Dissimilar sequence: similar structure of proteins
-
Mateusz Banach
Abstract
Sequence-to-structure relation is one of the major objects of the analysis of protein folding problem. The pair of two small proteins (domains) of similar structure (β-hairpin/α-helix/β-hairpin) generated by the chains of similar length (about 60 amino acids) with very low sequence similarity (15%) is the object of the comparable analysis of 3D structure. The criterion for similarity estimation is the status of polypeptide chain with respect to the hydrophobic core structure. The fuzzy oil drop model is applied to reveal the differentiated status of fragments of the well-defined secondary structure. This analysis allows the interpretation of the structure in other than the geometric form as it is made based on secondary structure classification. The two compared highly similar proteins appear to be different with respect to the hydrophobic core structure.
Acknowledgements
Many thanks to Anan Śmietańska for technical support.
Author contributions: All the authors have accepted responsibility for the entire content of this submitted manuscript and approved submission.
Research funding: The work was financially supported by Collegium Medicum grant system K/ZDS/006363.
Employment or leadership: None declared.
Honorarium: None declared.
Competing interests: The funding organization(s) played no role in the study design; in the collection, analysis, and interpretation of data; in the writing of the report; or in the decision to submit the report for publication.
References
1. Dill KA, MacCallum JL. The protein-folding problem, 50 years on. Science 2012;338:1042–6.10.1126/science.1219021Suche in Google Scholar
2. Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP) – round x. Proteins 2014;82:1–6.10.1002/prot.24452Suche in Google Scholar
3. Allison JR, Bergeler M, Hansen N, van Gunsteren WF. Current computer modeling cannot explain why two highly similar sequences fold into different structures. Biochemistry 2011;50:10965–73.10.1021/bi2015663Suche in Google Scholar
4. Khoury GA, Liwo A, Khatib F, Zhou H, Chopra G, Bacardit J, et al. WeFold: a coopetition for protein structure prediction. Proteins 2014;82:1850–68.10.1002/prot.24538Suche in Google Scholar
5. Konieczny L, Bryliński M, Roterman I. Gauss-function-based model of hydrophobicity density in proteins. In Silico Biol 2006;6:15–22.10.3233/ISB-00217Suche in Google Scholar
6. Gallagher T, Alexander P, Bryan P, Gilliland GL. Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR. Biochemistry 1994;33:4721–9.10.1021/bi00181a032Suche in Google Scholar
7. O’Neill JW, Kim DE, Baker D, Zhang KY. Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution. Acta Crystallogr D Biol Crystallogr 2001;57:480–7.10.1107/S0907444901000373Suche in Google Scholar
8. Levitt MA. A simplified representation of protein conformations for rapid simulation of protein folding. J Mol Biol 1976;104:59–107.10.1016/0022-2836(76)90004-8Suche in Google Scholar
9. Kullback S, Leibler RA. On information and sufficiency. Ann Math Stat 1951;22:79–86.10.1214/aoms/1177729694Suche in Google Scholar
10. Kalinowska B, Banach M, Konieczny L, Roterman I. Application of divergence entropy to characterize the structure of the hydrophobic core in DNA interacting proteins. Entropy 2015;17:1477–507.10.3390/e17031477Suche in Google Scholar
11. Kalinowska B, Banach M, Konieczny L, Marchewka D, Roterman I. Intrinsically disordered proteins – relation to general model expressing the active role of the water environment. Adv Protein Chem Struct Biol 2014;94:315–46.10.1016/B978-0-12-800168-4.00008-1Suche in Google Scholar PubMed
12. Banach M, Konieczny L, Roterman I. The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function. J Theor Biol 2014;359:6–17.10.1016/j.jtbi.2014.05.007Suche in Google Scholar PubMed
13. Banach M, Prudhomme N, Carpentier M, Duprat E, Papandreou N, Kalinowska B, et al. Contribution to the prediction of the fold code: application to immunoglobulin and flavodoxin cases. PLoS One 2015;10:e0125098.10.1371/journal.pone.0125098Suche in Google Scholar PubMed PubMed Central
14. Banach M, Kalinowska B, Konieczny L, Roterman I. Role of disulfide bonds in stabilizing the conformation of selected enzymes – an approach based on divergence entropy applied to the structure of hydrophobic core in proteins. Entropy 2016;18:67.10.3390/e18030067Suche in Google Scholar
©2016 Walter de Gruyter GmbH, Berlin/Boston
Artikel in diesem Heft
- Frontmatter
- Review
- Cognitive robots in the development and rehabilitation of children with developmental disorders
- Opinion Paper
- Fuzzy-based computational simulations of brain functions – preliminary concept
- Original Articles
- Usefulness of the measurement of saccadic refixation in the diagnosis of attention-deficit hyperactivity disorder/hyperkinetic disorder in adults
- Computer-aided analysis of data from evaluation sheets of subjects with autism spectrum disorders
- Dissimilar sequence: similar structure of proteins
- Shortening and dispersion of single-walled carbon nanotubes upon interaction with mixed supramolecular compounds
- Oblique-viewing endoscope calibration in the diagnostics and treatment in the pelvis minor area
- Short Communication
- Molecular models of human visual pigments: insight into the atomic bases of spectral tuning
Artikel in diesem Heft
- Frontmatter
- Review
- Cognitive robots in the development and rehabilitation of children with developmental disorders
- Opinion Paper
- Fuzzy-based computational simulations of brain functions – preliminary concept
- Original Articles
- Usefulness of the measurement of saccadic refixation in the diagnosis of attention-deficit hyperactivity disorder/hyperkinetic disorder in adults
- Computer-aided analysis of data from evaluation sheets of subjects with autism spectrum disorders
- Dissimilar sequence: similar structure of proteins
- Shortening and dispersion of single-walled carbon nanotubes upon interaction with mixed supramolecular compounds
- Oblique-viewing endoscope calibration in the diagnostics and treatment in the pelvis minor area
- Short Communication
- Molecular models of human visual pigments: insight into the atomic bases of spectral tuning
