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1.
Nat Commun ; 15(1): 3351, 2024 Apr 18.
Article En | MEDLINE | ID: mdl-38637543

While much prior work has explored the constraints on protein sequence and evolution induced by physical protein-protein interactions, the sequence-level constraints emerging from non-binding functional interactions in metabolism remain unclear. To quantify how variation in the activity of one enzyme constrains the biochemical parameters and sequence of another, we focus on dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), a pair of enzymes catalyzing consecutive reactions in folate metabolism. We use deep mutational scanning to quantify the growth rate effect of 2696 DHFR single mutations in 3 TYMS backgrounds under conditions selected to emphasize biochemical epistasis. Our data are well-described by a relatively simple enzyme velocity to growth rate model that quantifies how metabolic context tunes enzyme mutational tolerance. Together our results reveal the structural distribution of epistasis in a metabolic enzyme and establish a foundation for the design of multi-enzyme systems.


Thymidylate Synthase , Mutation , Thymidylate Synthase/metabolism
3.
bioRxiv ; 2023 Aug 17.
Article En | MEDLINE | ID: mdl-37645784

Enzyme abundance, catalytic activity, and ultimately sequence are all shaped by the need of growing cells to maintain metabolic flux while minimizing accumulation of deleterious intermediates. While much prior work has explored the constraints on protein sequence and evolution induced by physical protein-protein interactions, the sequence-level constraints emerging from non-binding functional interactions in metabolism remain unclear. To quantify how variation in the activity of one enzyme constrains the biochemical parameters and sequence of another, we focused on dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), a pair of enzymes catalyzing consecutive reactions in folate metabolism. We used deep mutational scanning to quantify the growth rate effect of 2,696 DHFR single mutations in 3 TYMS backgrounds under conditions selected to emphasize biochemical epistasis. Our data are well-described by a relatively simple enzyme velocity to growth rate model that quantifies how metabolic context tunes enzyme mutational tolerance. Together our results reveal the structural distribution of epistasis in a metabolic enzyme and establish a foundation for the design of multi-enzyme systems.

4.
Nat Ecol Evol ; 7(9): 1480-1489, 2023 09.
Article En | MEDLINE | ID: mdl-37500908

Estimates of deep-time biodiversity typically rely on statistical methods to mitigate the impacts of sampling biases in the fossil record. However, these methods are limited by the spatial and temporal scale of the underlying data. Here we use a spatially explicit mechanistic model, based on neutral theory, to test hypotheses of early tetrapod diversity change during the late Carboniferous and early Permian, critical intervals for the diversification of vertebrate life on land. Our simulations suggest that apparent increases in early tetrapod diversity were not driven by local endemism following the 'Carboniferous rainforest collapse'. Instead, changes in face-value diversity can be explained by variation in sampling intensity through time. Our results further demonstrate the importance of accounting for sampling biases in analyses of the fossil record and highlight the vast potential of mechanistic models, including neutral models, for testing hypotheses in palaeobiology.


Biological Evolution , Vertebrates , Animals , Selection Bias , Biodiversity , Fossils
5.
Genes (Basel) ; 14(1)2023 01 14.
Article En | MEDLINE | ID: mdl-36672956

Histone lysine methyltransferase and demethylase enzymes play a central role in chromatin organization and gene expression through the dynamic regulation of histone lysine methylation. Consistent with this, genes encoding for histone lysine methyltransferases (KMTs) and demethylases (KDMs) are involved in complex human syndromes, termed congenital regulopathies. In this report, we present several lines of evidence for the involvement of these genes in developmental ocular phenotypes, suggesting that individuals with structural eye defects, especially when accompanied by craniofacial, neurodevelopmental and growth abnormalities, should be examined for possible variants in these genes. We identified nine heterozygous damaging genetic variants in KMT2D (5) and four other histone lysine methyltransferases/demethylases (KMT2C, SETD1A/KMT2F, KDM6A and KDM5C) in unrelated families affected with developmental eye disease, such as Peters anomaly, sclerocornea, Axenfeld-Rieger spectrum, microphthalmia and coloboma. Two families were clinically diagnosed with Axenfeld-Rieger syndrome and two were diagnosed with Peters plus-like syndrome; others received no specific diagnosis prior to genetic testing. All nine alleles were novel and five of them occurred de novo; five variants resulted in premature truncation, three were missense changes and one was an in-frame deletion/insertion; and seven variants were categorized as pathogenic or likely pathogenic and two were variants of uncertain significance. This study expands the phenotypic spectra associated with KMT and KDM factors and highlights the importance of genetic testing for correct clinical diagnosis.


