Search NASA⌕ Search

SEARCH · Search NASA

Results for “Protein Design”

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 91 records · Page 5
All sourcesNASA NTRSDOE OSTI
NASA NTRS2001

Expression of the Acyl-Coenzyme A: Cholesterol Acyltransferase GFP Fusion Protein in Sf21 Insect Cells

The enzyme acyl-coenzyme A:cholesterol acyltransferase (ACAT) is an important contributor to the pathological expression of plaque leading to artherosclerosis n a major health problem. Adequate knowledge of the structure of this protein will enable pharmaceutical companies to design drugs specific to the enzyme. ACAT is a membrane protein located in the endoplasmic reticulum.t The protein has never been purified to homogeneity.T.Y. Chang's laboratory at Dartmouth College provided a 4-kb cDNA clone (K1) coding for a structural gene of the protein. We have modified the gene sequence and inserted the cDNA into the BioGreen His Baculovirus transfer vector. This was successfully expressed in Sf2l insect cells as a GFP-labeled ACAT protein. The advantage to this ACAT-GFP fusion protein (abbreviated GCAT) is that one can easily monitor its expression as a function of GFP excitation at 395 nm and emission at 509 nm. Moreover, the fusion protein GCAT can be detected on Western blots with the use of commercially available GFP antibodies. Antibodies against ACAT are not readily available. The presence of the 6xHis tag in the transfer vector facilitates purification of the recombinant protein since 6xHis fusion proteins bind with high affinity to Ni-NTA agarose. Obtaining highly pure protein in large quantities is essential for subsequent crystallization. The purified GCAT fusion protein can readily be cleaved into distinct GFP and ACAT proteins in the presence of thrombin. Thrombin digests the 6xHis tag linking the two protein sequences. Preliminary experiments have indicated that both GCAT and ACAT are expressed as functional proteins. The ultimate aim is to obtain large quantities of the ACAT protein in pure and functional form appropriate for protein crystal growth. Determining protein structure is the key to the design and development of effective drugs. X-ray analysis requires large homogeneous crystals that are difficult to obtain in the gravity environment of earth. Protein crystals grown in microgravity are often larger and have fewer defects than those grown on earth. The analysis of higher quality space-grown crystals will assist in structure-based drug design. We have successfully grown GCAT-infected Sf21 cells in both adhesion and suspension cultures. Expression levels of GCAT in cell lines such as Sf9 and High Five appear to be reduced. We intend to replicate GCAT expression in all three cell lines using the NASA rotating wall bioreactor which effectively duplicates a microgravity environment. The bioreactor itself could be launched to study the expression of the GFP and GCAT proteins in the actual microgravity environment achieved in orbit.

Mahtani, H. K.↗
NASA NTRS1994

The 1994 NASA/USRA/ADP Design Projects

The NASA/USRA/ADP Design Projects from Vanderbilt University, Department of Mechanical Engineering (1994) are enclosed in this final report. Design projects include: (1) Protein Crystal Growth, both facilities and methodology; (2) ACES Deployable Space Boom; (3) Hybrid Launch System designs for both manned and unmanned systems; (4) LH2 Fuel Tank design (SSTO); (5) SSTO design; and (6) Pressure Tank Feed System design.

Cruse, Thomas↗
NASA NTRS2001

Effects of Convective Transport of Solute and Impurities on Defect-Causing Kinetics Instabilities

For in-situ studies of the formation and evolution of step patterns during the growth of protein crystals, we have designed and assembled an experimental setup based on Michelson interferometry with the surface of the growing protein crystal as one of the reflective surfaces. The crystallization part of the device allows optical monitoring of a face of a crystal growing at temperature stable within 0.05 C in a developed solution flow of controlled direction and speed. The reference arm of the interferometer contains a liquid-crystal element that allows controlled shifts of the phase of the interferograms. We employ an image processing algorithm which combines five images with a pi/2 phase difference between each pair of images. The images are transferred to a computer by a camera capable of capturing 6-8 frames per second. The device allows data collection data regarding growth over a relatively large area (approximately .3 sq. mm) in-situ and in real time during growth. The estimated dept resolution of the phase shifting interferometry is about 100 A. The lateral resolution, depending on the zoom ratio, varies between 0.3 and 0.6 micrometers. We have now collected quantitative results on the onset, initial stages and development of instabilities in moving step trains on vicinal crystal surfaces at varying supersaturation, position on the facet, crystal size and temperature with the proteins ferritin, apoferritin and thaumatin. Comparisons with theory, especially with the AFM results on the molecular level processes, see below, allow tests of the rational for the effects of convective flows and, as a particular case, the lack thereof, on step bunching.

