Towards understanding the messengers of extracellular space: Computational models of outside-in integrin reaction networks

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[1]  J. Marshall,et al.  DNA Origami Nanoarrays for Multivalent Investigations of Cancer Cell Spreading with Nanoscale Spatial Resolution and Single-Molecule Control. , 2018, ACS nano.

[2]  Samuel I Stupp,et al.  Development of bioactive peptide amphiphiles for therapeutic cell delivery. , 2010, Acta biomaterialia.

[3]  Thomas R. Cox,et al.  Remodeling and homeostasis of the extracellular matrix: implications for fibrotic diseases and cancer , 2011, Disease Models & Mechanisms.

[4]  C. Cabañas,et al.  Conformational equilibria and intrinsic affinities define integrin activation , 2017, The EMBO journal.

[5]  Herbert M. Sauro,et al.  Tellurium: A Python Based Modeling and Reproducibility Platform for Systems Biology , 2016, bioRxiv.

[6]  Hong Li,et al.  Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. , 2004, The Journal of chemical physics.

[7]  Gregory A Voth,et al.  Multiscale model of integrin adhesion assembly , 2019, bioRxiv.

[8]  Richard M. Murray,et al.  BioCRNpyler: Compiling chemical reaction networks from biomolecular parts in diverse contexts , 2020, bioRxiv.

[9]  Arnoud Sonnenberg,et al.  Function and interactions of integrins , 2001, Cell and Tissue Research.

[10]  Nariyoshi Shinomiya,et al.  Proliferation and invasion: plasticity in tumor cells. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  S. Itzkovitz,et al.  Functional atlas of the integrin adhesome , 2007, Nature Cell Biology.

[12]  Yousef Jamali,et al.  An agent based model of integrin clustering: Exploring the role of ligand clustering, integrin homo-oligomerization, integrin-ligand affinity, membrane crowdedness and ligand mobility , 2013, J. Comput. Phys..

[13]  A. Ranga,et al.  Bioengineering approaches to guide stem cell-based organogenesis , 2014, Development.

[14]  Donald Gullberg,et al.  Integrins , 2009, Cell and Tissue Research.

[15]  Francisco Prieto-Castrillo,et al.  Research Techniques Made Simple: Analysis of Collective Cell Migration Using the Wound Healing Assay. , 2017, The Journal of investigative dermatology.

[16]  F. Smedts,et al.  Bioengineering of living renal membranes consisting of hierarchical, bioactive supramolecular meshes and human tubular cells. , 2011, Biomaterials.

[17]  Wan-Ju Li,et al.  Tissue Stiffness Dictates Development, Homeostasis, and Disease Progression , 2015, Organogenesis.

[18]  J. García-Aznar,et al.  A discrete approach for modeling cell–matrix adhesions , 2014, CPM 2014.

[19]  N. Seeman.  Nanomaterials based on DNA. , 2010, Annual review of biochemistry.

[20]  D. Lacroix,et al.  Heterogeneity in The Mechanical Properties of Integrins Determines Mechanotransduction Dynamics in Bone Osteoblasts , 2019, Scientific Reports.

[21]  Ulrich S Schwarz,et al.  United we stand – integrating the actin cytoskeleton and cell–matrix adhesions in cellular mechanotransduction , 2012, Journal of Cell Science.

[22]  H. Callender,et al.  Mathematical modeling of integrin dynamics in initial formation of focal adhesions , 2014 .

[23]  Richard O. Hynes,et al.  Integrins: A family of cell surface receptors , 1987, Cell.

[24]  A. Buskermolen,et al.  Functional peptide presentation on different hydrogen bonding biomaterials using supramolecular additives. , 2019, Biomaterials.

[25]  A. Huttenlocher,et al.  Integrins in cell migration. , 2011, Cold Spring Harbor perspectives in biology.

[26]  Joachim P Spatz,et al.  Activation of integrin function by nanopatterned adhesive interfaces. , 2004, Chemphyschem : a European journal of chemical physics and physical chemistry.

