Biophysical Reviews

, Volume 10, Issue 2, pp 473–480 | Cite as

Biophysical studies of protein solubility and amorphous aggregation by systematic mutational analysis and a helical polymerization model

Review

Abstract

At concentrations above solubility, a protein aggregates, most often into amorphous aggregates, and loses its function. However, unlike amyloidogenic aggregates, which are β-sheeted fibrillar aggregates often related to neurodegenerative diseases, amorphous aggregates, where proteins aggregate/oligomerize without forming specific high-order structures, are rarely the focus of biophysical studies. Hence, protein solubility with respect to amorphous aggregation remains to be fully characterized from a biophysical viewpoint. Here, I briefly describe the structural nature of proteins in amorphous aggregates before discussing systematic mutational analyses that aim to rationalize the contribution of individual amino acids to the solubility of a protein. The discussion is expected to demonstrate that protein solubility, and, accordingly, amorphous aggregation, can be understood using thermodynamic and biophysical rationales similar to those used in the study of protein stability or, more recently, amyloidogenesis. Finally, I will argue that the mathematical formalism of the helical polymerization model (HPM) proposed by Oosawa, Kasai, and Asakura’s group can be readily adapted to provide a thermodynamic description of a system containing amorphous aggregates and soluble particles. The HPM and HPM-derived models imply the presence of nuclei or seeds for amorphous aggregates, similar to those hypothesized in crystallogenesis and amyloidogenesis.

Keywords

Solubility Precipitation Mutational analysis Thermodynamics analysis Helical polymerization model (HPM) Amorphous aggregation 

Notes

Acknowledgements

This article is dedicated to the 70th birthday anniversary of Professor Fumio Arisaka. I thank laboratory members, especially Drs. Atsushi Kato, Mohammad M. Islam, and Alam M. Khan for discussion and experimental data, and Ms. Patricia McGahan for the English grammar editing. This work was supported by a Japan Society for the Promotion of Science (JSPS) Grant-in-Aid for Scientific Research (KAKENHI-21300110).

Compliance with ethical standards

Conflict of interest

Yutaka Kuroda declares that he has no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by the author.

