Free energy calculations of biopolymeric systems at cellular interface

I would like to thank Dr. Muhammad H. Zaman, my advisor, without whose support and guidance this work could not be finished. I would also like to express my thanks to the members of the thesis committee: Dr. Ernst-Ludwig Florin, Dr. Manfred Fink, Dr. Tomio Petrosky and Dr. Jack B. Swift for their advice and direction. The life in the graduate school would not be so fulfilling without the kind, honest, and friendly people around the department of physics. I would also like to express my thanks to the people in the Zaman lab, Ge Wang, Leandro Forciniti, Rajagopal Rangarajan, Dewi Harjanto and Erin Baker. I would like to express my deep gratitude to my father Songquan Yang, my mother Gumei Zhou and my wife Chunyan Li for their unselfish love and support.

[1]  L G Griffith,et al.  Integration of surface modification and 3D fabrication techniques to prepare patterned poly(L-lactide) substrates allowing regionally selective cell adhesion. , 1998, Journal of biomaterials science. Polymer edition.

[2]  M. Sheetz,et al.  Mutational Evidence for Control of Cell Adhesion Through Integrin Diffusion/Clustering, Independent of Ligand Binding , 1997, The Journal of experimental medicine.

[3]  W. Knoll,et al.  Measurement of ligand-receptor interactions. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Muhammad H. Zaman,et al.  Regulation of Cell Adhesion Free Energy by External Sliding Forces , 2009 .

[5]  S. Sarkar.  Focal adhesions , 1999, Current Biology.

[6]  M. Carignano,et al.  Pressure isotherms, phase transition, instability, and structure of tethered polymers in good, Θ, and poor solvents , 1994 .

[7]  P Bongrand,et al.  Cell adhesion. Competition between nonspecific repulsion and specific bonding. , 1984, Biophysical journal.

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

[9]  Sean P. Palecek,et al.  Integrin-ligand binding properties govern cell migration speed through cell-substratum adhesiveness , 1997, Nature.

[10]  Jeffrey A Hubbell,et al.  Photopolymerized hyaluronic acid-based hydrogels and interpenetrating networks. , 2003, Biomaterials.

[11]  George Oster,et al.  Polymer Motors: Pushing out the Front and Pulling up the Back , 2003, Current Biology.

[12]  P. Saffman,et al.  Brownian motion in biological membranes. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[13]  C Zhu,et al.  Cell mechanics: mechanical response, cell adhesion, and molecular deformation. , 2000, Annual review of biomedical engineering.

[14]  R. Fässler,et al.  β 1 integrin function in vivo: Adhesion, migration and more , 2005, Cancer and Metastasis Reviews.

[15]  S. C. Kuo,et al.  Relationship between receptor/ligand binding affinity and adhesion strength. , 1993, Biophysical journal.

[16]  A. Metters,et al.  Synthetic matrix metalloproteinase-sensitive hydrogels for the conduction of tissue regeneration: Engineering cell-invasion characteristics , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[17]  H. Goldsmith,et al.  Interaction forces between red cells agglutinated by antibody. II. Measurement of hydrodynamic force of breakup. , 1986, Biophysical journal.

[18]  M. Farrar,et al.  Regulation of L-Selectin–mediated Rolling through Receptor Dimerization , 1998, The Journal of experimental medicine.

[19]  H M Berman,et al.  Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution. , 1994, Science.

[20]  Helen M. Berman,et al.  Sequence dependent conformational variations of collagen triple-helical structure , 1999, Nature Structural Biology.

[21]  M. Balboa,et al.  Co-clustering of beta 1 integrins, cytoskeletal proteins, and tyrosine-phosphorylated substrates during integrin-mediated leukocyte aggregation. , 1993, Journal of immunology.

[22]  J. Sikora,et al.  Soluble Fas receptor and soluble Fas ligand in the serum of women with uterine tumors , 2005, Apoptosis.

[23]  J. Israelachvili.  Intermolecular and surface forces , 1985 .

[24]  D A Lauffenburger,et al.  Mathematical model for the effects of adhesion and mechanics on cell migration speed. , 1991, Biophysical journal.

[25]  Linda G Griffith,et al.  Simulations of cell-surface integrin binding to nanoscale-clustered adhesion ligands. , 2002, Biophysical journal.

[26]  N. Hogg,et al.  LFA-1–mediated Adhesion Is Regulated by Cytoskeletal Restraint and by a Ca2+-dependent Protease, Calpain , 1998, The Journal of cell biology.

