In silico Mapping of Protein Unfolding Mutations for Inherited Disease

Neuropathy target esterase activity defines phenotypes among PNPLA6 disorders

Biallelic pathogenic variants in the PNPLA6 gene cause a broad spectrum of disorders leading to gait disturbance, visual impairment, anterior hypopituitarism and hair anomalies. PNPLA6 encodes neuropathy target esterase (NTE), yet the role of NTE dysfunction on affected tissues in the large spectrum of associated disease remains unclear. We present a systematic evidence-based review of a novel cohort of 23 new patients along with 95 reported individuals with PNPLA6 variants that implicate missense variants as a driver of disease pathogenesis. Measuring esterase activity of 46 disease-associated and 20 common variants observed across PNPLA6-associated clinical diagnoses unambiguously reclassified 36 variants as pathogenic and 10 variants as likely pathogenic, establishing a robust functional assay for classifying PNPLA6 variants of unknown significance. Estimating the overall NTE activity of affected individuals revealed a striking inverse relationship between NTE activity and the presence of retinopathy and endocrinopathy. This phenomenon was recaptured in vivo in an allelic mouse series, where a similar NTE threshold for retinopathy exists. Thus, PNPLA6 disorders, previously considered allelic, are a continuous spectrum of pleiotropic phenotypes defined by an NTE genotype:activity:phenotype relationship. This relationship, and the generation of a preclinical animal model, pave the way for therapeutic trials, using NTE as a biomarker.

Neuropathy target esterase activity predicts retinopathy among PNPLA6 disorders

Biallelic pathogenic variants in the PNPLA6 gene cause a broad spectrum of disorders leading to gait disturbance, visual impairment, anterior hypopituitarism, and hair anomalies. PNPLA6 encodes Neuropathy target esterase (NTE), yet the role of NTE dysfunction on affected tissues in the large spectrum of associated disease remains unclear. We present a clinical meta-analysis of a novel cohort of 23 new patients along with 95 reported individuals with PNPLA6 variants that implicate missense variants as a driver of disease pathogenesis. Measuring esterase activity of 46 disease-associated and 20 common variants observed across PNPLA6 -associated clinical diagnoses unambiguously reclassified 10 variants as likely pathogenic and 36 variants as pathogenic, establishing a robust functional assay for classifying PNPLA6 variants of unknown significance. Estimating the overall NTE activity of affected individuals revealed a striking inverse relationship between NTE activity and the presence of retinopathy and endocrinopathy. This phenomenon was recaptured in vivo in an allelic mouse series, where a similar NTE threshold for retinopathy exists. Thus, PNPLA6 disorders, previously considered allelic, are a continuous spectrum of pleiotropic phenotypes defined by an NTE genotype:activity:phenotype relationship. This relationship and the generation of a preclinical animal model pave the way for therapeutic trials, using NTE as a biomarker.

In Vitro Reconstitution of the Melanin Pathway's Catalytic Activities Using Tyrosinase Nanoparticles

The melanogenesis pathway is characterized by a series of reactions catalyzed by key enzymes, such as tyrosinase (TYR), tyrosinase-related protein 2 (TYRP2), and tyrosinase-related protein 1 (TYRP1), to produce melanin pigment. However, in vitro studies of the catalytic activity were incomplete because of a lack of commercially available enzyme substrates, such as dopachrome. Herein, human recombinant intra-melanosomal domains of key enzymes were produced in Trichoplusia ni (T. ni) larvae and then purified using a combination of chromatography techniques in catalytically active form. Using Michaelis-Menten kinetics, the diphenol oxidase activity of tyrosinase achieved the maximum production of native dopachrome at 10 min of incubation at 37 °C for TYR immobilized to magnetic beads (TYR-MB). The presence of dopachrome was confirmed spectrophotometrically at 475 nm through HPLC analysis and in the TYRP2-catalyzed reaction, yielding 5,6-dihydroxyindole-2-carboxylic acid (DHICA). In the TYRP1-driven oxidation of DHICA, the formation of 5,6-indolequinone-2-carboxylic acid (IQCA) was confirmed at ~560 nm. This is the first in vitro reconstitution of the reactions from the melanogenic pathway based on intra-melanosomal domains. In the future, this approach could be used for quantitative in vitro analysis of the melanin pathway, biochemical effects associated with inherited disease-related mutations, and drug screens.

