Structural and Functional Analysis of Hemoglobin and Serum Albumin Through Protein Long-Range Interaction Networks

Long-range contacts in protein structures were demonstrated to be predictive of different physiological properties of hemoglobin and albumin proteins. Complex networks based approach was demonstrated to highlight ba- sic principles of protein folding and activity. The presence of a natural scaling region ending at an approximate thresh- old of 120-150 residues shared by proteins of different size and quaternary structure was highlighted. This threshold is reminiscent of the typical size for a macromolecule to have a binding site sensible to environmental regulation.

[1]  C. Anfinsen Principles that govern the folding of protein chains. , 1973, Science.

[2]  N. Go,et al.  Studies on protein folding, unfolding and fluctuations by computer simulation. I. The effect of specific amino acid sequence represented by specific inter-unit interactions. , 2009 .

[3]  M G Rossmann,et al.  The NADPH binding site on beef liver catalase. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[4]  P. Privalov,et al.  Intermediate states in protein folding. , 1996, Journal of molecular biology.

[5]  E. Shakhnovich Theoretical studies of protein-folding thermodynamics and kinetics. , 1997, Current opinion in structural biology.

[6]  A. Fersht Nucleation mechanisms in protein folding. , 1997, Current opinion in structural biology.

[7]  A. Poupon,et al.  Populations of hydrophobic amino acids within protein globular domains: Identification of conserved “topohydrophobic” positions , 1998, Proteins.

[8]  D. Baker,et al.  Contact order, transition state placement and the refolding rates of single domain proteins. , 1998, Journal of molecular biology.

[9]  M Karplus,et al.  The fundamentals of protein folding: bringing together theory and experiment. , 1999, Current opinion in structural biology.

[10]  D. Baker,et al.  A surprising simplicity to protein folding , 2000, Nature.

[11]  Lorna J. Smith,et al.  Understanding protein folding via free-energy surfaces from theory and experiment. , 2000, Trends in biochemical sciences.

[12]  M. Karplus,et al.  Three key residues form a critical contact network in a protein folding transition state , 2001, Nature.

[13]  M. Gromiha,et al.  Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. , 2001, Journal of molecular biology.

[14]  M Karplus,et al.  Small-world view of the amino acids that play a key role in protein folding. , 2002, Physical review. E, Statistical, nonlinear, and soft matter physics.

[15]  M E J Newman Assortative mixing in networks. , 2002, Physical review letters.

[16]  Gürol M. Süel,et al.  Evolutionarily conserved networks of residues mediate allosteric communication in proteins , 2003, Nature Structural Biology.

[17]  C. Dobson Protein folding and misfolding , 2003, Nature.

[18]  Victoria A. Higman,et al.  Uncovering network systems within protein structures. , 2003, Journal of molecular biology.

[19]  M. Michael Gromiha,et al.  Importance of Native-State Topology for Determining the Folding Rate of Two-State Proteins , 2003, J. Chem. Inf. Comput. Sci..

[20]  Christopher M Dobson,et al.  Principles of protein folding, misfolding and aggregation. , 2004, Seminars in cell & developmental biology.

[21]  M Michael Gromiha,et al.  Inter-residue interactions in protein folding and stability. , 2004, Progress in biophysics and molecular biology.

[22]  J. Ferry,et al.  Structural and Kinetic Analyses of Arginine Residues in the Active Site of the Acetate Kinase from Methanosarcina thermophila* , 2005, Journal of Biological Chemistry.

[23]  S. Vishveshwara,et al.  A network representation of protein structures: implications for protein stability. , 2005, Biophysical journal.

[24]  Alessandro Giuliani,et al.  A topologically related singularity suggests a maximum preferred size for protein domains , 2006, Proteins.

[25]  M. Brunori,et al.  Identification and characterization of protein folding intermediates. , 2007, Biophysical chemistry.

[26]  Ganesh Bagler,et al.  Assortative mixing in Protein Contact Networks and protein folding kinetics , 2007, Bioinform..

[27]  P Fariselli,et al.  The effect of backbone on the small-world properties of protein contact maps , 2008, Physical biology.

[28]  Ozlem Keskin,et al.  Topological properties of protein interaction networks from a structural perspective. , 2008, Biochemical Society transactions.

[29]  M. Michael Gromiha,et al.  Multiple Contact Network Is a Key Determinant to Protein Folding Rates , 2009, J. Chem. Inf. Model..

[30]  Alessandro Giuliani,et al.  Proteins as Networks: A Mesoscopic Approach Using Haemoglobin Molecule as Case Study , 2009 .

[31]  Md. Aftabuddin,et al.  AMINONET-A TOOL TO CONSTRUCT AND VISUALIZE AMINO ACID NETWORKS, AND TO CALCULATE TOPOLOGICAL PARAMETERS , 2010 .

[32]  Mark Newman,et al.  Networks: An Introduction , 2010 .

[33]  Daniele Santoni,et al.  Shedding light on protein-ligand binding by graph theory: the topological nature of allostery. , 2012, Biophysical chemistry.

[34]  Daniele Santoni,et al.  Proteins as Sponges: A Statistical Journey along Protein Structure Organization Principles , 2012, J. Chem. Inf. Model..