DOI: 10.1110/ps.04881304. To be folded or to be unfolded?

10.1110/ps.04881304

Crossref journal-article

Wiley

Protein Science (311)

Abstract

AbstractThe lack of ordered structure in “natively unfolded” proteins raises a general question: Are there intrinsic properties of amino acid residues that are responsible for the absence of fixed structure at physiological conditions? In this article, we demonstrate that the competence of a protein to be folded or to be unfolded may be determined by the property of amino acid residues to form a sufficient number of contacts in a globular state. The expected average number of contacts per residue calculated from the amino acid sequence alone (using the average number of contacts for 20 amino acid residues in globular proteins) can be used as one of the simple indicators of natively unfolded proteins. The prediction accuracy for the sets of 80 folded and 90 natively unfolded proteins reaches 89% if the expected average number of contacts is used as a parameter and 83% in the case of hydrophobicity. An optimal set of artificial parameters for 20 amino acid residues obtained by Monte Carlo algorithm to maximally separate the sets of 90 natively unfolded and 80 folded proteins demonstrates the upper limit for prediction accuracy, which is 95%.

Bibliography

Garbuzynskiy, S. O., Lobanov, M. Yu., & Galzitskaya, O. V. (2004). To be folded or to be unfolded? Protein Science, 13(11), 2871â2877. Portico.

Authors 3

Sergiy O. Garbuzynskiy (first)
Michail Yu. Lobanov (additional)
Oxana V. Galzitskaya (additional)

References 17 Referenced 64

10.1093/nar/28.1.45
10.1111/j.1432-1033.1977.tb11885.x
{'key': 'e_1_2_7_4_1', 'first-page': '473', 'article-title': 'Protein disorder and the evolution of molecular recognition: Theory, predictions and observations', 'author': 'Dunker A.K.', 'year': '1998', 'journal-title': 'Pac. Symp. Biocomput.'} / Pac. Symp. Biocomput. / Protein disorder and the evolution of molecular recognition: Theory, predictions and observations by Dunker A.K. (1998)
10.1016/S0065-3233(02)62012-1
{'key': 'e_1_2_7_6_1', 'first-page': '369', 'article-title': 'Hydrophobic parameters amino‐acid side chains from partitioning of N‐acetyl‐amino‐acid amides', 'volume': '18', 'author': 'Fauchere I.I.', 'year': '1983', 'journal-title': 'Eur. J. Med. Chem.‐Chim. Ther.'} / Eur. J. Med. Chem.‐Chim. Ther. / Hydrophobic parameters amino‐acid side chains from partitioning of N‐acetyl‐amino‐acid amides by Fauchere I.I. (1983)
10.1110/ps.9.3.580
10.1016/0022-2836(82)90515-0
10.1016/S0022-2836(05)80134-2
10.1002/prot.10532
10.1110/ps.03128904
{'key': 'e_1_2_7_12_1', 'first-page': '437', 'article-title': 'Thousands of proteins likely to have long disordered regions', 'author': 'Romero P.', 'year': '1998', 'journal-title': 'Pac. Symp. Biocomput.'} / Pac. Symp. Biocomput. / Thousands of proteins likely to have long disordered regions by Romero P. (1998)
10.1016/S0014-5793(99)01557-4
10.1046/j.0014-2956.2001.02649.x
10.1002/1097-0134(20001115)41:3<415::AID-PROT130>3.0.CO;2-7
10.1002/prot.10437
10.1016/0097-8485(94)85023-2
10.1006/jmbi.1999.3110

Dates

Type	When
Created	20 years, 10 months ago (Oct. 21, 2004, 1:28 p.m.)
Deposited	1 year, 10 months ago (Oct. 12, 2023, 4:36 p.m.)
Indexed	2 months ago (July 2, 2025, 2:32 p.m.)
Issued	20 years, 10 months ago (Nov. 1, 2004)
Published	20 years, 10 months ago (Nov. 1, 2004)
Published Online	16 years, 8 months ago (Dec. 29, 2008)
Published Print	20 years, 10 months ago (Nov. 1, 2004)

Funders 0

None

BibTeX

@article{Garbuzynskiy_2004, title={To be folded or to be unfolded?}, volume={13}, ISSN={1469-896X}, url={http://dx.doi.org/10.1110/ps.04881304}, DOI={10.1110/ps.04881304}, number={11}, journal={Protein Science}, publisher={Wiley}, author={Garbuzynskiy, Sergiy O. and Lobanov, Michail Yu. and Galzitskaya, Oxana V.}, year={2004}, month=nov, pages={2871–2877} }

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