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

Wall, Michael E.; Clarage, James; Phillips, George N.

doi:10.1016/s0969-2126(97)00308-0

Cited by 98 publications

(158 citation statements)

References 38 publications

(77 reference statements)

Supporting

Mentioning

144

Contrasting

Order By: Relevance

“…has previously been observed for liquid-like motions (LLM) models (18)(19)(20)(21), which provide a softer model of the protein than the TLS model. In the LLM model, the atoms in the protein are assumed to move randomly, like in a homogeneous medium; the motions were termed "liquid-like" by Caspar et al (19) because the correlations in the displacements were assumed to fall off exponentially with the distance between atoms.…”

Section: Significancementioning

confidence: 97%

“…When each unit cell varies independently, the diffuse intensity is proportional to the variance in the unit cell structure factor (17), which describes correlations in the charge density variations. This assumption is appropriate when analyzing the broadly distributed diffuse intensity that corresponds to small correlation lengths (18)(19)(20)(21), as the contribution of inter-unit cell atom pairs in this case is a small fraction of the total signal.Several approaches have been used to connect macromolecular diffuse scattering data to models of protein motion and lattice disorder. Peter Moore (22) has emphasized the need to validate TLS models using diffuse scattering, as has been performed in a limited number of cases (8,23,24).…”

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Measuring and modeling diffuse scattering in protein X-ray crystallography

Benschoten

Liu

González

et al. 2016

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

View full text Add to dashboard Cite

X-ray diffraction has the potential to provide rich information about the structural dynamics of macromolecules. To realize this potential, both Bragg scattering, which is currently used to derive macromolecular structures, and diffuse scattering, which reports on correlations in charge density variations, must be measured. Until now, measurement of diffuse scattering from protein crystals has been scarce because of the extra effort of collecting diffuse data. Here, we present 3D measurements of diffuse intensity collected from crystals of the enzymes cyclophilin A and trypsin. The measurements were obtained from the same X-ray diffraction images as the Bragg data, using best practices for standard data collection. To model the underlying dynamics in a practical way that could be used during structure refinement, we tested translation-libration-screw (TLS), liquid-like motions (LLM), and coarse-grained normal-modes (NM) models of protein motions. The LLM model provides a global picture of motions and was refined against the diffuse data, whereas the TLS and NM models provide more detailed and distinct descriptions of atom displacements, and only used information from the Bragg data. Whereas different TLS groupings yielded similar Bragg intensities, they yielded different diffuse intensities, none of which agreed well with the data. In contrast, both the LLM and NM models agreed substantially with the diffuse data. These results demonstrate a realistic path to increase the number of diffuse datasets available to the wider biosciences community and indicate that dynamics-inspired NM structural models can simultaneously agree with both Bragg and diffuse scattering.protein dynamics | normal modes | structural biology | diffuse scattering | liquid-like motions X -ray crystallography can be a key tool for elucidating the structural basis of protein motions that play critical roles in enzymatic reactions, protein-protein interactions, and signaling cascades (1). X-ray diffraction yields an ensemble-averaged picture of the protein structure: each photon simultaneously probes multiple unit cells that can vary because of internal rearrangements or changes to the crystal lattice. Bragg analysis of X-ray diffraction only yields the mean charge density of the unit cell, however, which fundamentally limits the information that can be obtained about protein dynamics (2, 3).An inherent limitation in Bragg analysis is that models with different concerted motions can yield the same mean charge density (4). The traditional approach assumes a single structural model with individual atomic displacement parameters (B factors). Given enough data, anisotropic displacement parameters can be modeled. When the data are more limited, translation-libration-screw (TLS) refinement, which models rigid-body motions of subdomains (5), is often used [22% of Protein Data Bank (PDB) depositions (6, 7)]. Variations in the TLS domains can predict very different motions that agree equally well with the Bragg data (8, 9).Bragg analysis can be combined ...

show abstract

Section: Significancementioning

confidence: 97%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Measuring and modeling diffuse scattering in protein X-ray crystallography

Benschoten

Liu

González

et al. 2016

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

View full text Add to dashboard Cite

show abstract

“…A shift toward this ''open'' CaM conformation is believed to be a prerequisite for interactions with many CaM-regulated proteins (1,32,39). Binding to most targets, including the CaM-binding domain of CaMKII (CaMKII-cbp), induces a conformation in which CaM wraps around the target domain, resulting in a coil-to-helix transition in the target (35,40) (Fig. 2C).…”

Section: Computationally Designed Mutant Cams That Bind Two Ca 2؉ Ionmentioning

confidence: 99%

Ca ²⁺ /calmodulin-dependent protein kinase II (CaMKII) is activated by calmodulin with two bound calciums

Shifman

Choi²,

Mihalaş³

et al. 2006

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

122

142

View full text Add to dashboard Cite

Changes in synaptic strength that underlie memory formation in the CNS are initiated by pulses of Ca 2؉ flowing through NMDAtype glutamate receptors into postsynaptic spines. Differences in the duration and size of the pulses determine whether a synapse is potentiated or depressed after repetitive synaptic activity. Calmodulin (CaM) is a major Ca 2؉ effector protein that binds up to four Ca 2؉ ions. CaM with bound Ca 2؉ can activate at least six signaling enzymes in the spine. In fluctuating cytosolic Ca 2؉ , a large fraction of free CaM is bound to fewer than four Ca 2؉ ions. Binding to targets increases the affinity of CaM's remaining Ca 2؉ -binding sites. Thus, initial binding of CaM to a target may depend on the target's affinity for CaM with only one or two bound Ca 2؉ ions. To study CaM-dependent signaling in the spine, we designed mutant CaMs that bind Ca 2؉ only at the two N-terminal or two C-terminal sites by using computationally designed mutations to stabilize the inactivated Ca 2؉ -binding domains in the ''closed'' Ca 2؉ -free conformation. We have measured their interactions with CaMKII, a major Ca 2؉ ͞CaM target that mediates initiation of long-term potentiation. We show that CaM with two Ca 2؉ ions bound in its C-terminal lobe not only binds to CaMKII with low micromolar affinity but also partially activates kinase activity. Our results support the idea that competition for binding of CaM with two bound Ca 2؉ ions may influence significantly the outcome of local Ca 2؉ signaling in spines and, perhaps, in other signaling pathways.postsynaptic ͉ protein design ͉ synaptic plasticity ͉ microdomains

show abstract

“…For instance, current data processing programs do not make use of diffuse scattering information, which can be evident in diffraction images but is lost upon conversion into structure factors (Fig. 1) (Glover et al, 1991;Wall et al, 1997). Thirdly, and most importantly, a centralized archive of raw X-ray data would ensure that this experimental evidence is preserved, to the long-term advantage of both depositors and users.…”

mentioning

confidence: 99%