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Ultrafast peptide and protein dynamics by vibrational spectroscopy


Hamm, P (2008). Ultrafast peptide and protein dynamics by vibrational spectroscopy. In: Braun, M; Gilch, P; Zinth, W. Ultrashort laser pulses in biology and medicine. Berlin: Springer, 77-94.

Abstract

Proteins are molecular machines with a well-defined 3D structure, and it is mainly the success of X-ray and NMR spectroscopic techniques that made the tremendous progress in structural biology happen. However, it is also clear that biomolecular processes generally involve conformational changes of proteins and enzymes. Mostly due to a lack of appropriate spectroscopic tools, much less is known about the dynamics of protein structures.
Protein dynamics occurs on a large range of time scales, which can coarsely be related to various length scales: Dynamics of tertiary and quaternary structure extends from milliseconds to seconds and even longer, while formation of secondary structure has been observed between 50 ns and a few microseconds [1–12]. Nevertheless, several experiments have provided strong hints for the relevance of even faster processes from the observation of large instantaneous signals, which could not be time-resolved [2, 7, 13]. For example, Thompson et al. [5] estimated a “zipping time” for a 21-residue α-helix of 300 ps (i.e., the time for closing of subsequent hydrogen bonds, once an initial helix turn is formed), while Huang et al. [7] indirectly concluded that helix nucleation might occur on a subnanosecond time scale. Also molecular dynamics (MD) simulations suggest that peptides and proteins can undergo considerable structural changes within 1 ns or less [8–10, 14, 15]. Hummer et al. [16] found the formation of the first α-helical turn within 0.1–1 ns in work on helix nucleation in short Ala and Gly based peptides. Daura et al. [9, 17] simulated equilibrium folding/unfolding of a β-heptapeptide at the melting point and above to obtain statistics on the populations of the folded and unfolded states. Several folding/unfolding events were observed in a 50 ns trajectory, where the actual transitions from unfolded to folded conformations could be as fast as 50–100ps.

Proteins are molecular machines with a well-defined 3D structure, and it is mainly the success of X-ray and NMR spectroscopic techniques that made the tremendous progress in structural biology happen. However, it is also clear that biomolecular processes generally involve conformational changes of proteins and enzymes. Mostly due to a lack of appropriate spectroscopic tools, much less is known about the dynamics of protein structures.
Protein dynamics occurs on a large range of time scales, which can coarsely be related to various length scales: Dynamics of tertiary and quaternary structure extends from milliseconds to seconds and even longer, while formation of secondary structure has been observed between 50 ns and a few microseconds [1–12]. Nevertheless, several experiments have provided strong hints for the relevance of even faster processes from the observation of large instantaneous signals, which could not be time-resolved [2, 7, 13]. For example, Thompson et al. [5] estimated a “zipping time” for a 21-residue α-helix of 300 ps (i.e., the time for closing of subsequent hydrogen bonds, once an initial helix turn is formed), while Huang et al. [7] indirectly concluded that helix nucleation might occur on a subnanosecond time scale. Also molecular dynamics (MD) simulations suggest that peptides and proteins can undergo considerable structural changes within 1 ns or less [8–10, 14, 15]. Hummer et al. [16] found the formation of the first α-helical turn within 0.1–1 ns in work on helix nucleation in short Ala and Gly based peptides. Daura et al. [9, 17] simulated equilibrium folding/unfolding of a β-heptapeptide at the melting point and above to obtain statistics on the populations of the folded and unfolded states. Several folding/unfolding events were observed in a 50 ns trajectory, where the actual transitions from unfolded to folded conformations could be as fast as 50–100ps.

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Additional indexing

Item Type:Book Section, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Chemistry
Dewey Decimal Classification:540 Chemistry
Language:English
Date:2008
Deposited On:16 Jan 2009 16:10
Last Modified:05 Apr 2016 12:49
Publisher:Springer
Series Name:Biological and medical physics, biomedical engineering
ISSN:1618-7210
ISBN:978-3-540-73565-6 (P) 978-3-540-73566-3 (E)
Additional Information:The original publication is available at www.springerlink.com
Publisher DOI:10.1007/978-3-540-73566-3_4
Related URLs:http://opac.nebis.ch/F/?local_base=NEBIS&con_lng=GER&func=find-b&find_code=SYS&request=005426787
Permanent URL: http://doi.org/10.5167/uzh-10232

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