Direct Observation of Global Protein Motion in Hemoglobin and Myoglobin on Picosecond Time Scales

Genberg, L.; Richard, L.; McLendon, George; Miller, R. J. Dwayne

doi:10.1126/science.1998121

Cited by 108 publications

(97 citation statements)

References 23 publications

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“…The dynamics of large-scale nuclear motions in polypeptides are expected to be substantially slower than those of most solvents. Relaxation times ranging from picoseconds to microseconds have been reported for the heme pocket of myoglobin (55)(56)(57)(58). Indeed, electrochemical measurements by Waldeck and coworkers (59) (Fig.…”

Section: Medium Dynamicsmentioning

confidence: 99%

Long-range electron transfer

Gray

Winkler

2005

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

761

841

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Recent investigations have shed much light on the nuclear and electronic factors that control the rates of long-range electron tunneling through molecules in aqueous and organic glasses as well as through bonds in donor-bridge-acceptor complexes. Couplings through covalent and hydrogen bonds are much stronger than those across van der Waals gaps, and these differences in coupling between bonded and nonbonded atoms account for the dependence of tunneling rates on the structure of the media between redox sites in Ru-modified proteins and protein-protein complexes.electron tunneling ͉ hopping ͉ glass ͉ protein

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Section: Medium Dynamicsmentioning

confidence: 99%

Long-range electron transfer

Gray

Winkler

2005

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

761

841

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“…Because of its simple structure relative to other proteins, its accessibility to various spectroscopies, and its physiological importance for oxygen storage, myoglobin has been extensively considered from both theoretical and experimental points of view. Even now, the relation between the structure and its function is not completely understood and much work continues on this protein (see Pauling, 1964;Olson et al, 1988;Rohlfs et al, 1990;Genberg et al, 1991;Springer et al, 1994).…”

Section: Introductionmentioning

confidence: 99%

Structure and dynamics of the water around myoglobin

Phillips

Pettitt

1995

Protein Science

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The interplay between simulations at various levels of hydration and experimental observables has led to a picture of the role of solvent in thermodynamics and dynamics of protein systems. One of the most studied proteinsolvent systems is myoglobin, which serves as a paradigm for the development of structure-function relationships in many biophysical studies. We review here some aspects of the solvation of myoglobin and the resulting implications. In particular, recent theoretical and simulation studies unify much of the diverse set of experimental results on water near proteins.Keywords: diffraction analysis; hydration; myoglobin; protein solutions; solvation; water dynamicsMyoglobin has a long history as a testing ground for ideas about the nature of proteins. The first protein whose structure was obtained at sufficient resolution to determine a complete set of atomic coordinates was myoglobin. This pioneering work revealed the now-classic globin fold of the 8 a-helices packed together into the tertiary structure (Kendrew et al., 1960(Kendrew et al., , 1961. Because of its simple structure relative to other proteins, its accessibility to various spectroscopies, and its physiological importance for oxygen storage, myoglobin has been extensively considered from both theoretical and experimental points of view. Even now, the relation between the structure and its function is not completely understood and much work continues on this protein (see Pauling, 1964;Olson et al., 1988;Rohlfs et al., 1990;Genberg et al., 1991;Springer et al., 1994).It is apparent that the environment surrounding the protein is critical in determining observable properties. Many experimental measurements depend in a sensitive way on the state of the system, including the solvating environment (or lack thereof). The term solvation refers to the general solution process; hydration refers specifically to the role of water as a solvent. In this review on the solvation of myoglobin, we concentrate mostly on aspects of the structure of water around myoglobin. Of primary interest to us are the cases where there are substantial overlaps in the study of hydration properties by different methods, and where there are also abundant comparisons between theory and experiment. Diffraction experiments carried out on protein crystals provide time-averaged atomic positions of both the solvent and the protein. In one sense, they give the best spatial information available at this time. There are difficulties in the interpretation of the less-ordered water molecules. Perhaps surprisingly, results derived from X-ray and neutron diffraction methods seem to differ in certain details, especially those concerned with the solvent. Other methods such as NMR and Mossbauer radiation spectroscopy provide information complementary to that of diffraction experiments, and the challenge now is to assemble these different results into a coherent picture.Computer simulations and simpler theoretical models have recently provided an interesting, and possibly unifying, ...

