Molecular mechanism of claudin-15 strand flexibility: A computational study

Claudins in tight junctions form ion channels that regulate paracellular permeability. We use molecular dynamics simulations of claudin-15 strands formed by up to 300 monomers to uncover the molecular mechanism of strand flexibility.

[1]  R. Stroud,et al.  Structural basis for Clostridium perfringens enterotoxin targeting of claudins at tight junctions in mammalian gut , 2021, Proceedings of the National Academy of Sciences.

[2]  J. Piontek,et al.  Molecular architecture and assembly of the tight junction backbone. , 2020, Biochimica et biophysica acta. Biomembranes.

[3]  Fatemeh Khalili-Araghi,et al.  Computational Modeling of Claudin Structure and Function , 2020, International journal of molecular sciences.

[4]  Ann L. Miller,et al.  Multiscale dynamics of tight junction remodeling , 2019, Journal of Cell Science.

[5]  R. Stroud,et al.  Claudin-9 structures reveal mechanism for toxin-induced gut barrier breakdown , 2019, Proceedings of the National Academy of Sciences.

[6]  J. Heymann,et al.  Carbon replicas reveal double stranded structure of tight junctions in phase-contrast electron microscopy , 2019, Communications Biology.

[7]  S. Tsukita,et al.  The Claudins: From Tight Junctions to Biological Systems. , 2019, Trends in biochemical sciences.

[8]  F. Benfenati,et al.  Molecular Dynamics Simulations of Ion Selectivity in a Claudin-15 Paracellular Channel. , 2018, The journal of physical chemistry. B.

[9]  Fatemeh Khalili-Araghi,et al.  Molecular determination of claudin-15 organization and channel selectivity , 2018, The Journal of general physiology.

[10]  C. V. Van Itallie,et al.  Multiple claudin–claudin cis interfaces are required for tight junction strand formation and inherent flexibility , 2018, Communications Biology.

[11]  F. Benfenati,et al.  A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations , 2017, PloS one.

[12]  H. Wolburg,et al.  Polar and charged extracellular residues conserved among barrier‐forming claudins contribute to tight junction strand formation , 2017, Annals of the New York Academy of Sciences.

[13]  C. V. Van Itallie,et al.  Visualizing the dynamic coupling of claudin strands to the actin cytoskeleton through ZO-1 , 2017, Molecular biology of the cell.

[14]  Ann L. Miller,et al.  Maintenance of the Epithelial Barrier and Remodeling of Cell-Cell Junctions during Cytokinesis , 2016, Current Biology.

[15]  M. Balda,et al.  Tight junctions: from simple barriers to multifunctional molecular gates , 2016, Nature Reviews Molecular Cell Biology.

[16]  R. Pastor,et al.  Mechanical properties of lipid bilayers from molecular dynamics simulation. , 2015, Chemistry and physics of lipids.

[17]  J. Piontek,et al.  Assembly and function of claudins: Structure-function relationships based on homology models and crystal structures. , 2015, Seminars in cell & developmental biology.

[18]  Hiroshi Suzuki,et al.  Structural insight into tight junction disassembly by Clostridium perfringens enterotoxin , 2015, Science.

[19]  Hiroshi Suzuki,et al.  Model for the architecture of claudin-based paracellular ion channels through tight junctions. , 2015, Journal of Molecular Biology.

[20]  J. Nagle,et al.  Experimental support for tilt-dependent theory of biomembrane mechanics. , 2014, Physical review letters.

[21]  O. Nureki,et al.  Crystal Structure of a Claudin Provides Insight into the Architecture of Tight Junctions , 2014, Science.

[22]  H. Wolburg,et al.  Claudin-3 and Claudin-5 Protein Folding and Assembly into the Tight Junction Are Controlled by Non-conserved Residues in the Transmembrane 3 (TM3) and Extracellular Loop 2 (ECL2) Segments* , 2014, The Journal of Biological Chemistry.

[23]  Vivian L. Hsieh,et al.  Robust measurement of membrane bending moduli using light sheet fluorescence imaging of vesicle fluctuations. , 2013, Langmuir : the ACS journal of surfaces and colloids.

[24]  A. Yu,et al.  Claudin-2 pore function requires an intramolecular disulfide bond between two conserved extracellular cysteines. , 2013, American journal of physiology. Cell physiology.

