1
|
Manning MC, Holcomb RE, Payne RW, Stillahn JM, Connolly BD, Katayama DS, Liu H, Matsuura JE, Murphy BM, Henry CS, Crommelin DJA. Stability of Protein Pharmaceuticals: Recent Advances. Pharm Res 2024; 41:1301-1367. [PMID: 38937372 DOI: 10.1007/s11095-024-03726-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Accepted: 06/03/2024] [Indexed: 06/29/2024]
Abstract
There have been significant advances in the formulation and stabilization of proteins in the liquid state over the past years since our previous review. Our mechanistic understanding of protein-excipient interactions has increased, allowing one to develop formulations in a more rational fashion. The field has moved towards more complex and challenging formulations, such as high concentration formulations to allow for subcutaneous administration and co-formulation. While much of the published work has focused on mAbs, the principles appear to apply to any therapeutic protein, although mAbs clearly have some distinctive features. In this review, we first discuss chemical degradation reactions. This is followed by a section on physical instability issues. Then, more specific topics are addressed: instability induced by interactions with interfaces, predictive methods for physical stability and interplay between chemical and physical instability. The final parts are devoted to discussions how all the above impacts (co-)formulation strategies, in particular for high protein concentration solutions.'
Collapse
Affiliation(s)
- Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO, USA.
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA.
| | - Ryan E Holcomb
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Robert W Payne
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO, USA
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | | | | | | | | | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO, USA
| | | |
Collapse
|
2
|
Toledo PL, Gianotti AR, Vazquez DS, Ermácora MR. Protein nanocondensates: the next frontier. Biophys Rev 2023; 15:515-530. [PMID: 37681092 PMCID: PMC10480383 DOI: 10.1007/s12551-023-01105-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 07/21/2023] [Indexed: 09/09/2023] Open
Abstract
Over the past decade, myriads of studies have highlighted the central role of protein condensation in subcellular compartmentalization and spatiotemporal organization of biological processes. Conceptually, protein condensation stands at the highest level in protein structure hierarchy, accounting for the assembly of bodies ranging from thousands to billions of molecules and for densities ranging from dense liquids to solid materials. In size, protein condensates range from nanocondensates of hundreds of nanometers (mesoscopic clusters) to phase-separated micron-sized condensates. In this review, we focus on protein nanocondensation, a process that can occur in subsaturated solutions and can nucleate dense liquid phases, crystals, amorphous aggregates, and fibers. We discuss the nanocondensation of proteins in the light of general physical principles and examine the biophysical properties of several outstanding examples of nanocondensation. We conclude that protein nanocondensation cannot be fully explained by the conceptual framework of micron-scale biomolecular condensation. The evolution of nanocondensates through changes in density and order is currently under intense investigation, and this should lead to the development of a general theoretical framework, capable of encompassing the full range of sizes and densities found in protein condensates.
Collapse
Affiliation(s)
- Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Roque Sáenz Peña 352, 1876, Bernal, Buenos Aires, Argentina
- Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Bernal, Argentina
| |
Collapse
|
3
|
Kudose S, Cossey LN, Canetta PA, Sekulic M, Vanbeek CA, Huls FB, Gupta I, Bu L, Alexander MP, Cornell LD, Fidler ME, Markowitz GS, Larsen CP, D’Agati VD, Nasr SH, Santoriello D. Clinicopathologic Spectrum of Lysozyme-Associated Nephropathy. Kidney Int Rep 2023; 8:1585-1595. [PMID: 37547521 PMCID: PMC10403676 DOI: 10.1016/j.ekir.2023.05.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 05/08/2023] [Indexed: 08/08/2023] Open
Abstract
Introduction Lysozyme-associated nephropathy (LyN), a rare cause of kidney injury in patients with chronic myelomonocytic leukemia (CMML), has not been well described to date. We report the clinicopathologic spectrum of LyN from a multi-institutional series. Method We identified 37 native kidney biopsies with LyN and retrospectively obtained clinicopathologic data. Results Thirty-seven patients had a median age of 74 years and included 78% males. Their most common presentation was acute kidney injury (AKI) or AKI on chronic kidney disease (CKD) (66%) with median estimated glomerular filtration rate (eGFR) of 21.7 ml/min per 1.73 m2, and proteinuria of 1.7 g. A minority (15%) had partial Fanconi syndrome. Serum lysozyme levels were elevated in all tested. Hematologic disorder (n = 28, 76%) was the most common etiology, including CMML (n = 15), acute myeloid leukemia (n = 5), and myelodysplastic syndrome (MDS) (n = 5). Nonhematologic causes (n = 5, 14%), included metastatic neuroendocrine carcinoma (n = 3), sarcoidosis, and leprosy. Etiology was unknown in 4 (11%). Pathology showed proximal tubulopathy with abundant hypereosinophilic intracytoplasmic inclusions, with characteristic staining pattern by lysozyme immunostain. Mortality was high (8/30). However, among the 22 alive, including 85% treated, 7 had improved kidney function, including 1 who discontinued dialysis and 6 with increase in eGFR >15 ml/min per 1.73 m2 compared with eGFR at the time of biopsy. Conclusion Increased awareness of the full clinicopathologic spectrum of LyN may lead to prompt diagnosis, earlier treatment, and potentially improved outcome of this rare entity.