Eye Abnormalities , Histones , Humans , Histones/genetics , Lysine/metabolism , Histone-Lysine N-Methyltransferase/genetics , Histone-Lysine N-Methyltransferase/metabolism , Eye Abnormalities/genetics , Histone Demethylases/genetics , Histone Demethylases/metabolism
6.
Eur J Hum Genet ; 31(3): 363-367, 2023 03.
Article En | MEDLINE | ID: mdl-36450800

ARHGAP35 has known roles in cell migration, invasion and division, neuronal morphogenesis, and gene/mRNA regulation; prior studies indicate a role in cancer in humans and in the developing eyes, neural tissue, and renal structures in mice. We identified damaging variants in ARHGAP35 in five individuals from four families affected with anophthalmia, microphthalmia, coloboma and/or anterior segment dysgenesis disorders, together with variable non-ocular phenotypes in some families including renal, neurological, or cardiac anomalies. Three variants affected the extreme C-terminus of the protein, with two resulting in a frameshift and C-terminal extension and the other a missense change in the Rho-GAP domain; the fourth (nonsense) variant affected the middle of the gene and is the only allele predicted to undergo nonsense-mediated decay. This study implicates ARHGAP35 in human developmental eye phenotypes. C-terminal clustering of the identified alleles indicates a possible common mechanism for ocular disease but requires further studies.


Anophthalmos , Coloboma , Eye Abnormalities , Microphthalmos , Humans , Animals , Mice , Eye Abnormalities/genetics , Microphthalmos/genetics , Anophthalmos/genetics , Coloboma/genetics , Phenotype , Mutation , Repressor Proteins/genetics , Guanine Nucleotide Exchange Factors/genetics
7.
J Med Genet ; 60(4): 368-379, 2023 04.
Article En | MEDLINE | ID: mdl-35882526

BACKGROUND: Axenfeld-Rieger syndrome (ARS) is characterised by typical anterior segment anomalies, with or without systemic features. The discovery of causative genes identified ARS subtypes with distinct phenotypes, but our understanding is incomplete, complicated by the rarity of the condition. METHODS: Genetic and phenotypic characterisation of the largest reported ARS cohort through comprehensive genetic and clinical data analyses. RESULTS: 128 individuals with causative variants in PITX2 or FOXC1, including 81 new cases, were investigated. Ocular anomalies showed significant overlap but with broader variability and earlier onset of glaucoma for FOXC1-related ARS. Systemic anomalies were seen in all individuals with PITX2-related ARS and the majority of those with FOXC1-related ARS. PITX2-related ARS demonstrated typical umbilical anomalies and dental microdontia/hypodontia/oligodontia, along with a novel high rate of Meckel diverticulum. FOXC1-related ARS exhibited characteristic hearing loss and congenital heart defects as well as previously unrecognised phenotypes of dental enamel hypoplasia and/or crowding, a range of skeletal and joint anomalies, hypotonia/early delay and feeding disorders with structural oesophageal anomalies in some. Brain imaging revealed highly penetrant white matter hyperintensities, colpocephaly/ventriculomegaly and frequent arachnoid cysts. The expanded phenotype of FOXC1-related ARS identified here was found to fully overlap features of De Hauwere syndrome. The results were used to generate gene-specific management plans for the two types of ARS. CONCLUSION: Since clinical features of ARS vary significantly based on the affected gene, it is critical that families are provided with a gene-specific diagnosis, PITX2-related ARS or FOXC1-related ARS. De Hauwere syndrome is proposed to be a FOXC1opathy.


