|
|
Studies on the Properties of Biomacromolecules under Molecular Crowded Conditions |
ZHANG Yu-jiao1, TANG Qian1, CAO Hong-yu1, ZHENG Xue-fang1,2 |
1. School of Life Science and Biotechnology, Dalian University, Dalian 116622, China; 2. Liaoning Key Lab of Bio-organic Chemistry, Dalian University, Dalian 116622, China |
|
|
Abstract Living cells contain a variety of biomolecules, they play their physiological functions in different concentrations, which is often neglected in vitro studies. With the molecular crowding theory put forward, the addition of crowding agents in vitro is valued by more and more biologists and chemists, many research results show that the molecular crowding has effects on the properties of the biomolecules. The properties and functions of biomolecules from the effects of molecular crowding on protein folding, aggregation, enzymatic activity, the nucleic acids molecular structure and properties under the crowding conditions were discussed, to provide more references for the further research.
|
Received: 03 August 2012
Published: 25 December 2012
|
|
|
|
[1] Swaminathan R, Hoang C P, Verkman A S. Photobleaching recovery and anisotropy decay of green fluorescent protein GFP-S65T in solution and cells: cytoplasmic viscosity probed by green fluorescent protein translational and rotational diffusion. Biophys J, 1997, 72(4):1900-1907. [2] Minton A P. The effect of volume occupancy upon the thermodynamic activity of proteins: some biochemical consequences.Mol Cell Biochemistry, 1983, 55(2):119-140. [3] Ellis R J. Macromolecular crowding: an important but neglected aspect of the intracellular environment. Curr Opin Struct Biology, 2001, 11(1):114-119. [4] 王莉衡, 钦传光, 尚晓娅等. 大分子拥挤环境中溶菌酶的去折叠过程.西北农林科技大学学报, 2009,37(9):187-192. Wang L H, Qin C G, Shang X Y, et al. Journal of Northwest,2009, 37(9): 187-192. [5] Wang Y, He H, Li S. Effect of Ficoll 70 on thermal stability and structure of creatine kinase. Biochemistry (Mosc), 2010, 75(5): 648-654. [6] Zhang D L, Wu L J, Chen J, et al. Effects of macromolecular crowding on the structural stability of human α-lactalbumin. Acta Biochim Biophys Sin (Shanghai),2012, 44(8):703-711. [7] 闫菡, 郭占云, 冯佑民. 大分子拥挤及其对蛋白质折叠的影响.陕西医学杂志, 2003, 32(3):246-247. Yan H, Guo Z Y, Feng Y M. Shaanxi Medical Journal, 2003, 32(3):246-247. [8] 赵明, 井健, 李森. 大分子拥挤试剂对人肌肌酸激酶折叠途径的影响作用研究. 北京师范大学学报, 2007,43(4):442-446. Zhao M, Jing J, Li S. Journal of Beijing Normal Unieversity, 2007, 43 (4):442-446. [9] 李剑, 王志珍. 细胞内的大分子拥挤环境. 生物化学与生物物理进展, 2001, 28(6):788-792. Li J, Wang Z Z, Progress in Biochemistry and Biophysics, 2001, 28(6):788-792. [10] Fan Y Q, Liu H J, Li C, et al. Effects of macromolecular crowding on refolding of recombinant human brain-type creatine kinase.Int J Biol Macromol, 2012, 51(1-2):113-118. [11] Fan Y Q, Lee J, Oh S, et al. Effects of osmolytes on human brain-type creatine kinase folding in dilute solutions and crowding systems.Int J Biol Macromol, 2012(in press). [12] McPhie P, Ni Y S, Minton A P. Macromolecular crowding stabilizes the molten globule form of apomyoglobin with respect to both cold and heat unfolding. J Mol Biol, 2006, 361(1):7-10. [13] Davis-Searles P R, Morar A S, Saunders A J, et al. Sugar-induced molten-globule model. Biochemistry,1998, 37 (48): 17048-17053. [14] Saunders A J, Davis-Searles P R, Allen D L, et al. Osmolyte-induced changes in protein conformational equilibria.Biopolymers, 2000, 53(4): 293-307. [15] Morar A S, Olteanu A, Young G B, et al. Solvent-induced collapse of alpha-synuclein and acid-denatured cytochrome c.Protein Sci, 2001, 10(11): 2195-2199. [16] Sasahara K, McPhie P, Minton A P. Effect of dextran on protein stability and conformation attributed to macromolecular crowding. J Mol Biol, 2003, 326(4): 1227-1236. [17] Cole N, Ralston G B. Enhancement of self-association of human spectrin by polyethylene glycol. Int J Biochemistry, 1994, 26(6): 799-804. [18] Lindner R A, Ralston G B. Effects of dextran on the self-association of human spectrin. Biophys Chemistry, 1995, 57(1): 15-25. [19] Rivas G, Fernandez J A, Minton A P. 