Macromolecular crowding modulates folding mechanism of alpha/beta protein apoflavodoxin.
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Dirar Homouz | Pernilla Wittung-Stafshede | P. Wittung-Stafshede | M. Cheung | D. Homouz | Loren J. Stagg | Margaret S Cheung | Loren Stagg
[1] Ruxandra I. Dima,et al. Asymmetry in the shapes of folded and denatured states of proteins , 2003, q-bio/0310023.
[2] O. Berg,et al. The influence of macromolecular crowding on thermodynamic activity: Solubility and dimerization constants for spherical and dumbbell‐shaped molecules in a hard‐sphere mixture , 1990, Biopolymers.
[3] Bengt Rippe,et al. Ficoll and dextran vs. globular proteins as probes for testing glomerular permselectivity: effects of molecular size, shape, charge, and deformability. , 2005, American journal of physiology. Renal physiology.
[4] C. Dobson,et al. Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell , 2000, The EMBO journal.
[5] Allen P. Minton,et al. Cell biology: Join the crowd , 2003, Nature.
[6] Entropically Driven Helix Formation , 2005, Science.
[7] A. Minton,et al. Effect of dextran on protein stability and conformation attributed to macromolecular crowding. , 2003, Journal of molecular biology.
[8] F. Hartl,et al. Principles of protein folding in the cellular environment. , 1999, Current opinion in structural biology.
[9] A. Minton,et al. Influence of macromolecular crowding upon the stability and state of association of proteins: predictions and observations. , 2005, Journal of pharmaceutical sciences.
[10] Adrian H Elcock,et al. Atomic-level observation of macromolecular crowding effects: Escape of a protein from the GroEL cage , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[11] D Thirumalai,et al. Simulations of β-hairpin folding confined to spherical pores using distributed computing , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[12] G. Rivas,et al. Protein self‐association in crowded protein solutions: A time‐resolved fluorescence polarization study , 2004, Protein science : a publication of the Protein Society.
[13] C. V. van Mierlo,et al. Protein topology affects the appearance of intermediates during the folding of proteins with a flavodoxin-like fold. , 2005, Biophysical chemistry.
[14] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.
[15] N. Go. Protein folding as a stochastic process , 1983 .
[16] J. Onuchic,et al. Interplay among tertiary contacts, secondary structure formation and side-chain packing in the protein folding mechanism: all-atom representation study of protein L. , 2003, Journal of molecular biology.
[17] Gideon Schreiber,et al. Protein-protein association in polymer solutions: from dilute to semidilute to concentrated. , 2007, Biophysical journal.
[18] Changbong Hyeon,et al. Effects of trimethylamine N-oxide (TMAO) and crowding agents on the stability of RNA hairpins. , 2008, Journal of the American Chemical Society.
[19] Pernilla Wittung-Stafshede,et al. Molecular crowding enhances native structure and stability of alpha/beta protein flavodoxin. , 2007, Proceedings of the National Academy of Sciences of the United States of America.
[20] D Thirumalai,et al. Exploring the kinetic requirements for enhancement of protein folding rates in the GroEL cavity. , 1999, Journal of molecular biology.
[21] D. Apiyo,et al. Presence of the cofactor speeds up folding of Desulfovibrio desulfuricans flavodoxin , 2002, Protein science : a publication of the Protein Society.
[22] A. Minton. Excluded volume as a determinant of macromolecular structure and reactivity , 1981 .
[23] Stephen Grossberg,et al. Art 2: Self-Organization Of Stable Category Recognition Codes For Analog Input Patterns , 1988, Other Conferences.
[24] J. Onuchic,et al. Investigation of routes and funnels in protein folding by free energy functional methods. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[25] D. Thirumalai,et al. Molecular crowding enhances native state stability and refolding rates of globular proteins. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[26] Javier Sancho,et al. Closure of a tyrosine/tryptophan aromatic gate leads to a compact fold in apo flavodoxin , 1996, Nature Structural Biology.
[27] Ken A Dill,et al. Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. , 2007, Journal of chemical theory and computation.
