Abstract
Proteins are macromolecular structures, functionally active in their three-dimensional state, and their entire machinery depends on involvement of number of polypeptides. A perceptive insight of protein folding mechanism is a remarkable task, and various studies in protein structure and function have investigated mechanism of determining protein’s three-dimensional details. Apart from understanding basic energy forces and molecules operational behind protein folding, various computational models have also been designed that outline essential aspects of protein folding mechanism. In the present chapter, we have exercised to bring all aspects of protein folding under one roof with all essential components affecting protein folding, which include major driving forces, mechanisms, folding pathways, thermodynamics, kinetics, effect of chemical reagents, pH, temperature, and computational model to analyze protein folding mechanisms. Reliable prediction of protein folding process allows deducing its appropriate function, and we believe that present chapter will prove a step forward in the respective study.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Abkevich VI, Shakhnovich EI (2000) What can disulfide bonds tell us about protein energetics, function and folding: simulations and bioinformatics analysis. J Mol Biol 300:975–985
Ahluwalia U, Katyal N, Deep S (2012) Models of protein folding. J Prot Proteo 3(2):85–93
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walters P (2002) The shape and structure of proteins. Molecular biology of the cell, 4th edn. Garland Science, New York/London. ISBN 0-8153-3218-1
Alberts B, Bray D, Hopkin K, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2010) Protein structure and function. Essential cell biology, 3rd edn. Garland Science, New York, pp 120–170. ISBN 978-0-8153-4454-4
Anfinsen CB (1972) The formation and stabilization of protein structure. Biochem J 128 (4):737–749. doi:10.1042/bj1280737. PMC 1173893 PMID 4565129
Berg JM, Tymoczko JL, Stryer L (2002) Protein structure and function. Biochemistry. W. H. Freeman, San Francisco. ISBN 0-7167-4684-0
Brandon C, Tooze J (1991) Introduction to protein structure. Garland Publishing, New York/London
Carrell RW, Lomas DA (1997) Conformational disease. Lancet 350(9071):134–138. doi:10.1016/S0140-6736(97)02073-4
Chiti F, Dobson CM (2006) Protein misfolding, functional amyloid, and human disease. Annu Rev Biochem 75(1):333–366. doi:10.1146/annurev.biochem.75.101304.123901
Creighton TE (1990) Protein folding. Biochem J 270:1–16
Darby NJ, Creighton TE (1993) Dissecting the disulphide-coupled folding pathway of bovine pancreatic trypsin inhibitor: forming the first disulphide bonds in analogues of the reduced protein. J Mol Biol 232:873–896
Dressler D, Potter H (1991) Discovering enzymes. W.H. Freeman, New York/Oxford
Essential Biochemistry (2016) www.wiley.com
Flory P (1953) Principles of polymer chemistry. Cornell University Press, Ithaca
Friedrich O (2006) Critical illness myopathy: what is happening? Curr Opin Clin Nutr Metab Care 9(4):403–409. doi:10.1097/01.mco.0000232900.59168.a0
Harel M, Su CT, Frolow F, Silman I, Sussman JL (1991) Gamma-chymotrypsin is a complex of alpha-chymotrypsin with its own autolysis products. Biochemist 30:5217
Haspel N, Tsai CJ, Wolfson H, Nussinov R (2003) Hierarchical protein folding pathways: a computational study of protein fragments. Prot Struc Func Genet 51:203–215
Hogg PJ (2003) Disulfide bonds as switches for protein function. Trends Biochem Sci 28(4):210–214
Hubbard RE, Haider MK (2010) Hydrogen bonds in proteins: role and strength. University of York, York. doi:10.1002/9780470015902.a0003011.pub2