Eye Abnormalities , Homeodomain Proteins , Humans , Homeodomain Proteins/genetics , Transcription Factors/genetics , Anterior Eye Segment/abnormalities , Eye Abnormalities/genetics , Eye Abnormalities/diagnosis , Forkhead Transcription Factors/genetics , Mutation
8.
Hum Genomics ; 16(1): 49, 2022 10 25.
Article En | MEDLINE | ID: mdl-36284357

FOXC1 encodes a forkhead-domain transcription factor associated with several ocular disorders. Correct FOXC1 dosage is critical to normal development, yet the mechanisms controlling its expression remain unknown. Together with FOXQ1 and FOXF2, FOXC1 is part of a cluster of FOX genes conserved in vertebrates. CRISPR-Cas9-mediated dissection of genomic sequences surrounding two zebrafish orthologs of FOXC1 was performed. This included five zebrafish-human conserved regions, three downstream of foxc1a and two remotely upstream of foxf2a/foxc1a or foxf2b/foxc1b clusters, as well as two intergenic regions between foxc1a/b and foxf2a/b lacking sequence conservation but positionally corresponding to the area encompassing a previously reported glaucoma-associated SNP in humans. Removal of downstream sequences altered foxc1a expression; moreover, zebrafish carrying deletions of two or three downstream elements demonstrated abnormal phenotypes including enlargement of the anterior chamber of the eye reminiscent of human congenital glaucoma. Deletions of distant upstream conserved elements influenced the expression of foxf2a/b or foxq1a/b but not foxc1a/b within each cluster. Removal of either intergenic sequence reduced foxc1a or foxc1b expression during late development, suggesting a role in transcriptional regulation despite the lack of conservation at the nucleotide level. Further studies of the identified regions in human patients may explain additional individuals with developmental ocular disorders.


Glaucoma , Zebrafish , Animals , Humans , Zebrafish/genetics , Zebrafish/metabolism , Zebrafish Proteins/genetics , Zebrafish Proteins/metabolism , CRISPR-Cas Systems/genetics , Gene Expression Regulation, Developmental , Forkhead Transcription Factors/genetics , Forkhead Transcription Factors/metabolism , Glaucoma/genetics , Genomics , DNA, Intergenic/genetics , DNA, Intergenic/metabolism , Nucleotides/metabolism
9.
J Phys Condens Matter ; 34(39)2022 Jul 29.
Article En | MEDLINE | ID: mdl-35853447

Melting experiments on Fe3S were conducted to 75 GPa and 2800 K in laser-heated and internally resistive-heated diamond anvil cells within-situx-ray diffraction and/or post-mortem textural observation. From the constrained melting curve, we assessed the thermal equation of state for Fe3S liquid. Then we constructed a thermodynamic model of melting of the system Fe-Fe3S including the eutectic relation under high pressures based on our new experimental data. The mixing properties of Fe-S liquids under high pressures were evaluated in order to account for existing experimental data on eutectic temperature. The results demonstrate that the mixing of Fe and S liquids are nonideal at any core pressure. The calculated sulphur content in eutectic point decreases with increasing pressure to 120 GPa and is fairly constant of 8 wt% at greater pressures. From the Gibbs free energy, we derived the parameters to calculate the crystallising point of an Fe-S core and its isentrope, and then we calculated the density and the longitudinal seismic wave velocity (Vp) of these liquids along each isentrope. While Fe3S liquid can account for the seismologically constrained density andVpprofiles over the outer core, the density of the precipitating phase is too low for the inner core. On the other hand, a hypothetical Fe-S liquid core with a bulk composition on the Fe-rich side of the eutectic point cannot represent the density andVpprofiles of the Earth's outer core. Therefore, Earth's core cannot be approximated by the system Fe-S and it should include another light element.

