Attempts at using protein structures to identify disease-causing mutations have been dominated by the idea that most pathogenic mutations are disruptive at a structural level. Therefore, computational stability predictors, which assess whether a mutation is likely to be stabilising or destabilising to protein structure, have been commonly used when evaluating new candidate disease variants, despite not having been developed specifically for this purpose. We therefore tested 13 different stability predictors for their ability to discriminate between pathogenic and putatively benign missense variants. We find that one method, FoldX, significantly outperforms all other predictors in the identification of disease variants. Moreover, we demonstrate that employing predicted absolute energy change scores improves performance of nearly all predictors in distinguishing pathogenic from benign variants. Importantly, however, we observe that the utility of computational stability predictors is highly heterogeneous across different proteins, and that they are all inferior to the best performing variant effect predictors for identifying pathogenic mutations. We suggest that this is largely due to alternate molecular mechanisms other than protein destabilisation underlying many pathogenic mutations. Thus, better ways of incorporating protein structural information and molecular mechanisms into computational variant effect predictors will be required for improved disease variant prioritisation.

Most known disease-causing mutations occur in protein-coding regions of DNA. While some of these involve a loss of protein function (e.g., through premature stop codons or missense changes that destabilize protein folding), many act via alternative molecular mechanisms and have dominant-negative or gain-of-function effects. In nearly all cases, these non-loss-of-function mutations can be understood by considering interactions of the wild-type and mutant protein with other molecules, such as proteins, nucleic acids, or small ligands and substrates. Here, we review the diverse molecular mechanisms by which pathogenic mutations can have non-loss-of-function effects, including by disrupting interactions, increasing binding affinity, changing binding specificity, causing assembly-mediated dominant-negative and dominant-positive effects, creating novel interactions, and promoting aggregation and phase separation. We believe that increased awareness of these diverse molecular disease mechanisms will lead to improved diagnosis (and ultimately treatment) of human genetic disorders. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

BackgroundImprovements in data processing, increased understanding of the biomechanical background behind kinetics and kinematics, and technological advancements in inertial measurement unit (IMU) sensors have enabled high precision in the measurement of joint angles and acceleration on human subjects. This has resulted in new devices that reportedly measure joint angles, arm speed, and stresses to the pitching arms of baseball players. This study seeks to validate one such sensor, the MotusBASEBALL unit, with a marker-based motion capture laboratory.HypothesisWe hypothesize that the joint angle measurements (“arm slot” and “shoulder rotation”) of the MotusBASEBALL device will hold a statistically significant level of reliability and accuracy, but that the “arm speed” and “stress” metrics will not be accurate due to limitations in IMU technology.MethodsA total of 10 healthy subjects threw five to seven fastballs followed by five to seven breaking pitches (slider or curveball) in the motion capture lab. Subjects wore retroreflective markers and the MotusBASEBALL sensor simultaneously.ResultsIt was found that the arm slot (R = 0.975, P < 0.001), shoulder rotation (R = 0.749, P < 0.001), and stress (R = 0.667, P = 0.001 when compared to elbow torque; R = 0.653, P = 0.002 when compared to shoulder torque) measurements were all significantly correlated with the results from the motion capture lab. Arm speed showed significant correlations to shoulder internal rotation speed (R = 0.668, P = 0.001) and shoulder velocity magnitude (R = 0.659, P = 0.002). For the entire sample, arm slot and shoulder rotation measurements were on a similar scale, or within 5–15% in absolute value, of magnitude to measurements from the motion capture test, averaging eight degrees less (12.9% relative differences) and nine degrees (5.4%) less, respectively. Arm speed had a much larger difference, averaging 3,745 deg/s (80.2%) lower than shoulder internal rotation velocity, and 3,891 deg/s (80.8%) less than the shoulder velocity magnitude. The stress metric was found to be 41 Newton meter (Nm; 38.7%) less when compared to elbow torque, and 42 Nm (39.3%) less when compared to shoulder torque. Despite the differences in magnitude, the correlations were extremely strong, indicating that the MotusBASEBALL sensor had high reliability for casual use.ConclusionThis study attempts to validate the use of the MotusBASEBALL for future studies that look at the arm slot, shoulder rotation, arm speed, and stress measurements from the MotusBASEBALL sensor. Excepting elbow extension velocity, all metrics from the MotusBASEBALL unit showed significant correlations to their corresponding metrics from motion capture and while some magnitudes differ substantially and therefore fall short in validity, the link between the metrics is strong enough to indicate reliable casual use. Further research should be done to further investigate the validity and reliability of the arm speed metric.

