Reaction kinetics in intracellular environments with macromolecular crowding: simulations and rate laws.

[1]  D. V. Slyke,et al.  THE MODE OF ACTION OF UREASE AND OF ENZYMES IN GENERAL , 1914 .

[2]  K. G. Falk,et al.  THE MODE OF ACTION OF UREASE AND OF ENZYMES IN GENERAL , 1917 .

[3]  George Kingsley Zipf,et al.  Human behavior and the principle of least effort , 1949 .

[4]  A. G. Ogston,et al.  The spaces in a uniform random suspension of fibres , 1958 .

[5]  A. Ogston,et al.  The partition of solutes between buffer solutions and solutions containing hyaluronic acid. , 1961, The Biochemical journal.

[6]  Some thermodynamic relationships in ternary systems, with special reference to the properties of systems containing hyaluronic acid and protein. , 1962 .

[7]  T. Laurent,et al.  THE INTERACTION BETWEEN POLYSACCHARIDES AND OTHER MACROMOLECULES. 4. THE OSMOTIC PRESSURE OF MIXTURES OF SERUM ALBUMIN AND HYALURONIC ACID. , 1963, The Biochemical journal.

[8]  T. Laurent.  THE INTERACTION BETWEEN POLYSACCHARIDES AND OTHER MACROMOLECULES. 5. THE SOLUBILITY OF PROTEINS IN THE PRESENCE OF DEXTRAN. , 1963, The Biochemical journal.

[9]  S. Caplan,et al.  Degree of coupling and its relation to efficiency of energy conversion , 1965 .

[10]  A. Ogston,et al.  An approach to the study of phase separation in ternary aqueous systems. , 1968, The Biochemical journal.

[11]  M. Savageau.  Biochemical systems analysis. II. The steady-state solutions for an n-pool system using a power-law approximation. , 1969, Journal of theoretical biology.

[12]  Effect of membranes and other porous networks on the equilibrium and rate constants of macromolecular reactions , 1970 .

[13]  T. Laurent.  Enzyme reactions in polymer media. , 1971, European journal of biochemistry.

[14]  Conformational transitions of polynucleotides in polymer media. , 1974, European journal of biochemistry.

[15]  R Heinrich,et al.  A linear steady-state treatment of enzymatic chains. Critique of the crossover theorem and a general procedure to identify interaction sites with an effector. , 1974, European journal of biochemistry.

[16]  Reinhart Heinrich,et al.  A Linear Steady-State Treatment of Enzymatic Chains Critique of the Crossover Theorem and a General Procedure to Identify Interaction Sites with an Effector , 1974 .

[17]  D. Gillespie.  A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .

[18]  M. Savageau.  Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology , 1976 .

[19]  D. Gillespie.  Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[20]  Benoit B. Mandelbrot,et al.  Fractal Geometry of Nature , 1984 .

[21]  J. Ovádi,et al.  Effect of association-dissociation on the catalytic properties of glyceraldehyde 3-phosphate dehydrogenase. , 1979, Archives of biochemistry and biophysics.

[22]  A. Kornberg,et al.  Enzymatic replication of the origin of the Escherichia coli chromosome. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[23]  A. Minton.  Excluded volume as a determinant of macromolecular structure and reactivity , 1981 .

[24]  Marc Mangel,et al.  Conditioned averages in chemical kinetics , 1981 .

[25]  A. Fulton,et al.  How crowded is the cytoplasm? , 1982, Cell.

[26]  Heterogeneous exciton kinetics: Triplet naphthalene homofusion in an isotopic mixed crystal , 1982 .

[27]  Foundation stones of biochemistry: By T. R. C. Boyde. Pp. 316. Voile et Aviron, Hong Kong (or 23 Hartington Grove, Cambridge). 1980. £10.00 , 1982 .

[28]  F. Wilczek,et al.  Particle–antiparticle annihilation in diffusive motion , 1983 .

[29]  B. H. Pheiffer,et al.  Macromolecular crowding allows blunt-end ligation by DNA ligases from rat liver or Escherichia coli. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[30]  Shlomo Havlin,et al.  Exact-enumeration approach to random walks on percolation clusters in two dimensions , 1984 .

[31]  J. Clegg,et al.  Properties and metabolism of the aqueous cytoplasm and its boundaries. , 1984, The American journal of physiology.

[32]  B. Trus,et al.  The cytoplasmic matrix: its volume and surface area and the diffusion of molecules through it. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[33]  J. Brickmann.  B. Mandelbrot: The Fractal Geometry of Nature, Freeman and Co., San Francisco 1982. 460 Seiten, Preis: £ 22,75. , 1985 .

[34]  S. Redner,et al.  Introduction To Percolation Theory , 2018 .

