DNA-Nanostructure-Guided Assembly of Proteins into Programmable Shapes

The development of methods to synthesize artificial protein complexes with precisely controlled configurations will enable diverse biological and medical applications. Using DNA to link proteins provides programmability that can be difficult to achieve with other methods. Here, we use DNA origami as an "assembler" to guide the linking of protein-DNA conjugates using a series of oligonucleotide hybridization and displacement operations. We constructed several isomeric protein nanostructures, including a dimer, two types of trimer structures, and three types of tetramer assemblies, on a DNA origami platform by using a C3-symmetric building block composed of a protein trimer modified with DNA handles. Our approach expands the scope for the precise assembly of protein-based nanostructures and will enable the formulation of functional protein complexes with stoichiometric and geometric control.

High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody

Multivalency enables nanostructures to bind molecular targets with high affinity. Although antibodies can be generated against a wide range of antigens, their shape and size cannot be tuned to match a given target. DNA nanotechnology provides an attractive approach for designing customized multivalent scaffolds due to the addressability and programmability of the nanostructure shape and size. Here, we design a nanoscale synthetic antibody ("nano-synbody") based on a three-helix bundle DNA nanostructure with one, two, or three identical arms terminating in a mini-binder protein that targets the SARS-CoV-2 spike protein. The nano-synbody was designed to match the valence and distance between the three receptor binding domains (RBDs) in the spike trimer, in order to enhance affinity. The protein-DNA nano-synbody shows tight binding to the wild-type, Delta, and several Omicron variants of the SARS-CoV-2 spike trimer, with affinity increasing as the number of arms increases from one to three. The effectiveness of the nano-synbody was also verified using a pseudovirus neutralization assay, with the three-arm nanostructure inhibiting two Omicron variants against which the structures with only one or two arms are ineffective. The structure of the three-arm nano-synbody bound to the Omicron variant spike trimer was solved by negative-stain transmission electron microscopy reconstruction, and shows the protein-DNA nanostructure with all three arms attached to the RBD domains, confirming the intended trivalent attachment. The ability to tune the size and shape of the nano-synbody, as well as its potential ability to attach two or more different binding ligands, will enable the high-affinity targeting of a range of proteins not possible with traditional antibodies.

Desmocollin-1 is associated with pro-metastatic phenotype of luminal A breast cancer cells and is modulated by parthenolide

BACKGROUND

Desmocollin-1 (DSC1) is a desmosomal transmembrane glycoprotein that maintains cell-to-cell adhesion. DSC1 was previously associated with lymph node metastasis of luminal A breast tumors and was found to increase migration and invasion of MCF7 cells in vitro. Therefore, we focused on DSC1 role in cellular and molecular mechanisms in luminal A breast cancer and its possible therapeutic modulation.

METHODS

Western blotting was used to select potential inhibitor decreasing DSC1 protein level in MCF7 cell line. Using atomic force microscopy we evaluated effect of DSC1 overexpression and modulation on cell morphology. The LC-MS/MS analysis of total proteome on Orbitrap Lumos and RNA-Seq analysis of total transcriptome on Illumina NextSeq 500 were performed to study the molecular mechanisms associated with DSC1. Pull-down analysis with LC-MS/MS detection was carried out to uncover DSC1 protein interactome in MCF7 cells.

RESULTS

Analysis of DSC1 protein levels in response to selected inhibitors displays significant DSC1 downregulation (p-value ≤ 0.01) in MCF7 cells treated with NF-κB inhibitor parthenolide. Analysis of mechanic cell properties in response to DSC1 overexpression and parthenolide treatment using atomic force microscopy reveals that DSC1 overexpression reduces height of MCF7 cells and conversely, parthenolide decreases cell stiffness of MCF7 cells overexpressing DSC1. The LC-MS/MS total proteome analysis in data-independent acquisition mode shows a strong connection between DSC1 overexpression and increased levels of proteins LACRT and IGFBP5, increased expression of IGFBP5 is confirmed by RNA-Seq. Pathway analysis of proteomics data uncovers enrichment of proliferative MCM_BIOCARTA pathway including CDK2 and MCM2-7 after DSC1 overexpression. Parthenolide decreases expression of LACRT, IGFBP5 and MCM_BIOCARTA pathway specifically in DSC1 overexpressing cells. Pull-down assay identifies DSC1 interactions with cadherin family proteins including DSG2, CDH1, CDH3 and tyrosine kinase receptors HER2 and HER3; parthenolide modulates DSC1-HER3 interaction.

CONCLUSIONS

Our systems biology data indicate that DSC1 is connected to mechanisms of cell cycle regulation in luminal A breast cancer cells, and can be effectively modulated by parthenolide.

