Signal Propagation in Proteins and Relation to Equilibrium Fluctuations

Correction for: Chennubhotla C, Bahar I (2007) Signal propagation in proteins and relation to equilibrium fluctuations. PLoS Comput Biol 3(9): e172. 10.1371/journal.pcbi.0030172 Four mathematical expressions appeared incorrectly. The correct expressions follow. The hitting time expression Equation 14 involves three different types of contributions: a one-body term that depends on the destination node, ; a two-body term that depends on the initial and final nodes, ; and a series of three-body terms that depend on intermediate nodes, in addition to the two end points, . Derivation of Equation 14. The discussion below borrows from results in [12,13]. Deriving from is a three-step process: …

[1]  M. Randic,et al.  Resistance distance , 1993 .

[2]  François Fouss,et al.  A novel way of computing similarities between nodes of a graph, with application to collaborative recommendation , 2005, The 2005 IEEE/WIC/ACM International Conference on Web Intelligence (WI'05).

[3]  A. B. Rami Shani,et al.  Matrices: Methods and Applications , 1992 .

[4]  I. Gutman,et al.  Resistance distance and Laplacian spectrum , 2003 .

[5]  C. Chennubhotla,et al.  Markov propagation of allosteric effects in biomolecular systems: application to GroEL–GroES , 2006, Molecular systems biology.

[6]  A. Atilgan,et al.  Small-world communication of residues and significance for protein dynamics. , 2003, Biophysical journal.

[7]  P. Flory,et al.  Statistical thermodynamics of random networks , 1976, Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences.

[8]  D. Matthews,et al.  Structure-assisted design of mechanism-based irreversible inhibitors of human rhinovirus 3C protease with potent antiviral activity against multiple rhinovirus serotypes. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Andrzej Kloczkowski,et al.  Chain dimensions and fluctuations in random elastomeric networks. 1. Phantom Gaussian networks in the undeformed state , 1989 .

[10]  Allan D. Jepson,et al.  Spectral Embedding and Min Cut for Image Segmentation , 2004, BMVC.

[11]  S. Withers,et al.  Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase. , 1999, Biochemistry.

[12]  I. Bahar,et al.  Normal mode analysis : theory and applications to biological and chemical systems , 2005 .

[13]  A. Atilgan,et al.  Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential. , 1997, Folding & design.

[14]  J. Louis,et al.  Hydrophilic peptides derived from the transframe region of Gag-Pol inhibit the HIV-1 protease. , 1998, Biochemistry.

[15]  Stéphane Lafon,et al.  Diffusion maps , 2006 .

[16]  H. Zhao,et al.  Structure of a snake venom phospholipase A2 modified by p-bromo-phenacyl-bromide. , 1998, Toxicon : official journal of the International Society on Toxinology.

[17]  Elisha Haas,et al.  The study of protein folding and dynamics by determination of intramolecular distance distributions and their fluctuations using ensemble and single-molecule FRET measurements. , 2005, Chemphyschem : a European journal of chemical physics and physical chemistry.

[18]  Jianpeng Ma,et al.  Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes. , 2005, Structure.

[19]  Peter G. Doyle,et al.  Random Walks and Electric Networks: REFERENCES , 1987 .

[20]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[21]  M. Wall,et al.  Quantifying allosteric effects in proteins , 2005, Proteins.

[22]  G. Milne,et al.  Structure-based identification of a ricin inhibitor. , 1997, Journal of molecular biology.

[23]  A. Maritan,et al.  Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models , 2004, Proteins.

[24]  Sean X. Sun,et al.  The elasticity of α-helices , 2005 .

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

[26]  Amos Maritan,et al.  Elastic properties of proteins: insight on the folding process and evolutionary selection of native structures. , 2002, Journal of molecular biology.

[27]  Y. Sanejouand,et al.  Functional modes of proteins are among the most robust. , 2005, Physical review letters.

[28]  I. Bahar,et al.  Coupling between catalytic site and collective dynamics: a requirement for mechanochemical activity of enzymes. , 2005, Structure.

[29]  I. Bahar,et al.  Gaussian Dynamics of Folded Proteins , 1997 .

[30]  A. Atilgan,et al.  Screened nonbonded interactions in native proteins manipulate optimal paths for robust residue communication. , 2006, Biophysical journal.

[31]  Takahisa Yamato,et al.  Energy transfer pathways relevant for long-range intramolecular signaling of photosensory protein revealed by microscopic energy conductivity analysis , 2006 .

[32]  D. Farrens,et al.  High-throughput protein structural analysis using site-directed fluorescence labeling and the bimane derivative (2-pyridyl)dithiobimane. , 2004, Biochemistry.