Rapid and automated design of two-component protein nanomaterials using ProteinMPNN.

The design of protein-protein interfaces using physics-based design methods such as Rosetta requires substantial computational resources and manual refinement by expert structural biologists. Deep learning methods promise to simplify protein-protein interface design and enable its application to a wide variety of problems by researchers from various scientific disciplines. Here, we test the ability of a deep learning method for protein sequence design, ProteinMPNN, to design two-component tetrahedral protein nanomaterials and benchmark its performance against Rosetta. ProteinMPNN had a similar success rate to Rosetta, yielding 13 new experimentally confirmed assemblies, but required orders of magnitude less computation and no manual refinement. The interfaces designed by ProteinMPNN were substantially more polar than those designed by Rosetta, which facilitated in vitro assembly of the designed nanomaterials from independently purified components. Crystal structures of several of the assemblies confirmed the accuracy of the design method at high resolution. Our results showcase the potential of deep learning-based methods to unlock the widespread application of designed protein-protein interfaces and self-assembling protein nanomaterials in biotechnology.

Design of amyloidogenic peptide traps.

Segments of proteins with high ß-strand propensity can self-associate to form amyloid fibrils implicated in many diseases. We describe a general approach to bind such segments in ß-strand and ß-hairpin conformations using de novo designed scaffolds that contain deep peptide-binding clefts. The designs bind their cognate peptides in vitro with nanomolar affinities. The crystal structure of a designed protein-peptide complex is close to the design model, and NMR characterization reveals how the peptide-binding cleft is protected in the apo state. We use the approach to design binders to the amyloid-forming proteins transthyretin, tau, serum amyloid A1 and amyloid ß1-42 (Aß42). The Aß binders block the assembly of Aß fibrils as effectively as the most potent of the clinically tested antibodies to date and protect cells from toxic Aß42 species.

De novo design of small beta barrel proteins.

Small beta barrel proteins are attractive targets for computational design because of their considerable functional diversity despite their very small size (<70 amino acids). However, there are considerable challenges to designing such structures, and there has been little success thus far. Because of the small size, the hydrophobic core stabilizing the fold is necessarily very small, and the conformational strain of barrel closure can oppose folding; also intermolecular aggregation through free beta strand edges can compete with proper monomer folding. Here, we explore the de novo design of small beta barrel topologies using both Rosetta energy-based methods and deep learning approaches to design four small beta barrel folds: Src homology 3 (SH3) and oligonucleotide/oligosaccharide-binding (OB) topologies found in nature and five and six up-and-down-stranded barrels rarely if ever seen in nature. Both approaches yielded successful designs with high thermal stability and experimentally determined structures with less than 2.4 Å rmsd from the designed models. Using deep learning for backbone generation and Rosetta for sequence design yielded higher design success rates and increased structural diversity than Rosetta alone. The ability to design a large and structurally diverse set of small beta barrel proteins greatly increases the protein shape space available for designing binders to protein targets of interest.

De novo designed ice-binding proteins from twist-constrained helices.

Attaining molecular-level control over solidification processes is a crucial aspect of materials science. To control ice formation, organisms have evolved bewildering arrays of ice-binding proteins (IBPs), but these have poorly understood structure-activity relationships. We propose that reverse engineering using de novo computational protein design can shed light on structure-activity relationships of IBPs. We hypothesized that the model alpha-helical winter flounder antifreeze protein uses an unusual undertwisting of its alpha-helix to align its putative ice-binding threonine residues in exactly the same direction. We test this hypothesis by designing a series of straight three-helix bundles with an ice-binding helix projecting threonines and two supporting helices constraining the twist of the ice-binding helix. Our findings show that ice-recrystallization inhibition by the designed proteins increases with the degree of designed undertwisting, thus validating our hypothesis, and opening up avenues for the computational design of IBPs.

Improving the secretion of designed protein assemblies through negative design of cryptic transmembrane domains.