[25]  A. Yu,et al.  Claudins and the modulation of tight junction permeability. , 2013, Physiological reviews.

[26]  Klaus Schulten,et al.  Further optimization of a hybrid united-atom and coarse-grained force field for folding simulations: Improved backbone hydration and interactions between charged side chains. , 2012, Journal of chemical theory and computation.

[27]  Alexander D. MacKerell,et al.  Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles. , 2012, Journal of chemical theory and computation.

[28]  Yun-Dong Wu,et al.  Parameterization of PACE Force Field for Membrane Environment and Simulation of Helical Peptides and Helix-Helix Association. , 2012, Journal of chemical theory and computation.

[29]  A. Watson,et al.  The epithelial barrier is maintained by in vivo tight junction expansion during pathologic intestinal epithelial shedding. , 2011, Gastroenterology.

[30]  Yun-Dong Wu,et al.  PACE Force Field for Protein Simulations. 1. Full Parameterization of Version 1 and Verification. , 2010, Journal of chemical theory and computation.

[31]  A. Vologodskii,et al.  Temperature dependence of DNA persistence length , 2010, Nucleic acids research.

[32]  Alexander D. MacKerell,et al.  Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types. , 2010, The journal of physical chemistry. B.

[33]  H. Wolburg,et al.  Participation of the second extracellular loop of claudin-5 in paracellular tightening against ions, small and large molecules , 2010, Cellular and Molecular Life Sciences.

[34]  C. Weber,et al.  Epithelial Myosin Light Chain Kinase Activation Induces Mucosal Interleukin-13 Expression to Alter Tight Junction Ion Selectivity* , 2010, The Journal of Biological Chemistry.

[35]  A. Yu,et al.  Structure-Function Studies of Claudin Extracellular Domains by Cysteine-scanning Mutagenesis* , 2009, The Journal of Biological Chemistry.

[36]  C. V. Van Itallie,et al.  Physiology and function of the tight junction. , 2009, Cold Spring Harbor perspectives in biology.

[37]  Heidelinde R. C. Dietrich,et al.  The persistence length of double stranded DNA determined using dark field tethered particle motion. , 2009, The Journal of chemical physics.

[38]  D. Sept,et al.  Microtubule elasticity: connecting all-atom simulations with continuum mechanics. , 2009, Physical review letters.

[39]  M. H. Cheng,et al.  Molecular Basis for Cation Selectivity in Claudin-2–based Paracellular Pores: Identification of an Electrostatic Interaction Site , 2009, The Journal of general physiology.

[40]  A. Yu,et al.  Biology of claudins. , 2008, American journal of physiology. Renal physiology.

[41]  C. Lim,et al.  Kinetics of adhesion mediated by extracellular loops of claudin-2 as revealed by single-molecule force spectroscopy. , 2008, Journal of molecular biology.

[42]  P. J. Kausalya,et al.  Probing effects of pH change on dynamic response of Claudin-2 mediated adhesion using single molecule force spectroscopy. , 2008, Experimental cell research.

[43]  J. Piontek,et al.  Structure and function of claudins. , 2008, Biochimica et biophysica acta.

[44]  B. Wiesner,et al.  Formation of tight junction: determinants of homophilic interaction between classic claudins , 2008, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

[45]  D. Tieleman,et al.  The MARTINI force field: coarse grained model for biomolecular simulations. , 2007, The journal of physical chemistry. B.

[46]  G. S. Manning The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force. , 2006, Biophysical journal.

[47]  Hideo Tashiro,et al.  Flexural rigidity of individual microtubules measured by a buckling force with optical traps. , 2006, Biophysical journal.

[48]  C. V. Van Itallie,et al.  Claudins and epithelial paracellular transport. , 2006, Annual review of physiology.

[49]  Laxmikant V. Kalé,et al.  Scalable molecular dynamics with NAMD , 2005, J. Comput. Chem..

[50]  Gregory A Voth,et al.  Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Alexander D. MacKerell,et al.  Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations , 2004, J. Comput. Chem..

[52]  S. Tsukita,et al.  Dynamic behavior of paired claudin strands within apposing plasma membranes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[53]  D. Goodenough,et al.  Paracellular ion channel at the tight junction. , 2003, Biophysical journal.