DNA replication is fundamental for cell proliferation in all organisms. Nonetheless, components of the replisome have been implicated in human disease, and here we report PRIM1 encoding the catalytic subunit of DNA primase as a novel disease gene. Using a variant classification agnostic approach, biallelic mutations in PRIM1 were identified in five individuals. PRIM1 protein levels were markedly reduced in patient cells, accompanied by replication fork asymmetry, increased interorigin distances, replication stress, and prolonged S-phase duration. Consequently, cell proliferation was markedly impaired, explaining the patients' extreme growth failure. Notably, phenotypic features distinct from those previously reported with DNA polymerase genes were evident, highlighting differing developmental requirements for this core replisome component that warrant future investigation.

Intraflagellar transport (IFT) is a highly conserved mechanism for motor-driven transport of cargo within cilia, but how this cargo is selectively transported to cilia is unclear. WDR35/IFT121 is a component of the IFT-A complex best known for its role in ciliary retrograde transport. In the absence of WDR35, small mutant cilia form but fail to enrich in diverse classes of ciliary membrane proteins. In Wdr35 mouse mutants, the non-core IFT-A components are degraded and core components accumulate at the ciliary base. We reveal deep sequence homology of WDR35 and other IFT-A subunits to α and ß' COPI coatomer subunits, and demonstrate an accumulation of 'coat-less' vesicles which fail to fuse with Wdr35 mutant cilia. We determine that recombinant non-core IFT-As can bind directly to lipids and provide the first in-situ evidence of a novel coat function for WDR35, likely with other IFT-A proteins, in delivering ciliary membrane cargo necessary for cilia elongation.

Approximately half of proteins with experimentally determined structures can interact with other copies of themselves and assemble into homomeric complexes, the overwhelming majority of which (>96%) are symmetric. Although homomerisation is often assumed to a functionally beneficial result of evolutionary selection, there has been little systematic analysis of the relationship between homomer structure and function. Here, utilizing the large numbers of structures and functional annotations now available, we have investigated how proteins that assemble into different types of homomers are associated with different biological functions. We observe that homomers from different symmetry groups are significantly enriched in distinct functions, and can often provide simple physical and geometrical explanations for these associations in regards to substrate recognition or physical environment. One of the strongest associations is the tendency for metabolic enzymes to form dihedral complexes, which we suggest is closely related to allosteric regulation. We provide a physical explanation for why allostery is related to dihedral complexes: it allows for efficient propagation of conformational changes across isologous (i.e. symmetric) interfaces. Overall we demonstrate a clear relationship between protein function and homomer symmetry that has important implications for understanding protein evolution, as well as for predicting protein function and quaternary structure.One of the fundamental challenges in the biological sciences is in understanding the relationship between protein structure and function. This problem is highly relevant not only to the understanding of the evolution of a protein's biological role, but for protein structure and function prediction, protein design, and the prediction of the phenotypic impact of mutations.Within protein families there is enormous functional diversity, and sequences, folds and domains can all code for different functionalities depending on their surroundings 1-3 . In the dynamic and crowded environment that is a living cell 4, 5 , proteins are in constant contact with each other and often carry out their functions as part of larger protein complexes [6][7][8][9] . The way that the subunits are organised to form the quaternary structure of a protein complex is a crucial piece of the protein structure-function relationship puzzle, alongside sequences, folds and domains.Most of the structural information on protein complexes that we have available today is for homomers, i.e. protein complexes that are formed by the assembly of multiple copies of a single type of polypeptide chain. Analysis of published X-ray crystal structures shows that roughly 45% of eukaryotic proteins and 60% of prokaryotic proteins can form homomeric complexes 10 . Whilst the high fraction of homomers does reflect biases in protein structure determination, and the fraction of heteromeric complexes (i.e. those formed from multiple distinct polypeptide chains) within cells is probably higher, homomerisation is ...

