Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “protein dynamics”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 523 records · Page 29

Influence of Electronic Polarization on the Spectral Density

Accurate spectral densities are necessary for computing realistic exciton dynamics and nonlinear optical spectra of chromophores in condensed-phase environments, including multichromophore pigment–protein systems. However, due to the significant computational cost of computing spectral densities from first principles, requiring many thousands of excited-state calculations, most simulations of realistic systems rely on treating the environment as fixed-point charges. In this work, using a number of representative systems ranging from solvated chromophores to the photoactive yellow protein (PYP), we demonstrate that the quantum mechanical (QM) electronic polarization of the environment is key to obtaining accurate spectral densities and line shapes within the cumulant framework. We show that the QM environment can enhance or depress the coupling of fast chromophore degrees of freedom to the energy gap, altering the electronic–vibrational coupling and the resulting vibronic progressions in the absorption spectrum. In analyzing the physical origin of peaks in the spectral density, we identify vibrational modes that couple the electron and the hole as being particularly sensitive to the QM screening of the environment. For PYP, we reveal the need for careful determination of the appropriate QM region to obtain reliable spectral densities. Our findings suggest that the QM polarization of the environment can be crucial not just for excitation energies but also for electronic–vibrational coupling in complex systems with implications for the correct modeling of linear and nonlinear optical spectroscopy in the condensed phase as well as energy transfer in pigment–protein complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Magnetic resonance control of spin-correlated radical pair dynamics in vivo

Magnetic fields can influence reactions involving spin-correlated radical pairs (SCRPs). This provides a mechanism by which both static and time-varying magnetic fields can affect living systems at the biomolecular level. However, an engineered SCRP system conferring magnetic sensitivity to a non-native biochemical process in a multicellular organism has not yet been demonstrated. Here, in this study, we demonstrate control of SCRP dynamics using magnetic resonance in a live transgenic animal. We show that the emission of various red fluorescent proteins (RFPs), in the presence of a flavin cofactor, can be modified by a combination of static and radiofrequency magnetic fields applied near the electron spin resonance frequency. This effect was measured at room temperature both in vitro and in the nematode Caenorhabditis elegans, genetically modified to express the RFP mScarlet. These observations suggest that the magnetic field effects measured in RFP-flavin systems are due to quantum-correlated radical pairs with a coherence time larger than 4 ns. Our experiments demonstrate that radiofrequency magnetic fields can influence dynamics of reactions involving SCRPs in vivo, potentially enabling new methods for remotely controlling biomolecular processes, such as gene expression, and suggest broader potential for quantum tools in biology.

Burd, Shaun C. [Stanford Univ., CA (United States)↗

End-to-end learning of multiple sequence alignments with differentiable Smith–Waterman

Abstract Motivation Multiple sequence alignments (MSAs) of homologous sequences contain information on structural and functional constraints and their evolutionary histories. Despite their importance for many downstream tasks, such as structure prediction, MSA generation is often treated as a separate pre-processing step, without any guidance from the application it will be used for. Results Here, we implement a smooth and differentiable version of the Smith–Waterman pairwise alignment algorithm that enables jointly learning an MSA and a downstream machine learning system in an end-to-end fashion. To demonstrate its utility, we introduce SMURF (Smooth Markov Unaligned Random Field), a new method that jointly learns an alignment and the parameters of a Markov Random Field for unsupervised contact prediction. We find that SMURF learns MSAs that mildly improve contact prediction on a diverse set of protein and RNA families. As a proof of concept, we demonstrate that by connecting our differentiable alignment module to AlphaFold2 and maximizing predicted confidence, we can learn MSAs that improve structure predictions over the initial MSAs. Interestingly, the alignments that improve AlphaFold predictions are self-inconsistent and can be viewed as adversarial. This work highlights the potential of differentiable dynamic programming to improve neural network pipelines that rely on an alignment and the potential dangers of optimizing predictions of protein sequences with methods that are not fully understood. Availability and implementation Our code and examples are available at: https://github.com/spetti/SMURF. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

