1
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Ruocco V, Grünwald-Gruber C, Rad B, Tscheliessnig R, Hammel M, Strasser R. Effects of N-glycans on the structure of human IgA2. Front Mol Biosci 2024; 11:1390659. [PMID: 38645274 PMCID: PMC11026580 DOI: 10.3389/fmolb.2024.1390659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 03/22/2024] [Indexed: 04/23/2024] Open
Abstract
The transition of IgA antibodies into clinical development is crucial because they have the potential to create a new class of therapeutics with superior pathogen neutralization, cancer cell killing, and immunomodulation capacity compared to IgG. However, the biological role of IgA glycans in these processes needs to be better understood. This study provides a detailed biochemical, biophysical, and structural characterization of recombinant monomeric human IgA2, which varies in the amount/locations of attached glycans. Monomeric IgA2 antibodies were produced by removing the N-linked glycans in the CH1 and CH2 domains. The impact of glycans on oligomer formation, thermal stability, and receptor binding was evaluated. In addition, we performed a structural analysis of recombinant IgA2 in solution using Small Angle X-Ray Scattering (SAXS) to examine the effect of glycans on protein structure and flexibility. Our results indicate that the absence of glycans in the Fc tail region leads to higher-order aggregates. SAXS, combined with atomistic modeling, showed that the lack of glycans in the CH2 domain results in increased flexibility between the Fab and Fc domains and a different distribution of open and closed conformations in solution. When binding with the Fcα-receptor, the dissociation constant remains unaltered in the absence of glycans in the CH1 or CH2 domain, compared to the fully glycosylated protein. These results provide insights into N-glycans' function on IgA2, which could have important implications for developing more effective IgA-based therapeutics in the future.
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Affiliation(s)
- Valentina Ruocco
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Clemens Grünwald-Gruber
- Core Facility Mass Spectrometry, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Behzad Rad
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rupert Tscheliessnig
- Division of Biophysics, Gottfried-Schatz-Research-Center, Medical University of Graz, Graz, Austria
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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2
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Yu T, Luo X, Prendergast D, Butterfoss GL, Rad B, Balsara NP, Zuckerman RN, Jiang X. The Structural Evolution of Polypeptoid Nanofibers Revealed by 3-D Cryo-TEM. Microsc Microanal 2023; 29:1722-1723. [PMID: 37613920 DOI: 10.1093/micmic/ozad067.890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Affiliation(s)
- Tianyi Yu
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xubo Luo
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Prendergast
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Glenn L Butterfoss
- Center for Genomics and Systems Biology, New York University, Abu Dhabi, United Arab Emirates
| | - Behzad Rad
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nitash P Balsara
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA
| | - Ronald N Zuckerman
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Xi Jiang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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3
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Tyler J, Ralston C, Rad B. Sneaking in SpyCatcher using cell penetrating peptides for in vivo imaging. Nanotechnology 2023. [PMID: 37336203 PMCID: PMC10396330 DOI: 10.1088/1361-6528/acdf65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
In vivo imaging of protein complexes is a powerful method for understanding the underlying biological function of these key biomolecules. Though the engineering of small, high affinity nanobodies have become more prevalent, the off-rates of these tags may result in incomplete or partial labeling of proteins in live cells. The SpyCatcher003 and SpyTag split protein system allow for irreversible, covalent binding to a short target peptide unlike nanobody-affinity based probes. However, delivering these tags into a cell without disrupting its normal function is a key challenge. Cell Penetrating Peptides (CPPs) are short peptide sequences that facilitate the transduction of otherwise membrane-impermeable "cargo" , such as proteins, into cells. Here we report on our efforts to engineer and characterize CPP-SpyCatcher003 fusions as modular imaging probes. We selected three CPPs, CUPID, Pentratin, and PVEC, to engineer fusion protein probes for superresolution microscopy, with the aim to eliminate prior permeabilization treatments that could introduce imaging artifacts. We find that fusing the CPP sequences to SpyCatcher003 resulted in dimer and multimer formation as determined by size exclusion chromatography, dynamic light scattering, and SDS resistant dimers on SDS-PAGE gels. By isolating and labeling the monomeric forms of the engineered protein, we show these constructs retained their ability to bind SpyTag and all three CPP sequences remain membrane active, as assessed by CD spectroscopy in the presence of SDS detergent. Using fluorescence and super resolution Lattice Structured Illumination Microscopy (Lattice SIM) imaging we show that the CPPs did not enhance uptake of SpyCatcher by E. coli, however with Caulobacter crescentus cells, we show that Penetratin, and to a lesser degree CUPID, does enhance uptake. Our results demonstrate the ability of the CPP-SpyCatcher003 to label targets within living cells, providing the groundwork for using split protein systems for targeted in vivo imaging.
