Browsing by Subject "Models, Structural"

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    Accelerating crystal structure determination with iterative AlphaFold prediction.
    (Acta crystallographica. Section D, Structural biology, 2023-03) Terwilliger, Thomas C; Afonine, Pavel V; Liebschner, Dorothee; Croll, Tristan I; McCoy, Airlie J; Oeffner, Robert D; Williams, Christopher J; Poon, Billy K; Richardson, Jane S; Read, Randy J; Adams, Paul D
    Experimental structure determination can be accelerated with artificial intelligence (AI)-based structure-prediction methods such as AlphaFold. Here, an automatic procedure requiring only sequence information and crystallographic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. Iterating through cycles of structure prediction is a key element of this procedure: a predicted model rebuilt in one cycle is used as a template for prediction in the next cycle. This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. In 87% of cases our procedure yielded a model with at least 50% of Cα atoms matching those in the deposited models within 2 Å. Predictions from the iterative template-guided prediction procedure were more accurate than those obtained without templates. It is concluded that AlphaFold predictions obtained based on sequence information alone are usually accurate enough to solve the crystallographic phase problem with molecular replacement, and a general strategy for macromolecular structure determination that includes AI-based prediction both as a starting point and as a method of model optimization is suggested.
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    ItemOpen Access
    Molecular endpoints of Ca2+/calmodulin- and voltage-dependent inactivation of Ca(v)1.3 channels.
    (J Gen Physiol, 2010-03) Tadross, Michael R; Ben Johny, Manu; Yue, David T
    Ca(2+)/calmodulin- and voltage-dependent inactivation (CDI and VDI) comprise vital prototypes of Ca(2+) channel modulation, rich with biological consequences. Although the events initiating CDI and VDI are known, their downstream mechanisms have eluded consensus. Competing proposals include hinged-lid occlusion of channels, selectivity filter collapse, and allosteric inhibition of the activation gate. Here, novel theory predicts that perturbations of channel activation should alter inactivation in distinctive ways, depending on which hypothesis holds true. Thus, we systematically mutate the activation gate, formed by all S6 segments within Ca(V)1.3. These channels feature robust baseline CDI, and the resulting mutant library exhibits significant diversity of activation, CDI, and VDI. For CDI, a clear and previously unreported pattern emerges: activation-enhancing mutations proportionately weaken inactivation. This outcome substantiates an allosteric CDI mechanism. For VDI, the data implicate a "hinged lid-shield" mechanism, similar to a hinged-lid process, with a previously unrecognized feature. Namely, we detect a "shield" in Ca(V)1.3 channels that is specialized to repel lid closure. These findings reveal long-sought downstream mechanisms of inactivation and may furnish a framework for the understanding of Ca(2+) channelopathies involving S6 mutations.