10.
J Pediatr Orthop ; 42(6): 314-320, 2022 Jul 01.
Article En | MEDLINE | ID: mdl-35667052

BACKGROUND: The optimal treatment of Gartland type IIa supracondylar humerus fractures remains controversial. We report the results of a series of patients with type IIa fractures who underwent closed reduction and immobilization using conscious sedation in the emergency department. Our goal was to identify variables associated with fractures that were successfully managed nonoperatively. METHODS: This was a retrospective cohort study of pediatric patients who underwent closed reduction of Gartland type IIa supracondylar humerus fractures with the use of conscious sedation in the emergency department. Prereduction and postreduction radiographs were reviewed to determine the degree of fracture extension, anterior humeral line index, Baumann angle, and splint flexion angle. The success of closed reduction was defined as a reduction that was maintained without the need for surgical intervention. RESULTS: A total of 54 patients (54 elbows) were included in this study. The mean overall age was 5.2±2.5 years. Following the closed reduction in the emergency department, 38 (70%) patients were successfully managed nonoperatively with casting, and 16 (30%) patients required operative intervention. The degree of fracture extension on the injury radiograph was 13.2±8.4 degrees in the nonoperative group compared with 19.8±7.5 degrees in the operative group (P=0.008). The postreduction degree of fracture extension was 3.0±3.4 degrees in the nonoperative group and 10.0±7.2 degrees in the operative group (P<0.0001). The mean anterior humeral line index on the injury radiograph was 0.34 in the nonoperative group and 0.13 in the operative group (P=0.104). The mean anterior humeral line index on the postreduction radiograph was 1.2 in the nonoperative group and 0.38 in the operative group (P=0.0002). Patient age, prereduction and postreduction Baumann angle, and the postreduction splint flexion angle did not differ significantly between groups. CONCLUSIONS: Closed reduction under conscious sedation in the emergency department is a viable treatment option for Gartland type IIa supracondylar humerus fractures. Increasing fracture extension on injury radiographs can help predict failure of nonoperative management following closed reduction. LEVEL OF EVIDENCE: Level III-retrospective comparative study.


Elbow Joint , Humeral Fractures , Child , Child, Preschool , Humans , Humeral Fractures/surgery , Humeral Fractures/therapy , Humerus , Retrospective Studies , Treatment Outcome , Elbow Injuries
11.
Elife ; 112022 06 28.
Article En | MEDLINE | ID: mdl-35762582

Members of the bacterial T6SS amidase effector (Tae) superfamily of toxins are delivered between competing bacteria to degrade cell wall peptidoglycan. Although Taes share a common substrate, they exhibit distinct antimicrobial potency across different competitor species. To investigate the molecular basis governing these differences, we quantitatively defined the functional determinants of Tae1 from Pseudomonas aeruginosa PAO1 using a combination of nuclear magnetic resonance and a high-throughput in vivo genetic approach called deep mutational scanning (DMS). As expected, combined analyses confirmed the role of critical residues near the Tae1 catalytic center. Unexpectedly, DMS revealed substantial contributions to enzymatic activity from a much larger, ring-like functional hot spot extending around the entire circumference of the enzyme. Comparative DMS across distinct growth conditions highlighted how functional contribution of different surfaces is highly context-dependent, varying alongside composition of targeted cell walls. These observations suggest that Tae1 engages with the intact cell wall network through a more distributed three-dimensional interaction interface than previously appreciated, providing an explanation for observed differences in antimicrobial potency across divergent Gram-negative competitors. Further binding studies of several Tae1 variants with their cognate immunity protein demonstrate that requirements to maintain protection from Tae activity may be a significant constraint on the mutational landscape of tae1 toxicity in the wild. In total, our work reveals that Tae diversification has likely been shaped by multiple independent pressures to maintain interactions with binding partners that vary across bacterial species and conditions.


Amidohydrolases , Peptidoglycan , Amidohydrolases/genetics , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/metabolism , Cell Wall/metabolism , Peptidoglycan/metabolism , Pseudomonas aeruginosa/metabolism
12.
Am J Clin Oncol ; 45(6): 268-272, 2022 06 01.
Article En | MEDLINE | ID: mdl-35588227