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Affiliation(s)
- James Tyler
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., MS:67R5115, Berkeley, California, 94720-8099, UNITED STATES
| | - Corie Ralston
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., MS:67R5115, Berkeley, California, 94720-8099, UNITED STATES
| | - Behzad Rad
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., MS:67R5115, Berkeley, California, 94720-8099, UNITED STATES
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4
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Yu T, Luo X, Prendergast D, Butterfoss GL, Rad B, Balsara NP, Zuckermann RN, Jiang X. Structural Elucidation of a Polypeptoid Chain in a Crystalline Lattice Reveals Key Morphology-Directing Role of the N-Terminus. ACS Nano 2023; 17:4958-4970. [PMID: 36821346 PMCID: PMC10018772 DOI: 10.1021/acsnano.2c12503] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/13/2023] [Indexed: 06/12/2023]
Abstract
The ability to engineer synthetic polymers with the same structural precision as biomacromolecules is crucial to enable the de novo design of robust nanomaterials with biomimetic function. Peptoids, poly(N-substituted) glycines, are a highly controllable bio-inspired polymer family that can assemble into a variety of functional, crystalline nanostructures over a wide range of sequences. Extensive investigation on the molecular packing in these lattices has been reported; however, many key atomic-level details of the molecular structure remain underexplored. Here, we use cryo-TEM 3D reconstruction to directly visualize the conformation of an individual polymer chain within a peptoid nanofiber lattice in real space at 3.6 Å resolution. The backbone in the N-decylglycine hydrophobic core is shown to clearly adopt an extended, all-cis-sigma strand conformation, as previously suggested in many peptoid lattice models. We also show that packing interactions (covalent and noncovalent) at the solvent-exposed N-termini have a dominant impact on the local chain ordering and hence the ability of the chains to pack into well-ordered lattices. Peptoids in pure water form fibers with limited growth in the a direction (<14 molecules in width), whereas in the presence of formamide, they grow to over microns in length in the a direction. This dependence points to the significant role of the chain terminus in determining the long-range order in the packing of peptoid lattices and provides an opportunity to modulate lattice stability and nanoscale morphology by the addition of exogenous small molecules. These findings help resolve a major challenge in the de novo structure-based design of sequence-defined biomimetic nanostructures based on crystalline domains and should accelerate the design of functional nanostructures.