[27]  Leah Edelstein-Keshet,et al.  A Comparison of Computational Models for Eukaryotic Cell Shape and Motility , 2012, PLoS Comput. Biol..

[28]  G. Voth,et al.  Coarse-Grained Simulation of Full-Length Integrin Activation. , 2019, Biophysical journal.

[29]  Nour Almouemen,et al.  Tissue Engineering: Understanding the Role of Biomaterials and Biophysical Forces on Cell Functionality Through Computational and Structural Biotechnology Analytical Methods , 2019, Computational and structural biotechnology journal.

[30]  G. Qiao,et al.  Integrin Clustering Matters: A Review of Biomaterials Functionalized with Multivalent Integrin‐Binding Ligands to Improve Cell Adhesion, Migration, Differentiation, Angiogenesis, and Biomedical Device Integration , 2018, Advanced healthcare materials.

[31]  Jens Friedrichs,et al.  Revealing Early Steps of α2β1 Integrin-mediated Adhesion to Collagen Type I by Using Single-Cell Force Spectroscopy , 2007 .

[32]  Klaus Schulten,et al.  Molecular Dynamics Simulations of Forced Unbending of Integrin αVβ3 , 2011, PLoS Comput. Biol..

[33]  Valerie M. Weaver,et al.  A tense situation: forcing tumour progression , 2009, Nature Reviews Cancer.

[34]  Konstantin Popov,et al.  MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks , 2016, PLoS Comput. Biol..

[35]  Adam Byron,et al.  Definition of a consensus integrin adhesome and its dynamics during adhesion complex assembly and disassembly , 2015, Nature Cell Biology.

[36]  Arnoud Sonnenberg,et al.  Integrin–TGF‐β crosstalk in fibrosis, cancer and wound healing , 2010, EMBO reports.

[37]  Richard O Hynes,et al.  Integrins Bidirectional, Allosteric Signaling Machines , 2002, Cell.

[38]  David J Odde,et al.  Traction Dynamics of Filopodia on Compliant Substrates , 2008, Science.

[39]  Douglas A Lauffenburger,et al.  Kinetic model for lamellipodal actin-integrin 'clutch' dynamics , 2008, Cell adhesion & migration.

[40]  Iain G. Johnston,et al.  The chaos within: exploring noise in cellular biology , 2012 .

[41]  H. Frieboes,et al.  Modeling the Kinetics of Integrin Receptor Binding to Hepatic Extracellular Matrix Proteins , 2017, Scientific Reports.

[42]  J. Couchman.  Syndecans: proteoglycan regulators of cell-surface microdomains? , 2003, Nature Reviews Molecular Cell Biology.

[43]  Radek Erban,et al.  STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB , 2011, Bioinform..

[44]  Bo Cheng,et al.  Cellular mechanosensing of the biophysical microenvironment: A review of mathematical models of biophysical regulation of cell responses. , 2017, Physics of life reviews.

[45]  Bo Cheng,et al.  Nanoscale integrin cluster dynamics controls cellular mechanosensing via FAKY397 phosphorylation , 2020, Science Advances.

[46]  Erik S. Welf,et al.  Stochastic Model of Integrin-Mediated Signaling and Adhesion Dynamics at the Leading Edges of Migrating Cells , 2010, PLoS Comput. Biol..

[47]  Stefano Schivo,et al.  Biological networks 101: computational modeling for molecular biologists. , 2014, Gene.

[48]  Adam Byron,et al.  Integrin ligands at a glance , 2006, Journal of Cell Science.

[49]  Thimo Rohlf,et al.  Receptor cross-talk in angiogenesis: mapping environmental cues to cell phenotype using a stochastic, Boolean signaling network model. , 2010, Journal of theoretical biology.