OBJECTIVES: Financial toxicity due to cancer treatment is a significant concern for patients. To increase transparency related to treatment costs, the Hospital Price Transparency Final Rule (HPTFR) was passed on January 1, 2021. We used hospital pricing documentation to explore the costs of head and neck cancer (HNC) radiotherapy in Ohio, hypothesizing a large variance in cost based on geography. MATERIALS AND METHODS: Radiation oncology facilities were identified using the Ohio Hospital Association (OHA) website. The reported technical charges for Current Procedural Terminology (CPT) codes commonly billed in the definitive management of HNC with radiotherapy were recorded, and total treatment costs (TTCs) were calculated. RESULTS: Of 254 OHA-listed hospitals, 102 had radiation oncology facilities. Seven facilities were excluded due to a lack of pricing data, leaving 95 facilities in 40 of 88 counties. Median TTC was $176,496. Average TTC was $184,831 (SD: $83,982). The 22 rural hospitals charged less compared with nonrural hospitals, with a difference in medians of $72,084.38 (P<0.001). No difference was found between the TTCs of nonprofit and public hospitals (P=0.348) nor between academically affiliated and nonacademically affiliated hospitals (P=0.247). There is no correlation between county median household income and TTC (R2=0.0007). Rather, TTCs varied drastically across counties, regardless of income levels. CONCLUSIONS: There is a wide range of treatment costs for HNC patients receiving definitive radiotherapy in Ohio, and no variables fully explain this variance. Further policies are needed to improve the quality, quantity, and accessibility of health care data to address financial toxicity.


Radiation Oncology , Delivery of Health Care , Health Care Costs , Hospital Costs , Hospitals , Humans
13.
Health Care Manage Rev ; 47(1): 78-85, 2022.
Article En | MEDLINE | ID: mdl-33399352

BACKGROUND: Voluntary turnover (VTO) of nursing employees is expensive for hospital systems and is often associated with lower levels of patient satisfaction, as well as adverse patient outcomes such as falls and medication errors. PURPOSE: The aim of this study was to establish nurses' electronic medical record (EMR) use patterns and test if they can be used to predict VTO. METHODOLOGY/APPROACH: The study followed 1,836 hospital nurses via the collection of EMR metadata through two 1-month time periods that were 1 year apart. Machine learning algorithms were then used to derive patterns of EMR utilization using VTO as a key variable for classification. Post hoc analysis of the most predictive variables was conducted. RESULTS: The predictive model was effective in identifying which nurses would turnover 73.4% of the time and which nurses would not turnover 84.1% of the time. PRACTICE APPLICATIONS: The ability to accurately predict nurses' intentions to leave is critical to reducing turnover. Early identification can lead to specific interventions to mitigate factors that are adversely impacting the nursing experience. Post hoc analysis and the key informant interviews indicated that many nurses do not appear to have good EMR navigation skills and spend significant effort in search of patient information.


Nursing Staff, Hospital , Personnel Turnover , Hospitals , Humans , Information Systems , Job Satisfaction , Surveys and Questionnaires
14.
Hum Genet ; 140(12): 1775-1789, 2021 Dec.
Article En | MEDLINE | ID: mdl-34642815

Missense variants located in the N-terminal region of WDR37 were recently identified to cause a multisystemic syndrome affecting neurological, ocular, gastrointestinal, genitourinary, and cardiac development. WDR37 encodes a WD40 repeat-containing protein of unknown function. We identified three novel WDR37 variants, two likely pathogenic de novo alleles and one inherited variant of uncertain significance, in individuals with phenotypes overlapping those previously reported but clustering in a different region of the protein. The novel alleles are C-terminal to the prior variants and located either within the second WD40 motif (c.659A>G p.(Asp220Gly)) or in a disordered protein region connecting the second and third WD40 motifs (c.778G>A p.(Asp260Asn) and c.770C>A p.(Pro257His)). The three novel mutants showed normal cellular localization but lower expression levels in comparison to wild-type WDR37. To investigate the normal interactions of WDR37, we performed co-immunoprecipitation and yeast two-hybrid assays. This revealed the ability of WDR37 to form homodimers and to strongly bind PACS1 and PACS2 phosphofurin acidic cluster sorting proteins; immunocytochemistry confirmed colocalization of WDR37 with PACS1 and PACS2 in human cells. Next, we analyzed previously reported and novel mutants for their ability to dimerize with wild-type WDR37 and bind PACS proteins. Interaction with wild-type WDR37 was not affected for any variant; however, one novel mutant, p.(Asp220Gly), lost its ability to bind PACS1 and PACS2. In summary, this study presents a novel region of WDR37 involved in human disease, identifies PACS1 and PACS2 as major binding partners of WDR37 and provides insight into the functional effects of various WDR37 variants.