GTP binding by Arabidopsis extra-large G protein 2 is not essential for its functions

The extra-large guanosine-5'-triphosphate (GTP)-binding protein 2, XLG2, is an unconventional Gα subunit of the Arabidopsis (Arabidopsis thaliana) heterotrimeric GTP-binding protein complex with a major role in plant defense. In vitro biochemical analyses and molecular dynamic simulations show that affinity of XLG2 for GTP is two orders of magnitude lower than that of the conventional Gα, AtGPA1. Here we tested the physiological relevance of GTP binding by XLG2. We generated an XLG2(T476N) variant with abolished GTP binding, as confirmed by in vitro GTPγS binding assay. Yeast three-hybrid, bimolecular fluorescence complementation, and split firefly-luciferase complementation assays revealed that the nucleotide-depleted XLG2(T476N) retained wild-type XLG2-like interactions with the Gβγ dimer and defense-related receptor-like kinases. Both wild-type and nucleotide-depleted XLG2(T476N) restored the defense responses against Fusarium oxysporum and Pseudomonas syringae compromised in the xlg2 xlg3 double mutant. Additionally, XLG2(T476N) was fully functional restoring stomatal density, root growth, and sensitivity to NaCl, but failed to complement impaired germination and vernalization-induced flowering. We conclude that XLG2 is able to function in a GTP-independent manner and discuss its possible mechanisms of action.

Plant Sciences↗

Integrating an Industrial Source and Commercial Algae Farm with Innovative CO 2 Transfer Membrane and Improved Strain Technologies

This report describes the overall findings of the research project “Integrating an Industrial Source and Commercial Algae Farm with Innovative CO 2 Transfer Membrane and Improved Strain Technologies”. The motivation and goal for this project were to increase the carbon utilization efficiency (CUE) and areal productivity for algal cultivations, thereby reducing CO 2 costs to cultivation operations and improving economics. This was achieved through a combination of enhanced delivery of inorganic carbon and improved strains of Nannochloropsis oceanica capable of higher rates of bicarbonate uptake and metabolism. The project succeeded in these goals. First, a bubble-free, membrane-based technology was developed for delivering CO 2 to cultivations, which increased the CUE from the 15-20% that is standard in the industry to more than 65%. In addition, N. oceanica was modified to express a bicarbonate transporter protein, BicA, which enabled the cells to grow more quickly. In addition, advances were made in the protein engineering of carbonic anhydrase (CA) for enhanced stability and catalytic performance, the computational fluid dynamics modeling of algal cultivation systems, and in the life-cycle assessment and technoeconomic analysis of algal production. Together, these outcomes contribute to advancing algal cultivation as an economically viable platform for production of fuels, materials, and other chemical products. The project results aid in addressing the dual challenges of reducing atmospheric CO 2 levels and achieving green energy solutions.

09 BIOMASS FUELS↗

Unraveling Electronic and Vibrational Coherences Following a Charge Transfer Process in a Photosystem II Reaction Center

A reaction center is a unique biological system that performs the initial charge separation within a Photosystem II (PSII) multiunit enzyme, which eventually drives the catalytic water-splitting in plants and algae. The possible role of quantum coherences coinciding with the energy and charge transfer processes in PSII reaction center is one of the active areas of research. Here, we study these quantum coherences by using a numerically exact method on an excitonic dimer model, including linear vibronic coupling and employing optimal parameters from experimental two-dimensional coherent spectroscopic measurements. This enables us to precisely capture the excitonic interaction between pigments and the dissipation of the energy from electronic and charge-transfer (CT) states to the protein environment. We employ the time nonlocal (TNL) quantum master equation to calculate the population dynamics, which yields numerically reliable results. The calculated results show that, due to the strong dissipation, the lifetime of electronic coherence is too short to have direct participation in the charge transfer processes. However, there are long-lived vibrational coherences present in the system at frequencies close to the excitionic energy gap. These are strongly coupled with the electronic coherences, which makes the detection of the electronic coherences with conventional techniques very challenging. Additionally, we unravel the strong excitonic interaction of radical pair (PD1 and PD2) in the reaction center, which results in a long-lived electronic coherence of >100 fs, even at room temperature. Our work provide important physical insight to the charge separation process in PSII reaction center, which may be helpful for better understanding of photophysical processes in other natural and artificial light-harvesting systems.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Conformational dynamics linked to domain closure and substrate binding explain the ERAP1 allosteric regulation mechanism

