The Amino Acid Sequences of Proteins Determine Folding and Non-folding

  • Richard Dods


This chapter (The Amino Acid Sequences of Proteins Determine Folding and Non-folding) continues where Chap.  1 left off. Amino acid sequences determine the folded structure of proteins. The manner in which the protein folds is visualized by an energy landscape called a protein folding funnel. This chapter describes the funnel and how it relates to three-dimensional protein structure. This chapter describes the spin glass theory which also visualizes protein folding. Regions of amino acids called foldons are described. The 20 amino acid building blocks of proteins are enumerated in this chapter. The ice-like blanket that surrounds a protein and its effects on folding are described in this chapter. Other forces that stabilize the folded structure are described. This chapter defines and describes intrinsically disordered proteins (IDP) and intrinsically disordered protein regions (IDPR) and their functions. Effects of hypoxia on protein structure are discussed. Scaffolding and hubs are described.




refers to proliferation of blood vessels.

Energy landscape

corresponds to all possible conformations of a protein i.e. all spatial positions of the protein molecule and therefore all its Gibbs free energies.


refers to protein function due to a random coil.


are protein regions that are folded.

Hub proteins

are proteins (at least ten) that bind each other.

Hydrophobic (hydropathy)

refers to avoidance of water.

Hydrophobic collapse

is a process in which newly synthesized proteins form secondary structure (α-helix and β-pleated) in regions of hydrophobicity. These protein regions then “collapse” (aggregate) by arranging the hydrophobic amino acids, so that their side chains face toward the interior of the molecule, thus creating tertiary conformation.


refers to lack of oxygen.

Intrinsically disordered proteins or regions

are proteins or regions of proteins that have a random coil conformation and do not have a three-dimensional folded structure.

Molten globules

are partially folded proteins that have a compact protein interior and have some secondary structure but lack tertiary structure. They can be isolated under moderately denaturing conditions and are separate from the native state by having a higher free energy.


refers to overlapping protein domains where other proteins bind.

Native state

of a protein is when the protein is in its lowest energy state and exhibits its natural functions.

Posttranslational modification

refers to chemical changes that occur to amino acids after they have come off the ribosomes as a polypeptide.

Pre-molten globule (early molten globule)

is an intermediate between the molten protein and the native protein. The protein is partially folded. Compactness is developing in the interior of the molecule. It may have some secondary structure, and has incomplete tertiary structure. It may be isolated.

Principle of minimal frustration

states that proteins have domains that avoid valleys that tend to fold to a lower Gibbs energy conformation.

Protein folding funnels

is the current hypothesis as to how a protein folds. Its width is the entropy (highest at the top, lowest at the bottom). The top of the funnel has the highest Gibbs free energy and the bottom the lowest Gibbs free energy. It has an infinite number of conformations at the top and the native conformation resides at the bottom. The sides of the funnel have “valleys” that trap certain conformations. The “smoother” the sides of the funnel the faster the native conformation is reached.

Random coil (loops)

is a protein conformation in which the amino acid sequence does not have a specific, rigid, geometric shape. Rather the amino acid sequence of a random coil is randomly orientated in all possible conformations. Random coils are detected by circular dichroism and nuclear magnetic resonance but not by X-ray diffraction. X-ray diffraction yields results only for rigid (ordered) portions of proteins.

Scaffold proteins

bind two or more other proteins.

Secondary structure

refers to two structures in a protein, α-helix and β-pleated sheets (further described in Chap.  2).

Site-directed mutagenesis

is replacing one amino acid by another using genetic engineering.

Steric hindrance

refers to repulsions by side chains of amino acids. There is much less steric hindrance in intrinsic disordered region than in ordered regions.

Tertiary structure

refers to the overall shape of a protein. The α-helixes, β-pleated sheets, and random coils in the protein fold themselves to form the overall shape, tertiary structure of the protein (further described in Chap.  3).

Theory of spin glasses

is applicable to folding of proteins. Spin glasses are a class of magnetic alloys that below a critical temperature have energy valleys separated by energy barriers and other characteristics similar to those found in the protein folding funnel hypothesis.


refers to binding of ubiquitin to a protein for its destruction.