Abnormalities, Multiple/genetics , Mutant Proteins/genetics , Nuclear Proteins/genetics , Abnormalities, Multiple/metabolism , Adolescent , Animals , Cells, Cultured , Child , Child, Preschool , Cognitive Dysfunction/genetics , Female , Humans , Male , Mutant Proteins/metabolism , Nuclear Proteins/metabolism , Pedigree , Protein Binding , Syndrome , Two-Hybrid System Techniques , Vesicular Transport Proteins/metabolism
15.
Elife ; 102021 06 16.
Article En | MEDLINE | ID: mdl-34132193

Our ability to rationally optimize allosteric regulation is limited by incomplete knowledge of the mutations that tune allostery. Are these mutations few or abundant, structurally localized or distributed? To examine this, we conducted saturation mutagenesis of a synthetic allosteric switch in which Dihydrofolate reductase (DHFR) is regulated by a blue-light sensitive LOV2 domain. Using a high-throughput assay wherein DHFR catalytic activity is coupled to E. coli growth, we assessed the impact of 1548 viable DHFR single mutations on allostery. Despite most mutations being deleterious to activity, fewer than 5% of mutations had a statistically significant influence on allostery. Most allostery disrupting mutations were proximal to the LOV2 insertion site. In contrast, allostery enhancing mutations were structurally distributed and enriched on the protein surface. Combining several allostery enhancing mutations yielded near-additive improvements to dynamic range. Our results indicate a path toward optimizing allosteric function through variation at surface sites.


Many proteins exhibit a property called 'allostery'. In allostery, an input signal at a specific site of a protein ­ such as a molecule binding, or the protein absorbing a photon of light ­ leads to a change in output at another site far away. For example, the protein might catalyze a chemical reaction faster or bind to another molecule more tightly in the presence of the input signal. This protein 'remote control' allows cells to sense and respond to changes in their environment. An ability to rapidly engineer new allosteric mechanisms into proteins is much sought after because this would provide an approach for building biosensors and other useful tools. One common approach to engineering new allosteric regulation is to combine a 'sensor' or input region from one protein with an 'output' region or domain from another. When researchers engineer allostery using this approach of combining input and output domains from different proteins, the difference in the output when the input is 'on' versus 'off' is often small, a situation called 'modest allostery'. McCormick et al. wanted to know how to optimize this domain combination approach to increase the difference in output between the 'on' and 'off' states. More specifically, McCormick et al. wanted to find out whether swapping out or mutating specific amino acids (each of the individual building blocks that make up a protein) enhances or disrupts allostery. They also wanted to know if there are many possible mutations that change the effectiveness of allostery, or if this property is controlled by just a few amino acids. Finally, McCormick et al. questioned where in a protein most of these allostery-tuning mutations were located. To answer these questions, McCormick et al. engineered a new allosteric protein by inserting a light-sensing domain (input) into a protein involved in metabolism (a metabolic enzyme that produces a biomolecule called a tetrahydrofolate) to yield a light-controlled enzyme. Next, they introduced mutations into both the 'input' and 'output' domains to see where they had a greater effect on allostery. After filtering out mutations that destroyed the function of the output domain, McCormick et al. found that only about 5% of mutations to the 'output' domain altered the allosteric response of their engineered enzyme. In fact, most mutations that disrupted allostery were found near the site where the 'input' domain was inserted, while mutations that enhanced allostery were sprinkled throughout the enzyme, often on its protein surface. This was surprising in light of the commonly-held assumption that mutations on protein surfaces have little impact on the activity of the 'output' domain. Overall, the effect of individual mutations on allostery was small, but McCormick et al. found that these mutations can sometimes be combined to yield larger effects. McCormick et al.'s results suggest a new approach for optimizing engineered allosteric proteins: by introducing mutations on the protein surface. It also opens up new questions: mechanically, how do surface sites affect allostery? In the future, it will be important to characterize how combinations of mutations can optimize allosteric regulation, and to determine what evolutionary trajectories to high performance allosteric 'switches' look like.


