Communication between noncontacting macromolecules

Annual Review of Biophysics and Biomolecular Structure

Volumn 34, Issue , 2005, Pages 21-42

  Völker, Jens ^a   Breslauer, Kenneth J ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Coupled equilibria; Linkage thermodynamics; Molecular crowding; Solute solvent interactions; Through solution communication

Indexed keywords

BIOPOLYMER; POLYMER; SODIUM ION; SOLVENT; WATER;

AQUEOUS SOLUTION; CONFORMATIONAL TRANSITION; COVALENT BOND; MACROMOLECULE; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; MOLECULAR MECHANICS; MOLECULAR PROBE; PH; PRIORITY JOURNAL; REGULATORY MECHANISM; REVIEW; SOLUTE; THEORY; THERMODYNAMICS;

BIOPHYSICS; BIOPOLYMERS; HYDROGEN-ION CONCENTRATION; IONS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MOLECULAR CONFORMATION; SODIUM; SOLVENTS; TEMPERATURE; THERMODYNAMICS; WATER;

EID: 20544468994     PISSN: 10568700     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.biophys.33.110502.133332     Document Type: Review

References (97)

1. Aalkjaer C, Peng HL. 1997. pH and smooth muscle. Acta Physiol. Scand. 161:557-66
2. Aickin CC. 1986. Intracellular pH regulation by vertebrate muscle. Annu. Rev. Physiol. 48:349-61
3. Baskakov I, Bolen DW. 1998. Forcing thermodynamically unfolded proteins to fold. J. Biol. Chem. 273:4831-34
4. Blake RD, Delcourt SG. 1987. Loop energy in DNA. Biopolymers 26:2009-26
5. Blokzijl W, Engberts JBFN. 1993. Hydrophobic effects. Opinions and fact. Angew. Chem. Int. Ed. Engl. 32:1545-79
6. Bloomfield VA. 1996. DNA condensation. Curr. Opin. Struct. Biol. 6:334-41
7. Bloomfield VA. 1997. DNA condensation by multivalent cations. Biopolymers 44:269-82
8. Bolen DW. 2001. Protein stabilization by naturally occurring osmolytes. Methods Mol. Biol. 168:17-36
9. Bolen DW, Baskakov IV. 2001. The osmophobic effect: natural selection of a thermodynamic force in protein folding. J. Mol. Biol. 310:955-63
10. Brunori M, Coletta M, Giardina B, Wyman J. 1978. A macromolecular transducer as illustrated by trout hemoglobin IV. Proc. Natl. Acad. Sci. USA 75:4310-12
11. Cayley DS, Guttman HJ, Record MT Jr. 2000. Biophysical characterization of changes in amounts and activity of Escherichia coli cell and compartment water and turgor pressure in response to osmotic stress. Biophys. J. 78:1748-64
12. Cayley S, Lewis BA, Guttman HJ, Record MT Jr. 1991. Characterization of the cytoplasm of Escherichia coli K-12 as a function of external osmolarity. Implications for protein-DNA interactions in vivo. J. Mol. Biol. 222:281-300
13. Cayley S, Lewis BA, Record MT Jr. 1992. Origins of the osmoprotective properties of betaine and proline in Escherichia coli K- 12. J. Bacteriol. 174:1586-95
14. Cayley S, Record MT Jr. 2003. Roles of cytoplasmic osmolytes, water, and crowding in the response of Escherichia coli to osmotic stress: biophysical basis of osmoprotection by glycine betaine. Biochemistry 42:12596-609
15. Chalikian TV. 2003. Volumetric properties of proteins. Annu. Rev. Biophys. Biomol. Struct. 32:207-35
16. Chalikian TV, Breslauer KJ. 1998. Thermodynamic analysis of biomolecules: a volumetric approach. Curr. Opin. Struct. Biol. 8:657-64
17. Chalikian TV, Breslauer KJ. 1998. Volumetric properties of nucleic acids. Blopolymers 48:264-80
18. Chalikian TV, Sarvazyan AP, Breslauer KJ. 1994. Hydration and partial compressibility of biological compounds. Biophys. Chem. 51:89-109
19. Chalikian TV, Totrov M, Abagyan R, Breslauer KJ. 1996. The hydration of globular proteins as derived from volume and compressibility measurements: cross correlating thermodynamic and structural data. J. Mol. Biol. 260:588-603