Vekilov, Peter G.↗
NASA NTRS1992

Commercial researcher perspective

Protein crystallography--a research tool used to study the structure of the complex building blocks of living systems--has a lot to gain from space-based research. In order to know how a protein works in the human body, researchers must understand its molecular structure. Researchers have identified 150,000 different proteins in the body, but they now know the structure of less than a third of them. The only viable technique for analyzing the structure of these proteins is x-ray diffraction of the proteins in their crystal form. The better the quality of a protein crystal, the more useful it is to researchers who are trying to delineate its structure. The microgravity environment of space allows protein crystals to grow nearly undisturbed by convection and other gravity-driven forces that cause flaws to form in them on the ground. In space, lack of convection enables protein crystals to grow more slowly than they do on Earth, and the slower a protein crystal grows, the fewer flaws it will have. Protein crystal growth experiments have already flown on 14 Space Shuttle missions. This year's USML-1 Spacelab mission included protein crystal growth experiments conducted for commercial researchers. The results of protein crystal experiments flown thus far have been larger crystals with more uniform morphologies. The Center for Macromolecular Crystallography (A NASA-cosponsored CCDS) currently builds flight hardware to meet researchers' needs and handles sample loading and retrieval for flight experiments. Protein crystallography enables 'rational drug design': the development of drugs that bind only with the target protein and, hence, do not cause side effects. For example, pharmaceutical companies presently are interested in developing drugs that can inhibit purine nucleoside phosphorylase (PNP), a protein that plays a role in auto-immune diseases. To continue these kinds of investigations, researchers need a constant supply of protein crystals that are as free of flaws as possible. Space Station Freedom will provide the kind of research environment that will enable the production of such supplies. In addition, Freedom will provide the kind of long-duration facility required by protein crystal researchers: 40 percent of proteins require more than two weeks to crystallize.

Delucas, Larry↗
DOE OSTI2025

Integrated thermal and biological conversion of microalgal proteins to lipids

Microalgal composition varies with cultivation strategy, and low-cost approaches often produce high-protein biomass. This presents challenges for biorefineries designed around static, lipid-rich feedstocks. In particular, hydrolysates from high-protein algae are nitrogen-rich and sugar-poor, limiting microbial conversion and reducing product yields. This study develops a sequential thermal conditioning and biological upgrading strategy to integrate high-protein hydrolysate processing within conventional lipid extraction and upgrading designs. Oxidative deconstruction was used to break down proteins into ammonium and short-chain carboxylates. Ammonium was subsequently removed to yield a nitrogen-depleted, carboxylate-rich medium suitable for microbial lipid production. Bioconversion trials with Cutaneotrichosporon oleaginosum showed lipid accumulation only from hydrolysates treated with both oxidative deconstruction and nitrogen removal, reaching 1.2 g/L lipids at 30 % intracellular content. This integrated approach enables protein-to-lipid conversion and improves flexibility to process variable algal feedstocks, advancing fuel-oriented microalgal biorefineries.

09 BIOMASS FUELS↗
NASA NTRS2002

Study of Fluid Flow Control In Protein Crystallization Using Strong Magnetic Fields

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in 'microgravity', researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. Once the basic understanding is obtained, the study will focus on testing the hypothesis on proteins of pyruvate dehydrogenase complex (PDC), proteins E1 and E3. Obtaining high crystal quality of these proteins is of great importance to structural biologists since their structures need to be determined.

Ramachandran, N.↗
NASA NTRS2002

Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. Once the basic understanding is obtained, the study will focus on testing the hypothesis on proteins of pyruvate dehydrogenase complex (PDC), proteins E1 and E3. Obtaining high crystal quality of these proteins is of great importance to structural biologists since their structures need to be determined. Specific goals for the investigation are: 1. To develop an understanding of convection control in diamagnetic fluids with concentration gradients through experimentation and numerical modeling. Specifically solutal buoyancy driven convection due to crystal growth will be considered. 2. To develop predictive measures for successful crystallization in a magnetic field using analyses and numerical modeling for use in future protein crystal growth experiments. This will establish criteria that can be used to estimate the efficacy of magnetic field flow damping on crystallization of candidate proteins. 3. To demonstrate the understanding of convection damping by high magnetic fields to a class of proteins that is of interest and whose structure is as yet not determined. 4. To compare quantitatively, the quality of the grown crystals with and without a magnetic field. X-ray diffraction techniques will be used for the comparative studies. In a preliminary set of experiments, we studied crystal dissolution effects in a 5 Tesla magnet available at NASA Marshall Space Flight Center (MSFC). Using a Schlieren setup, a 1mm crystal of Alum (Aluminum-Potassium Sulfate) was introduced in a 75% saturated solution and the resulting dissolution plume was observed. The experiment was conducted both in the presence and absence of a magnetic field gradient. The magnet produces a gradient field of approx. 1 Tesla2/cm. Image analysis of the recorded images indicated an enhanced plume velocity that was of the order of the measurement limit. For this experiment, both the gradient and gravity fields are in the same direction resulting in an enhanced effective gravity that tends to accelerate the observed plume velocity. While the results are not conclusive, pending further tests, it clearly points out the inadequacy of the MSFC magnet for conducting protein crystallization experiments and the need for a stronger magnet. In spacebased experiments, however, where the gravitational effects are small, only a weak magnetic field will be required to control or mitigate the effects of convective contamination.

