FKBP-12 complexes with FK506 and rapamycin. , 1993, Journal of molecular biology.

[46]  S. Schmid,et al.  The dynamin middle domain is critical for tetramerization and higher‐order self‐assembly , 2007, The EMBO journal.

[47]  P. Evans,et al.  Importance of the pleckstrin homology domain of dynamin in clathrin-mediated endocytosis , 1999, Current Biology.

[48]  P. Kollman,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .

[49]  B. Barylko,et al.  Dynamin 2 Mutants Linked to Centronuclear Myopathies Form Abnormally Stable Polymers* , 2010, The Journal of Biological Chemistry.

[50]  A. Scherer,et al.  Crystal structure of a dynamin GTPase domain in both nucleotide‐free and GDP‐bound forms , 2001, The EMBO journal.

[51]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[52]  J. Rush,et al.  Immunoaffinity profiling of tyrosine phosphorylation in cancer cells , 2005, Nature Biotechnology.

[53]  C. Blackstone,et al.  A Lethal de Novo Mutation in the Middle Domain of the Dynamin-related GTPase Drp1 Impairs Higher Order Assembly and Mitochondrial Division* , 2010, The Journal of Biological Chemistry.

[54]  T. Blundell,et al.  Crystal structure of the pleckstrin homology domain from dynamin , 1994, Nature Structural Biology.

[55]  P. Sigler,et al.  Crystal structure at 2.2 Å resolution of the pleckstrin homology domain from human dynamin , 1994, Cell.

[56]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[57]  N. Bache,et al.  The in Vivo Phosphorylation Sites of Rat Brain Dynamin I* , 2007, Journal of Biological Chemistry.