Further Reading

  1. Levinthal C (1968) Are there pathways for protein foldin? Extrait J Chim Phys 65:44CrossRefGoogle Scholar
  2. Dill KA, MacCallum JL (2012) The protein-folding problem, 50 years on. Science 338:1042CrossRefGoogle Scholar
  3. Leopard PE, Montal M, Onuchic JN. (1992)Protein folding funnels: A kinetic approach to the sequence-structure relationship. PNAS: 89:8721.CrossRefGoogle Scholar
  4. Bryngelson JD, Onuchic JN, Socci ND, et al. (1995) Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins:21:167.CrossRefGoogle Scholar
  5. Kauzmann W (1959) Some factors in the interpretation of protein denaturation. Adv Protein Chem: 14:1.CrossRefGoogle Scholar
  6. Fersht A (1999) Structure and mechanism in protein science: A guide to enzyme catalysis and protein folding. WH Freeman and Co. New York, NY: Chap. 19, p 598.Google Scholar
  7. Stein DL (1985) A model of protein conformational substates. PNAS 82:3670.CrossRefGoogle Scholar
  8. Wolynes PG, Onuchic JN, Thirumalai D (1995) Navigating the folding routes. Science 267:1619.CrossRefGoogle Scholar
  9. Bryngelson JD, Wolynes PG (1987) Spin glasses and the statistical mechanics of protein folding. PNAS 84:7524.CrossRefGoogle Scholar
  10. Goldstein RA, Luthey-Schulten, Wolynes PG (1992) Optimal protein-folding codes from spin-glass theory. PNAS 89:4918.CrossRefGoogle Scholar
  11. Maity H, Maity M, Krishna M, et al (2005) Protein folding: The stepwise assembly of foldon units. PNAS 102:4741.CrossRefGoogle Scholar
  12. Panchenko AR, Luthery-Schulten Z, Wolynes PG (1996) Foldons, protein structural modules, and exons. PNAS 93:2008CrossRefGoogle Scholar
  13. Stadtman TC (1996) Selenocysteine. Annu. Rev. Bio 65: 83. doi: Scholar
  14. Zinoni F, Birkmann A, Stadtman, TC, et al (1986) Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli. PNAS 83: 4650.CrossRefGoogle Scholar
  15. Ibba M, Söll D. (2002) Genetic code: Introducing pyrrolysine. Curr Bio 12:R464.CrossRefGoogle Scholar
  16. Lesser GJ, Rose GD (1990) Hydrophobicity of amino acid subgroups in proteins. Proteins 8:6.CrossRefGoogle Scholar
  17. Pace CN, Fu H, Fryar KL, et al (2011) Contribution of hydrophobic interactions to protein stability. J Mol Biol 408:514CrossRefGoogle Scholar
  18. Pace CN, Scholtz JM, Grimsley GR (2014) Forces stabilizing proteins. FEBS Lett. 588:2177.CrossRefGoogle Scholar
  19. Newberry RW, Barlett GJ, VanVeller B, et al. (2014). Signatures of n➔π interactions in proteins. Protein Sci: 23:284. doi: Scholar
  20. Bartlett GJ, Newberry RW, VanVeller B, et al. (2013) Interplay of hydrogen bonds and n➔ π∗ interactions in proteins. J Am Chem Soc: 135:18688. doi: Scholar
  21. Newberry RW, Raines RT(2016) A prevalent intraresidue hydrogen bond stabilizes proteins Nat Chem Bio 12:1084.CrossRefGoogle Scholar
  22. Baker EG, Williams C, Hudson KL, et al. (2017) Engineering protein stability with atomic precision in a monomeric miniprotein. Nat Chem Bio: 2017: Published Online May 22.Google Scholar
  23. Sippel KH, Quiocho FA (2015) Ion-dipole interactions and their functions in proteins. Protein Science 24:1040.CrossRefGoogle Scholar
  24. Necci M, Piovesan D, Tosatto S. (2016) Large-scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe. Protein Sci: 25:2164.CrossRefGoogle Scholar
  25. Uversky VN, Gillespie JR, Fink AL. (2000) Why are “natively unfolded” proteins unstructured under physiologic conditions? Proteins: 41:415.CrossRefGoogle Scholar
  26. Kyle J, Doolittle RF. (1982) A simple method for displaying the hydropathic character of a protein. J Mol Biol: 157:105.CrossRefGoogle Scholar
  27. Guy HR. (1985) Amino acid side-chain partition energies and distribution of residues in soluble proteins. Biophys J: 47:61.CrossRefGoogle Scholar
  28. Prilusky J, Felder CE, Zeev-Ben-Mordehai, et al. (2005) Foldindex©: a simple tool to predict whether a given protein sequence is intrinsically unfolded. Bioinformatics:21:3435.CrossRefGoogle Scholar
  29. Chothia C. (1976) The nature of the accessible and buried surfaces in proteins. J Mol Biol: 105:1.CrossRefGoogle Scholar
  30. Williams RM, Braun VM, Garner EC. (2001)The protein non-folding problem: Amino acid determinants of intrinsic order and disorder. Pac Symp Biocomput: 6:89.Google Scholar
