GTExome: Modeling commonly expressed missense mutations in the human genome.

A web application, GTExome, is described that quickly identifies, classifies, and models missense mutations in commonly expressed human proteins. GTExome can be used to categorize genomic mutation data with tissue specific expression data from the Genotype-Tissue Expression (GTEx) project. Commonly expressed missense mutations in proteins from a wide range of tissue types can be selected and assessed for modeling suitability. Information about the consequences of each mutation is provided to the user including if disulfide bonds, hydrogen bonds, or salt bridges are broken, buried prolines introduced, buried charges are created or lost, charge is swapped, a buried glycine is replaced, or if the residue that would be removed is a proline in the cis configuration. Also, if the mutation site is in a binding pocket the number of pockets and their volumes are reported. The user can assess this information and then select from available experimental or computationally predicted structures of native proteins to create, visualize, and download a model of the mutated protein using Fast and Accurate Side-chain Protein Repacking (FASPR). For AlphaFold modeled proteins, confidence scores for native proteins are provided. Using this tool, we explored a set of 9,666 common missense mutations from a variety of tissues from GTEx and show that most mutations can be modeled using this tool to facilitate studies of protein-protein and protein-drug interactions. The open-source tool is freely available at https://pharmacogenomics.clas.ucdenver.edu/gtexome/.

GTExome: Modeling commonly expressed missense mutations in the human genome.

A web application, GTExome, is described that quickly identifies, classifies, and models missense mutations in commonly expressed human proteins. GTExome can be used to categorize genomic mutation data with tissue specific expression data from the Genotype-Tissue Expression (GTEx) project. Commonly expressed missense mutations in proteins from a wide range of tissue types can be selected and assessed for modeling suitability. Information about the consequences of each mutation is provided to the user including if disulfide bonds, hydrogen bonds, or salt bridges are broken, buried prolines introduced, buried charges are created or lost, charge is swapped, a buried glycine is replaced, or if the residue that would be removed is a proline in the cis configuration. Also, if the mutation site is in a binding pocket the number of pockets and their volumes are reported. The user can assess this information and then select from available experimental or computationally predicted structures of native proteins to create, visualize, and download a model of the mutated protein using Fast and Accurate Side-chain Protein Repacking (FASPR). For AlphaFold modeled proteins, confidence scores for native proteins are provided. Using this tool, we explored a set of 9,666 common missense mutations from a variety of tissues from GTEx and show that most mutations can be modeled using this tool to facilitate studies of protein-protein and protein-drug interactions. The open-source tool is freely available at https://pharmacogenomics.clas.ucdenver.edu/gtexome/.

Assessing protein homology models with docking reproducibility.

Results of the recent Critical Assessment of Protein Structure (CASP) competitions demonstrate that protein backbones can be predicted with very high accuracy. In particular, the artificial intelligence methods of AlphaFold 2 from DeepMind were able to produce structures that were similar enough to experimental structures that many described the problem of protein prediction solved. However, for such structures to be used for drug docking studies requires precision in the placement of side chain atoms as well. Here we built a library of 1334 small molecules and examined how reproducibly they bound to the same site on a protein using QuickVina-W, a branch of the program Autodock that is optimized for blind searches. We discovered that the higher the backbone quality of the homology model the greater the similarity between the small molecule docking to the experimental and modeled structures. Furthermore, we found that specific subsets of this library were particularly useful for identifying small differences between the best of the best modeled structures. Specifically, when the number of rotatable bonds in the small molecule increased, differences in binding sites became more apparent.

Metabolovigilance: Associating Drug Metabolites with Adverse Drug Reactions.

