The Use of Variant Maps to Explore Domain-Specific Mutations of FGFR1.

Here we describe the genotype-phenotype correlations of diseases caused by variants in Fibroblast Growth Factor Receptor 1 ( FGFR1) and report a novel, de novo variant in FGFR1 in an individual with multiple congenital anomalies. The proband presented with bilateral cleft lip and palate, malformed auricles, and bilateral ectrodactyly of his hands and feet at birth. He was later diagnosed with diabetes insipidus, spastic quadriplegia, developmental delay, agenesis of the corpus callosum, and enlargement of the third cerebral ventricle. We noted the substantial phenotypic overlap with individuals with Hartsfield syndrome, the rare combination of holoprosencephaly and ectrodactyly. Sequencing of FGFR1 identified a previously unreported de novo variant in exon 11 (p.Gly487Cys), which we modeled to determine its predicted effect on the protein structure. Although it was not predicted to significantly alter protein folding stability, it is possible this variant leads to the formation of nonnative intra- or intermolecular disulfide bonds. We then mapped this and other disease-associated variants to a 3-dimensional model of FGFR1 to assess which protein domains harbored the highest number of pathogenic changes. We observed the greatest number of variants within the domains involved in FGF binding and FGFR activation. To further explore the contribution of each variant to disease, we recorded the phenotype resulting from each FGFR1 variant to generate a series of phenotype-specific protein maps and compared our results to benign variants appearing in control databases. It is our hope that the use of phenotypic maps such as these will further the understanding of genetic disease in general and diseases caused by variation in FGFR1 specifically.

Polarizable atomic multipole X-ray refinement: weighting schemes for macromolecular diffraction.

In the past, weighting between the sum of chemical and data-based targets in macromolecular crystallographic refinement was based on comparing the gradients or Hessian diagonal terms of the two potential functions. Here, limitations of this scheme are demonstrated, especially in the context of a maximum-likelihood target that is inherently weighted by the model and data errors. In fact, the congruence between the maximum-likelihood target and a chemical potential based on polarizable atomic multipole electrostatics evaluated with Ewald summation has opened the door to a transferable static weight. An optimal static weight is derived from first principles and is demonstrated to be transferable across a broad range of data resolutions in the context of a recent implementation of X-ray crystallographic refinement using the polarizable AMOEBA force field and it is shown that the resulting models are balanced with respect to optimizing both R(free) and MolProbity scores. Conversely, the classical automatic weighting scheme is shown to lead to underfitting or overfitting of the data and poor model geometry. The benefits of this approach for low-resolution diffraction data, where the need for prior chemical information is of particular importance, are also highlighted. It is demonstrated that this method is transferable between low- and high-resolution maximum-likelihood-based crystallographic refinement, which proves for the first time that resolution-dependent parameterization of either the weight or the chemical potential is unnecessary.

A smooth and differentiable bulk-solvent model for macromolecular diffraction.

Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute-solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, R(free) and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6 A) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography.

Assessing the accuracy of a prototype drill guide for fibular graft placement in femoral head necrosis.

A prototype drill guide was developed to improve the accuracy of surgical placement of fibular grafts for the treatment of femoral head necrosis. To document performance, two tantalum beads, one placed on the lateral femoral shaft and the other embedded in the superior portion of the head, were used to define the desired graft tract in a series of seven surrogate femurs. Two orthogonal x-rays of the drill guide mounted on each surrogate femur were taken both before and after drilling. After stylus digitization of each x-ray pair, a computer program calculated the achieved accuracy of the drill. The mean of the absolute error between the desired versus obtained position of the drill tip was 3.68 mm (s.d. 1.24 mm), and the random component of the error was 1.98 mm (s.d. 0.89 mm).