The endoplasmic-reticulum aminopeptidase ERAP1 processes antigenic peptides for loading on MHC-I proteins and recognition by CD8 T cells as they survey the body for infection and malignancy. Crystal structures have revealed ERAP1 in either open or closed conformations, but whether these occur in solution and are involved in catalysis is not clear. Here, we assess ERAP1 conformational states in solution in the presence of substrates, allosteric activators, and inhibitors by small-angle X-ray scattering. We also characterize changes in protein conformation by X-ray crystallography, and we localize alternate C-terminal binding sites by chemical crosslinking. Structural and enzymatic data suggest that the structural reconfigurations of ERAP1 active site are physically linked to domain closure and are promoted by binding of long peptide substrates. These results clarify steps required for ERAP1 catalysis, demonstrate the importance of conformational dynamics within the catalytic cycle, and provide a mechanism for the observed allosteric regulation and Lys/Arg528 polymorphism disease association.

59 BASIC BIOLOGICAL SCIENCES↗

Phosphorylation barcodes direct biased chemokine signaling at CXCR3

Chemokine receptors, a group of G protein-coupled receptors (GPCRs), interact with transducers such as G proteins, ß-arrestins, and GPCR kinases (GRKs). In the chemokine system, many chemokine agonists act as “biased agonists” that preferentially activate distinct signaling effectors when binding to the same receptor, resulting in distinct physiological effects. Although one third of FDA-approved drugs target GPCRs, there has been limited success in targeting the chemokine system. Currently, there is little evidence that differential receptor phosphorylation, or “phosphorylation barcodes,” direct these biased responses at chemokine receptors. To address this knowledge gap, we used mass spectrometry to demonstrate that chemokines of CXCR3 promote different ensembles of phosphorylation barcodes that are associated with differential activation of G proteins, ß-arrestins and GRKs. Chemokine stimulation also resulted in distinct changes throughout the kinome in global phosphoproteomic studies. Mutation of specific CXCR3 phosphosites altered ß-arrestin conformation and impacted ß-arrestin activation in molecular dynamics simulations. T-cells expressing phosphorylation-deficient CXCR3 mutants resulted in distinct agonist- and receptor-specific chemotactic and signaling profiles that were not completely explained by engagement of G proteins, ß-arrestins, and GRKs alone. In conclusion, our results directly link distinct GPCR phosphorylation patterns with non-redundant chemokine signaling (Figure 1).

CXCR3↗

Full scale structural, mechanical and dynamical properties of HIV-1 liposomes

Enveloped viruses are enclosed by a lipid membrane inside of which are all of the components necessary for the virus life cycle; viral proteins, the viral genome and metabolites. Viral envelopes are lipid bilayers that adopt morphologies ranging from spheres to tubes. The envelope is derived from the host cell during viral replication. Thus, the composition of the bilayer depends on the complex constitution of lipids from the host-cell’s organelle(s) where assembly and/or budding of the viral particle occurs. Here, molecular dynamics (MD) simulations of authentic, asymmetric HIV-1 liposomes are used to derive a unique level of resolution of its full-scale structure, mechanics and dynamics. Analysis of the structural properties reveal the distribution of thicknesses of the bilayers over the entire liposome as well as its global fluctuations. Moreover, full-scale mechanical analyses are employed to derive the global bending rigidity of HIV-1 liposomes. Finally, dynamical properties of the lipid molecules reveal important relationships between their 3D diffusion, the location of lipid-rafts and the asymmetrical composition of the envelope. Overall, our simulations reveal complex relationships between the rich lipid composition of the HIV-1 liposome and its structural, mechanical and dynamical properties with critical consequences to different stages of HIV-1’s life cycle.