Protein Biochemistry and Molecular Modeling of the Intra-Melanosomal Domain of Human Recombinant Tyrp2 Protein and OCA8-Related Mutant Variants

Tyrosinase-related protein 2 (Tyrp2) is involved in the melanogenesis pathway, catalyzing the tautomerization of dopachrome to 5,6-dihydroxyindole-2-carboxylic acid (DHICA). Recently, a new type of albinism was discovered with disease-causing mutations in the TYRP2 gene. Here, for the first time, we characterized the intra-melanosomal protein domain of Tyrp2 (residues 1-474) and missense variants C40S and C61W, which mimic the alterations found in genetic studies. Recombinant proteins were produced in the Trichoplusia Ni (Ti. Ni) larvae, purified by a combination of immobilized metal affinity (IMAC) and gel-filtration (GF) chromatography, and biochemically characterized. The mutants showed the protein expression in the lysates such as the wild type; however, undetectable protein yield after two steps of purification exhibited their misfolding and instability. In addition, the misfolding effect of the mutations was confirmed computationally using homology modeling and molecular docking. Together, experiments in vitro and computer simulations indicated the critical role of the Cys-rich domain in the Tyrp2 protein stability. The results are consistent with molecular modeling, global computational mutagenesis, and clinical data, proving the significance of genetic alterations in cysteine residues, which could cause oculocutaneous albinism type 8.

Tyrp1 Mutant Variants Associated with OCA3: Computational Characterization of Protein Stability and Ligand Binding

Oculocutaneous albinism type 3 (OCA3) is an autosomal recessive disorder caused by mutations in the TYRP1 gene. Tyrosinase-related protein 1 (Tyrp1) is involved in eumelanin synthesis, catalyzing the oxidation of 5,6-dihydroxyindole-2-carboxylic acid oxidase (DHICA) to 5,6-indolequinone-2-carboxylic acid (IQCA). Here, for the first time, four OCA3-causing mutations of Tyrp1, C30R, H215Y, D308N, and R326H, were investigated computationally to understand Tyrp1 protein stability and catalytic activity. Using the Tyrp1 crystal structure (PDB:5M8L), global mutagenesis was conducted to evaluate mutant protein stability. Consistent with the foldability parameter, C30R and H215Y should exhibit greater instability, and two other mutants, D308N and R326H, are expected to keep a native conformation. SDS-PAGE and Western blot analysis of the purified recombinant proteins confirmed that the foldability parameter correctly predicted the effect of mutations critical for protein stability. Further, the mutant variant structures were built and simulated for 100 ns to generate free energy landscapes and perform docking experiments. Free energy landscapes formed by Y362, N378, and T391 indicate that the binding clefts of C30R and H215Y mutants are larger than the wild-type Tyrp1. In docking simulations, the hydrogen bond and salt bridge interactions that stabilize DHICA in the active site remain similar among Tyrp1, D308N, and R326H. However, the strengths of these interactions and stability of the docked ligand may decrease proportionally to mutation severity due to the larger and less well-defined natures of the binding clefts in mutants. Mutational perturbations in mutants that are not unfolded may result in allosteric alterations to the active site, reducing the stability of protein-ligand interactions.

