Proteins in action: the physics of structural fluctuations and conformational changes.

Structural dynamics is essential for the biological function of proteins. Results from new experimental techniques should be compared with those from previous experiments in order to obtain a consistent picture of the physics of intramolecular fluctuations and conformational changes. The high intensity and time structure of synchrotron radiation have made possible time-resolved X-ray structure analysis and the determination of phonon density spectra through the Mössbauer effect. By combining results from Mössbauer absorption spectroscopy, incoherent neutron scattering, low-temperature crystallography and optical spectroscopy, a physical picture of protein dynamics emerges.

[1]  R. J. Dwayne Miller,et al.  Ultrafast Phase Grating Studies of Heme Proteins: Observation of the Low-Frequency Modes Directing Functionally Important Protein Motions , 1998 .

[2]  Hans Frauenfelder,et al.  Temperature-dependent X-ray diffraction as a probe of protein structural dynamics , 1979, Nature.

[3]  Aleksandr V. Smirnov,et al.  Watching a Protein as it Functions with 150-ps Time-Resolved X-ray Crystallography , 2003, Science.

[4]  A. Miele,et al.  Structural Dynamics of Myoglobin , 2002, The Journal of Biological Chemistry.

[5]  D Bourgeois,et al.  Photolysis of the Carbon Monoxide Complex of Myoglobin: Nanosecond Time-Resolved Crystallography , 1996, Science.

[6]  W. Doster,et al.  THE DYNAMICAL TRANSITION IN PROTEINS : THE ROLE OF HYDROGEN BONDS , 2022 .

[7]  F. Parak Physical aspects of protein dynamics , 2003 .

[8]  H. Frauenfelder,et al.  Slaving: Solvent fluctuations dominate protein dynamics and functions , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[9]  A. Nagy,et al.  Observation of the cascaded atomic-to-global length scales driving protein motion , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[10]  K. Achterhold,et al.  Phonon-Assisted Mössbauer Effect: The Vibrational Density of States of Myoglobin , 2002 .

[11]  K. Achterhold,et al.  Determination of the phonon spectrum of iron in myoglobin using inelastic X-ray scattering of synchrotron radiation , 1997, European Biophysics Journal.

[12]  D Bourgeois,et al.  Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction. , 2001, Biochemistry.

[13]  R. Miller,et al.  Diffractive optics-based heterodyne-detected four-wave mixing signals of protein motion: From “protein quakes” to ligand escape for myoglobin , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[14]  A. Miele,et al.  Controlling Ligand Binding in Myoglobin by Mutagenesis* , 2002, The Journal of Biological Chemistry.

[15]  R. Miller,et al.  Direct observation of global protein motion in hemoglobin and myoglobin on picosecond time scales. , 1991, Science.

[16]  K. Moffat,et al.  New techniques in fast time-resolved structure determination. , 2000, Cellular and molecular biology.

[17]  M. Lim,et al.  Complex nonexponential relaxation in myoglobin after photodissociation of MbCO: measurement and analysis from 2 ps to 56 υs , 1994 .

[18]  Robert M. Sweet,et al.  Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobin , 2000, Nature.

[19]  G. Nienhaus,et al.  Ligand binding and conformational motions in myoglobin , 2000, Nature.

[20]  G. Zaccai Moist and soft, dry and stiff: a review of neutron experiments on hydration-dynamics-activity relations in the purple membrane of Halobacterium salinarum. , 2000, Biophysical chemistry.

[21]  Marius Schmidt,et al.  Application of singular value decomposition to the analysis of time-resolved macromolecular x-ray data. , 2003, Biophysical journal.

[22]  G. Zaccai,et al.  How soft is a protein? A protein dynamics force constant measured by neutron scattering. , 2000, Science.

[23]  F. Parak,et al.  Hydrogen atoms in proteins: Positions and dynamics , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[24]  F. Parak,et al.  Hydrogen and deuterium in myoglobin as seen by a neutron structure determination at 1.5 A resolution. , 2002, Biophysical chemistry.

[25]  E. Alp,et al.  Long-range reactive dynamics in myoglobin. , 2001, Physical review letters.

[26]  H Frauenfelder,et al.  Dynamics of ligand binding to myoglobin. , 1975, Biochemistry.

[27]  M Brunori,et al.  Structural dynamics of myoglobin. , 2000, Biophysical chemistry.

[28]  K. Achterhold,et al.  Protein dynamics: determination of anisotropic vibrations at the haem iron of myoglobin , 2003 .

[29]  G Ulrich Nienhaus,et al.  Myoglobin, a paradigm in the study of protein dynamics. , 2002, Chemphyschem : a European journal of chemical physics and physical chemistry.

[30]  Wolfgang Doster,et al.  Dynamical transition of myoglobin revealed by inelastic neutron scattering , 1989, Nature.

[31]  G. Kachalova,et al.  A steric mechanism for inhibition of CO binding to heme proteins. , 1999, Science.

[32]  M. Tehei,et al.  Fast dynamics of halophilic malate dehydrogenase and BSA measured by neutron scattering under various solvent conditions influencing protein stability , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[33]  A. Miele,et al.  Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[34]  J. Skinner,et al.  Spectral diffusion and the energy landscape of a protein. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[35]  N. Go,et al.  Dynamical transition of myoglobin in a crystal: comparative studies of X-ray crystallography and Mössbauer spectroscopy , 2001, European Biophysics Journal.

[36]  M. Brunori,et al.  The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[37]  G. Zaccai,et al.  Protein flexibility from the dynamical transition: a force constant analysis. , 2001, Biophysical journal.

[38]  H Frauenfelder,et al.  The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin , 2001, Proceedings of the National Academy of Sciences of the United States of America.