[54]  C. V. Van Itallie,et al.  Claudins create charge-selective channels in the paracellular pathway between epithelial cells. , 2002, American journal of physiology. Cell physiology.

[55]  S. Tsukita,et al.  Conversion of Zonulae Occludentes from Tight to Leaky Strand Type by Introducing Claudin-2 into Madin-Darby Canine Kidney I Cells , 2001, The Journal of cell biology.

[56]  Shoichiro Tsukita,et al.  Multifunctional strands in tight junctions , 2001, Nature Reviews Molecular Cell Biology.

[57]  J. Howard,et al.  Mechanics of Motor Proteins and the Cytoskeleton , 2001 .

[58]  S. Tsukita,et al.  Manner of Interaction of Heterogeneous Claudin Species within and between Tight Junction Strands , 1999, The Journal of cell biology.

[59]  K. Fujimoto,et al.  A Single Gene Product, Claudin-1 or -2, Reconstitutes Tight Junction Strands and Recruits Occludin in Fibroblasts , 1998, The Journal of cell biology.

[60]  E. Dejana,et al.  Junctional Adhesion Molecule, a Novel Member of the Immunoglobulin Superfamily That Distributes at Intercellular Junctions and Modulates Monocyte Transmigration , 1998, The Journal of cell biology.

[61]  Kazushi Fujimoto,et al.  Claudin-1 and -2: Novel Integral Membrane Proteins Localizing at Tight Junctions with No Sequence Similarity to Occludin , 1998, The Journal of cell biology.

[62]  Alexander D. MacKerell,et al.  All-atom empirical potential for molecular modeling and dynamics studies of proteins. , 1998, The journal of physical chemistry. B.

[63]  M. Itoh,et al.  Interspecies diversity of the occludin sequence: cDNA cloning of human, mouse, dog, and rat-kangaroo homologues , 1996, The Journal of cell biology.

[64]  M. Schliwa,et al.  Flexural rigidity of microtubules measured with the use of optical tweezers. , 1996, Journal of cell science.

[65]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[66]  B. Brooks,et al.  Constant pressure molecular dynamics simulation: The Langevin piston method , 1995 .

[67]  A C Maggs,et al.  Analysis of microtubule rigidity using hydrodynamic flow and thermal fluctuations. , 1994, The Journal of biological chemistry.

[68]  M. Itoh,et al.  Occludin: a novel integral membrane protein localizing at tight junctions , 1993, The Journal of cell biology.

[69]  T. Mcnelley,et al.  Temperature dependence of , 1993, Metallurgical and Materials Transactions A.

[70]  M. Magnasco,et al.  Measurement of the persistence length of polymerized actin using fluorescence microscopy. , 1993, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

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

[72]  J. Howard,et al.  Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape , 1993, The Journal of cell biology.

[73]  Steven B. Smith,et al.  Electrophoretic charge density and persistence length of DNA as measured by fluorescence microscopy , 1990, Biopolymers.

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

[75]  Zvi Kam,et al.  Dependence of DNA conformation on the concentration of salt. , 1981, Biopolymers.

[76]  E. Gratton,et al.  An absolute method for the determination of the persistence length of native DNA from electron micrographs , 1979, Biopolymers.

[77]  P. Claude Morphological factors influencing transepithelial permeability: A model for the resistance of theZonula Occludens , 1978, The Journal of Membrane Biology.

[78]  P. Claude,et al.  FRACTURE FACES OF ZONULAE OCCLUDENTES FROM "TIGHT" AND "LEAKY" EPITHELIA , 1973, The Journal of cell biology.

[79]  J. Turner,et al.  The intestinal epithelial barrier: a therapeutic target? , 2017, Nature Reviews Gastroenterology &Hepatology.

[80]  L. Monticelli,et al.  The Membrane Bending Modulus in Experiments and Simulations: A Puzzling Picture , 2016 .

[81]  Mónica Díaz-Coránguez,et al.  Tight Junctions , 2022 .

[82]  M. Furuse Molecular basis of the core structure of tight junctions. , 2010, Cold Spring Harbor perspectives in biology.

[83]  T. Mukherjee,et al.  Freeze-etch appearance of the tight junctions in the epithelium of small and large intestine of mice , 2005, Protoplasma.

[84]  W. Wooster,et al.  Crystal structure of , 2005 .