Computationally designed protein nanoparticles have recently emerged as a promising platform for the development of new vaccines and biologics. For many applications, secretion of designed nanoparticles from eukaryotic cells would be advantageous, but in practice, they often secrete poorly. Here we show that designed hydrophobic interfaces that drive nanoparticle assembly are often predicted to form cryptic transmembrane domains, suggesting that interaction with the membrane insertion machinery could limit efficient secretion. We develop a general computational protocol, the Degreaser, to design away cryptic transmembrane domains without sacrificing protein stability. The retroactive application of the Degreaser to previously designed nanoparticle components and nanoparticles considerably improves secretion, and modular integration of the Degreaser into design pipelines results in new nanoparticles that secrete as robustly as naturally occurring protein assemblies. Both the Degreaser protocol and the nanoparticles we describe may be broadly useful in biotechnological applications.

Accurate computational design of three-dimensional protein crystals.

Protein crystallization plays a central role in structural biology. Despite this, the process of crystallization remains poorly understood and highly empirical, with crystal contacts, lattice packing arrangements and space group preferences being largely unpredictable. Programming protein crystallization through precisely engineered side-chain-side-chain interactions across protein-protein interfaces is an outstanding challenge. Here we develop a general computational approach for designing three-dimensional protein crystals with prespecified lattice architectures at atomic accuracy that hierarchically constrains the overall number of degrees of freedom of the system. We design three pairs of oligomers that can be individually purified, and upon mixing, spontaneously self-assemble into >100 µm three-dimensional crystals. The structures of these crystals are nearly identical to the computational design models, closely corresponding in both overall architecture and the specific protein-protein interactions. The dimensions of the crystal unit cell can be systematically redesigned while retaining the space group symmetry and overall architecture, and the crystals are extremely porous and highly stable. Our approach enables the computational design of protein crystals with high accuracy, and the designed protein crystals, which have both structural and assembly information encoded in their primary sequences, provide a powerful platform for biological materials engineering.

Toward net-zero sustainable aviation fuel with wet waste-derived volatile fatty acids.

With the increasing demand for net-zero sustainable aviation fuels (SAF), new conversion technologies are needed to process waste feedstocks and meet carbon reduction and cost targets. Wet waste is a low-cost, prevalent feedstock with the energy potential to displace over 20% of US jet fuel consumption; however, its complexity and high moisture typically relegates its use to methane production from anaerobic digestion. To overcome this, methanogenesis can be arrested during fermentation to instead produce C2 to C8 volatile fatty acids (VFA) for catalytic upgrading to SAF. Here, we evaluate the catalytic conversion of food waste-derived VFAs to produce n-paraffin SAF for near-term use as a 10 vol% blend for ASTM "Fast Track" qualification and produce a highly branched, isoparaffin VFA-SAF to increase the renewable blend limit. VFA ketonization models assessed the carbon chain length distributions suitable for each VFA-SAF conversion pathway, and food waste-derived VFA ketonization was demonstrated for >100 h of time on stream at approximately theoretical yield. Fuel property blending models and experimental testing determined normal paraffin VFA-SAF meets 10 vol% fuel specifications for "Fast Track." Synergistic blending with isoparaffin VFA-SAF increased the blend limit to 70 vol% by addressing flashpoint and viscosity constraints, with sooting 34% lower than fossil jet. Techno-economic analysis evaluated the major catalytic process cost-drivers, determining the minimum fuel selling price as a function of VFA production costs. Life cycle analysis determined that if food waste is diverted from landfills to avoid methane emissions, VFA-SAF could enable up to 165% reduction in greenhouse gas emissions relative to fossil jet.

Design of Diverse Asymmetric Pockets in De Novo Homo-oligomeric Proteins.