[35]  B O Palsson,et al.  Mathematical modelling of dynamics and control in metabolic networks. III. Linear reaction sequences. , 1985, Journal of theoretical biology.

[36]  D. Taylor,et al.  Structural organization of interphase 3T3 fibroblasts studied by total internal reflection fluorescence microscopy , 1985, The Journal of cell biology.

[37]  Raoul Kopelman,et al.  Rate processes on fractals: Theory, simulations, and experiments , 1986 .

[38]  D. Taylor,et al.  Hindered diffusion of inert tracer particles in the cytoplasm of mouse 3T3 cells. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[39]  D. Chandler,et al.  Introduction To Modern Statistical Mechanics , 1987 .

[40]  S. Zimmerman,et al.  Macromolecular crowding increases binding of DNA polymerase to DNA: an adaptive effect. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[41]  L S Liebovitch,et al.  Fractal analysis of a voltage-dependent potassium channel from cultured mouse hippocampal neurons. , 1987, Biophysical journal.

[42]  L S Liebovitch,et al.  Fractal model of ion-channel kinetics. , 1987, Biochimica et biophysica acta.

[43]  Raoul Kopelman,et al.  Fractal Reaction Kinetics , 1988, Science.

[44]  Daniel ben-Avraham,et al.  Computer simulation methods for diffusion‐controlled reactions , 1988 .

[45]  P. Halling.  Do the laws of chemistry apply to living cells? , 1989, TIBS -Trends in Biochemical Sciences. Regular ed.

[46]  F G Ball,et al.  Markov, fractal, diffusion, and related models of ion channel gating. A comparison with experimental data from two ion channels. , 1989, Biophysical journal.

[47]  G. Searby,et al.  Lattice gas experiments on a non-exothermic diffusion flame in a vortex field , 1989 .

[48]  Christopher K. Mathews,et al.  Structural and organizational aspects of metabolic regulation : proceedings of an Eli-Lilly directors/sponsors fund-UCLA Symposium held at Keystone, Colorado, April 17-24, 1989 , 1990 .

[49]  G. Ralston.  Effects of "crowding" in protein solutions , 1990 .

[50]  A. Minton,et al.  Holobiochemistry: the effect of local environment upon the equilibria and rates of biochemical reactions. , 1990, The International journal of biochemistry.

[51]  M. Record,et al.  Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo. , 1991, Journal of molecular biology.

[52]  D S Goodsell,et al.  Inside a living cell. , 1991, Trends in biochemical sciences.

[53]  S. Zimmerman,et al.  Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. , 1991, Journal of molecular biology.

[54]  Kapral,et al.  Oscillations and waves in a reactive lattice-gas automaton. , 1991, Physical review letters.

[55]  Anna T. Lawniczak,et al.  Reactive dynamics in a multispecies lattice‐gas automaton , 1992 .

[56]  D. Gillespie.  A rigorous derivation of the chemical master equation , 1992 .

[57]  S. Zimmerman,et al.  Macromolecular crowding effects on macromolecular interactions: some implications for genome structure and function. , 1993, Biochimica et biophysica acta.

[58]  L. Liebovitch.  Interpretation of protein structure and dynamics from the statistics of the open and closed times measured in a single ion-channel protein , 1993 .

[59]  A. Minton,et al.  Macromolecular crowding and molecular recognition , 1993, Journal of molecular recognition : JMR.

[60]  David S. Goodsell.  The machinery of life , 1993 .

[61]  A. Minton,et al.  Macromolecular crowding: biochemical, biophysical, and physiological consequences. , 1993, Annual review of biophysics and biomolecular structure.

[62]  Brian G. Cox,et al.  Modern Liquid Phase Kinetics , 1994 .

[63]  M. Sahini,et al.  Applications of Percolation Theory , 2023, Applied Mathematical Sciences.

[64]  T. Laurent.  An early look at macromolecular crowding. , 1995, Biophysical chemistry.

[65]  M. Savageau.  Michaelis-Menten mechanism reconsidered: implications of fractal kinetics. , 1995, Journal of theoretical biology.

[66]  Panos Argyrakis,et al.  Reaction-Diffusion Model for A + A Reaction , 1995 .

[67]  Gary A. Talbot.  Applications of Percolation Theory , 1995 .

[68]  Anna T. Lawniczak,et al.  Lattice gas automata for reactive systems , 1995, comp-gas/9512001.

[69]  Kopelman,et al.  Nonclassical kinetics in three dimensions: Simulations of elementary A+B and A+A reactions. , 1996, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[70]  R. Heinrich,et al.  The Regulation of Cellular Systems , 1996, Springer US.