Time trends in the relation between the achieved education and the cardiovascular risk factors prevalence and control in general population and in persons with coronary heart disease

Background

Achieved education is the most consistent and powerful socioeconomic status index and the differences in cardiovascular mortality (CV) according to achieved education in the Czech Republic are over a long period among most pronounced in Europe. Higher prevalence of CV risk factors in less educated is the major factor behind their higher CV morbidity and mortality.

Purpose

To analyse the changes in prevalence and control of CV risk factors according to achieved education in general population and in patients with stable CHD and their impact on CV mortality.

Methods

Based on data of 15 590 persons from 7 cross sectional epidemiological surveys carried through the Czech MONICA and post-MONICA project in 1985–2018 in identical 6 districts of the Czech Republic (general population) and on data of 2129 patients from 5 independent descriptive surveys of the Czech EUROASPIRE study in 1995–2018 (patients with stable CHD) time trends of major CV risk factors and their control in respondents with basic, secondary and university education were compared.

Results

The persons from general population as well as patients with CHD with higher education had consistently lower BMI and lower prevalence of obesity, the differences increased in due time (p<0,001), the prevalence of obesity increased in all educational strata (p<0,001). The total and non-HDL cholesterol were higher in lower educational population strata (p<0,01), but not in CHD patients, there was a very pronounced continuous decrease in all educational strata (p<0,001 for trend). Population systolic and diastolic blood pressures and prevalence of hypertension were higher in men and women with basic education (p<0,01) and decreased during the analysed period (p<0,001). In CHD patients the blood pressure was higher only in women. The prevalence of smoking was higher in men with basic education and decreased in all educational strata (p<0,0001), in women the prevalence of smoking increased in women with basic and decreased in women with secondary and university education (p<0,0001), in CHD patients the prevalence of smoking was lower and did not differ according to education. Prevalence of diabetes and of sedentary life style increased and was more prevalent in general as well as in CHD population in persons with lower education.

Conclusion

CV risk gradient in general population and in CHD patients decreased with level of education achieved, was present during the whole analysed period and became more pronounced in the 2016–18 survey. The education based differences were more pronounced in factors influenced by lifestyle (BMI, smoking) and less in factors influenced also by medical therapies (blood pressure, cholesterol levels). The impact on CV mortality is to be expected more pronounced in general CV prevention and less in already treated population. Observation of healthy life style remains a basic problem in CV prevention, particularly in persons with elementary education.

Funding Acknowledgement

Type of funding source: Public grant(s) – National budget only. Main funding source(s): Agency for Medical Research, Ministry of Health of the Czech Republic

P6230Gender disparities in serum uric acid levels associated increased cardiovascular risk. The Czech Post-MONICA study

Background

Recent European Society of Hypertension (ESH) guidelines have implemented serum uric acid (SUA) levels as cardiovascular (CV) risk factor and recommend routine SUA levels measurement in hypertensive patients. However, what is the appropriate SUA level threshold and whether all patients with so called asymptomatic hyperuricemia should be treated remain unclear.

Objective

To evaluate longitudinal trends and determinants of mean serum uric acid (SUA) levels in two representative Czech population surveys (2006–09 and 2015–18) and to determine the SUA levels associated with increased 10-year risk of cardiovascular (CV) death.

Methods

Two independent cross-sectional surveys of major CV risk factors were performed in the Czech Republic in 2006–09 and 2015–18; 1% percent random samples aged 25–64 years stratified by age and gender were examined. The number of participants was 3612 in 2006–09, and 2621 in 2015–18. Ten-year risk of CV death was categorized using the SCORE algorithm as low (<1%), intermediate (1% to <5%), high (≥5% to 10%), and very high (≥10%).

Results

Final analyses included 3542 individuals (48.2% men; mean age 47.1±11.3) in 2006–09, and 2304 individuals (47.4% men; mean age 47.9±10.9) in 2015–18. Over the past decade, there was a highly significant increase in SUA levels (μmol/l) from 344.6±81.1 to 374.4±73.3 in men, and from 250.1±73.8 to 278.9±66.1 in women. In gender-specific multivariate linear regression analyses conducted in the 2015–18 survey, SUA levels increased with use of diuretics, an increase in waist-to-height ratio, serum triglycerides, and aspartate aminotransferase, and a decrease in estimated glomerular filtration rate in both genders, whereas in men SUA levels increased also with an increase in quartiles of alcohol intake and gamma-glutamyl transferase, and a decrease in glycated haemoglobin. When analysing pooled data of the two surveys, mean SUA levels increased with each increase in 10-year CV risk category in women (P<0.001), but not in men (P=0.21). In receiver operating characteristic (ROC) curve analysis, the cut-off value of SUA levels discriminating between low/intermediate and high/very high CV risk category in women was 306 μmol/l (sensitivity 53%; specificity 82%; area under the ROC curve 0.713 [95% CI 0.683–0.743]).