A challenge for design of protein-small-molecule recognition is that incorporation of cavities with size, shape, and composition suitable for specific recognition can considerably destabilize protein monomers. This challenge can be overcome through binding pockets formed at homo-oligomeric interfaces between folded monomers. Interfaces surrounding the central homo-oligomer symmetry axes necessarily have the same symmetry and so may not be well suited to binding asymmetric molecules. To enable general recognition of arbitrary asymmetric substrates and small molecules, we developed an approach to designing asymmetric interfaces at off-axis sites on homo-oligomers, analogous to those found in native homo-oligomeric proteins such as glutamine synthetase. We symmetrically dock curved helical repeat proteins such that they form pockets at the asymmetric interface of the oligomer with sizes ranging from several angstroms, appropriate for binding a single ion, to up to more than 20 Å across. Of the 133 proteins tested, 84 had soluble expression in E. coli, 47 had correct oligomeric states in solution, 35 had small-angle X-ray scattering (SAXS) data largely consistent with design models, and 8 had negative-stain electron microscopy (nsEM) 2D class averages showing the structures coming together as designed. Both an X-ray crystal structure and a cryogenic electron microscopy (cryoEM) structure are close to the computational design models. The nature of these proteins as homo-oligomers allows them to be readily built into higher-order structures such as nanocages, and the asymmetric pockets of these structures open rich possibilities for small-molecule binder design free from the constraints associated with monomer destabilization.

Using TLC-MALDI-TOF to Interrogate In Vitro Peptidyl Proximal Preferences of PARP14 and Glycohydrolase Specificity.

The transfer of ADP-ribose (ADPr) from nicotinamide adenine dinucleotide (NAD+) to target proteins is mediated by a class of human diphtheria toxin-like ADP-ribosyltransferases (ARTDs; previously referred to as poly-ADP-ribose polymerases or PARPs) and the removal of ADPr is catalyzed by a family of glycohydrolases. Although thousands of potential ADPr modification sites have been identified using high-throughput mass-spectrometry, relatively little is known about the sequence specificity encoded near the modification site. Herein, we present a matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) method that facilitates the in vitro analysis of proximal factors that guide ARTD target selection. We identify a minimal 5-mer peptide sequence that is necessary and sufficient to drive glutamate/aspartate targeting using PARP14 while highlighting the importance of the adjacent residues in PARP14 targeting. We measure the stability of the resultant ester bond and show that non-enzymatic removal is pH and temperature dependent, sequence independent, and occurs within hours. Finally, we use the ADPr-peptides to highlight differential activities within the glycohydrolase family and their sequence preferences. Our results highlight (1) the utility of MALDI-TOF in analyzing proximal ARTD-substrate interactions and (2) the importance of peptide sequences in governing ADPr transfer and removal.

Utility of MRI in the identification of hippocampal sclerosis of aging.

INTRODUCTION: Hippocampal sclerosis of aging (HS) is a common pathology often misdiagnosed as Alzheimer's disease. We tested the hypothesis that participants with HS would have a magnetic resonance imaging (MRI)-detectable hippocampal pattern of atrophy distinct from participants without HS, both with and without Alzheimer's disease neuropathology (ADNP). METHODS: Query of the National Alzheimer's Coordinating Center database identified 198 participants with MRI and autopsy. Hippocampal subfields were segmented with FreeSurfer v6. Analysis of covariance for subfield volumes compared HS+ participants to those without HS, both with ADNP (HS-/ADNP+) and without (HS-/ADNP-). RESULTS: HS+ participants (N = 27, 14%) showed atrophied cornu ammonis 1 (CA1; left P < .001, ηp2  = 0.14; right P = .001, ηp2  = 0.09) and subiculum (left P < .001, ηp2  = 0.139; right P = .001, ηp2  = 0.085) compared to HS-/ADNP+ (N = 100, 51%). Compared to HS-/ADNP- (N = 71, 36%), HS+ also had atrophy in subiculum (left P < .001, ηp2  = 0.235; right P = .002, ηp2  = 0.137) and CA1 (left P < .001, ηp2  = 0.137; right P = .006, ηp2  = 0.070). DISCUSSION: Subiculum and CA1 atrophy from clinical MRI may be a promising in vivo biomarker for HS.

Interpersonal Psychotherapy-Adolescent Skills Training With Youth From Asian American and Immigrant Families: Cultural Considerations and Intervention Process.