20. Chalikian TV, Völker J, Srinivasan AR, Olson WK, Breslauer KJ. 1999. The hydration of nucleic acid duplexes as assessed by a combination of volumetric and structural techniques. Biopolymers 50:459-71
21. Chamberlin MJ. 1965. Comparative properties of DNA, RNA, and hybrid homopolymer pairs. Fed. Proc. 24:1446-57
22. Crnogorac MM, Ullmann GM, Kostic NM. 2001. Effects of pH on protein association: modification of the proton-linkage model and experimental verification of the modified model in the case of cytochrome c and plastocyanin. J. Am. Chem. Soc. 123:10789-98
23. De Cristofaro R, Landolfi R, De Candia E, Castagnola M, Di Cera E, Wyman J. 1988. Allosteric equilibria in the binding of fibrinogen to platelets. Proc. Natl. Acad. Sci. USA 85:8473-76
24. Di Cera E, Gill SJ, Wyman J. 1988. Canon-ical formulation of linkage thermodynamics. Proc. Natl. Acad. Sci. USA 85:5077-81
25. Ellis RJ, Minton AP. 2003. Cell biology: join the crowd. Nature 425:27-28
26. Fulton AB. 1982. How crowded is the cytoplasm? Cell 30:345-47
27. Garcia-Moreno B. 1995. Probing structural and physical basis of protein energetics linked to protons and salt. Methods Enzymol. 259:512-38
28. Gehring K, Leroy JL, Gueron M. 1993. A tetrameric DNA structure with protonated cytosine.cytosine base pairs. Nature 363:561-65
29. Gill SJ, Robert CH, Coletta M, Di Cera E, Brunori M. 1986. Cooperative free energies for nested allosteric models as applied to human hemoglobin. Biophys. J. 50:747-52
30. Goldbeter A, Dupont G. 1990. Allosteric regulation, cooperativity, and biochemical oscillations. Biophys. Chem. 37:341-53
31. Hall D, Minton AP. 2003. Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges. Biochim. Biophys. Acta 1649:127-39
32. Holcomb DN, Timasheff SN. 1968. Temperature dependence of the hydrogen ion equilibria in poly(riboadenylic acid). Biopolymers 6:513-29
33. Howard FB, Miles HT, Ross PD. 1995. The poly(dT)·2poly(dA) triple helix. Biochemistry 34:7135-44
34. Klump HH. 1988. Conformational transitions in nucleic acids. In Biochemical Thermodynamics: Studies in Modern Thermodynamics, ed. MN Jones, pp. xi, 403. New York: Elsevier
35. Leikin S, Parsegian VA, Rau DC, Rand RP. 1993. Hydration forces. Annu. Rev. Phys. Chem. 44:369-95
36. Leroy JL, Gehring K, Kettani A, Gueron M. 1993. Acid multimers of oligodeoxycytidine strands: stoichiometry, base-pair characterization, and proton exchange properties. Biochemistry 32:6019-31
37. Leroy JL, Gueron M. 1995. Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons. Structure 3: 101-20
38. Lonhienne TG, Reilly PE, Winzor DJ. 2003. Further evidence for the reliance of catalysis by rabbit muscle pyruvate kinase upon isomerization of the ternary complex between enzyme and products. Biophys. Chem. 104:189-98
39. Lonhienne TG, Winzor DJ. 2002. Calorimetric demonstration of the potential of molecular crowding to emulate the effect of an allosteric activator on pyruvate kinase kinetics. Biochemistry 41:6897-901
40. Manning GS. 1978. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q. Rev. Biophys. 11:179-246
41. Manning GS. 1984. Limiting laws and counterion condensation in polyelectrolyte solutions. 8. Mixtures of counterions, species selectivity and valence selectivity. J. Phys. Chem. 88:6654-61
42. Manning GS, Ray J. 1998. Counterion condensation revisited. J. Biomol. Struct. Dyn. 16:461-76
43. Manzini G, Yathindra N, Xodo LE. 1994. Evidence for intramolecularly folded i-DNA structures in biologically relevant CCC-repeat sequences. Nucleic Acids Res. 22:4634-40
44. Matthew JB, Gurd FR, Garcia-Moreno B, Flanagan MA, March KL, Shire SJ. 1985. pH-dependent processes in proteins. CRC Crit. Rev. Biochem. 18:91-197
45. Mergny J-L, Lacroix L, Han X, Leroy J-L, Helene C. 1995. Intramolecular folding of pyrimidine oligodeoxynucleotides into an i-DNAmotif. J. Am. Chem. Soc. 117:8887-98