Characterization of Temperature-Dependent Kinetics of Oculocutaneous Albinism-Causing Mutants of Tyrosinase

Human tyrosinase (Tyr) is a glycoenzyme that catalyzes the first and rate-limiting step in melanin production, and its gene (TYR) is mutated in many cases of oculocutaneous albinism type 1 (OCA1). The mechanisms by which individual mutations contribute to the diverse pigmentation phenotype in patients with OCA1 have only began to be examined and remain to be delineated. Here, we analyze the temperature-dependent kinetics of wild-type Tyr (WT) and two OCA1B mutant variants (R422Q and P406L) using Michaelis–Menten and Van’t Hoff analyses. Recombinant truncated human Tyr proteins (residues 19–469) were produced in the whole insect Trichoplusia Ni larvae. Proteins were purified by a combination of affinity and size-exclusion chromatography. The temperature dependence of diphenol oxidase protein activities and kinetic parameters were measured by dopachrome absorption. Using the same experimental conditions, computational simulations were performed to assess the temperature-dependent association of L-DOPA and Tyr. Our results revealed, for the first time, that the association of L-DOPA with R422Q and P406L followed by dopachrome formation is a complex reaction supported by enthalpy and entropy forces. We show that the WT has a higher turnover number as compared with both R422Q and P406L. Elucidating the kinetics and thermodynamics of mutant variants of Tyr in OCA1B helps to understand the mechanisms by which they lower Tyr catalytic activity and to discover novel therapies for patients.

An overview of germline variations in genes of primary immunodeficiences through integrative analysis of ClinVar, HGMD® and dbSNP databases

Primary immunodeficiencies (PID) are a diverse group of genetic disorders caused by inadequate development and function of immune system. Identifying genetic etiology is important for genetic counselling and treatment decisions. Clinical relevance of genetic variants is a complex problem depending on gene-specific and variant specific genotype-phenotype interactions. To address this challenge, we aimed to characterize the pathogenic landscape of PID genes by combining the analysis of germline variations reported in ClinVar and HGMD^® and identification of damaging variations available in dbSNP. We generated a joint ClinVar/HGMD database, which included 111,940 variants, among them 32,452 were classified as pathogenic/likely pathogenic. From a total of 5,415,794 bi- or multiallelic variants in PID genes recorded in dbSNP, we retrieved 38,291 high impact (HI) biallelic variants with presumably disruptive impact in the protein, of them 25,500 variants were not present in ClinVar/HGMD. Using a functional prediction algorithm, we additionally identified 28,507 deleterious and 56,016 neutral missense variants among dbSNP variants and created a collection of damaging and neutral variations in PID genes, not currently present in ClinVar/HGMD, with their allele frequencies and mappings to protein domains. The distribution of pathogenic variants from ClinVar/HGMD, HI variants and deleterious missense variants from dbSNP was analyzed in the context of hereditary pattern and gene specific metrics, such as pLI and haploinsufficiency. Our report summarized data on complex gene-specific variability in PID genes and might be useful for the identification of the most promising variants and gene regions for further study.

DESP: Deep Enhanced Sampling of Proteins' Conformation Spaces Using AI-Inspired Biasing Forces

The molecular structures (i.e., conformation spaces, CS) of bio-macromolecules and the dynamics that molecules exhibit are crucial to the understanding of the basis of many diseases and in the continuous attempts to retarget known drugs/medications, improve the efficacy of existing drugs, or develop novel drugs. These make a better understanding and the exploration of the CS of molecules a research hotspot. While it is generally easy to computationally explore the CS of small molecules (such as peptides and ligands), the exploration of the CS of a larger biomolecule beyond the local energy well and beyond the initial equilibrium structure of the molecule is generally nontrivial and can often be computationally prohibitive for molecules of considerable size. Therefore, research efforts in this area focus on the development of ways that systematically favor the sampling of new conformations while penalizing the resampling of previously sampled conformations. In this work, we present Deep Enhanced Sampling of Proteins’ Conformation Spaces Using AI-Inspired Biasing Forces (DESP), a technique for enhanced sampling that combines molecular dynamics (MD) simulations and deep neural networks (DNNs), in which biasing potentials for guiding the MD simulations are derived from the KL divergence between the DNN-learned latent space vectors of [a] the most recently sampled conformation and those of [b] the previously sampled conformations. Overall, DESP efficiently samples wide CS and outperforms conventional MD simulations as well as accelerated MD simulations. We acknowledge that this is an actively evolving research area, and we continue to further develop the techniques presented here and their derivatives tailored at achieving DNN-enhanced steered MD simulations and DNN-enhanced targeted MD simulations.