[27]  B. Anvari,et al.  Measurement of adhesive forces between S. epidermidis and fibronectin‐coated surfaces using optical tweezers , 2002, Lasers in Surgery and Medicine.

[28]  C. Heeschen,et al.  Soluble CD40 ligand in acute coronary syndromes. , 2003, New England Journal of Medicine.

[29]  D. Hammer,et al.  Statistics of cell adhesion under hydrodynamic flow: simulation and experiment. , 1993, Blood cells.

[30]  C. Zhu,et al.  Kinetics and mechanics of cell adhesion. , 2000, Journal of biomechanics.

[31]  G. Borisy,et al.  Cell Migration: Integrating Signals from Front to Back , 2003, Science.

[32]  Kenneth M. Yamada,et al.  Cell–matrix adhesion , 2007, Journal of cellular physiology.

[33]  M J Bissell,et al.  The interplay of matrix metalloproteinases, morphogens and growth factors is necessary for branching of mammary epithelial cells. , 2001, Development.

[34]  B. Döme,et al.  Adhesion dynamics and cytoskeletal structure of gliding human fibrosarcoma cells: a hypothetical model of cell migration. , 2003, Experimental cell research.

[35]  H. Eyring.  The Activated Complex in Chemical Reactions , 1935 .

[36]  R. Hynes.  Cell adhesion: old and new questions , 1999 .

[37]  D. Hammer,et al.  Morphology of cell-substratum adhesion , 1992, Cell Biophysics.

[38]  C. Stanners,et al.  A co‐clustering model involving α5β1 integrin for the biological effects of GPI‐anchored human carcinoembryonic antigen (CEA) , 2007 .

[39]  Jean Paul Thiery,et al.  Focal adhesions: Structure and dynamics , 2000, Biology of the cell.

[40]  Tianyi Yang,et al.  Estimation of Cellular Adhesion Forces Using Mean Field Theory , 2010 .

[41]  Peter G Wolynes,et al.  Nonequilibrium statistical mechanical models for cytoskeletal assembly: towards understanding tensegrity in cells. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[42]  H. Eyring.  Viscosity, Plasticity, and Diffusion as Examples of Absolute Reaction Rates , 1936 .

[43]  G. Mizejewski,et al.  Role of integrins in cancer: survey of expression patterns. , 1999, Proceedings of the Society for Experimental Biology and Medicine. Society for Experimental Biology and Medicine.

[44]  J. Israelachvili,et al.  Direct Measurement of a Tethered Ligand-Receptor Interaction Potential , 1997, Science.

[45]  Zhe Sun,et al.  Integrins and Regulation of the Microcirculation: From Arterioles to Molecular Studies using Atomic Force Microscopy , 2005, Microcirculation.

[46]  Van der Waals forces , 2005 .

[47]  Tianyi Yang,et al.  Free energy landscape of receptor-mediated cell adhesion. , 2007, The Journal of chemical physics.

[48]  M. Bissell,et al.  Extracellular matrix signaling: integration of form and function in normal and malignant cells. , 1998, Current opinion in cell biology.

[49]  D R Critchley,et al.  Focal adhesions - the cytoskeletal connection. , 2000, Current opinion in cell biology.

[50]  Daniel A. Hammer,et al.  A dynamical model for receptor-mediated cell adhesion to surfaces in viscous shear flow , 1989, Cell Biophysics.

[51]  D. Lauffenburger,et al.  A dynamical model for receptor-mediated cell adhesion to surfaces. , 1987, Biophysical journal.

[52]  N. Peppas,et al.  A Molecular Theory of Polymer Gels , 2002 .

[53]  K. Gottschalk,et al.  A computational model of transmembrane integrin clustering. , 2004, Structure.

[54]  Peter J. Woolf,et al.  Monte Carlo simulations of receptor dynamics: Insights into cell signaling , 2004, Journal of Molecular Histology.

[55]  V. Adrian Parsegian,et al.  Van Der Waals Forces: A Handbook for Biologists, Chemists, Engineers, and Physicists , 2005 .

[56]  R. Berry,et al.  Investigations into sequence and conformational dependence of backbone entropy, inter-basin dynamics and the Flory isolated-pair hypothesis for peptides. , 2003, Journal of molecular biology.

[57]  A Leung,et al.  Detachment of agglutinin-bonded red blood cells. I. Forces to rupture molecular-point attachments. , 1991, Biophysical journal.