The Metabolovigilance database (https://pharmacogenomics.clas.ucdenver.edu/pharmacogenomics/side-effect/) is a single repository of information on over 15,920 pharmaceuticals and the compounds expected to result from metabolism of these drugs. Metabolovigilance functions as both a web server, providing data directly to users and as a web application, applying user inputs to create logic statements that curate the data presented or downloaded. Using this tool, it is easy to collect information on drugs, their side effects, and the metabolites associated with specific side effects. Information on these compounds can be sorted based on physical properties of the drugs and their metabolites. All of this information can be viewed, sorted, and downloaded for use in other applications. This open-access tool will facilitate molecular studies on the causes of adverse drug reactions and is well suited to integrate with genomic data furthering the goals of personalized medicine.

Biochemically prepared C-reactive protein conformational states differentially affect C1q binding.

C-reactive protein (CRP) is commonly measured as an inflammatory marker in patient studies for coronary heart disease, autoimmune disease and recent acute infections. Due to a correlation of CRP to a vast number of disease states, CRP is a well-studied protein in medical literature with over 16000 references in PubMed [1]. However, the biochemical and structural variations of CRP are not well understood in regards to their binding of complement immune response proteins. Conformations of CRP are thought to affect disease states differently, with a modified form showing neoepitopes and activating the complement immune response through C1q binding. In this work, we compare the unfolding of CRP using chemical denaturants and identify which states of CRP bind a downstream complement immune response binding partner (C1q). We used guanidine HCl (GndHCl), urea/EDTA, and 0.01% SDS with heat to perturb the pentameric state. All treatments give rise to a monomeric state in non-denaturing polyacrylamide gel electrophoresis experiments, but only treatment with certain concentrations of denaturant or dilute SDS with heat maintains CRP function with a key downstream binding partner, C1q, as measured by enzyme-linked immunosorbent assays. The results suggest that the final form of modified CRP and its ability to mimic biological binding is dependent on the preparation method.

Dynamics of Serine-8 Side-Chain in Amyloid-ß Fibrils and Fluorenylmethyloxycarbonyl Serine Amino Acid, Investigated by Solid-State Deuteron NMR.

Serine side-chains are strategic sites of post-translational modifications, and it is important to establish benchmarks of their internal dynamics. In this work, we compare the dynamics of serine side-chains in several biologically important systems: serine-8 in the disordered domain of Aß1-40 fibrils in the hydrated and dry states and fluorenylmethyloxycarbonyl (Fmoc) serine with the bulky group that mimics the hydrophobicity of the fibril contacts yet lacks the complexity of the protein system. Using deuterium solid-state NMR static line shape and longitudinal relaxation techniques in the 310 to 180 K temperature range, we compare the main features of the dynamics in these systems. The main motional modes in the fibrils are large-scale fluctuations in the hydrated state of the fibrils as well as local motions such as 3-site jumps of the Cß deuterons at high temperatures and small-angle fluctuations of the Cα-Cß axis at low temperatures. In the hydrated fibrils, two distinct states are present with vastly different extents of large-scale diffusive motions and 3-site-jump rate constants. The hydrated state at the physiological conditions is dominated by the "free" state undergoing large-scale diffusive motions and very fast local 3-site jumps, while in the "bound" state, these large-scale motions are quenched due to transient inter- and intramolecular interactions. Additionally, in the bound state, the 3-site-jump motions are orders of magnitude slower. Details of the dynamics in the serine side-chain are dependent on fine structural features and hydration levels of the systems.

Lipid-Coated Gold Nanoparticles and FRET Allow Sensitive Monitoring of Liposome Clustering Mediated by the Synaptotagmin-7 C2A Domain.

