Conformational changes and small world association in proteins

Murat Cetinkaya, Lee Salway, Ozlem Keskin, Melik C. Demirel

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

A set of proteins which exhibit domain motions, are analyzed by an elastic network model. We calculated the fluctuation and cooperativity of residues with low amplitude fluctuations across different domain motions. Slow modes that are associated with the function of proteins have common features among different protein structures. In addition, we have calculated network parameters such as connectivity and path length for the same set of proteins. Higher level of connectivity and lower level of path length are obtained as the protein moves from open to closed conformation. This paper focuses on the importance of large degree of conformational freedom in proteins while maintain their native state.

Original languageEnglish (US)
Title of host publicationNanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium
EditorsM. Cahay, M. Urquidi-Macdonald, S. Bandyopadhyay, P. Guo, H. Hasegawa, N. Koshida, J.P. Leburton, D.J. Lockwood, S. Seal, A. Stella
Pages539-545
Number of pages7
VolumePV 2004-13
StatePublished - 2005
EventNanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium - Honolulu, HI, United States
Duration: Oct 3 2004Oct 8 2004

Other

OtherNanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium
CountryUnited States
CityHonolulu, HI
Period10/3/0410/8/04

Fingerprint

Association reactions
Proteins
Conformations

All Science Journal Classification (ASJC) codes

  • Engineering(all)

Cite this

Cetinkaya, M., Salway, L., Keskin, O., & Demirel, M. C. (2005). Conformational changes and small world association in proteins. In M. Cahay, M. Urquidi-Macdonald, S. Bandyopadhyay, P. Guo, H. Hasegawa, N. Koshida, J. P. Leburton, D. J. Lockwood, S. Seal, ... A. Stella (Eds.), Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium (Vol. PV 2004-13, pp. 539-545)
Cetinkaya, Murat ; Salway, Lee ; Keskin, Ozlem ; Demirel, Melik C. / Conformational changes and small world association in proteins. Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium. editor / M. Cahay ; M. Urquidi-Macdonald ; S. Bandyopadhyay ; P. Guo ; H. Hasegawa ; N. Koshida ; J.P. Leburton ; D.J. Lockwood ; S. Seal ; A. Stella. Vol. PV 2004-13 2005. pp. 539-545
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title = "Conformational changes and small world association in proteins",
abstract = "A set of proteins which exhibit domain motions, are analyzed by an elastic network model. We calculated the fluctuation and cooperativity of residues with low amplitude fluctuations across different domain motions. Slow modes that are associated with the function of proteins have common features among different protein structures. In addition, we have calculated network parameters such as connectivity and path length for the same set of proteins. Higher level of connectivity and lower level of path length are obtained as the protein moves from open to closed conformation. This paper focuses on the importance of large degree of conformational freedom in proteins while maintain their native state.",
author = "Murat Cetinkaya and Lee Salway and Ozlem Keskin and Demirel, {Melik C.}",
year = "2005",
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Cetinkaya, M, Salway, L, Keskin, O & Demirel, MC 2005, Conformational changes and small world association in proteins. in M Cahay, M Urquidi-Macdonald, S Bandyopadhyay, P Guo, H Hasegawa, N Koshida, JP Leburton, DJ Lockwood, S Seal & A Stella (eds), Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium. vol. PV 2004-13, pp. 539-545, Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium, Honolulu, HI, United States, 10/3/04.

Conformational changes and small world association in proteins. / Cetinkaya, Murat; Salway, Lee; Keskin, Ozlem; Demirel, Melik C.

Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium. ed. / M. Cahay; M. Urquidi-Macdonald; S. Bandyopadhyay; P. Guo; H. Hasegawa; N. Koshida; J.P. Leburton; D.J. Lockwood; S. Seal; A. Stella. Vol. PV 2004-13 2005. p. 539-545.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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Cetinkaya M, Salway L, Keskin O, Demirel MC. Conformational changes and small world association in proteins. In Cahay M, Urquidi-Macdonald M, Bandyopadhyay S, Guo P, Hasegawa H, Koshida N, Leburton JP, Lockwood DJ, Seal S, Stella A, editors, Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium. Vol. PV 2004-13. 2005. p. 539-545