Ramachandran, Narayanan↗
NASA NTRS2002

Countering Solutal Buoyant Convection with High Magnetic Fields

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemist, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitant, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in microgravity, we have been able to dramatically effect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the current status of the investigation and discuss results from the experimental and modeling efforts.

Ramachandran, N.↗
NASA NTRS2003

Using Strong Magnetic Fields to Control Solutal Convection

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in microgravity , we have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the experimental results using paramagnetic salts and solutions in magnetic fields and compare them to analytical predictions.

Ramachandran, N.↗
NASA NTRS2004

Magnetic Control of Convection during Protein Crystallization

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular Crystals for diffraction analyses has been the central focus for bio-chemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and Sedimentation as is achieved in "microgravity", we have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, f o d o n of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with counteracts on for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteract terrestrial gravity. The genera1 objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the experimental results using paramagentic salts and solutions in magnetic fields and compare them to analyticalpr~ctions.

Ramachandran, N.↗
DOE OSTI2024

Impact of temperature and concentration on flow behaviour of reconstituted lactose and protein–rich dairy powders

To help with designing the drying process, this study investigated the flow behaviour of lactose and protein-rich reconstituted dairy powders at 25°C and 50°C. Lactose-rich samples, 50% dried whey (DW) and 60% whey protein concentrate (WPC35) did not follow the Herschel–Bulkley model because of presence of lactose crystals. Reconstituted 50% skim milk powder (SMP) and protein-rich dairy powders exhibited shear-thinning behaviour (n < 0.3). With increasing concentration, whey protein concentrate/isolate (WPC80/WPI) and micellar casein concentrate high-solid dispersions exhibited more shear-thinning behaviour (n < 0.4). Furthermore, understanding shear-thinning behaviour of lactose-rich and protein-rich reconstituted dairy powders will provide basis for optimising drying parameters.

36 MATERIALS SCIENCE↗
NASA NTRS1990

Protein crystal growth in low gravity

The effect of low gravity on the growth of protein crystals and those parameters which will affect growth and crystal quality was studied. The proper design of the flight hardware and experimental protocols are highly dependent on understanding the factors which influence the nucleation and growth of crystals of biological macromolecules. Thus, those factors are investigated and the body of knowledge which has been built up for small molecule crystallization. These data also provide a basis of comparison for the results obtained from low-g experiments. The flows around growing crystals are detailed. The preliminary study of the growth of isocitrate lyase, the crystal morphologies found and the preliminary x ray results are discussed. The design of two apparatus for protein crystal growth by temperature control are presented along with preliminary results.

Feigelson, Robert S.↗
DOE OSTI2024

Functional anatomy of zinc finger antiviral protein complexes

Abstract ZAP is an antiviral protein that binds to and depletes viral RNA, which is often distinguished from vertebrate host RNA by its elevated CpG content. Two ZAP cofactors, TRIM25 and KHNYN, have activities that are poorly understood. Here, we show that functional interactions between ZAP, TRIM25 and KHNYN involve multiple domains of each protein, and that the ability of TRIM25 to multimerize via its RING domain augments ZAP activity and specificity. We show that KHNYN is an active nuclease that acts in a partly redundant manner with its homolog N4BP1. The ZAP N-terminal RNA binding domain constitutes a minimal core that is essential for antiviral complex activity, and we present a crystal structure of this domain that reveals contacts with the functionally required KHNYN C-terminal domain. These contacts are remote from the ZAP CpG binding site and would not interfere with RNA binding. Based on our dissection of ZAP, TRIM25 and KHNYN functional anatomy, we could design artificial chimeric antiviral proteins that reconstitute the antiviral function of the intact authentic proteins, but in the absence of protein domains that are otherwise required for activity. Together, these results suggest a model for the RNA recognition and action of ZAP-containing antiviral protein complexes.