Purpose Lamins are the major component of nuclear lamina, maintaining structural integrity of the nucleus. Lamin A/C variants are well established to cause a spectrum of disorders ranging from myopathies to progeria, termed laminopathies. Phenotypes resulting from variants in LMNB1 and LMNB2 have been much less clearly defined. Methods We investigated exome and genome sequencing from the Deciphering Developmental Disorders Study and the 100,000 Genomes Project to identify novel microcephaly genes. Results Starting from a cohort of patients with extreme microcephaly, 13 individuals with heterozygous variants in the two human B-type lamins were identified. Recurrent variants were established to be de novo in nine cases and shown to affect highly conserved residues within the lamin ɑ-helical rod domain, likely disrupting interactions required for higher-order assembly of lamin filaments. Conclusion We identify dominant pathogenic variants in LMNB1 and LMNB2 as a genetic cause of primary microcephaly, implicating a major structural component of the nuclear envelope in its etiology and defining a new form of laminopathy. The distinct nature of this lamin B–associated phenotype highlights the strikingly different developmental requirements for lamin paralogs and suggests a novel mechanism for primary microcephaly warranting future investigation.

BackgroundWeighted-baseball training programs are used at the high school, collegiate, and professional levels of baseball. The purpose of this study was to evaluate the effects of a six-week training period consisting of weighted implements, manual therapy, weightlifting, and other modalities on shoulder external rotation, elbow valgus stress, pitching velocity, and kinematics.HypothesisA six-week training program that includes weighted implements will increase pitching velocity along with concomitant increases in arm angular velocities, joint kinetics, and shoulder external rotation.MethodsSeventeen collegiate and professional baseball pitchers (age range 18–23, average: 19.9 ± 1.3) training at Driveline Baseball were evaluated via a combination of an eight-camera motion-capture system, range-of-motion measurements and radar- and pitch-tracking equipment, both before and after a six-week training period. Each participant received individualized training programs, with significant overlap in training methods for all athletes. Twenty-eight biomechanical parameters were computed for each bullpen trial, four arm range-of-motion measurements were taken, and pitching velocities were recorded before and after the training period. Pre- and post-training period data were compared via post-hoc paired t tests.ResultsThere was no change in pitching velocity across the seventeen subjects. Four biomechanical parameters for the holistic group were significantly changed after the training period: internal rotational velocity was higher (from 4,527 ± 470 to 4,759 ± 542 degrees/second), shoulder abduction was lower at ball release (96 ± 7.6 to 93 ± 5.4°), the shoulder was less externally rotated at ball release (95 ± 15 to 86 ± 18°) and shoulder adduction torque was higher (from 103 ± 39 to 138 ± 53 N-m). Among the arm range of motion measurements, four were significantly different after the training period: the shoulder internal rotation range of motion and total range of motion for both the dominant and non-dominant arm. When the group was divided into those who gained pitching velocity and those who did not, neither group showed a significant increase in shoulder external rotation, or elbow valgus stress.ConclusionsFollowing a six-week weighted implement program, pitchers did not show a significant change in velocity, joint kinetics, or shoulder external rotation range of motion. When comparing pitchers who gained velocity versus pitchers who did not, no statistically significant changes were seen in joint kinetics and shoulder range of motion.