[50]  T. Byzova,et al.  Mechanisms of Integrin–Vascular Endothelial Growth Factor Receptor Cross-Activation in Angiogenesis , 2007, Circulation research.

[51]  R. Fässler,et al.  Integrin-mediated mechanotransduction , 2016, The Journal of cell biology.

[52]  Monika Heiner,et al.  Snoopy’s hybrid simulator: a tool to construct and simulate hybrid biological models , 2017, BMC Systems Biology.

[53]  G Wayne Brodland,et al.  How computational models can help unlock biological systems. , 2015, Seminars in cell & developmental biology.

[54]  R. Hynes.  The emergence of integrins: a personal and historical perspective. , 2004, Matrix biology : journal of the International Society for Matrix Biology.

[55]  Herbert M. Sauro,et al.  Tellurium: An extensible python-based modeling environment for systems and synthetic biology , 2018, Biosyst..

[56]  David S. Harburger,et al.  Integrin signalling at a glance , 2009, Journal of Cell Science.

[57]  Hans Clevers,et al.  Designer matrices for intestinal stem cell and organoid culture , 2016, Nature.

[58]  J. Klafter,et al.  Accurate Quantification of Diffusion and Binding Kinetics of Non‐integral Membrane Proteins by FRAP , 2011, Traffic.

[59]  M. Merchant,et al.  The hepatic “matrisome” responds dynamically to injury: Characterization of transitional changes to the extracellular matrix in mice , 2017, Hepatology.

[60]  Xavier Trepat,et al.  Rigidity sensing and adaptation through regulation of integrin types , 2014, Nature materials.

[61]  J. Jansen,et al.  Mechanochemical mechanism of integrin clustering modulated by nanoscale ligand spacing and rigidity of extracellular substrates. , 2017, Journal of the mechanical behavior of biomedical materials.

[62]  E O Voit,et al.  Steps of Modeling Complex Biological Systems , 2008, Pharmacopsychiatry.

[63]  D. Critchley,et al.  Talin at a glance , 2008, Journal of Cell Science.

[64]  Chih-Kung Lee,et al.  Atomic force microscopy: determination of unbinding force, off rate and energy barrier for protein-ligand interaction. , 2007, Micron.

[65]  D. Keene,et al.  A Novel Binding Site in Collagen Type III for Integrins α1β1 and α2β1* , 2005, Journal of Biological Chemistry.

[66]  R. Del Maestro,et al.  Testing the “Go or Grow” Hypothesis in Human Medulloblastoma Cell Lines in Two and Three Dimensions , 2003, Neurosurgery.

[67]  Jennifer A. Craig,et al.  Design of a novel fibronectin-mimetic peptide-amphiphile for functionalized biomaterials. , 2006, Langmuir : the ACS journal of surfaces and colloids.

[68]  B. Eliceiri.  This Review is part of a thematic series on Integrins, which includes the following articles: Integrins and the Myocardium Functional Consequences of Integrin Gene Mutations in Mice Integrins in Vascular Development Integrin and Growth Factor Receptor Crosstalk , 2001 .

[69]  Kevin Burrage,et al.  Stochastic simulation in systems biology , 2014, Computational and structural biotechnology journal.

[70]  Huajian Gao,et al.  Modeling Active Mechanosensing in Cell-Matrix Interactions. , 2015, Annual review of biophysics.

[71]  Jing Fang,et al.  Influence of substrate rigidity on primary nucleation of cell adhesion: a thermal fluctuation model. , 2012, Journal of colloid and interface science.

[72]  Richard O. Hynes,et al.  The Evolution of Cell Adhesion , 2000, The Journal of cell biology.

[73]  E. W. Meijer,et al.  A modular approach to easily processable supramolecular bilayered scaffolds with tailorable properties. , 2014, Journal of materials chemistry. B.

[74]  A. Popel,et al.  Computational modeling of synergistic interaction between αVβ3 integrin and VEGFR2 in endothelial cells: Implications for the mechanism of action of angiogenesis-modulating integrin-binding peptides. , 2018, Journal of theoretical biology.