Although research has identified effective evidence-based depression prevention interventions for diverse youth, little is known about how the intervention process unfolds with immigrant family youth. This study utilized a qualitative approach to explore cultural and clinical differences in the implementation of Interpersonal Psychotherapy-Adolescent Skills Training (IPT-AST) in two schools, one serving youth from primarily immigrant, Asian American families and the second, youth from mostly nonimmigrant, non-Hispanic White families. A total of 131 IPT-AST sessions were audio recorded, transcribed, and coded for presence and patterns of cultural and clinical constructs. Results revealed that sessions with immigrant family youth were more likely to contain discussions of interpersonal problems characterized by estrangement, goals of spending time together with important others, mentions of emotion suppression and academic achievement expectations, conversations about acculturation, differences in value orientation, and discomfort with implementing new intervention skills. Dialogue from interventionist and youth exchanges is presented to illustrate how these themes emerged and were addressed by interventionists in a culturally responsive manner. The study highlights how IPT-AST with immigrant family and Asian American youth may unfold differently compared to youth from nonimmigrant families. Implications of findings for providers are discussed.

Nicotine Impairs the Response of Lung Epithelial Cells to IL-22.

Smoking is a major risk factor for pulmonary diseases that include chronic obstructive pulmonary diseases (COPD) and cancer. Nicotine is the toxic and addictive component of tobacco products, like cigarettes, that negatively affects the immune system. Here, we examined the effect of nicotine on the IL-22 pathway that protects lung function by increasing transepithelial resistance and epithelial cell regeneration and repair. Our results indicate that exposure to nicotine impairs the regenerative capacity of primary bronchial epithelial cells in scratch assays. IL-22 at 100 ng/ml significantly improved wound healing in epithelial cells; however, the exposure to nicotine hampered the IL-22-mediated effect of wound healing. Investigation into the mechanisms showed that IL-22 receptor, IL-22Rα1, was downregulated in the presence of nicotine as determined by q-PCR and flow cytometry. We also investigated the effect of nicotine on IL-22 production by T cells. Results indicate that nicotine inhibited the secretion of IL-22 from T cells in response to aryl hydrocarbon receptor (AHR) ligand, FICZ. Altogether, the data suggests that nicotine negatively influences the IL-22-IL-22R axis. This impairment may contribute to the nicotine-mediated detrimental effects on lung function.

Effects of Preference on Outcomes of Preventive Interventions among Ethnically Diverse Adolescents At-Risk of Depression.

Patient-centered care includes efforts to align treatment with patient preferences to improve outcomes and has not been studied in adolescent depression prevention. Within a school-based randomized trial, we examined the effects of offering a preference between two evidence-based preventive interventions for youth at risk of depression, Learning to BREATHE (L2B) and Interpersonal Therapy-Adolescent Skills Training. We examined the effects of 3 preference factors (assignment condition [preference vs. random], receipt of preferred program, and baseline program preference) on outcomes in a diverse sample of 111 adolescents (M age = 15.18 years, SD = .86): 81 (73%) girls, 45 (41%) White, 40 (36%) Asian American, 8 (7%) Latinx, 1 (1%) African American, and 17 (15%) multiracial or other race/ethnicity. Findings revealed little evidence that receiving a preferred intervention or being given a choice of interventions was linked to greater improvement or initial engagement. Further, analyses did not indicate that adolescents with baseline indications for a specific intervention would benefit more from that intervention; rather, adolescents with generally lower baseline functioning improved more regardless of the intervention received. However, receipt of L2B and a baseline preference for L2B were associated with greater improvements in about half of the outcomes examined, with effect sizes ranging from R 2 = 0.04 to 0.14. There was little support for the need to match interventions to adolescent preferences in school-based prevention efforts. Rather, the more scalable mindfulness-based intervention had stronger effects than the interpersonal intervention and may hold promise for diverse adolescents.

Correction to: "I was Confused About How to Take Care of Mom Because this Disease Is Different Everyday": Vietnamese American Caregivers' Understanding of Alzheimer's Disease.

The original version of this article unfortunately contained a mistake.

"I was Confused About How to Take Care of Mom Because this Disease is Different Everyday": Vietnamese American Caregivers' Understanding of Alzheimer's Disease.