[58]  S. Sen,et al.  Membrane mobility and clustering of Integrin Associated Protein (IAP, CD47)--major differences between mouse and man and implications for signaling. , 2006, Blood cells, molecules & diseases.

[59]  D. Taverna,et al.  The diverse roles of integrins and their ligands in angiogenesis. , 2002, Cold Spring Harbor symposia on quantitative biology.

[60]  E. Evans.  Detailed mechanics of membrane-membrane adhesion and separation. II. Discrete kinetically trapped molecular cross-bridges. , 1985, Biophysical journal.

[61]  B. Derjaguin,et al.  Theory of the stability of strongly charged lyophobic sols and of the adhesion of strongly charged particles in solutions of electrolytes , 1993 .

[62]  G. Whitesides,et al.  Measuring the forces involved in polyvalent adhesion of uropathogenic Escherichia coli to mannose-presenting surfaces. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[63]  D. Hanahan,et al.  The Hallmarks of Cancer , 2000, Cell.

[64]  R. Hynes,et al.  The integrin family of cell surface receptors. , 1987, Biochemical Society transactions.

[65]  J. Ramshaw,et al.  Amino acid propensities for the collagen triple-helix. , 2000, Biochemistry.

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

[67]  E. Verwey,et al.  Theory of the stability of lyophobic colloids. , 1955, The Journal of physical and colloid chemistry.

[68]  M. Ginsberg,et al.  Integrin signaling in vascular biology. , 1997, The Journal of clinical investigation.

[69]  Direct measurements of heterotypic adhesion between the cell surface proteins CD2 and CD48. , 2002, Biochemistry.

[70]  C. Rüegg,et al.  Integrin-mediated Adhesion and Soluble Ligand Binding Stabilize COX-2 Protein Levels in Endothelial Cells by Inducing Expression and Preventing Degradation* , 2005, Journal of Biological Chemistry.

[71]  Thilo Stehle,et al.  Crystal Structure of the Extracellular Segment of Integrin αVβ3 , 2001, Science.

[72]  E. Taylor,et al.  Cell Motility , 1986, Journal of Cell Science.

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

[74]  Mathew V. Jones,et al.  An Arginine Involved in GABA Binding and Unbinding But Not Gating of the GABAA Receptor , 2004, The Journal of Neuroscience.

[75]  Jennifer J Linderman,et al.  Integrin dimerization and ligand organization: key components in integrin clustering for cell adhesion. , 2005, Tissue engineering.

[76]  G. Sherbet,et al.  Characterisation of ionogenic groups and estimation of the net negative electric charge on the surface of cells using natural pH gradients. , 1972, Experimental cell research.

[77]  M. Dembo,et al.  Kinetics of cell detachment: Effect of ligand density , 1995, Annals of Biomedical Engineering.

[78]  D. Lauffenburger,et al.  Cell Migration: A Physically Integrated Molecular Process , 1996, Cell.

[79]  E. Evans.  Detailed mechanics of membrane-membrane adhesion and separation. I. Continuum of molecular cross-bridges. , 1985, Biophysical journal.

[80]  Christophe Chipot,et al.  Comprar Free Energy Calculations · Theory and Applications in Chemistry and Biology | Chipot, Christophe | 9783540736172 | Springer , 2007 .

[81]  H. Lodish.  Molecular Cell Biology , 1986 .

[82]  M. Carignano,et al.  Statistical thermodynamic theory of grafted polymeric layers , 1993 .

[83]  Renhao Li,et al.  Structural basis for integrin alphaIIbbeta3 clustering. , 2004, Biochemical Society transactions.

[84]  N. Peppas,et al.  Gel-gel adhesion by tethered polymers , 2001 .

[85]  P. C. Cross,et al.  Cell and Tissue Ultrastructure: A Functional Perspective , 1993 .

[86]  J. Marvaldi,et al.  Outside-in regulation of integrin clustering processes by ECM components per se and their involvement in actin cytoskeleton organization in a colon adenocarcinoma cell line , 2000, Histochemistry and Cell Biology.

[87]  Peter J Woolf,et al.  Self organization of membrane proteins via dimerization. , 2003, Biophysical chemistry.

[88]  B. Anvari,et al.  Measurement of Adhesive Forces between Individual Staphylococcus aureus MSCRAMMs and Protein-Coated Surfaces by Use of Optical Tweezers , 2003, Journal of bacteriology.

[89]  Koller Mr,et al.  Cell adhesion in animal cell culture: physiological and fluid-mechanical implications. , 1995 .

