Peptide-mediated intramolecular electron transfer: long-range distance dependence

Isied, Stephan S.; Ogawa, Michael Y.; Wishart, James F.

doi:10.1021/cr00011a002

Cited by 279 publications

(249 citation statements)

References 26 publications

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“…43 For instance, in electron transfer experiments, proline peptides provide predictable separation distance based on the number of proline residues. 45 The major concern in the design of a molecular ruler is the possibility of softening and structural failure that arises when the ruler is unable to provide a predictable separation distance between its bound moieties. An adequate cushion distance is often required when designing the linkers.…”

Section: Absence Of Flexibility: Molecular Rulersmentioning

confidence: 99%

Control of protein functional dynamics by peptide linkers

2005

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Control of structural flexibility is essential for the proper functioning of a large number of proteins and multiprotein complexes. At the residue level, such flexibility occurs due to local relaxation of peptide bond angles whose cumulative effect may result in large changes in the secondary, tertiary or quaternary structures of protein molecules. Such flexibility, and its absence, most often depends on the nature of interdomain linkages formed by oligopeptides. Both flexible and relatively rigid peptide linkers are found in many multidomain proteins. Linkers are thought to control favorable and unfavorable interactions between adjacent domains by means of variable softness furnished by their primary sequence. Large-scale structural heterogeneity of multidomain proteins and their complexes, facilitated by soft peptide linkers, is now seen as the norm rather than the exception. Biophysical discoveries as well as computational algorithms and databases have reshaped our understanding of the often spectacular biomolecular dynamics enabled by soft linkers. Absence of such motion, as in so-called molecular rulers, also has desirable functional effects in protein architecture. We review here the historic discovery and current understanding of the nature of domains and their linkers from a structural, computational, and biophysical point of view. A number of emerging applications, based on the current understanding of the structural properties

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Section: Absence Of Flexibility: Molecular Rulersmentioning

confidence: 99%

Control of protein functional dynamics by peptide linkers

2005

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“…It has to be noted that the tryptophan residues are about 30 Å away from the DNA surface (estimating the distance, using X-ray crystal structure of λ-repressor-operator DNA complex in VIEWER LITE software). In that case, the tryptophan residues may contribute in the process of long range ET through space, involving solvent, peptide bridge, or ion pairing to the operator DNA located at the N-terminal domain of the protein (57). The long range ET rates reportedly vary from ultrafast (10 10 /s) to very slow time scale (10 3 /s) depending on the distance as well as the system under study (57).…”

Section: Differential Electron Transfer Dynamics In Specific Protein-mentioning

confidence: 99%

“…In that case, the tryptophan residues may contribute in the process of long range ET through space, involving solvent, peptide bridge, or ion pairing to the operator DNA located at the N-terminal domain of the protein (57). The long range ET rates reportedly vary from ultrafast (10 10 /s) to very slow time scale (10 3 /s) depending on the distance as well as the system under study (57). The long range ET rates observed in our experiment are found to be well within the rates reported in the existing literature.…”

Section: Differential Electron Transfer Dynamics In Specific Protein-mentioning

confidence: 99%

Dynamical perspective of protein-DNA interaction

Batabyal

Choudhury

Sao

et al. 2014

BioMolecular Concepts

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Abstract:The interactions between protein-DNA are essential for various biological activities. In this review, we provide an overview of protein-DNA interactions that emphasizes the importance of dynamical aspects. We divide protein-DNA interactions into two categories: nonspecific and specific and both the categories would be discussed highlighting some of our relevant work. In the case of nonspecific protein-DNA interaction, solvation studies (picosecond and femtosecond-resolved) explore the role environmental dynamics and change in the micropolarity around DNA molecules upon complexation with histone protein (H1). While exploring the specific protein-DNA interaction at λ-repressor-operator sites interaction, particularly O R 1 and O R 2, it was observed that the interfacial water dynamics is minimally perturbed upon interaction with DNA, suggesting the labile interface in the protein-DNA complex. Förster resonance energy transfer (FRET) study revealed that the structure of the protein is more compact in repressor-O R 2 complex than in the repressor-O R 1 complex. Fluorescence anisotropy studies indicated enhanced flexibility of the C-terminal domain of the repressor at fast timescales after complex formation with O R 1. The enhanced flexibility and different conformation of the C-terminal domain of the repressor upon complexation with O R 1 DNA compared to O R 2 DNA were found to have pronounced effect on the rate of photoinduced electron transfer.

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“…One of these that is particularly relevant to bioelectrochemistry is the work of Isied et al [97] who studied the distance dependence of electron transfer between two metal complexes separated by an oligoproline bridge (Figure 1.38). Oligoproline bridges were selected because their rigidity allows the spacing between donor and acceptor to be well defined; the molecule cannot fold up to bring the donor and acceptor ends close to each other.…”

Section: Kinetics: Electron Transfer Rate Constantsmentioning

confidence: 99%

Bioenergetics and Biological Electron Transport

Bartlett

2008

Bioelectrochemistry

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Peptide-mediated intramolecular electron transfer: long-range distance dependence

Cited by 279 publications

References 26 publications

Control of protein functional dynamics by peptide linkers

Control of protein functional dynamics by peptide linkers

Dynamical perspective of protein-DNA interaction

Bioenergetics and Biological Electron Transport

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