Allosteric Regulation/genetics , Allosteric Site/genetics , Protein Binding/genetics , Computational Biology , Escherichia coli/genetics , Models, Molecular , Mutation/genetics , Protein Domains/genetics , Recombinant Fusion Proteins/chemistry , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Tetrahydrofolate Dehydrogenase/chemistry , Tetrahydrofolate Dehydrogenase/genetics , Tetrahydrofolate Dehydrogenase/metabolism
16.
Cell Syst ; 12(6): 547-560, 2021 06 16.
Article En | MEDLINE | ID: mdl-34139165

Folding a linear chain of amino acids into a three-dimensional protein is a complex physical process that ultimately confers an impressive range of diverse functions. Although recent advances have driven significant progress in predicting three-dimensional protein structures from sequence, proteins are not static molecules. Rather, they exist as complex conformational ensembles defined by energy landscapes spanning the space of sequence and conditions. Quantitatively mapping the physical parameters that dictate these landscapes and protein stability is therefore critical to develop models that are capable of predicting how mutations alter function of proteins in disease and informing the design of proteins with desired functions. Here, we review the approaches that are used to quantify protein stability at a variety of scales, from returning multiple thermodynamic and kinetic measurements for a single protein sequence to yielding indirect insights into folding across a vast sequence space. The physical parameters derived from these approaches will provide a foundation for models that extend beyond the structural prediction to capture the complexity of conformational ensembles and, ultimately, their function.


Protein Folding , Proteins , Kinetics , Protein Stability , Proteins/metabolism , Thermodynamics
17.
Hum Mol Genet ; 30(17): 1591-1606, 2021 08 12.
Article En | MEDLINE | ID: mdl-34046667

The forkhead transcription factor FOXE3 is critical for vertebrate eye development. Recessive and dominant variants cause human ocular disease but the full range of phenotypes and mechanisms of action for the two classes of variants are unknown. We identified FOXE3 variants in individuals with congenital eye malformations and carried out in vitro functional analysis on selected alleles. Sixteen new recessive and dominant families, including six novel variants, were identified. Analysis of new and previously reported genetic and clinical data demonstrated a broad phenotypic range with an overlap between recessive and dominant disease. Most families with recessive alleles, composed of truncating and forkhead-domain missense variants, had severe corneal opacity (90%; sclerocornea in 47%), aphakia (83%) and microphthalmia (80%), but some had milder features including isolated cataract. The phenotype was most variable for recessive missense variants, suggesting that the functional consequences may be highly dependent on the type of amino acid substitution and its position. When assessed, aniridia or iris hypoplasia were noted in 89% and optic nerve anomalies in 60% of recessive cases, indicating that these defects are also common and may be underrecognized. In dominant pedigrees, caused by extension variants, normal eye size (96%), cataracts (99%) and variable anterior segment anomalies were seen in most, but some individuals had microphthalmia, aphakia or sclerocornea, more typical of recessive disease. Functional studies identified variable effects on the protein stability, DNA binding, nuclear localization and transcriptional activity for recessive FOXE3 variants, whereas dominant alleles showed severe impairment in all areas and dominant-negative characteristics.


Eye Abnormalities/genetics , Eye/embryology , Forkhead Transcription Factors/genetics , Adolescent , Alleles , Cataract/genetics , Child , Corneal Opacity/genetics , Developmental Disabilities/genetics , Eye/growth & development , Eye Abnormalities/enzymology , Female , Forkhead Transcription Factors/metabolism , Humans , Male , Mutation , Pedigree , Phenotype
18.
Structure ; 29(1): 43-49.e3, 2021 01 07.
Article En | MEDLINE | ID: mdl-32937101

The Ni-Fe-S-containing A-cluster of acetyl-coenzyme A (CoA) synthase (ACS) assembles acetyl-CoA from carbon monoxide (CO), a methyl group (CH3+), and CoA. To accomplish this feat, ACS must bind CoA and interact with two other proteins that contribute the CO and CH3+, respectively: CO dehydrogenase (CODH) and corrinoid Fe-S protein (CFeSP). Previous structural data show that, in the model acetogen Moorella thermoacetica, domain 1 of ACS binds to CODH such that a 70-Å-long internal channel is created that allows CO to travel from CODH to the A-cluster. The A-cluster is largely buried and is inaccessible to CFeSP for methylation. Here we use electron microscopy to capture multiple snapshots of ACS that reveal previously uncharacterized domain motion, forming extended and hyperextended structural states. In these structural states, the A-cluster is accessible for methylation by CFeSP.


