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Liau B, Zhang L, Ang MJY, Ng JY, C V SB, Schneider S, Gudihal R, Bae KH, Yang YY. Quantitative analysis of mRNA-lipid nanoparticle stability in human plasma and serum by size-exclusion chromatography coupled with dual-angle light scattering. NANOMEDICINE : NANOTECHNOLOGY, BIOLOGY, AND MEDICINE 2024; 58:102745. [PMID: 38499167 DOI: 10.1016/j.nano.2024.102745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 03/20/2024]
Abstract
Understanding the stability of mRNA loaded lipid nanoparticles (mRNA-LNPs) is imperative for their clinical development. Herein, we propose the use of size-exclusion chromatography coupled with dual-angle light scattering (SEC-MALS) as a new approach to assessing mRNA-LNP stability in pure human serum and plasma. By applying a dual-column configuration to attenuate interference from plasma components, SEC-MALS was able to elucidate the degradation kinetics and physical property changes of mRNA-LNPs, which have not been observed accurately by conventional dynamic light scattering techniques. Interestingly, both serum and plasma had significantly different impacts on the molecular weight and radius of gyration of mRNA-LNPs, suggesting the involvement of clotting factors in desorption of lipids from mRNA-LNPs. We also discovered that a trace impurity (~1 %) in ALC-0315, identified as its O-tert-butyloxycarbonyl-protected form, greatly diminished mRNA-LNP stability in serum. These results demonstrated the potential utility of SEC-MALS for optimization and quality control of LNP formulations.
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Affiliation(s)
- Brian Liau
- Agilent Technologies, 1 Yishun Avenue 7, Singapore 768923, Republic of Singapore.
| | - Li Zhang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore 138668, Republic of Singapore
| | - Melgious Jin Yan Ang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore 138668, Republic of Singapore
| | - Jian Yao Ng
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore 138668, Republic of Singapore
| | - Suresh Babu C V
- Agilent Technologies, 1 Yishun Avenue 7, Singapore 768923, Republic of Singapore
| | - Sonja Schneider
- Agilent Technologies Deutschland GmbH, Hewlett-Packard Strasse 8, 76337 Waldbronn, Germany
| | - Ravindra Gudihal
- Agilent Technologies, 1 Yishun Avenue 7, Singapore 768923, Republic of Singapore
| | - Ki Hyun Bae
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore 138668, Republic of Singapore
| | - Yi Yan Yang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, Centros #06-01, Singapore 138668, Republic of Singapore.
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Fung HYJ, Neisman AB, Bernardes NE, Jiou J, Chook YM. Nap1 and Kap114 co-chaperone H2A-H2B and facilitate targeted histone release in the nucleus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.09.539987. [PMID: 37214964 PMCID: PMC10197623 DOI: 10.1101/2023.05.09.539987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Core histones are synthesized and processed in the cytoplasm before transport into the nucleus for assembly into nucleosomes; however, they must also be chaperoned as free histones are toxic. The importin Kap114 binds and transports histone H2A-H2B into the yeast nucleus, where RanGTP facilitates H2A-H2B release. Kap114 and H2A-H2B also bind the Nap1 histone chaperone, which is found in both the cytoplasm and the nucleus, but how Nap1 and Kap114 cooperate in H2A-H2B processing and nucleosome assembly has been unclear. To understand these mechanisms, we used biochemical and structural analyses to reveal how Nap1, Kap114, H2A-H2B and RanGTP interact. We show that Kap114, H2A-H2B and a Nap1 dimer (Nap1 2 ) assemble into a 1:1:1 ternary complex. Cryogenic electron microscopy revealed two distinct Kap114/Nap1 2 /H2A-H2B structures: one of H2A-H2B sandwiched between Nap1 2 and Kap114, and another in which Nap1 2 bound to the Kap114·H2A-H2B complex without contacting H2A-H2B. Another Nap1 2 ·H2A-H2B·Kap114·Ran GTP structure reveals the nuclear complex. Mutagenesis revealed shared critical interfaces in all three structures. Consistent with structural findings, DNA competition experiments demonstrated that Kap114 and Nap1 2 together chaperone H2A-H2B better than either protein alone. When RanGTP is present, Kap114's chaperoning activity diminishes. However, the presence of Nap1 2 within the Nap1 2 ·H2A-H2B·Kap114·Ran GTP quaternary complex restores its ability to chaperone H2A-H2B. This complex effectively deposits H2A-H2B into nucleosomes. Together, these findings suggest that Kap114 and Nap12 provide a sheltered path from cytoplasm to nucleus, facilitating the transfer of H2A-H2B from Kap114 to Nap1 2 , ultimately directing its specific deposition into nucleosomes.
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A comprehensive review of methods to study lncRNA-protein interactions in solution. Biochem Soc Trans 2022; 50:1415-1426. [PMID: 36250427 DOI: 10.1042/bst20220604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/10/2022] [Accepted: 09/27/2022] [Indexed: 11/17/2022]
Abstract
The long non-coding RNAs (lncRNAs) other than rRNA and tRNA were earlier assumed to be 'junk genomic material'. However, recent advancements in genomics methods have highlighted their roles not only in housekeeping but also in the progression of diseases like cancer as well as viral infections. lncRNAs owing to their length, have both short-range and long-range interactions resulting in complex folded structures that recruit various biomolecules enabling lncRNAs to undertake their various biological functions. Using cell lysate pull-down assays increasing number of lnRNAs-interacting proteins are being identified. These interactions can be further exploited to develop targeted novel therapeutic strategies to inhibit lncRNA-protein interactions. This review attempts to succinctly techniques that can identify and characterize the lnRNAs-protein interactions (i.e. affinity, stoichiometry, and thermodynamics). Furthermore, using other sophisticated biophysical techniques, one can also perform size estimations, and determine low-resolution structures. Since these methods study the biomolecules in solution, large-scale structural observations can be performed in real-time. This review attempts to briefly introduce the readers to biochemical and biophysical techniques, such that they can utilize these methods to obtain a holistic characterization of the biomolecules of interest. Additionally, it should be noted that the use of these methods is not limited to the characterization of the interacting molecules but can also be used to determine the efficacy of the therapeutic molecules to disrupt these interactions.