Family members provide the majority of caregiving to individuals living with Alzheimer's disease (AD) and related dementias. Asian American families are disproportionately impacted by the burden of caregiving due to limited knowledge about the disease in this community. This study explored how Vietnamese American caregivers understand AD and provide care to family members with AD. Twenty caregivers who have provided care to a family member with AD participated in a semi-structured qualitative interview. Data were analyzed using thematic analysis. Several themes were identified in the caregivers' understanding of AD: (a) "Now I know:" the disruptions, shocks and surprises leading up to the initial diagnosis; (b) The frustrations of managing family members' cognitive impairments; (c)"Going with the flow:" challenges in managing personality and behavioral changes; (d) The exhaustion of around-the-clock caregiving; (e)"Taking it day by day" in the face of progressively worsening symptoms. Underlining the participants' descriptions of AD was a shared understanding of the progressively worsening, complex and unpredictable nature of the disease that makes it challenging for family caregivers on a daily basis. Findings provide important implications for healthcare workers' outreach to Vietnamese American families to ease the caregiving experience through culturally-responsive education, thereby enhancing the families' ability to recognize the early symptoms and seek appropriate help.

"Living happily despite having an illness": Perceptions of healthy aging among Korean American, Vietnamese American, and Latino older adults.

BACKGROUND/OBJECTIVE: The growingly diverse aging population presents a challenge for the geriatric workforce, particularly its capacity to effectively respond to the sociocultural and linguistic needs of ethnic minority older adults. Informed by research on the importance of culturally-competent care in reducing racial and ethnic health disparities, this study sought to understand the meaning of healthy aging from the perspectives of Korean American, Vietnamese American, and Latino older adults. METHODS: Interviews were conducted with 30 participants recruited from community-based organizations in Southern California. RESULTS: Several dimensions emerged in the participants' understanding of healthy aging: (1) having good physical and mental health (2) optimism and acceptance; (3) social connectedness; (4) taking charge of one's health; and (5) independence and self-worth. CONCLUSIONS: Results could inform the development of a culturally-responsive geriatric healthcare system that takes into account older adults' beliefs, preferences, and needs to promote successful aging.

Quantitative Profiling of the Activity of Protein Lysine Methyltransferase SMYD2 Using SILAC-Based Proteomics.

The significance of non-histone lysine methylation in cell biology and human disease is an emerging area of research exploration. The development of small molecule inhibitors that selectively and potently target enzymes that catalyze the addition of methyl-groups to lysine residues, such as the protein lysine mono-methyltransferase SMYD2, is an active area of drug discovery. Critical to the accurate assessment of biological function is the ability to identify target enzyme substrates and to define enzyme substrate specificity within the context of the cell. Here, using stable isotopic labeling with amino acids in cell culture (SILAC) coupled with immunoaffinity enrichment of mono-methyl-lysine (Kme1) peptides and mass spectrometry, we report a comprehensive, large-scale proteomic study of lysine mono-methylation, comprising a total of 1032 Kme1 sites in esophageal squamous cell carcinoma (ESCC) cells and 1861 Kme1 sites in ESCC cells overexpressing SMYD2. Among these Kme1 sites is a subset of 35 found to be potently down-regulated by both shRNA-mediated knockdown of SMYD2 and LLY-507, a selective small molecule inhibitor of SMYD2. In addition, we report specific protein sequence motifs enriched in Kme1 sites that are directly regulated by endogenous SMYD2 activity, revealing that SMYD2 substrate specificity is more diverse than expected. We further show direct activity of SMYD2 toward BTF3-K2, PDAP1-K126 as well as numerous sites within the repetitive units of two unique and exceptionally large proteins, AHNAK and AHNAK2. Collectively, our findings provide quantitative insights into the cellular activity and substrate recognition of SMYD2 as well as the global landscape and regulation of protein mono-methylation.

Anticoagulant Use in High Stroke-Risk Patients With Nonvalvular Atrial Fibrillation.