Homology modeling and global computational mutagenesis of human myosin VIIa

Usher syndrome type 1B (USH1B) is a genetic disorder caused by mutations in the unconventional Myosin VIIa (MYO7A) protein. USH1B is characterized by hearing loss due to abnormalities in the inner ear and vision loss due to retinitis pigmentosa. Here, we present the model of human MYO7A homodimer, built using homology modeling, and refined using 5 ns molecular dynamics in water. Global computational mutagenesis was applied to evaluate the effect of missense mutations that are critical for maintaining protein structure and stability of MYO7A in inherited eye disease. We found that 43.26% (77 out of 178 in HGMD) and 41.9% (221 out of 528 in ClinVar) of the disease-related missense mutations were associated with higher protein structure destabilizing effects. Overall, most mutations destabilizing the MYO7A protein were found to associate with USH1 and USH1B. Particularly, motor domain and MyTH4 domains were found to be most susceptible to mutations causing the USH1B phenotype. Our work contributes to the understanding of inherited disease from the atomic level of protein structure and analysis of the impact of genetic mutations on protein stability and genotype-to-phenotype relationships in human disease.

Folliculin variants linked to Birt-Hogg-Dubé syndrome are targeted for proteasomal degradation

Germline mutations in the folliculin (FLCN) tumor suppressor gene are linked to Birt-Hogg-Dubé (BHD) syndrome, a dominantly inherited genetic disease characterized by predisposition to fibrofolliculomas, lung cysts, and renal cancer. Most BHD-linked FLCN variants include large deletions and splice site aberrations predicted to cause loss of function. The mechanisms by which missense variants and short in-frame deletions in FLCN trigger disease are unknown. Here, we present an integrated computational and experimental study that reveals that the majority of such disease-causing FLCN variants cause loss of function due to proteasomal degradation of the encoded FLCN protein, rather than directly ablating FLCN function. Accordingly, several different single-site FLCN variants are present at strongly reduced levels in cells. In line with our finding that FLCN variants are protein quality control targets, several are also highly insoluble and fail to associate with the FLCN-binding partners FNIP1 and FNIP2. The lack of FLCN binding leads to rapid proteasomal degradation of FNIP1 and FNIP2. Half of the tested FLCN variants are mislocalized in cells, and one variant (ΔE510) forms perinuclear protein aggregates. A yeast-based stability screen revealed that the deubiquitylating enzyme Ubp15/USP7 and molecular chaperones regulate the turnover of the FLCN variants. Lowering the temperature led to a stabilization of two FLCN missense proteins, and for one (R362C), function was re-established at low temperature. In conclusion, we propose that most BHD-linked FLCN missense variants and small in-frame deletions operate by causing misfolding and degradation of the FLCN protein, and that stabilization and resulting restoration of function may hold therapeutic potential of certain disease-linked variants. Our computational saturation scan encompassing both missense variants and single site deletions in FLCN may allow classification of rare FLCN variants of uncertain clinical significance.