59 BASIC BIOLOGICAL SCIENCES↗

Structural evidence for a dynamic metallocofactor during N 2 reduction by Mo-nitrogenase

The enzyme nitrogenase uses a suite of complex metallocofactors to reduce dinitrogen (N 2 ) to ammonia. Mechanistic details of this reaction remain sparse. We report a 1.83-angstrom crystal structure of the nitrogenase molybdenum-iron (MoFe) protein captured under physiological N 2 turnover conditions. This structure reveals asymmetric displacements of the cofactor belt sulfurs (S2B or S3A and S5A) with distinct dinitrogen species in the two αβ dimers of the protein. The sulfur-displaced sites are distinct in the ability of protein ligands to donate protons to the bound dinitrogen species, as well as the elongation of either the Mo–O5 (carboxyl) or Mo–O7 (hydroxyl) distance that switches the Mo-homocitrate ligation from bidentate to monodentate. These results highlight the dynamic nature of the cofactor during catalysis and provide evidence for participation of all belt-sulfur sites in this process.

Science & Technology - Other Topics↗

Primary biomolecular adsorption energetics of core–shell nanocomplexes: Implications for biological interactions

Molecular organization at the nano-bio interface governing the colloidal stability, reactivity, immune recognition, and drug delivery performance of nanoparticles remains difficult to predict. Quantifying the primary hydration energetics of biomolecule-coated nanomaterials can determine those interactions and provide a basis for engineered nanocarriers with tailored behavior in biological systems. Here, we measured the thermodynamics of water adsorption on patchy dry magnetite (Fe 3 O 4 ) nanoparticles coated with three model biomolecules, bovine serum albumin, potato starch, and lauric acid and compared these properties to the hydration energetics of the corresponding free dry biomolecules. The results demonstrate how the surface functionalization alters the hydrophilicity, the accessible hydrophilic surface, and the interaction potential of the nanocomplex surface with biological media. The protein coating increases the interaction potential of the surface of the nanocomplex. The weaker interaction potential of the polysaccharide coating and the relatively large hydrophilic surface area allow dynamic and reversible binding, while the fatty acid rearranges into a partial bilayer with very strong hydrophilicity. The findings establish the hydration enthalpy as a quantitative basis to determine and interpret nanoparticle interactions with proteins, membranes, and biological fluids, and provide a thermodynamic foundation for designing nanocarriers with predictable biological reactivity.

59 BASIC BIOLOGICAL SCIENCES↗

Emerging protein sequencing technologies: proteomics without mass spectrometry?

Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has been a leading method for proteomics for 30 years. Advantages provided by LC-MS/MS are offset by significant disadvantages, including cost. Recently, several non-mass spectrometric methods have emerged, but little information is available about their capacity to analyze the complex mixtures routine for mass spectrometry. Areas Covered: We review recent non-mass-spectrometric methods for sequencing proteins and peptides, including those using nanopores, sequencing by degradation, reverse translation, and short-epitope mapping, with comments on bioinformatics challenges, fundamental limitations, and areas where new technologies will be more or less competitive with LC-MS/MS. In addition to conventional literature searches, instrument vendor websites, patents, webinars, and preprints were also consulted to give a more up-to-date picture. Expert Opinion: Many new technologies are promising. However, demonstrations that they outperform mass spectrometry in terms of peptides and proteins identified have not yet been published, and astute observers note important disadvantages, especially relating to the dynamic range of single-molecule measurements of complex mixtures. Still, even if the performance of emerging methods proves inferior to LC-MS/MS, their low cost could create a different kind of revolution: a dramatic increase in the number of biology laboratories engaging in new forms of proteomics research.

