Conformational changes and small world association in proteins

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

Conformational changes and small world association in proteins

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

Research output: Chapter in Book/Report/Conference proceeding › Conference 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 language	English (US)
Title of host publication	Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium
Editors	M. Cahay, M. Urquidi-Macdonald, S. Bandyopadhyay, P. Guo, H. Hasegawa, N. Koshida, J.P. Leburton, D.J. Lockwood, S. Seal, A. Stella
Pages	539-545
Number of pages	7
Volume	PV 2004-13
State	Published - 2005
Event	Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium - Honolulu, HI, United States Duration: Oct 3 2004 → Oct 8 2004

Other

Other	Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium
Country/Territory	United States
City	Honolulu, HI
Period	10/3/04 → 10/8/04

All Science Journal Classification (ASJC) codes

General Engineering

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 et al. / 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",

language = "English (US)",

volume = "PV 2004-13",

pages = "539--545",

editor = "M. Cahay and M. Urquidi-Macdonald and S. Bandyopadhyay and P. Guo and H. Hasegawa and N. Koshida and J.P. Leburton and D.J. Lockwood and S. Seal and A. Stella",

booktitle = "Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium",

note = "Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium ; Conference date: 03-10-2004 Through 08-10-2004",

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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 et al.
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 proceeding › Conference contribution

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AU - Keskin, Ozlem

AU - Demirel, Melik C.

PY - 2005

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N2 - 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.

AB - 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.

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VL - PV 2004-13

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BT - Nanoscale Devices, Materials, and Biological Systems: Fundamental and Applications - Proceedings of the International Symposium

A2 - Cahay, M.

A2 - Urquidi-Macdonald, M.

A2 - Bandyopadhyay, S.

A2 - Guo, P.

A2 - Hasegawa, H.

A2 - Koshida, N.

A2 - Leburton, J.P.

A2 - Lockwood, D.J.

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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

Conformational changes and small world association in proteins

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