Functional in silico analysis of human tyrosinase and OCA1 associated mutations

Oculocutaneous albinism type 1 (OCA1) is an autosomal recessive disorder caused by mutations in the tyrosinase gene. OCA1 exists in two forms: OCA1A and OCA1B. OCA1A is caused by a full loss of the human tyrosinase protein (Tyr), leading to an absence of pigment in skin, hair, and eyes, while OCA1B has reduced Tyr catalytic activity and pigment. The current understanding of the disease is hampered by the absence of information regarding the alterations of protein structure and the effects leading to either form of OCA1. Here, we used computational methods to find a general mechanism for establishing this link. Tyr and mutant variants were built through homology modeling, glycosylated in silico, minimized, and simulated using 100 ns molecular dynamics in water. For OCA1B mutants, cavity size is linked to ΔΔG values for mutants, suggesting that partial loss of Tyr is associated with the destabilizing effect of the EGF-like domain movement. In OCA1A, active site mutation simulations indicate that the absence of O₂ leads to protein instability. OCA1B mutants are described in severity by the size of the cavity within the EGF-Tyr interface, while active site OCA1A mutants are unable to fully coordinate copper, leading to an absence of O₂ and Tyr instability. In patients with known genotypes, free energy changes may help identify the severity of the disease by assessing either the allosteric effect of the EGF-Tyr cavity in OCA1B or the active site instability in OCA1A.

Model for Counterion Binding and Charge Reversal on Protein Surfaces

The structural stability and solubility of proteins in liquid therapeutic formulations is important, especially since new generations of therapeutics are designed for efficacy before consideration of stability. We introduce an electrostatic binding model to measure the net charge of proteins with bound ions in solution. The electrostatic potential on a protein surface is used to separately group together acidic and basic amino acids into patches, which are then iteratively bound with oppositely charged counterions. This model is aimed toward formulation chemists for initial screening of a range of conditions prior to lab-work. Computed results compare well with experimental zeta potential measurements from the literature covering a range of solution conditions. Importantly, the binding model reproduces the charge reversal phenomenon that is observed with polyvalent ion binding to proteins and its dependence on ion charge and concentration. Intriguingly, protein sequence can be used to give similarly good agreement with experiment as protein structure, interpreted as resulting from the close proximity of charged side chains on a protein surface. Further, application of the model to human proteins suggests that polyanion binding and overcharging, including charge reversal for cationic proteins, is a general feature. These results add to evidence that addition of polyanions to protein formulations could be a general mechanism for modulating solution stability.

Comprehensive structure-function analysis of causative variants in retinal pigment epithelium specific 65 kDa protein associated Leber Congenital Amaurosis

A recent study published to screen RPE65 in 187 families with Leber Congenital Amaurosis (LCA) by Zilin Zhong in 2019. There are seven novel variants were identified in RPE65, which was associated with LCA, but among only five were missense mutations [(c.124C > T, p.(Leu42Phe), c.149T > C, p. (Phe50Ser), c.340A > C, p.(Asn114His), c.425A > G, p.(Asp142Gly) and c.1399C > G, p.(Pro467Ala)] in the Chinese population and potentially facilitates its clinical implementation. Further in-continuation of this study to the target of five novel missense mutations were the analysis of both structural and functional impact by the molecular dynamics and simulation. The result of five missense mutations might in critical structural alterations of RPE65 protein, disrupt its membrane association or rescue the activity of enzyme due to thermodynamics stability, and for this reason impair its isomerohydrolase activity, resulting in retinal dystrophy. These observations suggest that the reduced protein stability and altered subcellular localization of RPE65 might signify a mechanism for these mutations to lead to vision loss in LCA patients.

Global computational mutagenesis of domain structures associated with inherited eye disease

Multidomain proteins account for 70% of the eukaryotic proteome. In genetic disease, multidomain proteins are often affected by numerous mutations, but the effects of these mutations on protein stability and their roles in genetic disease are not well understood. Here, we analyzed protein globular domains to understand how genetic mutations affect the stability of multidomain proteins in inherited disease. In total, 291 domain atomic structures from nine multidomain proteins were modeled by homology, equilibrated using molecular dynamics in water, and subjected to global computational mutagenesis. The domains were separated into 7 groups based on protein fold homology. Mutation propensities within each group of domains were then averaged to select residues critical for domain fold stability. The consensus derived from the sequence alignment shows that the critical residues determined by global mutagenesis are conserved within each group. From this analysis, we concluded that 80% of known disease-related genetic variants are associated with critical residues and are expected to have significant destabilizing effects on domain structure. Our work provides an in silico quantification of protein stability and could help to analyze the complex relationship among missense mutations, multidomain protein stability, and disease phenotypes in inherited eye disease.

