Abstract
Proteins are important biomolecules, which perform diverse structural and functional roles in living systems. Starting from a linear chain of amino acids, proteins fold to different secondary structures, which then fold through short- and long-range interactions to give rise to the final three-dimensional shapes useful to carry out the biophysical and biochemical functions. Proteins are defined as having a common ‘fold’ if they have major secondary structural elements with same topological connections. It is known that folding mechanisms are largely determined by a protein’s topology rather than its interatomic interactions. The native state protein structures can, thus, be modelled, using a graph-theoretical approach, as coarse-grained networks of amino acid residues as ‘nodes’ and the inter-residue interactions/contacts as ‘links’. Using the network representation of protein structures and their 2D contact maps, we have identified the conserved contact patterns (groups of contacts) representing two typical folds — the EF-hand and the ubiquitin-like folds. Our results suggest that this direct and computationally simple methodology can be used to infer about the presence of specific folds from the protein’s contact map alone.
Similar content being viewed by others
References
L H Greene and V A Higman, J. Mol. Biol. 334, 781 (2003)
N Kannan and S Vishveshwara, J. Mol. Biol. 292, 441 (1999)
K V Brinda and S Vishveshwara, Biophys. J. 89, 4159 (2005)
K V Brinda and S Vishveshwara, Biophys. J. 92, 2523 (2007)
Md. Aftabuddina and S Kundu, Physica A396, 896 (2006)
M Vendruscolo, N V Dokholyan, E Paci and M Karplus, Phys. Rev. E65, 061910 (2002)
U K Muppirala and Zhijun Li, Protein Engineering, Design & Selection 19, 265 (2006)
G Bagler and Somdatta Sinha, Physica A346, 27 (2005)
G Bagler and Somdatta Sinha, Bioinformatics 23, 1760 (2007)
N S Shiju Lal and Somdatta Sinha, Proceedings of the 11th ADNAT Convention on Advances in Structural Biology and Structure Prediction 134 (2007)
Murzin et al, J. Mol. Biol. 247, 536 (1995)
G Pollastri and P Baldi, Bioinformatics 18, S62 (2002)
D R Westhead, D C Hatton and J M Thornton, Trends in Biochem. Sci. 23, 35 (1998)
A Godzik, J Skolnick and A Kolinski, J. Mol. Biol. 227, 227 (1999)
J Selbig and P Argos, Proteins: Struct. Funct. Genet. 31, 172 (1998)
A M Lesk, L L Conte and T J P Hubbard, Proteins 45(S5), 98 (2001)
A R Ortiz, A Kolinski, P Rotkiewiez and J Skolnick, Proteins Suppl. 3, 177 (1999)
Bernstein et al, J. Mol. Biol. 112, 535 (1977)
H M Berman, J Westbrook, Z Feng, G Gilliland, T N Bhat, H Weissig, I N Shindyalov and P E Bourne, Nucleic Acids Res. 28, 235 (2000)
W L DeLano, The PyMOL Molecular Graphics System (2002), www.pymol.org
The MathWorks, Inc. (www.mathworks.com/)
V Batagelj and A Mrvar, in Graph drawing software edited by M Jünger and P Mutzel (Springer, Berlin, 2003) p. 77
C Rao-Naik, W delaCruz, J M Laplaza, S Tan, J Callis and A J Fisher, J. Biol. Chem. 273, 34976 (1998)
A Buchberger, M J Howard, M Proctor and M Bycroft, J. Mol. Biol. 307, 17 (2001)
W Gronwald, F Huber, P Grunewald, M Sporner, S Wohlgemuth, C Herrmann and H R Kalbitzer, Structure 9, 1029 (2001)
J L Enmon, T de Beer and M Overduin, Biochemistry 39, 4309 (2000)
S Kim, D N Cullis, L A Feig and J D Baleja, Biochemistry 40, 6776 (2001)
M Andersson, A Malmendal, S Linse, I Ivarsson, S Forsen and L A Svensson, Protein Sci. 6, 1139 (1997)
J P Declercq, C Evrard, V Lamzin and J Parello, Protein Sci. 8, 2194 (1999)
S Nakayama, N D Moncrief and R H Kretsinger, J. Mol. Evol. 34, 416 (1992)
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Barah, P., Sinha, S. Analysis of protein folds using protein contact networks. Pramana - J Phys 71, 369–378 (2008). https://doi.org/10.1007/s12043-008-0170-5
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12043-008-0170-5