Literature DB >> 23897064

Network model of a protein globule.

E Z Meilikhov1, R M Farzetdinova.   

Abstract

Phase transition of a protein globule is considered in the frameworks of (i) the generalized mean-field theory for the order parameter, characterizing the extent of the deviation of a protein three-dimensional structure from its native state and (ii) the network model that treats a protein globule as a small-world network with a significant percent of long-range links between amino acid residues. Temperature dependencies of the introduced order parameter are defined and phase-transition temperatures are found on the basis of the function defining the distribution of links' numbers for protein residues. An important role of long-range links, promoting considerable rise of thermal protein stability, is demonstrated by the example of a correlation between protein melting temperature and a fraction of disulfide bonds.

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Year:  2013        PMID: 23897064      PMCID: PMC3758824          DOI: 10.1007/s10867-013-9326-8

Source DB:  PubMed          Journal:  J Biol Phys        ISSN: 0092-0606            Impact factor:   1.365


  21 in total

1.  Small-world communication of residues and significance for protein dynamics.

Authors:  Ali Rana Atilgan; Pelin Akan; Canan Baysal
Journal:  Biophys J       Date:  2004-01       Impact factor: 4.033

2.  Ising model in small-world networks.

Authors:  Carlos P Herrero
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2002-06-18

3.  Announcing the worldwide Protein Data Bank.

Authors:  Helen Berman; Kim Henrick; Haruki Nakamura
Journal:  Nat Struct Biol       Date:  2003-12

Review 4.  Network biology: understanding the cell's functional organization.

Authors:  Albert-László Barabási; Zoltán N Oltvai
Journal:  Nat Rev Genet       Date:  2004-02       Impact factor: 53.242

5.  Exact solution of Ising model on a small-world network.

Authors:  J Viana Lopes; Yu G Pogorelov; J M B Lopes dos Santos; R Toral
Journal:  Phys Rev E Stat Nonlin Soft Matter Phys       Date:  2004-08-25

Review 6.  Network-based models as tools hinting at nonevident protein functionality.

Authors:  Canan Atilgan; Osman Burak Okan; Ali Rana Atilgan
Journal:  Annu Rev Biophys       Date:  2012-02-23       Impact factor: 12.981

7.  Native proteins are surface-molten solids: application of the Lindemann criterion for the solid versus liquid state.

Authors:  Y Zhou; D Vitkup; M Karplus
Journal:  J Mol Biol       Date:  1999-01-29       Impact factor: 5.469

8.  Contact order, transition state placement and the refolding rates of single domain proteins.

Authors:  K W Plaxco; K T Simons; D Baker
Journal:  J Mol Biol       Date:  1998-04-10       Impact factor: 5.469

Review 9.  Stability of proteins. Proteins which do not present a single cooperative system.

Authors:  P L Privalov
Journal:  Adv Protein Chem       Date:  1982

10.  Spin glasses and the statistical mechanics of protein folding.

Authors:  J D Bryngelson; P G Wolynes
Journal:  Proc Natl Acad Sci U S A       Date:  1987-11       Impact factor: 11.205

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