Aldehyde Oxidoreductases/chemistry , Bacterial Proteins/chemistry , Multienzyme Complexes/chemistry , Aldehyde Oxidoreductases/metabolism , Bacterial Proteins/metabolism , Iron/chemistry , Iron/metabolism , Molecular Dynamics Simulation , Moorella/enzymology , Multienzyme Complexes/metabolism , Nickel/chemistry , Nickel/metabolism , Protein Domains , Sulfur/chemistry , Sulfur/metabolism
19.
Ind Eng Chem Res ; 59(12): 5287-5295, 2020 Mar 25.
Article En | MEDLINE | ID: mdl-33208988

Pore functionalized membranes with appropriate ion exchange/chelate groups allow toxic metal sorption under convective flow conditions. This study explores the sorption capacity of ionic mercury in a polyvinylidene fluoride-poly(acrylic acid) (PVDFs-PAA) functionalized membrane immobilized with cysteamine (MEA). Two methods of MEA immobilization to the PVDF-PAA membrane have been assessed: (i) ion exchange (IE) and (ii) carbodiimide cross-linker chemistry using 1-(3-dimethylaminopropyl)-3-ethyl carbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS), known as EDC/NHS coupling. The ion exchange method demonstrates that cysteamine (MEA) can be immobilized effectively on PVDF-PAA membranes without covalent attachment. The effectiveness of the MEA immobilized membranes to remove ionic mercury from the water was evaluated by passing a dissolved mercury(II) nitrate solution through the membranes. The sorption capacity of mercury for MEA immobilized membrane prepared by the IE method is 1015 mg/g PAA. On the other hand, the sorption capacity of mercury for MEA immobilized membrane prepared by EDC/NHS chemistry is 2446 mg/g PAA, indicating that membrane functionalization by EDC/NHS coupling enhanced mercury sorption 2.4 times compared to the IE method. The efficiencies of Hg removal are 94.1 ± 1.1 and 99.1 ± 0.1% for the MEA immobilized membranes prepared by IE and EDC/NHS coupling methods, respectively. These results show potential applications of MEA immobilized PVDF-PAA membranes for industrial wastewater treatment specifically from energy and mining industries to remove mercury and other toxic metals.

20.
Orthopedics ; 43(6): e561-e566, 2020 Nov 01.
Article En | MEDLINE | ID: mdl-32745226

Traumatic lower-extremity amputations often result in complications and surgical revisions. The authors report the in-hospital morbidity and mortality of traumatic lower-extremity amputations at a metropolitan level I trauma center for a large rural region and compare below-knee (BK) vs higher-level amputation complications. They retrospectively reviewed 168 adult patients during a 10-year period (2005 to 2015) who had a traumatic injury to the lower extremity that required an amputation. Main outcome measurements included amputation level, complication rates, intensive care unit (ICU) admission rates, length of stay, total trips to the operating room (OR), and Injury Severity Score (ISS). A total of 95 patients had through-knee/above-knee (TK/AK) amputations, and 73 patients had BK amputations. The majority of injuries occurred in the non-urban setting. The TK/AK group had higher ICU admission rates (76% vs 35%, P<.0001), longer overall hospital length of stay (22.0 vs 15.5 days, P=.01), more total OR trips (6.5 vs 5.0, P=.04), and higher ISS (17.0 vs 11.5, P<.0001). A complication was experienced by 64% of all patients during the initial hospitalization. The TK/AK group had higher complication rates than the BK group, including wound infection, pulmonary embolus, rhabdomyolysis, compartment syndrome, and death. Patients with TK/AK traumatic amputations have a greater burden of injury with higher complication rates, increased ICU admissions, increased length of stay, and increased ISS and require more return trips to the OR compared with patients with BK amputations. [Orthopedics. 2020;43(6):e561-e566.].


Amputation, Surgical , Amputation, Traumatic/surgery , Leg Injuries/surgery , Adult , Amputation, Traumatic/complications , Amputation, Traumatic/mortality , Compartment Syndromes/etiology , Female , Hospitalization , Humans , Injury Severity Score , Leg Injuries/complications , Leg Injuries/mortality , Male , Middle Aged , Reoperation , Retrospective Studies , Wound Infection/etiology
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