Science & Technology - Other Topics↗
DOE OSTI2024

Induced Chirality in QDs Using Thermoresponsive Elastin-like Polypeptides

Circular dichroism (CD) spectroscopy has emerged as a potent tool for probing chiral small-molecule ligand exchange on natively achiral quantum dots (QDs). In this study, we report a novel approach to identifying QD–biomolecule interactions by inducing chirality in CdS QDs using thermoresponsive elastin-like polypeptides (ELPs) engineered with C-terminal cysteine residues. Our method is based on a versatile two-step ligand exchange process starting from monodisperse oleate-capped QDs in nonpolar media and proceeding through an easily accessed achiral glycine-capped QD intermediate. Successful conjugation of the ELPs onto the QDs is confirmed by the diagnostic CD response corresponding to the QD electronic transitions in the visible range. The resulting ELP:CdS conjugates demonstrate thermally reversible coacervation, as observed through dynamic light scattering, small-angle X-ray scattering, and electron microscopy. Furthermore, this research provides a foundation for using induced chirality in QD electronic transitions to probe QD conjugation to complex peptides and proteins, opening pathways for designing dynamic, stimuli-responsive hybrid nanomaterials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A family portrait of lanmodulin selectivity for enhanced rare-earth separations

Proteins offer a molecular design space to create bespoke ligands for the separation of critical metals like rare earth elements (REs). However, data-intensive approaches to tune metalloprotein selectivity are constrained by the low-throughput nature of existing characterization methods. Here we invented an assay called ‘SpyTag-Catcher Immobilization of Lanmodulin for Assaying Metal-Binding Selectivity’ (SpyCI-LAMBS) to measure metalloprotein selectivity en masse. This 96-format workflow was used to study the selectivity of 621 lanmodulin (LanM) orthologs for 15 REs, revealing eight distinct selectivity profiles based on sequence-to-function analyses. We discovered >200 LanMs with stronger selectivity against low-value LaIII relative to the prototypical LanM. This includes a LanM that can perform a challenging one-stage separation of PrIII from LaIII with up to >99.9 mol% purity and 83% yield. SpyCI-LAMBS is a powerful tool that can rapidly collect high-fidelity selectivity data to inform metal ion separations and machine-learning-assisted metalloprotein design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Targeted sulfur(VI) fluoride exchange-mediated covalent modification of a tyrosine residue in the catalytic pocket of tyrosyl-DNA phosphodiesterase 1

Abstract Developing effective inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1 (TDP1) has been challenging because of the enzyme shallow catalytic pocket and non-specific substrate binding interactions. Recently, we discovered a quinolone-binding hot spot in TDP1’s active site proximal to the evolutionary conserved Y204 and F259 residues that position DNA. Sulfur (VI) fluoride exchange (SuFEx) is a biocompatible click chemistry reaction that enables acylation of protein residues, including tyrosine. Selective protein modifications can provide insights into the biological roles of proteins and inform ligand design. As we report herein, we used SuFEx chemistries to prepare covalent TDP1-bound binders showing site-specific covalent bonds with Y204. Our work presents the first application of SuFEx chemistries to TDP1 ligands. It validates the ability to covalently modify specific TDP1 residues by designed targeting and adds to the chemical biology resource toolbox for studying TDP1.

Chemistry↗
DOE OSTI2025

Generating forces in confinement via polymerization

Understanding how to produce forces using biomolecular building blocks is essential for the development of adaptive synthetic cells and living materials. Here we ask whether a dynamic polymer system can generate deformation forces in soft shells by pure self-assembly, motivated by the fact that biological polymer networks like the cytoskeleton can exert forces, move objects, and deform membranes by simply growing, even in the absence of molecular motors. We address this question by investigating polymer force generation by varying the release rate, the structure, and the interactions of self-assembling monomers. First, we develop a toy computational model of polymerization in a soft elastic shell that reveals the emergence of spontaneous bundling which enhances shell deformation. We then extend our model to account more explicitly for monomer binding dynamics. We find that the rate at which monomers are released into the interior of the shell is a crucial parameter for achieving deformation through polymer growth. Lastly, we demonstrate that the introduction of multivalent particles that can join polymers can either improve or impede polymer performance, depending on the amount and on the structure of the multivalent particles. Our results provide guidance for the experimental realization of polymer systems that can perform work at the nanoscale, for example through rationally designed self-assembling proteins or nucleic acids.

Osmanović, Dino [University of California at Los A↗