Loops, linkages, rings, catenanes, cages, and crowders: entropy-based strategies for stabilizing proteins.

A protein molecule exists in either a compact folded state or a variable and open unfolded state. Since the unfolded state is favored by chain entropy, restricting its entropy is an attractive mechanism for shifting the equilibrium toward the folded state. A number of entropy-based strategies have been engineered or used by natural proteins to increase the folding stability: (a) shortening of loop lengths, (b) covalent linkage of dimeric proteins, (c) backbone cyclization, (d) catenation, (e) spatial confinement, and (f) macromolecular crowding. Theoretical analyses demonstrate the importance of accounting for consequences on the folded as well as the unfolded state and provide guidance for further exploitation of these stabilization strategies.

[1]  T. Hazbun,et al.  Single-chain lambda Cro repressors confirm high intrinsic dimer-DNA affinity. , 1998, Biochemistry.

[2]  Homer Jacobson,et al.  Intramolecular Reaction in Polycondensations. I. The Theory of Linear Systems , 1950 .

[3]  Shoji Takada,et al.  How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: Molecular simulations , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[4]  Huan‐Xiang Zhou.  Protein folding and binding in confined spaces and in crowded solutions , 2004, Journal of molecular recognition : JMR.

[5]  J. Valentine,et al.  Molecular confinement influences protein structure and enhances thermal protein stability , 2001, Protein science : a publication of the Protein Society.

[6]  Huan-Xiang Zhou,et al.  Loops in Proteins Can Be Modeled as Worm-Like Chains , 2001 .

[7]  S. Edwards,et al.  The Theory of Polymer Dynamics , 1986 .

[8]  STATISTICAL MECHANICS OF WORMLIKE CHAINS , 1977 .

[9]  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.

[10]  G. Petsko,et al.  Crystal structures of Escherichia coli and Salmonella typhimurium 3-isopropylmalate dehydrogenase and comparison with their thermophilic counterpart from Thermus thermophilus. , 1997, Journal of molecular biology.

[11]  Huan‐Xiang Zhou.  Effect of catenation on protein folding stability. , 2003, Journal of the American Chemical Society.

[12]  A. Fersht,et al.  The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. , 1995, Journal of molecular biology.

[13]  T. Terwilliger,et al.  Genetic fusion of subunits of a dimeric protein substantially enhances its stability and rate of folding. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[14]  A. Minton,et al.  Effect of a concentrated "inert" macromolecular cosolute on the stability of a globular protein with respect to denaturation by heat and by chaotropes: a statistical-thermodynamic model. , 2000, Biophysical journal.

[15]  M. Smoluchowski.  Versuch einer mathematischen Theorie der Koagulationskinetik kolloider Lösungen , 1918 .

[16]  John E. Johnson,et al.  Topologically linked protein rings in the bacteriophage HK97 capsid. , 2000, Science.

[17]  A. Fersht,et al.  Glutamine, alanine or glycine repeats inserted into the loop of a protein have minimal effects on stability and folding rates. , 1997, Journal of molecular biology.

[18]  T. Creighton,et al.  Folding pathway of a circular form of bovine pancreatic trypsin inhibitor. , 1984, Journal of Molecular Biology.

[19]  M Karplus,et al.  Comment on: 'The entropy cost of protein association'. , 1999, Protein engineering.

[20]  J. Lebowitz,et al.  Thermodynamic Properties of Mixtures of Hard Spheres , 1964 .

[21]  A. Kentsis,et al.  Transition state heterogeneity in GCN4 coiled coil folding studied by using multisite mutations and crosslinking. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

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

[23]  D Baker,et al.  Long-range order in the src SH3 folding transition state. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[24]  J. Kelly,et al.  The effect of backbone cyclization on the thermodynamics of beta-sheet unfolding: stability optimization of the PIN WW domain. , 2002, Journal of the American Chemical Society.

[25]  H. Zhou,et al.  The affinity-enhancing roles of flexible linkers in two-domain DNA-binding proteins. , 2001, Biochemistry.

[26]  P. Dawson,et al.  Thermodynamics of a designed protein catenane. , 2003, Journal of molecular biology.

[27]  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.

[28]  A. Tamura,et al.  The entropy cost of protein association. , 1997, Journal of molecular biology.

[29]  K A Dill,et al.  Stabilization of proteins in confined spaces. , 2001, Biochemistry.

[30]  David J Craik,et al.  Circular proteins--no end in sight. , 2002, Trends in biochemical sciences.

[31]  L. Serrano,et al.  Loop length, intramolecular diffusion and protein folding , 1997, Nature Structural Biology.

[32]  Szabó,et al.  Diffusion-controlled reactions with mobile traps. , 1988, Physical review letters.

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

[34]  L Regan,et al.  An inverse correlation between loop length and stability in a four-helix-bundle protein. , 1997, Folding & design.

[35]  D. Baker,et al.  Functional rapidly folding proteins from simplified amino acid sequences , 1997, Nature Structural Biology.

[36]  Walter H. Stockmayer,et al.  Statistical Mechanics of Wormlike Chains. I. Asymptotic Behavior , 1972 .

[37]  Huan-Xiang Zhou,et al.  Effect of backbone cyclization on protein folding stability: chain entropies of both the unfolded and the folded states are restricted. , 2003, Journal of molecular biology.

[38]  R. Sauer,et al.  Equilibrium stability and sub-millisecond refolding of a designed single-chain Arc repressor. , 1996, Biochemistry.

[39]  D. W. Bolen,et al.  Efficacy of macromolecular crowding in forcing proteins to fold. , 2002, Biophysical chemistry.

[40]  A. Fersht,et al.  Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2. , 1997, Journal of molecular biology.

[41]  Single-chain versus dimeric protein folding: thermodynamic and kinetic consequences of covalent linkage. , 2001, Journal of the American Chemical Society.