Synaptotagmin (Syt) family proteins contain tandem C2 domains, C2A and C2B, which insert into anionic membranes in response to increased cytosolic Ca2+ concentration and facilitate exocytosis in neuronal and endocrine cells. The C2A domain from Syt7 binds lipid membranes much more tightly than the corresponding domain from Syt1, but the implications of this difference for protein function are not yet clear. In particular, the ability of the isolated Syt7 C2A domain to initiate membrane apposition and/or aggregation has been previously unexplored. Here, we demonstrate that Syt7 C2A induces apposition and aggregation of liposomes using Förster resonance energy transfer (FRET) assays, dynamic light scattering, and spectroscopic techniques involving lipid-coated gold nanoparticles (LCAuNPs). Protein-membrane binding, membrane apposition, and macroscopic aggregation are three separate phenomena with distinct Ca2+ requirements: the threshold Ca2+ concentration for membrane binding is lowest, followed by apposition and aggregation. However, aggregation is highly sensitive to protein concentration and can occur even at submicromolar Syt7 C2A; thus, highly sensitive assays are needed for measuring apposition without complications arising from aggregation. Notably, the localized surface plasmon resonance of the LCAuNP is sensitive to ≤10 nM Syt7 C2A concentrations. Furthermore, when the LCAuNPs were added into a FRET-based liposome apposition assay, the resultant energy transfer increased; possible explanations are discussed. Overall, LCAuNP-based methods allow for highly sensitive detection of protein-induced membrane apposition under conditions that miminize large-scale aggregation.

Conformational Changes in C-Reactive Protein Affect Binding to Curved Membranes in a Lipid Bilayer Model of the Apoptotic Cell Surface.

C-reactive protein (CRP) is a serum protein that binds to damaged membranes through a phosphatidylcholine binding site. The membrane binding process can initiate the complement immune response and facilitates the clearance of apoptotic cells, likely aiding in the protection of autoimmunity. The initiation of an immune response relies on a conformation change from a native, pentameric form to a modified form, where the modified form binds complement proteins (i.e., C1q) and regulatory proteins substantially better than the native form. In vitro, this reactivity is observed when CRP is monomeric, and a modified form has also been observed at sites of inflammation. Despite evidence that the monomeric form has much higher affinities for almost all proteinaceous binding partners, the role of CRP conformation on lipid binding is yet unknown. In this work, we mimic the outer leaflet of apoptotic cell membranes using a nanopatterned substrate to create curved, supported lipid bilayers and then characterize how CRP conformation affects the interactions between CRP and target membranes. In this assay, the chemical composition and shape are separately tunable parameters. The lipids consisted primarily of palmitoyloleoylphosphatidylcholine, with and without lysophosphatidylcholine, and the curvature had a radius of 27-55 nm. Using this model system combined with quantitative fluorescence microscopy methods, CRP binding to lipid membranes was measured as a function of different conformations of CRP. The modified form of CRP bound curved membranes, but the pentameric form did not for the range of curvatures measured. Unlike most other curvature-sensing proteins, modified CRP accumulated more at a moderate curvature, rather than highly curved or flat regions, suggesting that the membrane bound form does not solely depend on a defect binding mechanism. The presence of lysophosphatidylcholine, a component of apoptotic membranes, increased CRP binding to all types of membranes. Overall, our results show that CRP interactions vary with protein form, lipid composition, and membrane shape. The mechanism by which CRP recognizes damaged membranes depends on the combination of all three.

Polymer mediated layer-by-layer assembly of different shaped gold nanoparticles.

Gold nanoparticles (GNPs) have a wide range of properties with potential applications in electronics, optics, catalysis, and sensing. In order to demonstrate that dense, stable, and portable samples could be created for these applications, multiple layers of GNPs were assembled via drop casting on glass substrates by layer-by-layer (LBL) techniques. Two cationic polyelectrolytes, poly(diallyldimethylammonium chloride) and polyethyleneimine, one anionic polyelectrolyte, poly(sodium 4-styrene sulfonate), and one neutral polymer, polyvinylpyrrolidone, were combined with four different shapes of GNPs (spherical, rod, triangular prismatic, and octahedral) to prepare thin films. A subset of these polymer nanoparticle combinations were assembled into thin films. Synthesized GNPs were characterized via dynamic light scattering, UV-vis spectroscopy, and transmission electron microscopy and the LBL thin films were characterized using UV-vis spectroscopy and atomic force microscopy. Sensing applications of the nanoparticles in solution and thin films were tested by monitoring the localized surface plasmon resonance of the GNPs. LBL thin films were prepared ranging from 25 to 100 layers with optical densities at plasmon from 0.5 to 3.0. Sensitivity in solutions ranged from 14 to 1002nm/refractive index units (RIU) and films ranged from 18.8 to 135.1nm/RIU suggesting reduced access to the GNPs within the films.