Collapse
Affiliation(s)
- Satoru Kudose
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Pietro A. Canetta
- Department of Medicine, Division of Nephrology, Columbia University Irving Medical Center, New York, New York, USA
| | - Miroslav Sekulic
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Forest B. Huls
- Department of Pathology, Division of Laboratory Medicine, University of Alabama, Birmingham, Alabama, USA
| | - Isha Gupta
- Middletown Medical, Middletown, New York, USA
| | - Lihong Bu
- Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | - Glen S. Markowitz
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Vivette D. D’Agati
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Dominick Santoriello
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, New York, USA
| |
Collapse
|
4
|
Sun X, Chintakunta PK, Badachhape AA, Bhavane R, Lee H, Yang DS, Starosolski Z, Ghaghada KB, Vekilov PG, Annapragada AV, Tanifum EA. Rational Design of a Self-Assembling High Performance Organic Nanofluorophore for Intraoperative NIR-II Image-Guided Tumor Resection of Oral Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2206435. [PMID: 36721029 PMCID: PMC10074073 DOI: 10.1002/advs.202206435] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 12/30/2022] [Indexed: 06/18/2023]
Abstract
The first line of treatment for most solid tumors is surgical resection of the primary tumor with adequate negative margins. Incomplete tumor resections with positive margins account for over 75% of local recurrences and the development of distant metastases. In cases of oral cavity squamous cell carcinoma (OSCC), the rate of successful tumor removal with adequate margins is just 50-75%. Advanced real-time imaging methods that improve the detection of tumor margins can help improve success rates,overall safety, and reduce the cost. Fluorescence imaging in the second near-infrared (NIR-II) window has the potential to revolutionize the field due to its high spatial resolution, low background signal, and deep tissue penetration properties, but NIR-II dyes with adequate in vivo performance and safety profiles are scarce. A novel NIR-II fluorophore, XW-03-66, with a fluorescence quantum yield (QY) of 6.0% in aqueous media is reported. XW-03-66 self-assembles into nanoparticles (≈80 nm) and has a systemic circulation half-life (t1/2 ) of 11.3 h. In mouse models of human papillomavirus (HPV)+ and HPV- OSCC, XW-03-66 outperformed indocyanine green (ICG), a clinically available NIR dye, and enabled intraoperative NIR-II image-guided resection of the tumor and adjacent draining lymph node with negative margins. In vitro and in vivo toxicity assessments revealed minimal safety concerns for in vivo applications.
