Erratum: Signal propagation in proteins and relation to equilibrium fluctuations (PLoS Computational Biology (2007) 3, 9, (e172) DOI: 10.1371/journal.pcbi.0030172));Signal propagation in proteins and relation to equilibrium fluctuations

PLoS Computational Biology

Volumn 3, Issue 9, 2007, Pages 1716-1726

  Chennubhotla, Chakra ^a   Bahar, Ivet ^a  

^a UNIVERSITY OF PITTSBURGH SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INFORMATION THEORY; MARKOV PROCESSES; NETWORK ARCHITECTURE; SIGNAL TRANSDUCTION;

BIOLOGICAL FUNCTIONS; COMMUNICATION MECHANISMS; COMPUTATIONAL BIOLOGY; DISCRETE TIME; ELASTIC NETWORK MODELS; EQUILIBRIUM FLUCTUATION; NATIVE STRUCTURES; PROTEIN DYNAMICS; SIGNAL PROPAGATION; STOCHASTICS;

PROTEINS;

ARTICLE; ELASTICITY; MATHEMATICAL ANALYSIS; MEASUREMENT; MOLECULAR DYNAMICS; MOTION; NONHUMAN; PROBABILITY; PROTEIN FUNCTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SIGNAL TRANSDUCTION; STOCHASTIC MODEL;

EID: 34848882812     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0030223     Document Type: Erratum

References (37)

1. Bahar I, Atilgan A, Erman B (1997) Direct evaluation of thermal fluctuations in protein using a single parameter harmonic potential. Folding Design 2: 173-181.
2. Haliloglu T, Bahar I, Erman B (1997) Gaussian dynamics of folded proteins. Phys Rev Lett 79: 3090-3093.
3. Bahar I, Atilgan AR, Demirel MC, Erman B (1998) Vibrational dynamics of proteins: Significance of slow and fast modes in relation to function and stability. Phys Rev Lett 80: 2733-2736.
4. Cui Q, Bahar Ieditors (2006) Normal Mode Analysis: Theory and applications to biological and chemical systems. Boca Raton (Florida): CRC Press.
5. Bahar I, Rader AJ (2005) Coarse-grained normal modes in structural biology. Curr Opin Struct Bio 15: 1-7.
6. Micheletti C, Carloni P, Maritan A (2004) Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models. Proteins 55: 635.
7. Nicolay S, Sanejouand YH (2006) Functional modes of proteins are among the most robust. Phys Rev Lett 96: 078104.
8. Yang LW, Bahar I (2005) Coupling between catalytic sites and collective dynamics: A requirement for mechanochemical activity of enzymes. Structure 279: 893-904.
9. Ma J (2005) Usefulness and limitations of normal mode analysis modeling dynamics of biomolecular complexes. Structure 13: 373-380.
10. Norris JR (1997) Markov chains. Cambridge (United Kingdom): Cambridge University Press.
11. Doyle PG, Snell JL (1984) Random walks and electric networks. The Mathematical Association of America.
12. Barnett S (1992) Matrices: Methods and applications. Oxford: Oxford University Press.
13. Fouss F, Pirotte A, Renders JM, Saerens M (2005) A novel way of computing similarities between nodes of a graph, with application to collaborative recommendation. In: Proceedings of the IEEE International Conference on Web Intelligence; 19-22 September 2005; Compiegne, France. Institute of Electrical and Electronics Engineers. pp. 550-556.
14. Xiao W, Gutman I (2003) Resistance distance and Laplacian spectrum. Theo Chem Acc 110: 284-289.
15. Brinda K, Vishveshwara S (2005) A network representation of protein structures: Implications for protein stability. Biophys J 89: 4159-4170.
16. Chung FRK (1997) Spectral Graph Theory. In: CBMS Lectures Regional Conference Series in Mathematics; February 1997; Providence, Rhode Island. American Mathematical Society.
17. Aldous D, Fill J (2001) Reversible Markov chains and random walks on graphs. Chapter 2. Available: http://www.stat.berkeley.edu/~aldous/RWG/book. html.
18. Klein DJ, Randic M (1993) Resistance distance. J Math Chem 12: 81-85.
19. Berman H, Westbrook J, Feng Z, Gilliland G, Bhat T, et al. (2000) The Protein Data Bank. Nucleic Acids Res 28: 235-242.
20. Zhao H, Tang L, Wang X, Zhou Y, Lin Z (1998) Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide. Toxicon 36: 875.
21. Louis J, Dyda F, Nashed NT, Kimmel AR, Davies DR (1998) Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease. Biochemistry 37: 2105-2110.
22. Yan X, Hollis T, Svinth M, Monzingo AF, Milne GW, et al. (1997) Structure-based identification of a ricin inhibitor. J Mol Biol 266: 1043-1049.
23. Matthews DA, Dragovich PS, Webber SA, Fuhrman SA, Patick AK, et al. (1999) Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. Proc Natl Acad Sci U S A 96: 11000-11007.
24. Sidhu G, Withers SG, Nguyen NT, McIntosh NT, Ziser LP (1999) Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase. Biochemistry 38: 5346-5354.
25. Flory PJ (1976) Statistical thermodynamics of random networks. Proc Roy Soc A 351: 351-380.
26. Kloczkowski A, Mark JE, Erman B (1989) Chain dimensions and fluctuations in random elastomeric networks I: Phantom Gaussian networks in the undeformed state. Macromolecules 22: 1423-1432.
27. Coifman R, Lafon S (2006) Diffusion maps. App Comp Harmonic Analysis 21: 5-30.
28. Estrada F, Jepson A, Chennubhotla C (2004) Spectral embedding and mincut for image segmentation. In Proceedings of the British Machine Vision Conference (BMVC); 7-9 September 2004; Kingston, United Kingdom.
29. Chennubhotla C, Bahar I (2006) Markov propagation of allosteric effects in biomolecular systems. Mol Sys Biol 2: 36.
30. Ming D, Wall ME (2005) Quantifying allosteric effects in proteins. Proteins 59: 697-707.
31. Atilgan AR, Akan P, Baysal C (2004) Small world communication of residues and significance for protein dynamics. Biophys J 86: 85-91.
32. Atilgan AR, Turgut D, Atilgan C (2007) Screened non-bonded interactions in native proteins manipulate optimal paths for robust residue communication. Biophys J BioFAST. doi:10.1529/biophysj.106.099440
33. Ishikura T, Yamato T (2006) Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis. Chem Phy Lett 432: 533-537.
34. Choe S, Sun S (2005) The elasticity of α-helices. J Chem Phy 122: 244912.
35. Micheletti C, Lattanzi G, Maritan A (2002) Elastic properties of proteins: Insight on the folding process and evolutionary selection of native structures. J Mol Biol 321: 909-921.
36. Mansoor S, Farrens D (2004) High-throughput protein structural analysis using site-directed fluorescence labeling and the bimane derivative (2-pyridyl)dithiobimane. Biochemistry 43: 9426-9438.
37. Haas E (2005) The study of protein folding and dynamics by determination of intramolecular distance distributions and their fluctuations using ensemble and single-molecule FRET measurements. Chem Phys Chem 6: 858-870.