Constraint network analysis (CNA): A python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function

Journal of Chemical Information and Modeling

Volumn 53, Issue 4, 2013, Pages 1007-1015

  Pfleger, Christopher ^a   Rathi, Prakash Chandra ^a   Klein, Doris L ^a   Radestock, Sebastian ^a,b   Gohlke, Holger ^a  

^a HEINRICH HEINE UNIVERSITY   (Germany)

^b Elsevier Information Systems GmbH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

GRAPHIC METHODS; HIGH LEVEL LANGUAGES; LIGANDS; MOLECULES; NONPROFIT ORGANIZATION; PROTEINS; SOFTWARE PACKAGES; STABILITY; TEMPERATURE DISTRIBUTION;

ANALYSIS SOFTWARES; CONSTRAINT NETWORK ANALYSIS; HYDROPHOBIC TETHERS; PHASE TRANSITION POINT; PROTEIN ENGINEERING; PROTEIN STRUCTURES; TEMPERATURE DEPENDENCE; THERMAL UNFOLDING;

RIGIDITY;

HEN EGG LYSOZYME; LIGAND; LYSOZYME;

ANIMAL; ARTICLE; CHEMICAL PHENOMENA; CHEMICAL STRUCTURE; CHEMISTRY; CHICKEN; COMPUTER PROGRAM; COMPUTER SIMULATION; MOLECULAR LIBRARY; PHYSIOLOGY; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STABILITY; TEMPERATURE; THERMODYNAMICS;

ANIMALS; CHICKENS; COMPUTER SIMULATION; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; LIGANDS; MODELS, MOLECULAR; MURAMIDASE; PROTEIN ENGINEERING; PROTEIN FOLDING; PROTEIN STABILITY; SMALL MOLECULE LIBRARIES; SOFTWARE; TEMPERATURE; THERMODYNAMICS;

EID: 84876551539     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci400044m     Document Type: Article

References (68)