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Affiliation(s)
- Tianyi Yu
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xubo Luo
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - David Prendergast
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Glenn L. Butterfoss
- Center
for Genomics and Systems Biology, New York
University, Abu Dhabi, United Arab Emirates
| | - Behzad Rad
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Nitash P. Balsara
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- Molecular
Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Xi Jiang
- Materials
Sciences Division, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
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5
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Tow EW, Rad B, Kostecki R. Biofouling of filtration membranes in wastewater reuse: In situ visualization with confocal laser scanning microscopy. J Memb Sci 2022. [DOI: 10.1016/j.memsci.2021.120019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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6
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Gupta S, Russell B, Kristensen L, Rad B, Ralston C. Synergetic combination of photoluminescence spectroscopy with microsecond X-ray footprinting. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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7
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Kristensen LG, Holton JM, Rad B, Chen Y, Petzold CJ, Gupta S, Ralston CY. Hydroxyl radical mediated damage of proteins in low oxygen solution investigated using X-ray footprinting mass spectrometry. J Synchrotron Radiat 2021; 28:1333-1342. [PMID: 34475282 PMCID: PMC8415330 DOI: 10.1107/s1600577521004744] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/04/2021] [Indexed: 05/12/2023]
Abstract
In the method of X-ray footprinting mass spectrometry (XFMS), proteins at micromolar concentration in solution are irradiated with a broadband X-ray source, and the resulting hydroxyl radical modifications are characterized using liquid chromatography mass spectrometry to determine sites of solvent accessibility. These data are used to infer structural changes in proteins upon interaction with other proteins, folding, or ligand binding. XFMS is typically performed under aerobic conditions; dissolved molecular oxygen in solution is necessary in many, if not all, the hydroxyl radical modifications that are generally reported. In this study we investigated the result of X-ray induced modifications to three different proteins under aerobic versus low oxygen conditions, and correlated the extent of damage with dose calculations. We observed a concentration-dependent protecting effect at higher protein concentration for a given X-ray dose. For the typical doses used in XFMS experiments there was minimal X-ray induced aggregation and fragmentation, but for higher doses we observed formation of covalent higher molecular weight oligomers, as well as fragmentation, which was affected by the amount of dissolved oxygen in solution. The higher molecular weight products in the form of dimers, trimers, and tetramers were present in all sample preparations, and, upon X-ray irradiation, these oligomers became non-reducible as seen in SDS-PAGE. The results provide an important contribution to the large body of X-ray radiation damage literature in structural biology research, and will specifically help inform the future planning of XFMS, and well as X-ray crystallography and small-angle X-ray scattering experiments.
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Affiliation(s)
- Line G Kristensen
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Behzad Rad
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Yan Chen
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Christopher J Petzold
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Sayan Gupta
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Corie Y Ralston
- Molecular Foundry Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720, USA
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8
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Rad B, Ajo-Franklin CM, Manea F, Garda VG. Engineering Crystalline Protein Arrays for Functionalized 2D and 3D Biomaterials. Biophys J 2021. [DOI: 10.1016/j.bpj.2020.11.742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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9
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Nielsen AR, Jelavić S, Murray D, Rad B, Andersson MP, Ceccato M, Mitchell AC, Stipp SLS, Zuckermann RN, Sand KK. Thermodynamic and Kinetic Parameters for Calcite Nucleation on Peptoid and Model Scaffolds: A Step toward Nacre Mimicry. Cryst Growth Des 2020; 20:3762-3771. [PMID: 33192182 PMCID: PMC7660692 DOI: 10.1021/acs.cgd.0c00029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/22/2020] [Indexed: 06/11/2023]
Abstract
The production of novel composite materials, assembled using biomimetic polymers known as peptoids (N-substituted glycines) to nucleate CaCO3, can open new pathways for advanced material design. However, a better understanding of the heterogeneous CaCO3 nucleation process is a necessary first step. We determined the thermodynamic and kinetic parameters for calcite nucleation on self-assembled monolayers (SAMs) of nanosheet-forming peptoid polymers and simpler, alkanethiol analogues. We used nucleation rate studies to determine the net interfacial free energy (γ net) for the peptoid-calcite interface and for SAMs terminated with carboxyl headgroups, amine headgroups, or a mix of the two. We compared the results with γ net determined from dynamic force spectroscopy (DFS) and from density functional theory (DFT), using COSMO-RS simulations. Calcite nucleation has a lower thermodynamic barrier on the peptoid surface than on carboxyl and amine SAMs. From the relationship between nucleation rate (J 0) and saturation state, we found that under low-saturation conditions, i.e. <3.3 (pH 9.0), nucleation on the peptoid substrate was faster than that on all of the model surfaces, indicating a thermodynamic drive toward heterogeneous nucleation. When they are taken together, our results indicate that nanosheet-forming peptoid monolayers can serve as an organic template for CaCO3 polymorph growth.