[28] Dirar Homouz,et al. Crowded, cell-like environment induces shape changes in aspherical protein , 2008, Proceedings of the National Academy of Sciences.
[29] Leslie L. Chavez,et al. Multiple routes lead to the native state in the energy landscape of the β-trefoil family , 2006, Proceedings of the National Academy of Sciences.
[30] P. Wittung-Stafshede,et al. Macromolecular crowding increases structural content of folded proteins , 2007, FEBS letters.
[31] G. Vriend,et al. Molecular docking using surface complementarity , 1996, Proteins.
[32] 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.
[33] D. Thirumalai,et al. Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties. , 1996, Folding & design.
[34] Thomas M Truskett,et al. Coarse-grained strategy for modeling protein stability in concentrated solutions. II: phase behavior. , 2006, Biophysical journal.
[35] Loops, Linkages, Rings, Catenanes, Cages, and Crowders: Entropy‐Based Strategies for Stabilizing Proteins , 2004 .
[36] J. Onuchic,et al. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[37] C M Dobson,et al. Effects of macromolecular crowding on protein folding and aggregation , 1999, The EMBO journal.
[38] S. Takada,et al. Effects of macromolecular crowding on protein folding and aggregation studied by density functional theory: statics. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.
[39] C. Brooks,et al. Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. , 1993, Biochemistry.
[40] Conggang Li,et al. Residue-level interrogation of macromolecular crowding effects on protein stability. , 2008, Journal of the American Chemical Society.
[41] J. Onuchic,et al. Folding funnels and frustration in off-lattice minimalist protein landscapes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[42] C. V. van Mierlo,et al. Structural characterisation of apoflavodoxin shows that the location of the stable nucleus differs among proteins with a flavodoxin-like topology. , 1998, Journal of molecular biology.
[43] Margaret S. Cheung,et al. Exploring the Interplay between Topology and Secondary Structural Formation in the Protein Folding Problem , 2003 .
[44] D Thirumalai,et al. Effects of crowding and confinement on the structures of the transition state ensemble in proteins. , 2007, The journal of physical chemistry. B.
[45] J. Onuchic,et al. Theory of protein folding: the energy landscape perspective. , 1997, Annual review of physical chemistry.
[46] A. Minton,et al. Macromolecular crowding: biochemical, biophysical, and physiological consequences. , 1993, Annual review of biophysics and biomolecular structure.
[47] R. J. Speedy,et al. Cavities in the hard sphere crystal and fluid , 1994 .
[48] 15N NMR spin relaxation dispersion study of the molecular crowding effects on protein folding under native conditions. , 2006, Journal of the American Chemical Society.
[49] Fumio Oosawa,et al. On Interaction between Two Bodies Immersed in a Solution of Macromolecules , 1954 .
[50] Shaw,et al. Free polymer in a colloidal solution. , 1991, Physical review. A, Atomic, molecular, and optical physics.
[51] A. Minton,et al. Models for excluded volume interaction between an unfolded protein and rigid macromolecular cosolutes: macromolecular crowding and protein stability revisited. , 2005, Biophysical journal.
[52] B. Pettitt,et al. An analysis of the molecular origin of osmolyte‐dependent protein stability , 2007, Protein science : a publication of the Protein Society.
[53] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[54] Marta Bueno,et al. Do proteins with similar folds have similar transition state structures? A diffuse transition state of the 169 residue apoflavodoxin. , 2006, Journal of molecular biology.
[55] N. Grishin,et al. Alternate pathways for folding in the flavodoxin fold family revealed by a nucleation-growth model. , 2006, Journal of Molecular Biology.
[56] B. Halle,et al. Protein self-association induced by macromolecular crowding: a quantitative analysis by magnetic relaxation dispersion. , 2005, Biophysical journal.
[57] C. Brooks,et al. From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding. , 2001, Annual review of physical chemistry.
[58] D. Thirumalai,et al. The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus. , 1997, Folding & design.
[59] P. Wittung-Stafshede,et al. Molecular crowding enhances native structure and stability of α/β protein flavodoxin , 2007, Proceedings of the National Academy of Sciences.