1. Ahmed, A.; Kazemi, S.; Gohlke, H. Protein flexibility and mobility in structure-based drug design Front. Drug Des. Discovery 2007, 3, 455-476
2. Heal, J. W.; Jimenez-Roldan, J. E.; Wells, S. A.; Freedman, R. B.; Romer, R. A. Inhibition of HIV-1 protease: The rigidity perspective Bioinformatics 2012, 28, 350-357
3. Jagodzinski, F.; Hardy, J.; Streinu, I. Using rigidity analysis to probe mutation-induced structural changes in proteins J. Bioinf. Comput. Biol. 2012, 10
4. Radestock, S.; Gohlke, H. Protein rigidity and thermophilic adaptation Proteins 2011, 79, 1089-1108
5. Tan, H. P.; Rader, A. J. Identification of putative, stable binding regions through flexibility analysis of HIV-1 gp120 Proteins 2009, 74, 881-894
6. Halle, B. Flexibility and packing in proteins Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 1274-1279
7. Dokholyan, N. V.; Li, L.; Ding, F.; Shakhnovich, E. I. Topological determinants of protein folding Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 8637-8641
8. Vendruscolo, M.; Dokholyan, N. V.; Paci, E.; Karplus, M. Small-world view of the amino acids that play a key role in protein folding Phys. Rev. E 2002, 65, 1-4
9. Böde, C.; Kovács, I. A.; Szalay, M. S.; Palotai, R.; Korcsmáros, T.; Csermely, P. Network analysis of protein dynamics FEBS Lett. 2007, 581, 2776-2782
10. Greene, L. H.; Higman, V. A. Uncovering network systems within protein structures J. Mol. Biol. 2003, 334, 781-791
11. Heringa, J.; Argos, P. Side-chain clusters in protein structures and their role in protein folding J. Mol. Biol. 1991, 220, 151-171
12. Heringa, J.; Argos, P.; Egmond, M. R.; Devlieg, J. Increasing thermal stability of subtilisin from mutations suggested by strongly interacting side-chain clusters Protein Eng. 1995, 8, 21-30
13. Jacobs, D. J.; Rader, A. J.; Kuhn, L. A.; Thorpe, M. F. Protein flexibility predictions using graph theory Proteins 2001, 44, 150-165
14. Rader, A. J.; Hespenheide, B. M.; Kuhn, L. A.; Thorpe, M. F. Protein unfolding: Rigidity lost Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 3540-3545
15. Whiteley, W. Counting out to the flexibility of molecules Phys. Biol. 2005, 2, S116-S126
16. Jacobs, D. J.; Thorpe, M. F. Generic rigidity percolation: The pebble game Phys. Rev. Lett. 1995, 75, 4051-4054
17. Jacobs, D. J.; Hendrickson, B. An algorithm for two-dimensional rigidity percolation: The pebble game J. Comput. Phys. 1997, 137, 346-365
18. Katoh, N.; Tanigawa, S. A proof of the molecular conjecture Discrete Comput. Geom. 2011, 45, 647-700
19. Hespenheide, B. M.; Rader, A. J.; Thorpe, M. F.; Kuhn, L. A. Identifying protein folding cores from the evolution of flexible regions during unfolding J. Mol. Graphics Modell. 2002, 21, 195-207
20. Jacobs, D. J.; Dallakyan, S.; Wood, G. G.; Heckathorne, A. Network rigidity at finite temperature: Relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems Phys. Rev. E 2003, 68
21. Gohlke, H.; Kuhn, L. A.; Case, D. A. Change in protein flexibility upon complex formation: Analysis of Ras-Raf using molecular dynamics and a molecular framework approach Proteins 2004, 56, 322-337
22. Rader, A. J.; Anderson, G.; Isin, B.; Khorana, H. G.; Bahar, I.; Klein-Seetharaman, J. Identification of core amino acids stabilizing rhodopsin Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 7246-7251
23. Rader, A. J.; Bahar, I. Folding core predictions from network models of proteins Polymer 2004, 45, 659-668
24. Mamonova, T.; Hespenheide, B.; Straub, R.; Thorpe, M. F.; Kurnikova, M. Protein flexibility using constraints from molecular dynamics simulations Phys. Biol. 2005, 2, S137-S147
25. Wells, S.; Menor, S.; Hespenheide, B. M.; Thorpe, M. F. Constrained geometric simulation of diffusive motion in proteins Phys. Biol. 2005, 2, S127-S136
26. Livesay, D. R.; Jacobs, D. J. Conserved quantitative stability/ flexibility relationships (QSFR) in an orthologous RNase H pair Proteins 2006, 62, 130-143
27. Ahmed, A.; Gohlke, H. Multiscale modeling of macromolecular conformational changes combining concepts from rigidity and elastic network theory Proteins 2006, 63, 1038-1051
28. Radestock, S.; Gohlke, H. Exploiting the link between protein rigidity and thermostability for data-driven protein engineering Eng. Life Sci. 2008, 8, 507-522
29. Fulle, S.; Gohlke, H. Analyzing the flexibility of RNA structures by constraint counting Biophys. J. 2008, 94, 4202-4219
30. Fulle, S.; Gohlke, H. Constraint counting on RNA structures: Linking flexibility and function Methods 2009, 49, 181-188
31. Fulle, S.; Gohlke, H. Statics of the ribosomal exit tunnel: Implications for cotranslational peptide folding, elongation regulation, and antibiotics binding J. Mol. Biol. 2009, 387, 502-517
32. Fulle, S.; Christ, N. A.; Kestner, E.; Gohlke, H. HIV-1 TAR RNA spontaneously undergoes relevant apo-to-holo conformational transitions in molecular dynamics and constrained geometrical simulations J. Chem. Inf. Model. 2010, 50, 1489-1501
33. Mottonen, J. M.; Jacobs, D. J.; Livesay, D. R. Allosteric response is both conserved and variable across three CheY orthologs Biophys. J. 2010, 99, 2245-2254
34. Rader, A. J. Thermostability in rubredoxin and its relationship to mechanical rigidity Phys. Biol. 2010, 7, 016002
35. Rathi, P. C.; Radestock, S.; Gohlke, H. Thermostabilizing mutations preferentially occur at structural weak spots with a high mutation ratio J. Biotechnol. 2012, 159, 135-144