59 BASIC BIOLOGICAL SCIENCES↗

Role of carboxysomes in cyanobacterial CO 2 assimilation: CO 2 concentrating mechanisms and metabolon implications

Many carbon-fixing organisms have evolved CO 2 concentrating mechanisms (CCMs) to enhance the delivery of CO 2 to RuBisCO, while minimizing reactions with the competitive inhibitor, molecular O 2 . These distinct types of CCMs have been extensively studied using genetics, biochemistry, cell imaging, mass spectrometry, and metabolic flux analysis. Highlighted in this paper, the cyanobacterial CCM features a bacterial microcompartment (BMC) called ‘carboxysome’ in which RuBisCO is co-encapsulated with the enzyme carbonic anhydrase (CA) within a semi-permeable protein shell. Further, the cyanobacterial CCM is capable of increasing CO 2 around RuBisCO, leading to one of the most efficient processes known for fixing ambient CO 2 . The carboxysome life cycle is dynamic and creates a unique subcellular environment that promotes activity of the Calvin–Benson (CB) cycle. The carboxysome may function within a larger cellular metabolon, physical association of functionally coupled proteins, to enhance metabolite channelling and carbon flux. In light of CCMs, synthetic biology approaches have been used to improve enzyme complex for CO 2 fixations. Research on CCM-associated metabolons has also inspired biologists to engineer multi-step pathways by providing anchoring points for enzyme cascades to channel intermediate metabolites towards valuable products.

59 BASIC BIOLOGICAL SCIENCES↗

HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation

The spatial segregation of pericentromeric heterochromatin (PCH) into distinct, membrane-less nuclear compartments involves the binding of Heterochromatin Protein 1 (HP1) to H3K9me2/3-rich genomic regions. While HP1 exhibits liquid–liquid phase separation properties in vitro, its mechanistic impact on the structure and dynamics of PCH condensate formation in vivo remains largely unresolved. Here, using a minimal theoretical framework, we systematically investigate the mutual coupling between self-interacting HP1-like molecules and the chromatin polymer. We reveal that the specific affinity of HP1 for H3K9me2/3 loci facilitates coacervation in nucleo and promotes the formation of stable PCH condensates at HP1 levels far below the concentration required to observe phase separation in purified protein assays in vitro. These heterotypic HP1–chromatin interactions give rise to a strong dependence of the nucleoplasmic HP1 density on HP1-H3K9me2/3 stoichiometry, consistent with the thermodynamics of multicomponent phase separation. The dynamical cross talk between HP1 and the viscoelastic chromatin scaffold also leads to anomalously slow equilibration kinetics, which strongly depend on the genomic distribution of H3K9me2/3 domains and result in the coexistence of multiple long-lived, microphase-separated PCH compartments. The morphology of these complex coacervates is further found to be governed by the dynamic establishment of the underlying H3K9me2/3 landscape, which may drive their increasingly abnormal, aspherical shapes during cell development. These findings compare favorably to 4D microscopy measurements of HP1 condensate formation in live Drosophila embryos and suggest a general quantitative model of PCH formation based on the interplay between HP1-based phase separation and chromatin polymer mechanics.

3D genomics↗

Modeling Interactions within and between Peptide Amphiphile Supramolecular Filaments