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Affiliation(s)
- Anne R. Nielsen
- Nano-Science
Center, Department of Chemistry, University
of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Nano-Science
Center, Department of Chemistry, University
of Copenhagen, Copenhagen, Denmark
| | - Daniel Murray
- Biological
Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States
| | - Behzad Rad
- Biological
Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States
| | - Martin P. Andersson
- Nano-Science
Center, Department of Chemistry, University
of Copenhagen, Copenhagen, Denmark
| | - Marcel Ceccato
- Nano-Science
Center, Department of Chemistry, University
of Copenhagen, Copenhagen, Denmark
| | - Andrew C. Mitchell
- Department
of Geography & Earth Sciences, Aberystwyth
University, Aberystwyth, United Kingdom
| | - Susan L. S. Stipp
- Nano-Science
Center, Department of Chemistry, University
of Copenhagen, Copenhagen, Denmark
| | - Ronald N. Zuckermann
- Biological
Nanostructures Facility, The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California, United States
| | - Karina K. Sand
- Department
of Geography & Earth Sciences, Aberystwyth
University, Aberystwyth, United Kingdom
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10
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Manea F, Garda VG, Rad B, Ajo-Franklin CM. Programmable assembly of 2D crystalline protein arrays into covalently stacked 3D bionanomaterials. Biotechnol Bioeng 2020; 117:912-923. [PMID: 31885073 DOI: 10.1002/bit.27261] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 12/31/2022]
Abstract
Rational embellishment of self-assembling two-dimensional (2D) proteins make it possible to build 3D nanomaterials with novel catalytic, optoelectronic and mechanical properties. However, introducing multiple sites of embellishment into 2D protein arrays without affecting the self-assembly is challenging, limiting the ability to program in additional functionality and new 3D configurations. Here we introduce two orthogonal covalent linkages at multiple sites in a 2D crystalline-forming protein without affecting its self-assembly. We first engineered the surface-layer protein SbsB from Geobacillus stearothermophilus pV72/p2 to display isopeptide bond-forming protein conjugation pairs, SpyTag or SnoopTag, at four positions spaced 5.7-10.5 nm apart laterally and 3 nm axially. The C-terminal and two newly-identified locations within SbsB monomer accommodated the short SpyTag or SnoopTag peptide tags without affecting the 2D lattice structure. Introducing tags at distinct locations enabled orthogonal and covalent binding of SpyCatcher- or SnoopCatcher-protein fusions to micron-sized 2D nanosheets. By introducing different types of bifunctional cross-linkers, the dual-functionalized nanosheets were programmed to self-assemble into different 3D stacks, all of which retain their nanoscale order. Thus, our work creates a modular protein platform that is easy to program to create dual-functionalized 2D and lamellar 3D nanomaterials with new catalytic, optoelectronic, and mechanical properties.
