[19]Study of protein dynamics by X-ray diffraction

摘要: Properly carried out, high-resolution X-ray diffraction data collection followed by careful least-squares refinement can give the spatial distribution of high-frequency mean-square displacements in a protein. These reflect both individual atomic fluctuations hard variables (bond lengths and bond angles) collective motions involving soft (torsion angles, nonbonded interactions). Lower frequency, large amplitude rapid but improbable are not quantifiable, they may lead to such complete disorder that their existence at least be inferred from absence interpretable electron density for some sections structure. Interior residues more rigid than groups on surface, structural constraints reflected restricted motion even surface residues. Amplitudes 0.5 A or greater uncommon. The temperature dependence these fast varies considerably over In general, 〈x2〉 values have dependence, while small less affected temperature; however, exceptions common. Significant reduction cooling establishes proteins mobile crystalline state, static is dominant contributor mean square displacements. Disordered regions maps no longer automatically taken as signs errors structure determination. It now recognized strong often an indicator conformational flexibility. Some functional roles protein dynamics beginning understood. Missing results physicochemical details extracted thermal analysis molecule crystal structures. Application methods very difficult, it well remember just 10 years ago was commonly felt structures could refined. Certainly small, well-diffracting should amenable many sophisticated small-molecule analyses, yield resolutions comparable simple organic structures. The most important type awaits anisotropic B factor refinement, which would principal directions added information obtained. Unfortunately, unrestrained elipsoids requires six parameters each atom instead single isotropic parameter, 1.5 resolution do provide enough overdeterminacy. An alternative approach refine selected anisotropically holding rest fixed. only published procedure restrained implements restraints based directions29; this invalidated result molecular destroy correlation. Optimally, coupled with few proteins. studies develop group-atom light unbiased information. Blundell associates undertaken precisely study avian pancreatic polypeptide, measuring beyond 1 refining procedures, including full model.89 X-Ray atomic-resolution about initial final states process ligand binding triggered change, pathway much difficult unravel. Ringe has shown bulky used prevent return channel its resting state after binding, allowing move form identified.14 Ligands chemical “tails” might investigate other channels Intermediate changes trapped low temperatures90,91 choice inhibitors, examination abortive complexes multisubstrate reactions. The determined nonexistent average molecule. will best fit measured scattering amplitudes. contains contributions all different substates generated thermally driven during time collection,92 being weighted according probability lifetime. Any ideal angles merely one representative ensemble conformations. Most spectroscopic probes activity also properties molecule, sensitive members so see slightly average. certain cases, conformations seen particular technique, react substance. This picture emerged crystallographic dynamics.