Improved methods for evaluating the environmental impact of nanoparticle synthesis†.

With the market for products containing nanoparticles growing, improvements in the efficiency of nanoparticle synthesis are poised to have significant positive economic and environmental impacts. While many metrics have been designed for measuring the efficiency of small molecule synthesis, the use of these metrics for evaluating nanoparticle preparation has not been optimized. Here a critical evaluation of various green chemistry metrics is provided as they are applied to a common set of nanoparticle synthetic methods. The effect of the nanoparticle polydispersity on the relative greenness of different synthetic methods is also examined. Using metrics modified to account for polydispersity, a case study of gold nanoparticle syntheses is provided and three different methods of preparing monodisperse gold nanoparticles are compared. Interestingly, not all of the metrics provide the same rankings for the synthetic methods. And when polydispersity is ignored, the metrics provide a different rank order of the methods, highlighting the importance of clearly defining the desired nanoparticle size range to avoid underestimating the environmental impact.

Mixtures of supported and hybrid lipid membranes on heterogeneously modified silica nanoparticles.

Simple supported lipid bilayers do not accurately reflect the complex heterogeneity of cellular membranes; however, surface modification makes it possible to tune membrane properties to better mimic biological systems. Here, 3-[2-(2-aminoethylamino)ethylamino]propyl-trimethoxysilane (DETAS), a silica modifier, facilitated formation of supported lipid bilayers on silica nanoparticles. Evidence for a stable supported bilayer came from the successful entrapment of a soluble fluorophore within an interstitial water layer. A fluorescence-quenching assay that utilized a pore-forming peptide was used to demonstrate the existence of two separate lipid leaflets. In this assay, fluorescence was quenched by dithionite in roughly equal proportions prior to and after addition of melittin. When a hydrophobic modifier, octadecyltriethoxysilane, was codeposited on the nanoparticles with DETAS, there was a decrease in the amount of supported bilayer on the nanoparticles and an increase in the quantity of hybrid membrane. This allowed for a controlled mixture of two distinct types of membranes on a single substrate, one separated by a water cushion and the other anchored directly on the surface, thereby providing a new mimic of cellular membranes.

Using the Localized Surface Plasmon Resonance of Gold Nanoparticles to Monitor Lipid Membrane Assembly and Protein Binding.

Gold nanoparticles provide a template for preparing supported lipid layers with well-defined curvature. Here, we utilize the localized surface plasmon resonance (LSPR) of gold nanoparticles as a sensor for monitoring the preparation of lipid layers on nanoparticles. The LSPR is very sensitive to the immediate surroundings of the nanoparticle surface and it is used to monitor the coating of lipids and subsequent conversion of a supported bilayer to a hybrid membrane with an outer lipid leaflet and an inner leaflet containing hydrophobic alkanethiol. We demonstrate that both decanethiol and propanethiol are able to form hybrid membranes and that the membrane created over the shorter thiol can be stripped from the gold along with the lipid leaflet using ß-mercaptoethanol. The sensitivity of the nanoparticle LSPR to the refractive index (RI) of its surroundings is greater when the shorter thiol is used (37.8 ± 1.5 nm per RI unit) than when the longer thiol is used (27.5 ± 0.5 nm per RI unit). Finally, C-reactive protein binding to the membrane is measured using this sensor allowing observation of both protein-membrane and nanoparticle-nanoparticle interactions without chemical labeling of protein or lipids.

Membrane curvature recognition by C-reactive protein using lipoprotein mimics.