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Kumar M, Tomar M, Potkule J, Reetu, Punia S, Dhakane-Lad J, Singh S, Dhumal S, Chandra Pradhan P, Bhushan B, Anitha T, Alajil O, Alhariri A, Amarowicz R, Kennedy JF. Functional characterization of plant-based protein to determine its quality for food applications. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2021.106986] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Sarkar D, Vijayan R, Gourinath S, Sau AK. A unique aromatic cluster near the active site of H. pylori CPA is essential for catalytic function. Biophys J 2022; 121:248-262. [PMID: 34932956 PMCID: PMC8790187 DOI: 10.1016/j.bpj.2021.12.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/16/2021] [Accepted: 12/16/2021] [Indexed: 01/21/2023] Open
Abstract
Polyamines are essential for cell growth and proliferation. In plants and many bacteria, including Helicobacter pylori, the parent polyamine putrescine is only produced through the metabolism of N-carbamoylputrescine by N-carbamoylputrescine amidase (CPA). Thus, CPA is a crucial intermediate enzyme. Moreover, the absence of CPA in humans makes its presence in H. pylori a potential target for the development of new therapeutics against this pathogen. Despite this enzyme's presence in plants and bacteria, its function is not completely explored. Using structure-guided biochemical and biophysical studies on H. pylori CPA, we discovered an aromatic cluster containing four conserved tryptophans near the catalytic site and elucidated its role. Mutational studies revealed that they are individually vital to enzyme function. Unlike wild-type, which forms a hexamer, the Trp to Ala mutants only formed dimers. Interestingly, two other conserved residues, Gln155 and Asp278, interact with the tryptophan cluster and perform similar roles. Our results indicate that aromatic-aromatic and H-bonding contacts between the residues (Trp156-Trp273, Trp196-Gln155, and Trp153-Asp278) play a crucial role in stimulating activity through hexamer formation. Additionally, Trp156 is essential to generating a catalytically efficient hexamer. These results suggest dual roles for the tryptophans; in hexamer formation and in generating its functionally active form, thereby providing a mechanistic understanding into the role of the cluster. We also elucidated the catalytic roles of Glu43, Lys115, and Cys152, which are present at the active site. Our findings highlight, for the first time, the importance of a tryptophan cluster in H. pylori CPA that can be exploited to design therapeutic inhibitors.
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Affiliation(s)
- Ditsa Sarkar
- National Institute of Immunology, New Delhi, India
| | | | | | - Apurba Kumar Sau
- National Institute of Immunology, New Delhi, India,Correspondence:
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Methodological innovations drive conceptual innovations forward in chromatin biology. Methods 2020; 184:1-3. [PMID: 33069800 DOI: 10.1016/j.ymeth.2020.10.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Akhavantabib N, Krzizike DD, Neumann V, D'Arcy S. Stoichiometry of Rtt109 complexes with Vps75 and histones H3-H4. Life Sci Alliance 2020; 3:3/11/e202000771. [PMID: 32913112 PMCID: PMC7494816 DOI: 10.26508/lsa.202000771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 08/31/2020] [Accepted: 09/01/2020] [Indexed: 11/24/2022] Open
Abstract
The work determines the relative and absolute stoichiometry of a 5-chain protein complex involved in histone chaperoning and acetylation. Using sedimentation velocity and light scattering, it uncovers a dynamic equilibrium of complex self-association. Histone acetylation is one of many posttranslational modifications that affect nucleosome accessibility. Vps75 is a histone chaperone that stimulates Rtt109 acetyltransferase activity toward histones H3-H4 in yeast. In this study, we use sedimentation velocity and light scattering to characterize various Vps75–Rtt109 complexes, both with and without H3-H4. These complexes were previously ill-defined because of protein multivalency and oligomerization. We determine both relative and absolute stoichiometry and define the most pertinent and homogeneous complexes. We show that the Vps75 dimer contains two unequal binding sites for Rtt109, with the weaker binding site being dispensable for H3-H4 acetylation. We further show that the Vps75–Rtt109–(H3-H4) complex is in equilibrium between a 2:1:1 species and a 4:2:2 species. Using a dimerization mutant of H3, we show that this equilibrium is mediated by the four-helix bundle between the two copies of H3. We optimize the purity, yield, and homogeneity of Vps75–Rtt109 complexes and determine optimal conditions for solubility when H3-H4 is added. Our comprehensive biochemical and biophysical approach ultimately defines the large-scale preparation of Vps75–Rtt109–(H3-H4) complexes with precise stoichiometry. This is an essential prerequisite for ongoing high-resolution structural and functional analysis of this important multi-subunit complex.
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Affiliation(s)
- Noushin Akhavantabib
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Daniel D Krzizike
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, USA
| | - Victoria Neumann
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, TX, USA
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