  31. Campen A, Williams RM, Brown CJ, et al. (2008) TOP-IDP-Scale: A new amino acid scale measuring propensity for intrinsic disorder. Protein Pept Lett: 15:956.CrossRefGoogle Scholar
  32. Radivojac P, Obradovic Z, Smith DK, et al. (2004) Protein flexibility and intrinsic disorder. Protein Sci: 13:71.CrossRefGoogle Scholar
  33. Rhodes G (2006) Crystallography made crystal clear: A guide for users of macromolecular models. 3rd ed pp. 257, 267, 281. Academic Press. San Diego, CA.CrossRefGoogle Scholar
  34. Huang F, Oldfield CJ, Xue B, et al. (2014) Improving protein order-disorder classification using charge-hydropathy plots. Bioinformatics: 15 (suppl 17):54.Google Scholar
  35. Dods R. (2013) Chapter 7. Diagnosis of diabetes mellitus. In: Understanding diabetes: a biochemical perspective. Wiley, Hoboken, NJ.CrossRefGoogle Scholar
  36. Van der Lee R, Buljan M, Lang B, et al. (2014) Classification of intrinsically disordered regions and proteins. Chem Rev: 114:6589. Doi: Scholar
  37. Dyson HJ. (2016) Making sense of intrinsically disordered. Biophys J: 110:1013.CrossRefGoogle Scholar
  38. Forman-Kay JD, Mittag T. (2013) From sequence and forces to structure, function and evolution of intrinsically disordered proteins. Stucture: 21:1492. Doi: Scholar
  39. Lando D, Peet DJ, Gorman JJ, et al. (2002) FIH-1 is an asparaginyl hydroxylase enzyme that regulates the transcriptional activity of hypoxia-inducible factor. Genes Dev: 16:1466.CrossRefGoogle Scholar
  40. Berlow RB, Dyson J, Wright PE. (2017) Hypersensitive termination of the hypoxic response by a disordered protein switch. Nature: 543:447.CrossRefGoogle Scholar
  41. Krock BL, Skuli N, Simon MC. (2011) Hypoxia-induced angiogenesis: Good and evil. Genes & Cancer:2:1117.CrossRefGoogle Scholar
  42. Masoud GN, Li Wei. (2015) HIF-1α pathway: role, regulation and intervention for cancer therapy. Acta Pharm Sinica B: 5:378. doi: Scholar
  43. Lee S, Kwon OS, Lee C-S, et al. (2017) Synthesis and biological evaluation of kresoxim-methyl analogues as novel inhibitors of hypoxia-inducible factor (HIF-1) accumulation in cancer cells. Bioorganic & Medicinal Chem Lett: 27:3026.CrossRefGoogle Scholar
  44. Kapur S, Silverman AP, Ye AZ, et al. (2016) Engineering ligand-based VEGFR antagonists with increased receptor binding affinity more effectively inhibit angiogenesis. Bioengineering & Translational Med: 2:81.Doi: Scholar
  45. Kim DM, Nimigean CM. (2016) Voltage-gated potassium channels: A structural examination of selectivity and gating. Cold Spring Harbor perspectives in biology. Online: Accessed 18 Jun 2017. Doi: Scholar
  46. Hoshi T, Zagotta WN, Aldrich RW. (1990) Biophysical and molecular mechanisms of Shaker potassium channel inactivation. Science: 250:533. Doi: Scholar
  47. Zagoota WN, Hoshi T, Aldrich RW. (1990) Restoration of inactivation in mutants of Shaker potassium channels by a peptide derived from ShB. Science: 250:568. Doi: Scholar
  48. Uversky VN, Dunker AK. (2010). Understanding protein non-folding. Biochim Biophys Acta: 1804:1231. Doi: Scholar
  49. Van der Lee R, Buljan M, Lang B, et al.(2014) Classification of intrinsically disordered regions and proteins. Chem Rev 114:6589. Doi: Scholar
  50. Dunker AK, Lawson JD, Brown CJ, et al. (2001) Intrinsically disordered protein. J Mol Graphics Modelling: 19:26. Doi: Scholar
  51. Dunker AK, Brown CJ, Lawson JD, et al. (2002) Intrinsic disorder and protein function. Biochemistry: 41:6573. Doi: Scholar
  52. Uversky VN. (2013) A decade and a half of protein intrinsic disorder: Biology still waits for physics. Protein Science: 22:693. Doi: Scholar
  53. Dods R. (2013) Chapter 4. Diagnosis of diabetes mellitus. In: Understanding diabetes: a biochemical perspective. Wiley, Hoboken, NJ.CrossRefGoogle Scholar
  54. Ekman D, Light S, Björklund A, et al. (2006). What properties characterize the hub proteins of the protein-protein interaction of saccharomyces cerevisiae? Genome Biology: 7:R45. doi: Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Richard Dods
    • 1
  1. 1.Illinois Mathematics and Science AcademyPalatineUSA

Personalised recommendations