References

  1. Arakawa T, Tsumoto K (2003) The effects of arginine on refolding of aggregated proteins: not facilitate refolding, but suppress aggregation. Biochem Biophys Res Commun 304(1):148–152CrossRefPubMedGoogle Scholar
  2. Arisaka F, Noda H, Maruyama K (1975) Kinetic analysis of the polymerization process of actin. Biochim Biophys Acta 400(2):263–274CrossRefPubMedGoogle Scholar
  3. Baldwin RL (2012) Gas–liquid transfer data used to analyze hydrophobic hydration and find the nature of the Kauzmann–Tanford hydrophobic factor. Proc Natl Acad Sci U S A 109(19):7310–7313CrossRefPubMedPubMedCentralGoogle Scholar
  4. Boatz JC, Whitley MJ, Li M, Gronenborn AM, van der Wel PCA (2017) Cataract-associated P23T gammaD-crystallin retains a native-like fold in amorphous-looking aggregates formed at physiological pH. Nat Commun 8:15137CrossRefPubMedPubMedCentralGoogle Scholar
  5. Hall D, Minton AP (2002) Effects of inert volume-excluding macromolecules on protein fiber formation. I. Equilibrium models. Biophys Chem 98(1–2):93–104CrossRefPubMedGoogle Scholar
  6. Hall D, Kardos J, Edskes H, Carver JA, Goto Y (2015) A multi-pathway perspective on protein aggregation: implications for control of the rate and extent of amyloid formation. FEBS Lett 589(6):672–679CrossRefPubMedPubMedCentralGoogle Scholar
  7. Hamada H, Shiraki K (2007) L-argininamide improves the refolding more effectively than L-arginine. J Biotechnol 130(2):153–160CrossRefPubMedGoogle Scholar
  8. Islam MM, Khan MA, Kuroda Y (2012) Analysis of amino acid contributions to protein solubility using short peptide tags fused to a simplified BPTI variant. Biochim Biophys Acta 1824(10):1144–1150CrossRefPubMedGoogle Scholar
  9. Iwura T, Fukuda J, Yamazaki K, Arisaka F (2014) Conformational stability, reversibility and heat-induced aggregation of alpha-1-acid glycoprotein. J Biochem 156(6):345–352CrossRefPubMedGoogle Scholar
  10. Kamal MZ, Kumar V, Satyamurthi K, Das KK, Rao NM (2016) Mutational probing of protein aggregates to design aggregation-resistant proteins. FEBS Open Biol 6(2):126–134CrossRefGoogle Scholar
  11. Kato A, Maki K, Ebina T, Kuwajima K, Soda K, Kuroda Y (2007) Mutational analysis of protein solubility enhancement using short peptide tags. Biopolymers 85(1):12–18CrossRefPubMedGoogle Scholar
  12. Kauzmann W (1959) Some factors in the interpretation of protein denaturation. Adv Protein Chem 14:1–63CrossRefPubMedGoogle Scholar
  13. Khan MA, Islam MM, Kuroda Y (2013) Analysis of protein aggregation kinetics using short amino acid peptide tags. Biochim Biophys Acta 1834(10):2107–2115CrossRefPubMedGoogle Scholar
  14. Klug A, Durham ACH (1972) The disk of TMV protein and its relation to the helical and other modes of aggregation. Cold Spring Harb Symp Quant Biol 36:449–460CrossRefPubMedGoogle Scholar
  15. Kramer RM, Shende VR, Motl N, Pace CN, Scholtz JM (2012) Toward a molecular understanding of protein solubility: increased negative surface charge correlates with increased solubility. Biophys J 102(8):1907–1915CrossRefPubMedPubMedCentralGoogle Scholar
  16. Kuroda Y, Kim PS (2000) Folding of bovine pancreatic trypsin inhibitor (BPTI) variants in which almost half the residues are alanine. J Mol Biol 298(3):493–501CrossRefPubMedGoogle Scholar
  17. Kuroda Y, Suenaga A, Sato Y, Kosuda S, Taiji M (2016) All-atom molecular dynamics analysis of multi-peptide systems reproduces peptide solubility in line with experimental observations. Sci Rep 6:19479CrossRefPubMedPubMedCentralGoogle Scholar
  18. Kyte J, Doolittle RF (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol 157(1):105–132CrossRefPubMedGoogle Scholar
  19. Lide DR (ed) (2009) CRC handbook of chemistry and physics. 90th Edition, Section 7–1.Google Scholar
  20. Nohara D, Mizutani A, Sakai T (1999) Kinetic study on thermal denaturation of hen egg-white lysozyme involving precipitation. J Biosci Bioeng 87(2):199–205CrossRefPubMedGoogle Scholar
  21. Nozaki Y, Tanford C (1971) The solubility of amino acids and two glycine peptides in aqueous ethanol and dioxane solutions. Establishment of a hydrophobicity scale. J Biol Chem 246(7):2211–2217PubMedGoogle Scholar
  22. Oosawa F, Asakura S (1975) Thermodynamics of the polymerization of protein. Academic Press, New YorkGoogle Scholar
  23. Oosawa F, Kasai M (1962) A theory of linear and helical aggregations of macromolecules. J Mol Biol 4:10–21CrossRefPubMedGoogle Scholar
  24. Schön A, Clarkson BR, Jaime M, Freire E (2017) Temperature stability of proteins: analysis of irreversible denaturation using isothermal calorimetry. Proteins 85(11):2009–2016CrossRefPubMedPubMedCentralGoogle Scholar
  25. Shiraki K, Kudou M, Fujiwara S, Imanaka T, Takagi M (2002) Biophysical effect of amino acids on the prevention of protein aggregation. J Biochem 132(4):591–595CrossRefPubMedGoogle Scholar
  26. Sutherland JW, Sturtevant JM (1976) Calorimetric studies of the in vitro polymerization of brain tubulin. Proc Natl Acad Sci U S A 73(10):3565–3569CrossRefPubMedPubMedCentralGoogle Scholar
  27. Tanford C (1997) How protein chemists learned about the hydrophobic factor. Protein Sci 6(6):1358–1366CrossRefPubMedPubMedCentralGoogle Scholar
  28. Trevino SR, Scholtz JM, Pace CN (2007) Amino acid contribution to protein solubility: Asp, Glu, and Ser contribute more favorably than the other hydrophilic amino acids in RNase Sa. J Mol Biol 366(2):449–460CrossRefPubMedGoogle Scholar
  29. Trevino SR, Scholtz JM, Pace CN (2008) Measuring and increasing protein solubility. J Pharm Sci 97(10):4155–4166CrossRefPubMedGoogle Scholar
  30. Wolfenden R, Andersson L, Cullis PM, Southgate CCB (1981) Affinities of amino acid side chains for solvent water. Biochemistry 20:849–855CrossRefPubMedGoogle Scholar
  31. Xue WF (2015) Nucleation: the birth of a new protein phase. Biophys J 109(10):1999–2000CrossRefPubMedPubMedCentralGoogle Scholar
  32. Zimmerman SB, Minton AP (1993) Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu Rev Biophys Biomol Struct 22:27–65CrossRefPubMedGoogle Scholar

Copyright information

© International Union for Pure and Applied Biophysics (IUPAB) and Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Department of Biotechnology and Life Sciences, Graduate School of EngineeringTokyo University of Agriculture and TechnologyKoganei-shiJapan

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