Conclusions

Over the past decade, there was a significant increase in uricemia in the Czech adult population. However, increasing SUA levels were associated with increased 10-year CV death risk only in women. The SUA levels associated with high/very high CV risk were substantially lower in Czech women than the currently used cut-off values for hyperuricemia.

Acknowledgement/Funding

Grant number 15-27109A from Czech health research council

On the biophysics and kinetics of toehold-mediated DNA strand displacement

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

On the biophysics and kinetics of toehold-mediated DNA strand displacement

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

DNA hybridization kinetics: zippering, internal displacement and sequence dependence

Although the thermodynamics of DNA hybridization is generally well established, the kinetics of this classic transition is less well understood. Providing such understanding has new urgency because DNA nanotechnology often depends critically on binding rates. Here, we explore DNA oligomer hybridization kinetics using a coarse-grained model. Strand association proceeds through a complex set of intermediate states, with successful binding events initiated by a few metastable base-pairing interactions, followed by zippering of the remaining bonds. But despite reasonably strong interstrand interactions, initial contacts frequently dissociate because typical configurations in which they form differ from typical states of similar enthalpy in the double-stranded equilibrium ensemble. Initial contacts must be stabilized by two or three base pairs before full zippering is likely, resulting in negative effective activation enthalpies. Non-Arrhenius behavior arises because the number of base pairs required for nucleation increases with temperature. In addition, we observe two alternative pathways—pseudoknot and inchworm internal displacement—through which misaligned duplexes can rearrange to form duplexes. These pathways accelerate hybridization. Our results explain why experimentally observed association rates of GC-rich oligomers are higher than rates of AT- rich equivalents, and more generally demonstrate how association rates can be modulated by sequence choice.

Non-Gaussianity in single-particle tracking: use of kurtosis to learn the characteristics of a cage-type potential

Nonlinear interaction of membrane proteins with cytoskeleton and membrane leads to non-Gaussian structure of their displacement probability distribution. We propose a statistical analysis technique for learning the characteristics of the nonlinear potential from the time dependence of the cumulants of the displacement distribution. The efficiency of the approach is demonstrated on the analysis of the kurtosis of the displacement distribution of the particle traveling on a membrane in a cage-type potential. Results of numerical simulations are supported by analytical predictions. We show that the approach allows robust identification of some characteristics of the potential for the much lower temporal resolution compared with the mean-square displacement analysis and we demonstrate robustness to experimental errors in determining the particle positions.

Quantifying slow evolutionary dynamics in RNA fitness landscapes

We re-examine the evolutionary dynamics of RNA secondary structures under directional selection towards an optimum RNA structure. We find that the punctuated equilibria lead to a very slow approach to the optimum, following on average an inverse power of the evolutionary time. In addition, our study of the trajectories shows that the out-of-equilibrium effects due to the evolutionary process are very weak. In particular, the distribution of genotypes is close to that arising during equilibrium stabilizing selection. As a consequence, the evolutionary dynamics leave almost no measurable out-of-equilibrium trace, only the transition genotypes (close to the border between different periods of stasis) have atypical mutational properties.

Return probabilities and hitting times of random walks on sparse Erdös-Rényi graphs

We consider random walks on random graphs, focusing on return probabilities and hitting times for sparse Erdös-Rényi graphs. Using the tree approach, which is expected to be exact in the large graph limit, we show how to solve for the distribution of these quantities and we find that these distributions exhibit a form of self-similarity.

Experimental rabbit model of meningitis produced by Haemophilus influenzae serotype c

The virulence of Haemophilus influenzae type c when inoculated intracisternally (i.c.) into rabbits was evaluated. Rabbits are relatively resistant to infection with H. influenzae type b, such that inocula of the order of 10(6-9) cfu are required to produce meningitis in this model. In contrast, fatal meningitis was produced in this study when 10(3) cfu of a type-c strain were injected i.c. into rabbits. Numbers of bacteria in cerebrospinal fluid (CSF) of control (untreated) animals generally increased to 10(7) cfu/ml. Increases in white blood cells, protein and lactate in the CSF were similar to those which had been observed during meningitis due to Streptococcus pneumoniae in rabbits. The infection was amenable to therapy with ampicillin 50 mg/kg given intravenously 12 h after infection. Numbers of bacteria in CSF were reduced to 2.2 x 10(3) cfu/ml (SEM 0.2 x 10(3)) at 8 h after treatment with a single dose of ampicillin. Two doses of ampicillin, given 12 and 20 h after infection, significantly increased the mean survival time. In contrast to previous experimental studies with rabbits, the penetration of ampicillin into the CSF was high--46 (SEM 10) % of the blood level. Since considerable replication of H. influenzae type c occurred within the CSF in this model, the nature of the meningeal damage produced was likely to be similar to that which takes place in man. Hence, H. influenzae type c meningitis in rabbits may provide a useful model in which therapeutic and other experimental studies of H. influenzae meningitis can be performed.