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J B Clarage

Publications and source records attributed to J B Clarage.

8 recordsLinked to original sources
PubMed1998

Characterizing global substates of myoglobin.

BACKGROUND: The massive amount of information generated from current molecular dynamics simulations makes the data difficult to analyze efficiently. Principal component analysis has been used for almost a century to detect and characterize data relationships and to reduce the dimensionality for problems in many fields. Here, we present an adaptation of principal component analysis using a partial singular value decomposition (SVD) for investigating both the localized and global motions of macromolecules. RESULTS: Configuration space projections from the SVD analysis of a variety of myoglobin simulations are used to characterize the dynamics of the protein. This technique reveals new dynamical motifs, which quantify proposed hierarchical structures of conformational substates for proteins and provide a means by which configuration space sampling efficiency may be probed. The SVD clearly shows that solvent effects facilitate transitions between global conformational substates for myoglobin molecular dynamics simulations. Lyapunov exponents calculated from the configuration space divergence of 15 trajectories agree with previous predictions for the chaotic behavior of complex protein systems. CONCLUSIONS: Configuration space projections provide invaluable information about protein motions that would be extremely difficult to obtain otherwise. While the configuration space for myoglobin is quite large, it does have structure. Our analysis of this structure shows that the protein hops between a number of distinct global conformational states, much like the local behavior observed for an individual residue.

Computer Simulation↗
PubMed1997

Motions of calmodulin characterized using both Bragg and diffuse X-ray scattering.

BACKGROUND: Calmodulin is a calcium-activated regulatory protein which can bind to many different targets. The protein resembles a highly flexible dumbbell, and bends in the middle as it binds. This and other motions must be understood to formulate a realistic model of calmodulin function. RESULTS: Using the Bragg reflections from X-ray crystallography, a multiple-conformer refinement of a calmodulin-peptide complex shows anisotropic displacements, with high variations of dihedral angles in several nonhelical domains: the flexible linker; three of the four calcium-binding sites (including both of the N-terminal sites); and a turn connecting the C-terminal EF-hand calcium-binding domains. Three-dimensional maps of the large scale diffuse X-ray scattering data show isotropic liquid-like motions with an unusually small correlation length. Three-dimensional maps of the small scale diffuse streaks show highly coupled, anisotropic motions along the head-to-tail molecular packing direction in the unit cell. There is also weak coupling perpendicular to the head-to-tail packing direction, particularly across a cavity occupied by the disordered linker domain of the molecule. CONCLUSIONS: Together, the Bragg and diffuse scattering present a self-consistent description of the motions in the flexible linker of calmodulin. The other mobile regions of the protein are also of great interest. In particular, the high variations in the calcium-binding sites are likely to influence how strongly they bind ions. This is especially important in the N-terminal sites, which regulate the activity of the molecule.

Algorithms↗
PubMed1995

A sampling problem in molecular dynamics simulations of macromolecules.

Correlations in low-frequency atomic displacements predicted by molecular dynamics simulations on the order of 1 ns are undersampled for the time scales currently accessible by the technique. This is shown with three different representations of the fluctuations in a macromolecule: the reciprocal space of crystallography using diffuse x-ray scattering data, real three-dimensional Cartesian space using covariance matrices of the atomic displacements, and the 3N-dimensional configuration space of the protein using dimensionally reduced projections to visualize the extent to which phase space is sampled.

Computer Simulation↗
PubMed1995

Automatic identification of discrete substates in proteins: singular value decomposition analysis of time-averaged crystallographic refinements.

The singular value decomposition (SVD) provides a method for decomposing a molecular dynamics trajectory into fundamental modes of atomic motion. The right singular vectors are projections of the protein conformations onto these modes showing the protein motion in a generalized low-dimensional basis. Statistical analysis of the right singular vectors can be used to classify discrete configurational substates in the protein. The configuration space portraits formed from the right singular vectors can also be used to visualize complex high-dimensional motion and to examine the extent of configuration space sampling by the simulation.

Computer Simulation↗
PubMed1994

Analysis of diffuse scattering from yeast initiator tRNA crystals.

Yeast initiator tRNA crystals exhibit strong X-ray diffuse scattering. This scattering can be used to extract information about lattice-coupled and intramolecular motions in the crystals. The amplitudes and correlation distances of these motions can be estimated by calculating the diffuse scattering and comparing the results with the observed scattering. Results indicate that both anisotropic, lattice-coupled motions as well as short-range correlated local disorder in the anticodon arm contribute to the overall disorder in the crystals. These types of motions can be correlated with aspects of tRNA function. This additional information complements the results from analysis of crystallographic data and provides a more detailed picture of the structure and dynamics of the molecule. The degree to which the methodology presented here can account for the observed diffuse scattering from tRNA represents a significant step forward in the ability to use this conventionally discarded information, and encourages the ultimate extension of these ideas to a wide variety of macromolecular systems.

Journal Article↗
PubMed1994

Cross-validation tests of time-averaged molecular dynamics refinements for determination of protein structures by X-ray crystallography.

Time-averaged structure-factor restraints have been used in two molecular dynamics refinement schemes to define ensembles of conformations for myoglobin that fit the experimentally measured Bragg scattering from P6 crystals. The geometries of the structures have been maintained to the same currently acceptable limits in all cases. Free R value analysis was used to assess the validity of the two approaches. In the first scheme, where atoms have no B values, the decrease in R value was found to be spurious as judged by a concomitant increase in the free R value. The other scheme, however, which retains individual B values, was found to yield both low R values and low free R values; thus, here the additional variables introduced by modeling the protein in terms of an evolving ensemble of states do not overfit the data. For comparison, refinements were also carried out on the system using several other techniques for isotropic and anisotropic crystallographic refinement. The time-averaged refinements with B values compare quite favorably with the standard methods, but yield additional information about substates of the system. Hence, correctly applied time-averaged refinements can yield accurate models for protein molecules; moreover, by essentially relaxing the harmonic approximation from the refinement process, these refinements allow a more detailed description of the motions of complex molecules, such as proteins, to be determined from X-ray crystallographic data.

Journal Article↗
PubMed1992

Correlations of atomic movements in lysozyme crystals.

Diffuse scattering data have been collected on two crystal forms of lysozyme, tetragonal and triclinic, using synchrotron radiation. The observed diffraction patterns were simulated using an exact theory for simple model crystals which relates the diffuse scattering intensity distribution to the amplitudes and correlations of atomic movements. Although the mean square displacements in the tetragonal form are twice that in the triclinic crystal, the predominant component of atomic movement in both crystals is accounted for by short-range coupled motions where displacement correlations decay exponentially as a function of atomic separation, with a relaxation distance of approximately 6 A. Lattice coupled movements with a correlation distance approximately 50 A account for only about 5-10% of the total atomic mean square displacements in the protein crystals. The results contradict various presumptions that the disorder in protein crystals can be modeled predominantly by elastic vibrations or rigid body movements.

Crystallization↗