Many peptides are able to self-assemble into one-dimensional (1D) nanostructures, such as cylindrical fibers or ribbons of variable widths, but the relationship between the morphology of 1D objects and their molecular structure is not well understood. Here, we use coarse-grained molecular dynamics (CG-MD) simulations to study the nanostructures formed by self-assembly of different peptide amphiphiles (PAs). The results show that ribbons are hierarchical superstructures formed by laterally assembled cylindrical fibers. Simulations starting from bilayer structures demonstrate the formation of filaments, whereas other simulations starting from filaments indicate varying degrees of interaction among them depending on chemical structure. These interactions are verified by observations using atomic force microscopy of the various systems. The interfilament interactions are predicted to be strongest in supramolecular assemblies that display hydrophilic groups on their surfaces, while those with hydrophobic ones are predicted to interact more weakly as confirmed by viscosity measurements. The simulations also suggest that peptide amphiphiles with hydrophobic termini bend to reduce their interfacial energy with water, which may explain why these systems do not collapse into superstructures of bundled filaments. The simulations suggest that future experiments will need to address mechanistic questions about the self-assembly of these systems into hierarchical structures, namely, the preformation of interactive filaments vs equilibration of large assemblies into superstructures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Designing efficient genetic code expansion in Bacillus subtilis to gain biological insights

Abstract Bacillus subtilis is a model gram-positive bacterium, commonly used to explore questions across bacterial cell biology and for industrial uses. To enable greater understanding and control of proteins in B. subtilis , here we report broad and efficient genetic code expansion in B. subtilis by incorporating 20 distinct non-standard amino acids within proteins using 3 different families of genetic code expansion systems and two choices of codons. We use these systems to achieve click-labelling, photo-crosslinking, and translational titration. These tools allow us to demonstrate differences between E. coli and B. subtilis stop codon suppression, validate a predicted protein-protein binding interface, and begin to interrogate properties underlying bacterial cytokinesis by precisely modulating cell division dynamics in vivo. We expect that the establishment of this simple and easily accessible chemical biology system in B. subtilis will help uncover an abundance of biological insights and aid genetic code expansion in other organisms.

59 BASIC BIOLOGICAL SCIENCES↗

Increased Attack Rates and Decreased Incubation Periods in Raccoons with Chronic Wasting Disease Passaged through Meadow Voles

Chronic wasting disease (CWD) is a naturally-occurring neurodegenerative disease of cervids. Raccoons (Procyon lotor) and meadow voles (Microtus pennsylvanicus) have previously been shown to be susceptible to the CWD agent. To investigate the potential for transmission of the agent of CWD from white-tailed deer to voles and subsequently to raccoons, we intracranially inoculated raccoons with brain homogenate from a CWD-affected white-tailed deer (CWD Wtd ) or derivatives of this isolate after it had been passaged through voles 1 or 5 times. We found that passage of the CWDWtd isolate through voles led to a change in the biologic behavior of the CWD agent, including increased attack rates and decreased incubation periods in raccoons. A better understanding of the dynamics of cross-species transmission of CWD prions can provide insights into how these infectious proteins evolve in new hosts.

59 BASIC BIOLOGICAL SCIENCES↗

Characterizing Binding Interactions That Are Essential for Selective Transport through the Nuclear Pore Complex

Specific macromolecules are rapidly transported across the nuclear envelope via the nuclear pore complex (NPC). The selective transport process is facilitated when nuclear transport receptors (NTRs) weakly and transiently bind to intrinsically disordered constituents of the NPC, FG Nups. These two types of proteins help maintain the selective NPC barrier. To interrogate their binding interactions in vitro, we deployed an NPC barrier mimic. We created the stationary phase by covalently attaching fragments of a yeast FG Nup called Nsp1 to glass coverslips. We used a tunable mobile phase containing NTR, nuclear transport factor 2 (NTF2). In the stationary phase, three main factors affected binding: the number of FG repeats, the charge of fragments, and the fragment density. We also identified three main factors affecting binding in the mobile phase: the avidity of the NTF2 variant for Nsp1, the presence of nonspecific proteins, and the presence of additional NTRs. We used both experimentally determined binding parameters and molecular dynamics simulations of Nsp1FG fragments to create an agent-based model. The results suggest that NTF2 binding is negatively cooperative and dependent on the density of Nsp1FG molecules. Our results demonstrate the strengths of combining experimental and physical modeling approaches to study NPC-mediated transport.

59 BASIC BIOLOGICAL SCIENCES↗