36. Pfleger, C.; Radestock, S.; Schmidt, E.; Gohlke, H. Global and local indices for characterizing biomolecular flexibility and rigidity J. Comput. Chem. 2013, 34, 220-233
37. Wells, S. A.; Jimenez-Roldan, J. E.; Romer, R. A. Comparative analysis of rigidity across protein families Phys. Biol. 2009, 6
38. Zaccai, G. Biochemistry-How soft is a protein? A protein dynamics force constant measured by neutron scattering Science 2000, 288, 1604-1607
39. Jacobs, D. J.; Dallakyan, S. Elucidating protein thermodynamics from the three-dimensional structure of the native state using network rigidity Biophys. J. 2005, 88, 903-915
40. Gonzalez, L. C.; Wang, H.; Livesay, D. R.; Jacobs, D. J. Calculating ensemble averaged descriptions of protein rigidity without sampling PLoS One 2012, 7
41. Cock, P. J.; Antao, T.; Chang, J. T.; Chapman, B. A.; Cox, C. J.; Dalke, A.; Friedberg, I.; Hamelryck, T.; Kauff, F.; Wilczynski, B.; de Hoon, M. J. Biopython: Freely available Python tools for computational molecular biology and bioinformatics Bioinformatics 2009, 25, 1422-1423
42. Joosten, R. P.; Beek, T. A. H. T.; Krieger, E.; Hekkelman, M. L.; Hooft, R. W. W.; Schneider, R.; Sander, C.; Vriend, G. A series of PDB related databases for everyday needs Nucleic Acids Res. 2011, 39, D411-D419
43. Kabsch, W.; Sander, C. Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22, 2577-2637
44. Ascher, D.;; Dubois, P. F.;; Hinsen, K.;; Hugunin, J.; Oliphant, T. Numerical Python, 2001.
45. Jones, E.; Oliphant, T.; Peterson, P. SciPy: Open Source Scientific tools for Python, 2001
46. O'Boyle, N. M.; Banck, M.; James, C. A.; Morley, C.; Vandermeersch, T.; Hutchison, G. R. Open Babel: An open chemical toolbox J. Cheminform. 2011, 3
47. O'Boyle, N. M.; Morley, C.; Hutchison, G. R. Pybel: A Python wrapper for the OpenBabel cheminformatics toolkit Chem. Cent. J. 2008, 2
48. Beazley, D. M. Automated scientific software scripting with SWIG Future Gener. Comput. Syst. 2003, 19, 599-609
49. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank Nucleic Acids Res. 2000, 28, 235-242
50. Case, D.A.; T, A. D.; Cheatham, T.E.;, III; Simmerling, C.L.; Wang, J.; Duke, R.E.; Luo, R.; Walker, R.C.; Zhang, W.; Merz, K.M.; Roberts, B.; Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; I. Kolossváry; Wong, K.F.; Paesani, F.; Vanicek, J.; Liu, J.; Wu, X.; Brozell, S.R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D.R.; Mathews, D.H.; Seetin, M.G.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P.A. AMBER 11; University of California: San Francisco, 2010.
51. Dahiyat, B. I.; Gordon, D. B.; Mayo, S. L. Automated design of the surface positions of protein helices Protein Sci. 1997, 6, 1333-1337
52. Privalov, P. L.; Gill, S. J. Stability of protein-structure and hydrophobic interaction Adv. Protein Chem. 1988, 39, 191-234
53. Schellman, J. A. Temperature, stability, and the hydrophobic interaction Biophys. J. 1997, 73, 2960-2964
54. Burnham, K. P.; Anderson, D. R. Model Selection and Multimodel Inference: A Practical Information-Theoretic Approach, 2. ed.; Springer: New York, 2002; pp XXVI, 488 S.
55. Radford, S. E.; Dobson, C. M.; Evans, P. A. The folding of hen lysozyme involves partially structured intermediates and multiple pathways Nature 1992, 358, 302-307
56. Matagne, A.; Radford, S. E.; Dobson, C. M. Fast and slow tracks in lysozyme folding: Insight into the role of domains in the folding process J. Mol. Biol. 1997, 267, 1068-1074
57. Dinner, A. R.; Sali, A.; Smith, L. J.; Dobson, C. M.; Karplus, M. Understanding protein folding via free-energy surfaces from theory and experiment Trends Biochem. Sci. 2000, 25, 331-339
58. Kiefhaber, T. Kinetic traps in lysozyme folding Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 9029-9033
59. Wildegger, G.; Kiefhaber, T. Three-state model for lysozyme folding: Triangular folding mechanism with an energetically trapped intermediate J. Mol. Biol. 1997, 270, 294-304
60. Haliloglu, T.; Bahar, I. Structure-based analysis of protein dynamics: Comparison of theoretical results for hen lysozyme with X-ray diffraction and NMR relaxation data Proteins 1999, 37, 654-667
61. Radford, S. E.; Buck, M.; Topping, K. D.; Dobson, C. M.; Evans, P. A. Hydrogen-exchange in native and denatured states of hen egg-white lysozyme Proteins 1992, 14, 237-248
62. McCammon, J. A.; Gelin, B. R.; Karplus, M.; Wolynes, P. G. The hinge-bending mode in lysozyme Nature 1976, 262, 325-6
63. Kohn, J. E.; Afonine, P. V.; Ruscio, J. Z.; Adams, P. D.; Head-Gordon, T. Evidence of functional protein dynamics from X-ray crystallographic ensembles PLoS Comput. Biol. 2010, 6
64. Ahmed, A.; Rippmann, F.; Barnickel, G.; Gohke, H. A normal mode-based geometric simulation approach for exploring biologically relevant conformational transitions in proteins J. Chem. Inf. Model. 2011, 51, 1604-1622
65. Smith, L. J.; Sutcliffe, M. J.; Redfield, C.; Dobson, C. M. Structure of hen lysozyme in solution J. Mol. Biol. 1993, 229, 930-944
66. Tzeng, S. R.; Kalodimos, C. G. Dynamic activation of an allosteric regulatory protein Nature 2009, 462, 368-U139
67. Metz, A.; Pfleger, C.; Kopitz, H.; Pfeiffer-Marek, S.; Baringhaus, K. H.; Gohlke, H. Hot spots and transient pockets: Predicting the determinants of small-molecule binding to a protein-protein interface J. Chem. Inf. Model. 2011, 52, 120-133
68. Krüger, D. M.; Rathi, P. C.; Pfleger, C.; Gohlke, H. CNA Web server: Rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo)stability, and function Nucleic Acids Res. 2013, 10.1093/nar/gkt292