[90]  D. A. Hammer,et al.  Kinetics and Mechanics of Cell Adhesion under Hydrodynamic Flow: Two Cell Systems , 1994 .

[91]  G. Oster,et al.  Shrinking Gels Pull Cells , 2003, Science.

[92]  P. Hein,et al.  Carcinoma-associated fibroblasts stimulate tumor progression of initiated human epithelium , 2000, Breast Cancer Research.

[93]  J. Aplin,et al.  Cell adhesion on model substrata: threshold effects and receptor modulation. , 1981, Journal of cell science.

[94]  J. Hubbell,et al.  Molecularly engineered PEG hydrogels: a novel model system for proteolytically mediated cell migration. , 2005, Biophysical journal.

[95]  C. Figdor,et al.  Avidity regulation of integrins: the driving force in leukocyte adhesion. , 2000, Current opinion in cell biology.

[96]  Sean P. Palecek,et al.  Kinetic Model for Integrin-mediated Adhesion Release During Cell Migration , 1999, Annals of Biomedical Engineering.

[97]  D. Hammer,et al.  Simulation of cell rolling and adhesion on surfaces in shear flow: general results and analysis of selectin-mediated neutrophil adhesion. , 1992 .

[98]  I. Szleifer,et al.  Ligand-receptor interactions in tethered polymer layers. , 2005, Langmuir : the ACS journal of surfaces and colloids.

[99]  William H. Press,et al.  Numerical recipes in C. The art of scientific computing , 1987 .

[100]  P. Friedl,et al.  The biology of cell locomotion within three-dimensional extracellular matrix , 2000, Cellular and Molecular Life Sciences CMLS.

[101]  M. de Virgilio,et al.  Detection of Integrin αIIbβ3Clustering in Living Cells* , 2003, The Journal of Biological Chemistry.

[102]  Hermann E. Gaub,et al.  Measuring Cell Adhesion Forces with the Atomic Force Microscope at the Molecular Level , 2002, Cells Tissues Organs.

[103]  G. Oster,et al.  Cell motility driven by actin polymerization. , 1996, Biophysical journal.

[104]  L. Liaw,et al.  Soluble forms of the Notch ligands Delta1 and Jagged1 promote in vivo tumorigenicity in NIH3T3 fibroblasts with distinct phenotypes. , 2008, The American journal of pathology.

[105]  M. Carignano,et al.  Tethered Polymer Layers , 1996 .

[106]  V. Parsegian.  Long-range physical forces in the biological milieu. , 1973, Annual review of biophysics and bioengineering.

[107]  S. Shattil,et al.  Complementary Roles for Receptor Clustering and Conformational Change in the Adhesive and Signaling Functions of Integrin αIIbβ3 , 1998, The Journal of cell biology.

[108]  Z. Werb,et al.  New functions for the matrix metalloproteinases in cancer progression , 2002, Nature Reviews Cancer.

[109]  Z. Werb,et al.  How matrix metalloproteinases regulate cell behavior. , 2001, Annual review of cell and developmental biology.

[110]  G. I. Bell.  Models for the specific adhesion of cells to cells. , 1978, Science.

[111]  H. Kleinman,et al.  Matrigel: basement membrane matrix with biological activity. , 2005, Seminars in cancer biology.

[112]  T. Creighton.  Proteins: Structures and Molecular Properties , 1986 .

[113]  George Oster,et al.  Force generation by actin polymerization II: the elastic ratchet and tethered filaments. , 2003, Biophysical journal.

[114]  R. Tranquillo,et al.  A stochastic model for adhesion-mediated cell random motility and haptotaxis , 1993, Journal of mathematical biology.

[115]  Cheng-Hsien Liu,et al.  Measurement of the adhesive force between a single Klebsiella pneumoniae type 3 fimbria and collagen IV using optical tweezers. , 2006, Biochemical and biophysical research communications.

[116]  B. Anvari,et al.  Adherence of Staphylococcus aureus fibronectin binding protein A mutants: an investigation using optical tweezers. , 2004, Biomolecular engineering.

[117]  Tianyi Yang,et al.  Thermodynamics of clustered and unclustered receptor systems in cell adhesion , 2008 .

[118]  B. Hinz,et al.  Myofibroblast contraction activates latent TGF-β1 from the extracellular matrix , 2007, The Journal of cell biology.

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

[120]  W. Helfrich.  Elastic Properties of Lipid Bilayers: Theory and Possible Experiments , 1973, Zeitschrift fur Naturforschung. Teil C: Biochemie, Biophysik, Biologie, Virologie.