[75]  Michael A. Gibson,et al.  Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .

[76]  M. Humphries,et al.  The integrin adhesome network at a glance , 2016, Journal of Cell Science.

[77]  Maike Werner,et al.  Cellular Geometry Sensing at Different Length Scales and its Implications for Scaffold Design , 2020, Materials.

[78]  K. Schaller,et al.  'Go or grow': the key to the emergence of invasion in tumour progression? , 2012, Mathematical medicine and biology : a journal of the IMA.

[79]  Kevin T. O'Brien,et al.  Computational and experimental analysis of bioactive peptide linear motifs in the integrin adhesome , 2019, PloS one.

[80]  Christian A. Yates,et al.  Spatially extended hybrid methods: a review , 2017, Journal of The Royal Society Interface.

[81]  Corrado Priami,et al.  Stochastic simulation algorithms for computational systems biology: Exact, approximate, and hybrid methods , 2019, Wiley interdisciplinary reviews. Systems biology and medicine.

[82]  Shantanu Singh,et al.  How Not To Drown in Data: A Guide for Biomaterial Engineers. , 2017, Trends in biotechnology.

[83]  J. Worthington,et al.  TGFβ: a sleeping giant awoken by integrins. , 2011, Trends in biochemical sciences.

[84]  Pere Roca-Cusachs,et al.  Control of Mechanotransduction by Molecular Clutch Dynamics. , 2018, Trends in cell biology.

[85]  M. Corada,et al.  Vascular Endothelial Growth Factor Induces Shc Association With Vascular Endothelial Cadherin: A Potential Feedback Mechanism to Control Vascular Endothelial Growth Factor Receptor-2 Signaling , 2002, Arteriosclerosis, thrombosis, and vascular biology.

[86]  Walter de Back,et al.  Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology , 2014, Bioinform..

[87]  N. Hogg,et al.  Integrins take partners: cross-talk between integrins and other membrane receptors. , 1998, Trends in cell biology.

[88]  S. Coons,et al.  Dichotomy of astrocytoma migration and proliferation , 1996, International journal of cancer.

[89]  Weihong Tan,et al.  Mapping receptor density on live cells by using fluorescence correlation spectroscopy. , 2009, Chemistry.

[90]  M. Simons,et al.  Syndecan-4 signaling at a glance , 2013, Journal of Cell Science.

[91]  David P. Nickerson,et al.  Improving reproducibility in computational biology research , 2020, PLoS Comput. Biol..

[92]  Thomas Boudou,et al.  A hitchhiker's guide to mechanobiology. , 2011, Developmental cell.

[93]  Z. Kam,et al.  Differential Effect of Actomyosin Relaxation on the Dynamic Properties of Focal Adhesion Proteins , 2013, PloS one.

[94]  Lin Yu,et al.  Matrix Stiffness and Nanoscale Spatial Organization of Cell-Adhesive Ligands Direct Stem Cell Fate. , 2015, Nano letters.

[95]  Milan Mrksich,et al.  Using model substrates to study the dependence of focal adhesion formation on the affinity of integrin-ligand complexes. , 2004, Biochemistry.

[96]  D. Navajas,et al.  Force loading explains spatial sensing of ligands by cells , 2017, Nature.

[97]  David A. Calderwood,et al.  Calpain Cleavage Promotes Talin Binding to the β3Integrin Cytoplasmic Domain* , 2001, The Journal of Biological Chemistry.

[98]  B. Yaspan,et al.  Calpain cleavage promotes talin binding to the beta 3 integrin cytoplasmic domain. , 2001, The Journal of biological chemistry.

[99]  T. Barker,et al.  Feeling Things Out: Bidirectional Signaling of the Cell–ECM Interface, Implications in the Mechanobiology of Cell Spreading, Migration, Proliferation, and Differentiation , 2020, Advanced healthcare materials.