It has been reported that the oxidation of phosphatidylcholine (PC) is necessary for C-reactive protein (CRP) to bind to lipid membranes, but it remains elusive why CRP only binds oxidized membranes. Here we offer a new perspective on the role of membrane curvature and CRP binding using engineered lipoprotein particle (LPP) mimics. We show that CRP binds preferentially to LPP mimics with diameters of ≤ 28 nm, and binding of CRP to these mimics leads to the dissociation of native CRP into monomeric CRP, exposing CRP neo-epitopes that bind C1q. We also show that the smaller LPP mimics compete for CRP binding to oxidized low density lipoproteins (oxLDLs), suggesting that these mimics expose the same PC epitopes as those found on oxLDLs. Results from this study suggest that membrane curvature could be an additional factor influencing CRP binding of damaged membranes distinct from the oxidation of PC lipids.

Direct visualization of electrophoretic mobility shift assays using nanoparticle-aptamer conjugates.

Here, we demonstrate that aptamers tethered to gold nanoparticles enable direct visualization of protein-oligonucleotide interactions during gel electrophoresis. This technique is used to confirm that an aptamer previously identified as binding to C-reactive protein (CRP) only binds to the monomeric form of CRP. While native, pentameric CRP (pCRP) is used in clinical assays to predict cardiovascular disease (CVD) risk, it is the monomeric isoform that is more strongly associated with pro-inflammatory and pro-atherogenic effects. To visualize this selectivity, the CRP-aptamer was conjugated to streptavidin-coated gold nanoparticles and the mobility of the free oligonucleotide-nanoparticle conjugate (ON-NP) and the protein/ON-NP complex bands were visualized and recorded during electrophoresis using a simple digital camera. At a concentration of 6 µg/mL, monomeric CRP showed a significant decrease in the observed ON-NP mobility, whereas no change in mobility was observed with pCRP up to 18 µg/mL. Advantages of this nanoparticle-based electrophoretic mobility shift assay (NP-EMSA) over the traditional EMSA include real-time detection of protein-oligonucleotide interactions, the avoidance of harmful radioisotopes, and elimination of the need for expensive gel imagers. The availability of both the NP-EMSA technique and an mCRP-specific probe will allow for improved clinical diagnostic to more accurately predict future CVD risk.

C-reactive protein (CRP) aptamer binds to monomeric but not pentameric form of CRP.

Native C-reactive protein (CRP) is composed of five identical subunits arranged in a pentameric structure (pCRP). Binding of pCRP to damaged cell membranes produces a second isoform, modified CRP, which has similar antigenicity to isolated monomeric subunits of CRP (mCRP). Emerging evidence indicates that modified CRP plays a role in inflammation and atherosclerosis, however, there are very few techniques that can distinguish the different isoforms of CRP. Here we show that an RNA aptamer binds specifically to mCRP and not to pCRP. Using this aptamer, we describe a simple, fast, and sensitive assay to detect nanomolar concentrations of mCRP using fluorescence anisotropy. In addition, we show that this aptamer can be used to detect mCRP in polyacrylamide gels and bound to a surface using total internal reflection fluorescence microscopy. The biological activity of the mCRP we prepared by heating pCRP with 0.1% sodium dodecyl sulfate was confirmed by observing binding to the complement protein, C1q. This probe provides an important tool for CRP research and has the potential to improve clinical diagnostics that predict risk for cardiovascular disease.

Electrophoretic Mobility of Lipoprotein Nanoparticle Mimics.

Lipoprotein particles (LPPs) are biological nanoparticles whose physiological roles are greatly influenced by their sizes. The four major classes of LP are: very low density lipoprotein, intermediate density lipoprotein, low density lipoprotein (LDL) and high density lipoprotein. Since the predominance of small, dense LDLs is associated with increased risk of coronary artery disease (CAD) and diabetes mellitus, LPP profiling can be used to predict metabolic risk factors. Highly tunable LPP mimics can be synthesized using nanoparticles to carefully control for size, lipid composition and surface charge to facilitate the study LPPs in CAD. Here, we engineered LPP mimics using gold nanoparticles between 10-50 nm in diameters. We measured the mobility and zeta potential of these LPP mimics and showed that each mimics have distinct electrokinetic properties and are electrostatically stable.

