Glasses and proteins: Similarities and differences in their spectral diffusion dynamics

Schlichter, J.; Friedrich, J.

doi:10.1063/1.1367382

Cited by 17 publications

(26 citation statements)

References 35 publications

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“…Hence, we can safely assume that spectral diffusion in proteins is qualitatively drastically different from glasses. The dynamics in the waiting time domain as well as in the aging time domain seem to be governed by power laws with rather uniform exponents [86,87].…”

Section: Dynamics Of Fluctuation and Aging Processes In Heme Proteinsmentioning

confidence: 98%

Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles

Berlin

Burin

Friedrich

et al. 2006

Physics of Life Reviews

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Section: Dynamics Of Fluctuation and Aging Processes In Heme Proteinsmentioning

confidence: 98%

Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles

Berlin

Burin

Friedrich

et al. 2006

Physics of Life Reviews

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“…As a consequence, the pigments react to conformational changes of the protein with changes of their electronic energies, making them suited to monitor the dynamics of a protein with optical spectroscopy. Valuable information about the dynamics of proteins and the related time scales has been obtained by persistent spectral hole-burning spectroscopy (7,(12)(13)(14).Here, we report the observation of CSs in single-molecule experiments on light-harvesting complex 2 (LH2) complexes from Rhodospirillum molischianum. The salient feature of this technique is that it allows us to elucidate information that is commonly washed out by ensemble averaging in bulk measurements, by allowing direct observation of the dynamics of molecular processes without the need for synchronization of events.…”

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confidence: 95%

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confidence: 99%

Direct observation of tiers in the energy landscape of a chromoprotein: A single-molecule study

Hofmann

Aartsma

Michel

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

147

175

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Single-molecule spectroscopic techniques were applied to individual pigments embedded in a chromoprotein. A sensitive tool to monitor structural fluctuations of the protein backbone in the local environment of the chromophore is provided by recording the changes of the spectral positions of the pigment absorptions as a function of time. The data provide information about the organization of the energy landscape of the protein in tiers that can be characterized by an average barrier height. Additionally, a correlation between the average barrier height within a distinct tier and the time scale of the structural fluctuations is observed. P roteins are supramolecular machines that perform a tremendous variety of tasks in living organisms, such as the transport of electrons and small molecules, catalysis of biochemical reactions, or storage of energy to fuel metabolic processes. Despite the multitude of functions associated with proteins, they all consist of a linear chain of covalently linked amino acids. The high specificity of a particular protein results from its complex three-dimensional structure. The primary polypeptide sequence folds into secondary structural elements, such as ␣-helices and ␤-sheets, and the secondary structures are folded into a compact three-dimensional tertiary arrangement that determines the biological role and the status of activity of the protein. Proteins are remarkably robust despite the fact that their structure is stabilized only by relatively weak peptide-peptide and proteinsolvent interactions, such as hydrogen bonds and hydrophobic interactions. The connection among protein folding, protein structure, and protein function is one of the greatest challenges of current research. A major question that arises is: how does a protein fold within a reasonable time into its biologically active form?Even for a small protein consisting of Ϸ100 amino acids, the number of possible conformations is Ϸ10 100. Because of the weak interactions that stabilize the protein and the many degrees of freedom of such a large molecule, the lowest energy state is not unique, and description in terms of a rugged energy landscape is appropriate. The term ''energy landscape'' refers to the potential energy hypersurface of Ϸ 3,000 dimensions, resulting from the coordinates of the atoms of the protein. It features a large number of minima, maxima, and saddle points, and each minimum in this landscape represents a different conformational substate (CS) that corresponds to a different arrangement of the atoms. However, the number of possible conformations of a protein is so large that folding into the native state within a reasonable time by a process of statistical trial and error is impossible (Levinthal's paradox). The contemporary picture is that protein folding occurs by a progressive stabilization of intermediates that retains partially ''correct'' folding units guided by interactions that stabilize subdomains and domains of the final folded state.To describe protein dynamics and function, a model has been ...

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“…In our earlier works we tried to analyze our spectral diffusion measurements in the framework of a TLS-theory, which is well known from the theory of low temperature glasses [5]. However, when we started to pay more attention to the aging effects which can be observed in protein dynamics, it turned out that a satisfactory explanation of our data with a TLS-theory was impossible [6]. This is seen very well in Fig.…”

Section: Typical Experimental Observationsmentioning

confidence: 80%

Structural fluctuations and aging processes in deeply frozen proteins

Schlichter

Ponkratov

Friedrich

2003

Low Temperature Physics

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Frozen proteins are nonergodic systems and are subject to two types of structural motions, namely relaxation and fluctuation. Relaxation manifests itself in aging processes which slow the fluctuations. Within certain approximations we are able to experimentally separate the aging dynamics from the fluctuation dynamics by introducing two time parameters, namely an aging time t a and a waiting time t w . Both processes follow power laws in time. The fluctuation dynamics shows features of universality characterized by a rather uniform exponent of 1 4/ . This universality features were shown to be possible due to a random walk on a 1D random trajectory in conformational phase space. A very interesting aspect of protein dynamics concerns the influence of the host solvent on structural motions of the protein cores. We present results for sugar solvents and discuss possible mechanisms.

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Glasses and proteins: Similarities and differences in their spectral diffusion dynamics

Cited by 17 publications

References 35 publications

Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles

Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles

Direct observation of tiers in the energy landscape of a chromoprotein: A single-molecule study

Structural fluctuations and aging processes in deeply frozen proteins

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