46. Minton AP. 1983. The effect of volume occupancy upon the thermodynamic activity of proteins: some biochemical consequences. Mol. Cell. Biochem. 55:119-40
47. Minton AP. 1998. Molecular crowding: analysis of effects of high concentrations of inert cosolutes on biochemical equilibria and rates in terms of volume exclusion. Methods Enzymol. 295:127-49
48. Minton AP. 2001. The influence of macro-molecular crowding and macromolecular confinement on biochemical reactions in physiological media. J. Biol. Chem. 276: 10577-80
49. Minton AP, Colclasure GC, Parker JC. 1992. Model for the role of macromolecular crowding in regulation of cellular volume. Proc. Natl. Acad. Sci. USA 89:10504-6
50. Monod J, Wyman J, Changeux JP. 1965. On the nature of allosteric transitions: a plausible model. J. Mol. Biol. 12:88-118
51. Oliver AL, Wartell RM, Ratliff RL. 1977. Helix coil transitions of d(A)n-d(T)n, d(A-T)n-d(A-T)n, and d(A-A-T)n- d(A-T-T)n: evaluation of parameters governing DNA stability. Biopolymers 16:1115-37
52. Omta AW, Kropman MF, Woutersen S, Bakker HJ. 2003. Negligible effect of ions on the hydrogen-bond structure in liquid water. Science 301:347-49
53. Orchard CH, Kentish JC. 1990. Effects of changes of pH on the contractile function of cardiac muscle. Am. J. Physiol. 258:C967-81
54. Parsegian VA. 1995. Solvation: hopes for Hofmeister. Nature 378:335-36
55. Parsegian VA, Rand RP, Fuller NL, Rau DC. 1986. Osmotic stress for the direct measurement of intermolecular forces. Methods Enzymol. 127:400-16
56. Parsegian VA, Rand RP, Rau DC. 1995. Macromolecules and water: probing with osmotic stress. Methods Enzymol. 259:43-94
57. Parsegian VA, Rand RP, Rau DC. 2000. Osmotic stress, crowding, preferential hydration, and binding: a comparison of perspectives. Proc. Natl. Acad. Sci. USA 97: 3987-92
58. Paulsen MD, Anderson CF, Record MT Jr. 1988. Counterion exchange reactions on DNA: Monte Carlo and Poisson-Boltzmann analysis. Biopolymers 27:1249-65
59. Podgornik R, Strey HH, Rau DC, Parsegian VA. 1995. Watching molecules crowd: DNA double helixes under osmotic stress. Biophys. Chem. 57:111-21
60. Qu Y, Bolen CL, Bolen DW. 1998. Osmolyte-driven contraction of a random coil protein. Proc. Natl. Acad. Sci. USA 95: 9268-73
61. Qu Y, Bolen DW. 2002. Efficacy of macromolecular crowding in forcing proteins to fold. Biophys. Chem. 101-102:155-65
62. Ray J, Manning GS. 1992. Theory of delocalized ionic binding to polynucleotides: structural and excluded-volume effects. Biopolymers 32:541-49
63. Ray J, Manning GS. 1994. An attractive force between two rodlike polyions mediated by the sharing of condensed counterions. Langmuir 10:2450-61
64. Record MT Jr, Anderson CF. 1995. Interpretation of preferential interaction coefficients of nonelectrolytes and of electrolyte ions in terms of a two-domain model. Biophys. J. 68:786-94
65. Record MT Jr, Anderson CF, Lohman TM. 1978. Thermodynamic analysis of ion effects on the binding and conformational equilibriums of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q. Rev. Biophys. 11:103-78
66. Record MT Jr, Courtenay ES, Cayley DS, Guttman HJ. 1998. Responses of E. coli to osmotic stress: large changes in amounts of cytoplasmic solutes and water. Trends Biochem. Sci. 23:143-48
67. Record MT Jr, Courtenay ES, Cayley S, Guttman HJ. 1998. Biophysical compensation mechanisms buffering E. coli protein-nucleic acid interactions against changing environments. Trends Biochem. Sci. 23: 190-94
68. Record MT Jr, Woodbury CP, Lohman TM. 1976. Sodium ion effects on transitions of DNA and poly nucleotides of variable linear charge density. Biopolymers 15:893-915