C-reactive protein induced rearrangement of phosphatidylcholine on nanoparticle mimics of lipoprotein particles.

Lipid-coated metal nanoparticles are developed here as a mimic of low-density lipoprotein (LDL) particles and used to study C-reactive protein (CRP) binding to highly curved lipid membranes. A 12 nm shift in the localized surface plasmon resonance (LSPR) was observed when CRP was added to the lipid-coated gold nanoparticles. Transmission electron microscopy (TEM) revealed that CRP induced a structural change to the lipids, resulting in clusters of nanoparticles. This clustering provides a visualization of how CRP could cause the aggregation of LDL particles, which is a key step in atherosclerosis. The cluster formation and resultant LSPR shift requires the presence of both CRP and calcium. Fluorescence anisotropy, using a CRP-specific, fluorophore-labeled aptamer confirmed that CRP was bound to the lipid-coated nanoparticles. An increase in the fluorescence anisotropy (Delta r = +0.261 +/- 0.004) of the aptamer probe occurs in the presence of CRP, PC-coated nanoparticles, and calcium. Subsequent sequestration of calcium by EDTA leads to a decrease in the anisotropy (Delta r = -0.233 +/- 0.011); however, there is no change in the LSPR and no change to the cluster structure observed by TEM. This indicates that CRP binds to the PC membrane on the nanoparticle surface reversibly through a calcium bridging mechanism while changing the underlying membrane structure irreversibly as a result of binding.

Parallel factor analysis of spider fluorophores.

Fluorophores from the hemolymph of yellow sac spiders (Cheiracanthium mildei) have been characterized using excitation emission matrix (EEM) fluorescence spectroscopy. This approach provides characterization of fluorophores present in the organism without having to isolate pure samples. Minimal variation occurs between individual samples and each EEM has two distinct peaks, suggesting two fluorophores may be present in the hemolymph. Parallel factor analysis reveals that three fluorophores (with excitation and emission maxima at 270/319, 330/389, and 350/465 nm) best explains the sample to sample variation. By comparing the spectra of the three individual components to fluorophores found in scorpions it is shown that these spiders possess different fluorophores than scorpions. Furthermore, the fluorescence observed is not consistent with beta-carboline or 4-methyl-7-hydroxycoumarin, two compounds previously described in scorpions.

Gold nanoparticles become stable to cyanide etch when coated with hybrid lipid bilayers.

Hybrid bilayers composed of the lipid phosphatidylcholine (PC) and a submonolayer of 1-decanethiol bound to gold nanoparticles are very stable to potassium cyanide.

Porphyrin conjugated to DNA by a 2'-amido-2'-deoxyuridine linkage.

A porphyrin that contains a single carboxylic acid group was synthesized and coupled to 2'-amino-2'-deoxyuridine. The resultant product contained a free 3' hydroxyl group and a 4,4'-dimethoxytrityl (DMT) protecting group on the 5' hydroxyl of the uridine, making it suitable for use in oligonucleotide synthesis. The 3' H-phosphonate derivative of this molecule was synthesized and used to form a conjugate with a 19 nucleotide sequence of DNA (5'-CCTCCAGTGGAAATCAAGG-3'). This was carried out with the DNA attached at the 3' end to a control pore glass (CPG) substrate, allowing for rapid purification. After removal of the DMT group, an additional three nucleotides were added, leaving the porphyrin as an internal modification. This is the first report of porphyrin attached internally to an oligonucleotide using a hydrogen-bonding nucleoside analog. This allows oligonucleotides to be used as a scaffold for precise positioning of multiple porphyrins within biomimetic arrays.