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Affiliation(s)
- Francesca Manea
- The Molecular Foundry, Molecular Biophysics and Integrated Bioimaging Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Virginia G Garda
- The Molecular Foundry, Molecular Biophysics and Integrated Bioimaging Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Behzad Rad
- The Molecular Foundry, Molecular Biophysics and Integrated Bioimaging Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California
| | - Caroline M Ajo-Franklin
- The Molecular Foundry, Molecular Biophysics and Integrated Bioimaging Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California
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11
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Charrier M, Li D, Mann VR, Yun L, Jani S, Rad B, Cohen BE, Ashby PD, Ryan KR, Ajo-Franklin CM. Engineering the S-Layer of Caulobacter crescentus as a Foundation for Stable, High-Density, 2D Living Materials. ACS Synth Biol 2019; 8:181-190. [PMID: 30577690 DOI: 10.1021/acssynbio.8b00448] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Materials synthesized by organisms, such as bones and wood, combine the ability to self-repair with remarkable mechanical properties. This multifunctionality arises from the presence of living cells within the material and hierarchical assembly of different components across nanometer to micron scales. While creating engineered analogues of these natural materials is of growing interest, our ability to hierarchically order materials using living cells largely relies on engineered 1D protein filaments. Here, we lay the foundation for bottom-up assembly of engineered living material composites in 2D along the cell body using a synthetic biology approach. We engineer the paracrystalline surface-layer (S-layer) of Caulobacter crescentus to display SpyTag peptides that form irreversible isopeptide bonds to SpyCatcher-modified proteins, nanocrystals, and biopolymers on the extracellular surface. Using flow cytometry and confocal microscopy, we show that attachment of these materials to the cell surface is uniform, specific, and covalent, and its density can be controlled on the basis of the insertion location within the S-layer protein, RsaA. Moreover, we leverage the irreversible nature of this attachment to demonstrate via SDS-PAGE that the engineered S-layer can display a high density of materials, reaching 1 attachment site per 288 nm2. Finally, we show that ligation of quantum dots to the cell surface does not impair cell viability, and this composite material remains intact over a period of 2 weeks. Taken together, this work provides a platform for self-organization of soft and hard nanomaterials on a cell surface with precise control over 2D density, composition, and stability of the resulting composite, and is a key step toward building hierarchically ordered engineered living materials with emergent properties.
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12
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Zajdel TJ, Nam A, Yuan J, Shirsat VR, Rad B, Maharbiz MM. Applying machine learning to the flagellar motor for biosensing. Annu Int Conf IEEE Eng Med Biol Soc 2018; 2018:1-4. [PMID: 30440274 DOI: 10.1109/embc.2018.8512907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Escherichia coli detects and follows chemical gradients in its environment in a process known as chemotaxis. The performance of chemotaxis approaches fundamental biosensor speed and sensitivity limits, but there have been relatively few attempts to incorporate the response into a functional biosensor. Toward that end, we have developed software to process digital microscope images of a large number of tethered E. coli responding to different chemical perturbations. Upwards of fifty cells can be recorded in one experiment, allowing for rapid labeling of the chemotactic responses of multiple cells. After we collected hundreds of wild-type chemotactic E. coli motor responses to dilutions of aspartate and leucine, we trained a support vector classifier (SVC) to estimate the order of magnitude of aspartate concentration between 0M, 100nM, and 1μM with a single cell classification subset accuracy of 69%. We trained another SVC to differentiate between aspartate and leucine with a single cell classification subset accuracy of 83%. Using a majority-vote method on a bacterial population of size N, estimates have 95% confidence for N = 27 bacteria for concentration detection and N = 9 bacteria for chemical differentiation. These methods are a step towards adaptable chemotaxis-based biosensing.
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13
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Stel B, Cometto F, Rad B, De Yoreo JJ, Lingenfelder M. Dynamically resolved self-assembly of S-layer proteins on solid surfaces. Chem Commun (Camb) 2018; 54:10264-10267. [PMID: 30151543 DOI: 10.1039/c8cc04597f] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
By using high-speed and high-resolution Atomic Force Microscopy (AFM), it was possible to resolve within a single experiment the kinetic pathway in S-layer self-assembly at the solid-liquid interface, obtaining a model that accounts for the nucleation, growth and structural rearrangements in 2D protein self assembly across time (second to hours) and spatial scales (nm to microns).
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Affiliation(s)
- Bart Stel
- Max Planck-EPFL Laboratory for Molecular Nanoscience, École Polytechnique Fédérale de Lausanne, Switzerland.