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, 1999, 38(29): 9379-9388. [20] Minton A P. Implications of macromolecular crowding for protein assembly. Curr Opin Struct Biol, 2000, 10(1): 34-39. [21] Ptitsyn O B. Molten globule and protein folding. Adv Protein Chem, 1995, 47, 83-229. [22] Arai M, Kuwajima K. Role of the molten globule state in protein folding. Adv Protein Chem, 2000, 53: 209-282. [23] Wanker E E. Protein aggregation in Huntington’ s and Parkinson’ s disease: implications for therapy. Mol Med Today, 2000, 6(10): 387-391. [24] Zhang X P, Liu F, Cheng Z, et al. Cell fate decision mediated by p53 pulses.Proc Natl Acad Sci USA, 2009, 106(30): 12245-12250. [25] Kim J S, Yethiraj A. Crowding effects on protein association: effect of interactions between crowding agents. J Phys Chem B, 2011, 115(2): 347-353. [26] Miyoshi D, Nakamura K, Muhui S, et al. Thermodynamics of DNA structures under molecular crowding conditions with neutral and positive charged cosolutes. Nucleic Acids Symp Ser(Oxf), 2008, (52): 413-414. [27] Livolant F, Amelie L. Condensed phases of DNA: structures and phase transitions. Prog Polym Sci, 1996, 21: 1115-1164. [28] Bloomfield V A. DNA condensation. Curr Opin Struct Biol, 1996, 6(3): 334-341. [29] Vitiello L, Chonn A, Wasserman J D, et al. Condensation of plasmid DNA with polylysine improves liposome-mediated gene transfer into established and primary muscle cells. Gene Ther, 1996, 3(5): 396-404. [30] De Smedt S C, Demeester J, Hennink W E. Cationic polymer based gene delivery systems. Pharm Res, 2000, 17(2): 113-126. [31] Marky L A, Kupke D W. Enthalpy-entropy compensations in nucleic acids: contribution of electrostriction and structural hydration. Methods Enzymol, 2000, 323: 419-441. [32] Spink C H, Chaires J B. Effects of hydration, ion release, and excluded volume on the melting of triplex and duplex DNA. Biochemistry, 1999, 38(1): 496-508. [33] Nakano S I, Karimata H, Ohmichi T, et al. The effect of molecular crowding with nucleotide length and cosolute structure on DNA duplex stability. J Am Chem Soc, 2004, 126(44): 14330-14331. [34] Karimata H, Nakano S, Ohmichi T, et al. Stabilization of a DNA duplex under molecular crowding conditions of PEG. Nucleic Acids Symp Ser (Oxf),2004,(48):107-108. [35] Spink C H, Chaires J B. Selective stabilization of triplex DNA by poly(ethylene glycols). J Am Chem Soc, 1995, 117: 12887-12888. [36] Goobes R, Minsky A. Thermodynamic aspects of triplex DNA formation in crowded environments. J Am Chem Soc, 2001, 123(50): 12692-12693. [37] Goobes R, Cohen O, Minsky A. Unique condensation patterns of triplex DNA: physical aspects and physiological implications. Nucleic Acids Res, 2002, 30(10): 2154-2161. [38] Miyoshi D, Nakamura K, Tateishi-Karimata H, et al. Hydration of Watson-Crick base pairs and dehydration of Hoogsteen base pairs inducing structural polymorphism under molecular crowding conditions. J Am Chem Soc, 2009,131(10):3522-3531. [39] Goobes R, Kahana N. Cohen O, et al. Metabolic buffering exerted by macromolecular crowding on DNA-DNA interactions: origin and physiological significance. Biochemistry, 2003, 42(8): 2431-2440. [40] Li J, Correia J J, Wang L, et al. Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids Res, 2005, 33(14): 4649-4659. [41] Xue Y, Kan Z Y, Wang Q, et al. Human telomeric DNA forms parallel-stranded intramolecular G-quadruplex in K+ solution under molecular crowding conditions. J Am Chem Soc, 2007, 129(36): 11185-11191. [42] Xu L, Feng S, Zhou X. Human telomeric G-quadruplexes undergo dynamic conversion in a molecular crowding environment. Chem Commun, 2011, 47(12): 3517-3519. [43] Miyoshi D, Nakao A, Sugimoto N. Molecular crowding regulates the structural switch of the DNA G-quadruplex. Biochemistry, 2002, 41(50): 15017-15024. [44] Zhou Jun, Wei Chunying, Jia Guoqing, et al. The structural transition and compaction of human telomeric G-quadruplex induced by excluded volume effect under cation-deficient conditions. Biophys Chem, 2008,136(2-3):124-127. [45] Fujimoto T, Nakano S, Miyoshi D, et al. The effects of molecular crowding on the structure and stability of G-quadruplexes with an abasic site. Journal of Nucleic Acids, 2011,(2011):857149-857157. [46] Zimmerman S B, Minton A P. Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu Rev Biophys Biomol Struct, 1993, 22: 27-65. [47] Zhao S, Zhu Q, Somerville R L. The sigma(70) transcription factor TyrR has zinc-stimulated phosphatase activity that is inhibited by ATP and tyrosine. J Bacteriol, 2000, 182(4):1053-1061. [48] Poon J, Bailey M, Winzor D J, et al. Effects of molecular crowding on the interaction between DNA and the Escherichia coli regulatory protein TyrR. Biophys J, 1997, 73(6):3257-3264. [49] Grzegorz Wieczorek, Piotr Zielenkiewicz. Influence of macromolecular crowding on protein-protein association rates—a Brownian dynamics study. Biophys J, 2008,95(11): 5030-5036. |
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
|
Shared |
|
|
|
|
|
Discussed |
|
|
|
|