69. Record MT Jr, Zhang W, Anderson CF. 1998. Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. Adv. Protein Chem. 51:281-353
70. Rich A. 1958. Formation of two and three-stranded helical molecules by polyinosinic acid and polyadenylic acid. Nature 181:521-25
71. Rich A, Davis DR, Crick FHC, Watson JD. 1961. The molecular structure of polyadenylic acid. J. Mol. Biol. 3:71-86
72. Ripoll C, Norris V, Thellier M. 2004. Ion condensation and signal transduction. Bioessays 26:549-57
73. Rivas G, Fernandez JA, Minton AP. 1999. 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. Biochemistry 38:9379-88
74. Scatchard G. 1946. Physical chemistry of protein solutions. I. Derivation of the equations for the osmotic pressure. J. Am. Chem. Soc. 68:2315-19
75. Schellman JA. 1978. Solvent denaturation. Biopolymers 17:1305-22
76. Schellman JA. 1987. Selective binding and solvent denaturation. Biopolymers 26:549-5 9
77. Schellman JA. 1987. The thermodynamic stability of proteins. Annu. Rev. Biophys. Biophys. Chem. 16:115-37
78. Schellman JA. 1990. A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures. Biophys. Chem. 37:121-40
79. Schellman JA. 1994. The thermodynamics of solvent exchange. Biopolymers 34: 1015-26
80. Tang KE, Bloomfield VA. 2002. Assessing accumulated solvent near a macromolecular solute by preferential interaction coefficients. Biophys. J. 82:2876-91
81. Timasheff SN. 1991. Solvent effects on protein stability. Curr. Opin. Struct. Biol. 2: 35-39
82. Timasheff SN. 1993. The control of protein stability and association by weak interactions with water: How do solvents affect these processes? Annu. Rev. Biophys. Biomol. Struct. 22:67-97
83. Timasheff SN. 1998. Control of protein stability and reactions by weakly interacting cosolvents: the simplicity of the complicated. Adv. Protein Chem. 51:355-432
84. Timasheff SN. 1998. In disperse solution, "osmotic stress" is a restricted case of preferential interactions. Proc. Natl. Acad. Sci. USA 95:7363-67
85. Timasheff SN. 2002. Protein hydration, thermodynamic binding, and preferential hydration. Biochemistry 41:13473-82
86. Timasheff SN. 2002. Protein-solvent preferential interactions, protein hydration, and the modulation of biochemical reactions by solvent components. Proc. Natl. Acad. Sci. USA 99:9721-26
87. Timasheff SN. 2002. Thermodynamic binding and site occupancy in the light of the Schellman exchange concept. Biophys. Chem. 101-102:99-111
88. Vogler EA. 1998. Structure and reactivity of water at biomaterial surfaces. Adv. Colloid Interface Sci. 74:69-117
89. Völker J, Klump HH, Breslauer KJ. 2001. Communication between noncontacting macromolecules. Proc. Natl. Acad. Sci. USA 98:7694-99
90. Völker J, Klump HH, Manning GS, Breslauer KJ. 2001. Counterion association with native and denatured nucleic acids: an experimental approach. J. Mol. Biol. 310:1011-25
91. Wadsworth WG, Riddle DL. 1988. Acidic intracellular pH shift during Caenorhabditis elegans larval development. Proc. Natl. Acad. Sci. USA 85:8435-38
92. Wyman J. 1948. Heme proteins. Adv. Protein Chem. 4:407-531
93. Wyman J. 1964. Linked functions and reciprocal effects in hemoglobin: a second look. Adv. Protein Chem. 19:223-86
94. Wyman J. 1968. Regulation in macromolecules as illustrated by haemoglobin. Q. Rev. Biophys. 1:35-80
95. Wyman J, Gill SJ. 1990. Binding and Linkage. Functional Chemistry of Biological Macromolecules. Mill Valley, CA: Univ. Sci. Books
96. Zimmerman SB, Minton AP. 1993. Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu. Rev. Biophys. Biomol. Struct. 22:27-65
97. Zimmerman SB, Trach SO. 1991. Estimation of macromolecule concentrations and excluded volume effects for the cytoplasm of Escherichia coli. J. Mol. Biol. 222:599-620