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14
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Fukushima T, Gupta S, Rad B, Cornejo JA, Petzold CJ, Chan LJG, Mizrahi RA, Ralston CY, Ajo-Franklin CM. The Molecular Basis for Binding of an Electron Transfer Protein to a Metal Oxide Surface. J Am Chem Soc 2017; 139:12647-12654. [DOI: 10.1021/jacs.7b06560] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Tatsuya Fukushima
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Sayan Gupta
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Behzad Rad
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jose A. Cornejo
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J. Petzold
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Leanne Jade G. Chan
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Rena A. Mizrahi
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Corie Y. Ralston
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Caroline M. Ajo-Franklin
- Molecular Foundry, Molecular
Biophysics and Integrated Biosciences, and Biological Systems and
Engineering Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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15
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Rad B, Haxton TK, Shon A, Shin SH, Whitelam S, Ajo-Franklin CM. Ion-specific control of the self-assembly dynamics of a nanostructured protein lattice. ACS Nano 2015; 9:180-90. [PMID: 25494454 PMCID: PMC4310639 DOI: 10.1021/nn502992x] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 12/10/2014] [Indexed: 05/22/2023]
Abstract
Self-assembling proteins offer a potential means of creating nanostructures with complex structure and function. However, using self-assembly to create nanostructures with long-range order whose size is tunable is challenging, because the kinetics and thermodynamics of protein interactions depend sensitively on solution conditions. Here we systematically investigate the impact of varying solution conditions on the self-assembly of SbpA, a surface-layer protein from Lysinibacillus sphaericus that forms two-dimensional nanosheets. Using high-throughput light scattering measurements, we mapped out diagrams that reveal the relative yield of self-assembly of nanosheets over a wide range of concentrations of SbpA and Ca(2+). These diagrams revealed a localized region of optimum yield of nanosheets at intermediate Ca(2+) concentration. Replacement of Mg(2+) or Ba(2+) for Ca(2+) indicates that Ca(2+) acts both as a specific ion that is required to induce self-assembly and as a general divalent cation. In addition, we use competitive titration experiments to find that 5 Ca(2+) bind to SbpA with an affinity of 67.1 ± 0.3 μM. Finally, we show via modeling that nanosheet assembly occurs by growth from a negligibly small critical nucleus. We also chart the dynamics of nanosheet size over a variety of conditions. Our results demonstrate control of the dynamics and size of the self-assembly of a nanostructured lattice, the constituents of which are one of a class of building blocks able to form novel hybrid nanomaterials.
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Affiliation(s)
- Behzad Rad
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
| | - Thomas K. Haxton
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
| | - Albert Shon
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
- Department of Chemical and Biomolecular Engineering, UC Berkeley, Berkeley, California 94720-1462, United States
| | - Seong-Ho Shin
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
- Department of Chemistry, UC Berkeley, Berkeley, California 94720-1460, United States
| | - Stephen Whitelam
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
| | - Caroline M. Ajo-Franklin
- Materials Sciences Division, Physical Biosciences Division, and Synthetic Biology Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720-8075, United States
- Address correspondence to
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16
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Rad B, Shon A, Shin SH, Haxton T, Whitelam S, Ajo-Franklin CM. Modulating the Yield But Not Pathway of Protein Self-Assembly by the Surface-Layer Protein SbpA in Solution. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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17
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Abstract
A member of the SF2 family of helicases, Escherichia coli RecQ, is involved in the recombination and repair of double-stranded DNA breaks and single-stranded DNA (ssDNA) gaps. Although the unwinding activity of this helicase has been studied biochemically, the mechanism of translocation remains unclear. To this end, using ssDNA of varying lengths, the steady-state ATP hydrolysis activity of RecQ was analyzed. We find that the rate of ATP hydrolysis increases with DNA length, reaching a maximum specific activity of 38 ± 2 ATP/RecQ/s. Analysis of the rate of ATP hydrolysis as a function of DNA length implies that the helicase has a processivity of 19 ± 6 nucleotides on ssDNA and that RecQ requires a minimal translocation site size of 10 ± 1 nucleotides. Using the T4 phage encoded gene 32 protein (G32P), which binds ssDNA cooperatively, to decrease the lengths of ssDNA gaps available for translocation, we observe a decrease in the rate of ATP hydrolysis activity that is related to lattice occupancy. Analysis of the activity in terms of the average gap sizes available to RecQ on the ssDNA coated with G32P indicates that RecQ translocates on ssDNA on average 46 ± 11 nucleotides before dissociating. Moreover, when bound to ssDNA, RecQ hydrolyzes ATP in a cooperative fashion, with a Hill coefficient of 2.1 ± 0.6, suggesting that at least a dimer is required for translocation on ssDNA. We present a kinetic model for translocation by RecQ on ssDNA based on this characterization.