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“…Because the CO-iron bonds in a Mb ensemble can be coherently photolysed with a laser flash within only 50 fs (4), a range of time-resolved techniques has been applied to probe various aspects of the structural dynamics after CO photodissociation, such as energy dissipation, CO dynamics, or heme doming (5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15). Three-dimensional movies of Mb conformational transitions were derived by means of time-resolved crystallography, which recently reached subpicosecond time resolution (16)(17)(18)(19).…”

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confidence: 99%

Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin

Brinkmann

Hub

2016

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

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"Protein quake" denotes the dissipation of excess energy across a protein, in response to a local perturbation such as the breaking of a chemical bond or the absorption of a photon. Femtosecond timeresolved small-and wide-angle X-ray scattering (TR-SWAXS) is capable of tracking such ultrafast protein dynamics. However, because the structural interpretation of the experiments is complicated, a molecular picture of protein quakes has remained elusive. In addition, new questions arose from recent TR-SWAXS data that were interpreted as underdamped oscillations of an entire protein, thus challenging the long-standing concept of overdamped global protein dynamics. Based on molecular-dynamics simulations, we present a detailed molecular movie of the protein quake after carbon monoxide (CO) photodissociation in myoglobin. The simulations suggest that the protein quake is characterized by a single pressure peak that propagates anisotropically within 500 fs across the protein and further into the solvent. By computing TR-SWAXS patterns from the simulations, we could interpret features in the reciprocalspace SWAXS signals as specific real-space dynamics, such as CO displacement and pressure wave propagation. Remarkably, we found that the small-angle data primarily detect modulations of the solvent density but not oscillations of the bare protein, thereby reconciling recent TR-SWAXS experiments with the notion of overdamped global protein dynamics.time-resolved SAXS/WAXS | free-electron laser | molecular dynamics F unctional protein dynamics occur on various timescales, ranging from tens of femtoseconds for bond breaking, up to milliseconds and seconds for large-scale conformational transitions or protein folding. Observing and explaining such transitions, if possible in a time-resolved manner, has remained a central goal of molecular biophysics. A popular model system used to study proteins dynamics has been the 18-kDa protein myoglobin (Mb), the protein of first known tertiary structure (1). Mb contains an iron-porphyrin heme group that reversibly binds small gas molecules such as molecular oxygen (O 2 ) or carbon monoxide (CO). Mb is abundant in the muscle tissue of vertebrates, where it plays an important role in the transport and storage of O 2 and in the biochemistry of nitric oxide (2, 3).Because the CO-iron bonds in a Mb ensemble can be coherently photolysed with a laser flash within only 50 fs (4), a range of time-resolved techniques has been applied to probe various aspects of the structural dynamics after CO photodissociation, such as energy dissipation, CO dynamics, or heme doming (5-15). Three-dimensional movies of Mb conformational transitions were derived by means of time-resolved crystallography, which recently reached subpicosecond time resolution (16-19). These experimental studies were complemented by several pioneering molecular-dynamics (MD) simulations that revealed the Mb dynamics with atomic detail, with some focus on heat dissipation, vibrational dynamics, as well as ligand migration (20-28).Time-re...

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Direct Observation of Global Protein Motion in Hemoglobin and Myoglobin on Picosecond Time Scales

Cited by 108 publications

References 23 publications

Long-range electron transfer

Long-range electron transfer

Structure and dynamics of the water around myoglobin

Ultrafast anisotropic protein quake propagation after CO photodissociation in myoglobin

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