Global computational mutagenesis provides a critical stability framework in protein structures

A protein’s amino acid sequence dictates the folds and final structure the macromolecule will form. We propose that by identifying critical residues in a protein’s atomic structure, we can select a critical stability framework within the protein structure essential to proper protein folding. We use global computational mutagenesis based on the unfolding mutation screen to test the effect of every possible missense mutation on the protein structure to identify the residues that cannot tolerate a substitution without causing protein misfolding. This method was tested using molecular dynamics to simulate the stability effects of mutating critical residues in proteins involved in inherited disease, such as myoglobin, p53, and the 15^th sushi domain of complement factor H. In addition we prove that when the critical residues are in place, other residues may be changed within the structure without a stability loss. We validate that critical residues are conserved using myoglobin to show that critical residues are the same for crystal structures of 6 different species and comparing conservation indices to critical residues in 9 eye disease-related proteins. Our studies demonstrate that by using a selection of critical elements in a protein structure we can identify a critical protein stability framework. The frame of critical residues can be used in genetic engineering to improve small molecule binding for drug studies, identify loss-of-function disease-causing missense mutations in genetics studies, and aide in identifying templates for homology modeling.

Frequent hypomorphic alleles account for a significant fraction of ABCA4 disease and distinguish it from age-related macular degeneration

BACKGROUND

Variation in the ABCA4 gene is causal for, or associated with, a wide range of phenotypes from early onset Mendelian retinal dystrophies to late-onset complex disorders such as age-related macular degeneration (AMD). Despite substantial progress in determining the causal genetic variation, even complete sequencing of the entire open reading frame and splice sites of ABCA4 identifies biallelic mutations in only 60%-70% of cases; 20%-25% remain with one mutation and no mutations are found in 10%-15% of cases with clinically confirmed ABCA4 disease. This study was designed to identify missing causal variants specifically in monoallelic cases of ABCA4 disease.

METHODS

Direct sequencing and analysis were performed in a large familial ABCA4 disease cohort of predominately European descent (n=643). Patient phenotypes were assessed from clinical and retinal imaging data.

RESULTS

We determined that a hypomorphic ABCA4 variant c.5603A>T (p.Asn1868Ile), previously considered benign due to high minor allele frequency (MAF) (~7%) in the general population, accounts for 10% of the disease, >50% of the missing causal alleles in monoallelic cases, ~80% of late-onset cases and distinguishes ABCA4 disease from AMD. It results in a distinct clinical phenotype characterised by late-onset of symptoms (4th decade) and foveal sparing (85%). Intragenic modifying effects involving this variant and another, c.2588G>C (p.Gly863Ala) allele, were also identified.

CONCLUSIONS

These findings substantiate the causality of frequent missense variants and their phenotypic outcomes as a significant contribution to ABCA4 disease, particularly the late-onset phenotype, and its clinical variation. They also suggest a significant revision of diagnostic screening and assessment of ABCA4 variation in aetiology of retinal diseases.

Dataset of eye disease-related proteins analyzed using the unfolding mutation screen

A number of genetic diseases are a result of missense mutations in protein structure. These mutations can lead to severe protein destabilization and misfolding. The unfolding mutation screen (UMS) is a computational method that calculates unfolding propensities for every possible missense mutation in a protein structure. The UMS validation demonstrated a good agreement with experimental and phenotypical data. 15 protein structures (a combination of homology models and crystal structures) were analyzed using UMS. The standard and clustered heat maps, and patterned protein structure from the analysis were stored in a UMS library. The library is currently composed of 15 protein structures from 14 inherited eye diseases including retina degenerations, glaucoma, and cataracts, and contains data for 181,110 mutations. The UMS protein library introduces 13 new human models of eye disease related proteins and is the first collection of the consistently calculated unfolding propensities, which could be used as a tool for the express analysis of novel mutations in clinical practice, next generation sequencing, and genotype-to-phenotype relationships in inherited eye disease.