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Affiliation(s)
- Behzad Rad
- Department of Microbiology, Department of Molecular and Cellular Biology, Graduate Group in Biophysics, University of California, Davis, Davis, California 95616-8665, United States
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Rad B, Haxton T, Shin SH, Whitelam S, Ajo-Franklin C. Self Assembly Pathways of Surface-Layer Proteins. Biophys J 2012. [DOI: 10.1016/j.bpj.2011.11.1437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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Rouhani S, Facciotti MT, Woodcock G, Cheung V, Cunningham C, Nguyen D, Rad B, Lin CT, Lunde CS, Glaeser RM. Crystallization of membrane proteins from media composed of connected-bilayer gels. Biopolymers 2003; 66:300-16. [PMID: 12539259 DOI: 10.1002/bip.10310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The use of hydrated-lipid gels in which the bilayer is an infinitely periodic (or at least continuous), three-dimensional structure offers a relatively new approach for the crystallization of membrane proteins. While excellent crystals of the Halobacterial rhodopsins have been obtained with such media, success remains poor in extending their use to other membrane proteins. Experience with crystallization of bacteriorhodopsin has led us to recognize a number of improvements that can be made in the use of such hydrated-gel media, which may now prove to be of general value for the crystallization of other membrane proteins.
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Affiliation(s)
- Shahab Rouhani
- Life Sciences Division, Donner Laboratory, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA
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20
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Abstract
Several recent studies have shown that certain forms of genetic or acquired hypertension are associated with oxidative stress and that animals with those types of hypertension respond favorably to antioxidant therapy. We hypothesize that oxidative stress may cause hypertension via (among other mechanisms) enhanced oxidation and inactivation of nitric oxide (NO). To test this hypothesis, Sprague-Dawley rats were subjected to oxidative stress by glutathione (GSH) depletion by means of the GSH synthase inhibitor buthionine sulfoximine (BSO, 30 mmol/L in drinking water) for 2 weeks. The control group was given drug-free drinking water. In parallel experiments, subgroups of animals were provided vitamin E-fortified chow and vitamin C-supplemented drinking water. The BSO-treated group showed a 3-fold decrease in tissue GSH content, a marked elevation in blood pressure, and a significant reduction in the urinary excretion of the NO metabolite nitrate plus nitrite, which suggests depressed NO availability. These characteristics were associated with a significant accumulation in various tissues of nitrotyrosine, which is the footprint of NO inactivation by reactive oxygen species. Administration of vitamin E plus vitamin C ameliorated hypertension, improved urinary nitrate-plus-nitrite excretion, and mitigated nitrotyrosine accumulation (despite GSH depletion) in the BSO-treated animals but had no effect in the control group. In conclusion, GSH depletion resulted in perturbation of the NO system and severe hypertension in normal animals. The effects of BSO were mitigated by concomitant antioxidant therapy despite GSH depletion, which supports the notion that oxidative stress was involved in the pathogenesis of hypertension in this model.
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Affiliation(s)
- N D Vaziri
- Division of Nephrology and Hypertension, Department of Medicine, University of California, Irvine 92868, USA.
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