Karplus M, Weaver DL (1994) Protein folding dynamics: The diffusion-collision model and experimental data. Prot Sci 3:650–668
Lovell SC, Davis IW, Arendall WB III, de Bakker PIW, Word JM, Prisant MG, Richardson JS, Richardson DC (2003) Structure validation by Cα geometry: φ/ψ and Cβ deviation. Prot Struc Func Genet 50:437–450
Luheshi M, Crowther DC, Dobson CM (2008) Protein misfolding and disease: from the test tube to the organism. Curr Opin Chem Bio 12(1):25–31. doi:10.1016/j.cbpa.2008.02.011
Marnathambika BS, Bardwell JC (2008) Disulfide-linked protein folding pathways. Annu Rev Cell Dev Biol 24:211–235
Mogk A, Mayer MP, Deuerling E (2002) Mechanisms of protein folding: molecular chaperones and their application in biotechnology. Chem Bio Chem 3(9):807–814
Myers JK, Pace CN, Scholtz JM (1995) Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci Publ Protein Soc 4(10):2138–2148
Pace CN, Grimsley GR, Thomson JA, Barnett BJ (1988) Conformational stability and activity of ribonuclease T1 with zero, one, and two intact disulfide bonds. J Biol Chem 263:11820–11825
Privalov PL, Khechinashvili NN (1974) J Mol Bio 86:665–684
Schmidt B, Ho L, Hogg PJ (2006) Allosteric disulfide bonds. Biochemistry 45(24):7429–7433
Qin M, Wang W, Thirumalai D (2015) Protein folding guides disulfide bond formation. PNAS 112(36):11241–11246
Ramachandran GN, Sasisekaran V (1968) Conformation of polypeptides and proteins. Adv Prot Chem 23:284–438
Saibil H (2013) Chaperone machines for protein folding, unfolding and disaggregation. Nat Rev Mol Cell Biol 14(10):630–642. doi:10.1038/nrm3658
Saunders R, Deane CM (2010) Synonymous codon usage influences the local protein structure observed. Nucl Acids Res 38(19):6719–6728. doi:10.1093/nar/gkq495
Selkoe DJ (2003) Folding proteins in fatal ways. Nature 426(6968):900–904. doi:10.1038/nature02264
Spinner NB (2000) CADASIL: notch signaling defect or protein accumulation problem? J Clin Invest 105(5):561–562. doi:10.1172/JCI9511
Thornton JM (1981) Disulphide bridges in globular proteins. J Mol Biol 151:261–287
Valastyan JS, Lindquist S (2014) Mechanisms of protein-folding diseases at a glance. Disease Mod Mech 7:9–14. doi:10.1242/dmm.013474
Van den Berg B, Wain R, Dobson CM, Ellis RJ (2000) Macromolecular crowding perturbs protein refolding kinetics: implications for folding inside the cell. EMBO J 19(15):3870–3875. doi:10.1093/emboj/19.15.3870
Walker LC, LeVine H III (2000) The cerebral proteopathies: neurodegenerative disorders of protein conformation and assembly. Mol Neurobiol 21(1–2):83–95. doi:10.1385/MN:21:1-2:083
Westermark P et al (2007) A primer of amyloid nomenclature. Amyloid 14(3):179–183. doi:10.1080/13506120701460923
Yennawar NH, Yennawar HP, Farber GK (1994) X-ray crystal structure of gamma-chymotrypsin in hexane. Biochemistry 33:7326
Acknowledgment
The author extends her acknowledgment to Science and Engineering Research Board, New Delhi, for providing research support [project file number: DST/SERB YSS/2015/002072] and also extends her thanks to her Ph.D. student Ms. Meenal Rastogi at Amity Institute of Biotechnology, Amity University Uttar Pradesh, Noida, India.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 The Author(s)
About this chapter
Cite this chapter
Shrivastava, S. (2017). Protein Folding. In: Misra, G. (eds) Introduction to Biomolecular Structure and Biophysics. Springer, Singapore. https://doi.org/10.1007/978-981-10-4968-2_2
Download citation
DOI: https://doi.org/10.1007/978-981-10-4968-2_2
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-10-4967-5
Online ISBN: 978-981-10-4968-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)