Background Oral anticoagulants (OACs) are recommended for nonvalvular atrial fibrillation (NVAF) patients with moderate-to high-stroke risk. Objective To examine nationally reflective OAC usage in incident NVAF patients longitudinally. Design Three-year retrospective cohort analysis. Setting Medicare Part D recipients in the contiguous United States. PARTICIPANTS: 52,465 Medicare beneficiaries with incident NVAF in 2010 with two or more atrial fibrillation diagnoses seven or more days apart. Main outcome measure Stroke risk via congestive heart failure, hypertension, age greater than or equal to 75, diabetes, stroke, vascular disease, age 65-74, sex category (CHA2DS2-VASc) score. Primary outcome was proportion of patients receiving one or more OACs post-NVAF diagnoses. Results Of 48,980 high-risk patients, 32.7% received one or more OAC within 60 days of diagnosis. By close of 2011, 48% had one or more OAC. OAC use increased to 52.9% by close of 2012. Conclusions Fewer than 33% of high-risk NVAF patients received OACs within 60 days of diagnosis in 2010. Despite increased use over time, oral anticoagulation was below 53% at study end. Use of OACs declined with CHA2DS2-VASc greater than 6. Expanded efforts are warranted to augment OAC use in high stroke-risk patients.

LLY-507, a Cell-active, Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2.

SMYD2 is a lysine methyltransferase that catalyzes the monomethylation of several protein substrates including p53. SMYD2 is overexpressed in a significant percentage of esophageal squamous primary carcinomas, and that overexpression correlates with poor patient survival. However, the mechanism(s) by which SMYD2 promotes oncogenesis is not understood. A small molecule probe for SMYD2 would allow for the pharmacological dissection of this biology. In this report, we disclose LLY-507, a cell-active, potent small molecule inhibitor of SMYD2. LLY-507 is >100-fold selective for SMYD2 over a broad range of methyltransferase and non-methyltransferase targets. A 1.63-Å resolution crystal structure of SMYD2 in complex with LLY-507 shows the inhibitor binding in the substrate peptide binding pocket. LLY-507 is active in cells as measured by reduction of SMYD2-induced monomethylation of p53 Lys(370) at submicromolar concentrations. We used LLY-507 to further test other potential roles of SMYD2. Mass spectrometry-based proteomics showed that cellular global histone methylation levels were not significantly affected by SMYD2 inhibition with LLY-507, and subcellular fractionation studies indicate that SMYD2 is primarily cytoplasmic, suggesting that SMYD2 targets a very small subset of histones at specific chromatin loci and/or non-histone substrates. Breast and liver cancers were identified through in silico data mining as tumor types that display amplification and/or overexpression of SMYD2. LLY-507 inhibited the proliferation of several esophageal, liver, and breast cancer cell lines in a dose-dependent manner. These findings suggest that LLY-507 serves as a valuable chemical probe to aid in the dissection of SMYD2 function in cancer and other biological processes.

Application of the Extended Health Control Belief Model to Predict Hepatitis A and B Vaccinations.

BACKGROUND: Adult vaccination compliance rates vary according to sample and type of vaccine administered (influenza, pneumococcal). This study looked at vaccination of a community sample of low-income, minority adults. METHODS: Nurses offered free vaccination for hepatitis A and B in the form of the combined Twinrix vaccine to adults on a walk-in basis. In addition to dosing information, participants completed the Risk Behavior Assessment, the Coping Strategies Indicator and the Cardiovascular Risk Assessment. Skaff's extended Health Belief Model was used as the theoretical framework. Count regression was used to model receipt of one, two, or three doses. RESULTS: The majority of participants were male with a mean age of 40 years. The distribution of doses was: 173 individuals (27.6%) received one dose only, 261 (41.7%) received two doses, and 191 (30.5%) received three doses of vaccine. The multivariate count regression model including being male, having previously been told by a health care provider that one has syphilis, having severe negative emotions, and perceived social support were associated with participants' receiving fewer doses of hepatitis vaccine. A greater problem-solving score was associated with a higher number of vaccine doses received. CONCLUSION: Despite free vaccinations offered in an easily accessible community setting, the majority of participants failed to complete the hepatitis vaccine series. More effort is needed to get adult men to participate in hepatitis vaccination clinics. Additional research is necessary to understand barriers other than cost to adults receiving vaccination.