[71]  Spatially Resolved Anomalous Kinetics of a Catalytic Reaction: Enzymatic Glucose Oxidation in Capillary Spaces , 1997 .

[72]  A. Fersht.  Structure and mechanism in protein science , 1998 .

[73]  A. Minton,et al.  Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion. , 1998, Methods in enzymology.

[74]  Bengt Nölting,et al.  Protein Folding Kinetics: Biophysical Methods , 1999 .

[75]  C M Dobson,et al.  Effects of macromolecular crowding on protein folding and aggregation , 1999, The EMBO journal.

[76]  A. Arkin,et al.  It's a noisy business! Genetic regulation at the nanomolar scale. , 1999, Trends in genetics : TIG.

[77]  M. Elowitz,et al.  Protein Mobility in the Cytoplasm ofEscherichia coli , 1999, Journal of bacteriology.

[78]  G. Rivas,et al.  Direct observation of the self-association of dilute proteins in the presence of inert macromolecules at high concentration via tracer sedimentation equilibrium: theory, experiment, and biological significance. , 1999, Biochemistry.

[79]  A Hunding,et al.  The effect of slow allosteric transitions in a coupled biochemical oscillator model. , 1999, Journal of theoretical biology.

[80]  D. Brooks.  Can cytoplasm exist without undergoing phase separation? , 2000, International review of cytology.

[81]  C. Dobson,et al.  Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell , 2000, The EMBO journal.

[82]  H. Walter.  Consequences of phase separation in cytoplasm. , 2000, International review of cytology.

[83]  C. Haynes,et al.  Macromolecular crowding and its consequences. , 2000, International review of cytology.

[84]  P. Maini,et al.  Enzyme kinetics at high enzyme concentration , 2000, Bulletin of mathematical biology.

[85]  K. Luby-Phelps,et al.  Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area. , 2000, International review of cytology.

[86]  A. Minton.  Implications of macromolecular crowding for protein assembly. , 2000, Current opinion in structural biology.

[87]  H. Kuthan.  Self-organisation and orderly processes by individual protein complexes in the bacterial cell. , 2001, Progress in biophysics and molecular biology.

[88]  M. Al-Habori,et al.  Macromolecular crowding and its role as intracellular signalling of cell volume regulation. , 2001, The international journal of biochemistry & cell biology.

[89]  Simulation of enzymatic cellular reactions complicated by phase separation. , 2000, Physical review. E, Statistical, nonlinear, and soft matter physics.

[90]  R. Ellis.  Macromolecular crowding : obvious but underappreciated , 2022 .

[91]  R. Ellis,et al.  Macromolecular crowding: an important but neglected aspect of the intracellular environment. , 2001, Current opinion in structural biology.

[92]  A. Minton,et al.  The Influence of Macromolecular Crowding and Macromolecular Confinement on Biochemical Reactions in Physiological Media* , 2001, The Journal of Biological Chemistry.

[93]  G. Rivas,et al.  Direct observation of the enhancement of noncooperative protein self-assembly by macromolecular crowding: Indefinite linear self-association of bacterial cell division protein FtsZ , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[94]  O. Monasterio.  Rate constants determined by nuclear magnetic resonance. , 2001, Methods.

[95]  T. Kepler,et al.  Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. , 2001, Biophysical journal.

[96]  Hugues Berry,et al.  Monte carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation. , 2002, Biophysical journal.

[97]  A. Verkman.  Solute and macromolecule diffusion in cellular aqueous compartments. , 2002, Trends in biochemical sciences.

[98]  W. Baumeister,et al.  Macromolecular Architecture in Eukaryotic Cells Visualized by Cryoelectron Tomography , 2002, Science.

[99]  Damien Hall,et al.  Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges. , 2003, Biochimica et biophysica acta.

[100]  A. Minton,et al.  Effect of dextran on protein stability and conformation attributed to macromolecular crowding. , 2003, Journal of molecular biology.

[101]  P. Maini,et al.  A Century of Enzyme Kinetics: Reliability of the K M and v v max Estimates , 2003 .

[102]  K. Burrage,et al.  Bistability and switching in the lysis/lysogeny genetic regulatory network of bacteriophage lambda. , 2004, Journal of theoretical biology.

[103]  Allen P. Minton,et al.  The effect of volume occupancy upon the thermodynamic activity of proteins: some biochemical consequences , 2004, Molecular and Cellular Biochemistry.

[104]  Tianhai Tian,et al.  A multi-scaled approach for simulating chemical reaction systems. , 2004, Progress in biophysics and molecular biology.

[105]  H. Rottenberg.  The mechanism of energy-dependent ion transport in mitochondria , 2005, The Journal of Membrane Biology.