Collapse
Affiliation(s)
- Xianwei Sun
- Department of RadiologyBaylor College of MedicineHoustonTX77030USA
| | - Praveen Kumar Chintakunta
- Department of RadiologyBaylor College of MedicineHoustonTX77030USA
- Present address:
Sai Life Sciences LtdTurakapallyTelanganaIndia
| | | | - Rohan Bhavane
- Department of RadiologyBaylor College of MedicineHoustonTX77030USA
- Department of RadiologyTexas Children's HospitalHoustonTX77030USA
| | - Huan‐Jui Lee
- Department of Chemical and Biomolecular EngineeringUniversity of HoustonHoustonTX77204USA
| | - David S. Yang
- Department of Chemical and Biomolecular EngineeringUniversity of HoustonHoustonTX77204USA
| | - Zbigniew Starosolski
- Department of RadiologyBaylor College of MedicineHoustonTX77030USA
- Department of RadiologyTexas Children's HospitalHoustonTX77030USA
| | - Ketan B. Ghaghada
- Department of RadiologyBaylor College of MedicineHoustonTX77030USA
- Department of RadiologyTexas Children's HospitalHoustonTX77030USA
| | - Peter G. Vekilov
- Department of Chemical and Biomolecular EngineeringUniversity of HoustonHoustonTX77204USA
- Department of ChemistryUniversity of HoustonHoustonTX77204USA
| | - Ananth V. Annapragada
- Department of RadiologyBaylor College of MedicineHoustonTX77030USA
- Department of RadiologyTexas Children's HospitalHoustonTX77030USA
| | - Eric A. Tanifum
- Department of RadiologyBaylor College of MedicineHoustonTX77030USA
- Department of RadiologyTexas Children's HospitalHoustonTX77030USA
| |
Collapse
|
5
|
Mafimoghaddam S, Xu Y, Sherman MB, Orlova EV, Karki P, Orman MA, Vekilov PG. Suppression of amyloid-β fibril growth by drug-engineered polymorph transformation. J Biol Chem 2022; 298:102662. [PMID: 36334629 PMCID: PMC9720346 DOI: 10.1016/j.jbc.2022.102662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 10/24/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Fibrillization of the protein amyloid β is assumed to trigger Alzheimer's pathology. Approaches that target amyloid plaques, however, have garnered limited clinical success, and their failures may relate to the scarce understanding of the impact of potential drugs on the intertwined stages of fibrillization. Here, we demonstrate that bexarotene, a T-cell lymphoma medication with known antiamyloid activity both in vitro and in vivo, suppresses amyloid fibrillization by promoting an alternative fibril structure. We employ time-resolved in situ atomic force microscopy to quantify the kinetics of growth of individual fibrils and supplement it with structure characterization by cryo-EM. We show that fibrils with structure engineered by the drug nucleate and grow substantially slower than "normal" fibrils; remarkably, growth remains stunted even in drug-free solutions. We find that the suppression of fibril growth by bexarotene is not because of the drug binding to the fibril tips or to the peptides in the solution. Kinetic analyses attribute the slow growth of drug-enforced fibril polymorph to the distinctive dynamics of peptide chain association to their tips. As an additional benefit, the bexarotene fibrils kill primary rat hippocampal neurons less efficiently than normal fibrils. In conclusion, the suggested drug-driven polymorph transformation presents a mode of action to irreversibly suppress toxic aggregates not only in Alzheimer's but also potentially in myriad diverse pathologies that originate with protein condensation.
Collapse
Affiliation(s)
- Sima Mafimoghaddam
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Yuechuan Xu
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Michael B. Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Elena V. Orlova
- Department of Biological Sciences, Institute for Structural and Molecular Biology, Birkbeck University of London, London, UK
| | - Prashant Karki
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Mehmet A. Orman
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, Texas, USA
| | - Peter G. Vekilov
- William A. Brookshire Department of Chemical & Biomolecular Engineering, University of Houston, Houston, Texas, USA,Department of Chemistry, University of Houston, Houston, Texas, USA,For correspondence: Peter G. Vekilov
| |
Collapse
|
6
|
Vazquez DS, Toledo PL, Gianotti AR, Ermácora MR. Protein conformation and biomolecular condensates. Curr Res Struct Biol 2022; 4:285-307. [PMID: 36164646 PMCID: PMC9508354 DOI: 10.1016/j.crstbi.2022.09.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 10/27/2022] Open
Abstract
Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.
Collapse
Affiliation(s)
- Diego S. Vazquez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Pamela L. Toledo
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Alejo R. Gianotti
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| | - Mario R. Ermácora
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes and Grupo de Biología Estructural y Biotecnología, IMBICE, CONICET, Universidad Nacional de Quilmes, Argentina
| |
Collapse
|
7
|
The Ambiguous Functions of the Precursors That Enable Nonclassical Modes of Olanzapine Nucleation and Growth. CRYSTALS 2021. [DOI: 10.3390/cryst11070738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
One of the most consequential assumptions of the classical theories of crystal nucleation and growth is the Szilard postulate, which states that molecules from a supersaturated phase join a nucleus or a growing crystal individually. In the last 20 years, observations in complex biological, geological, and engineered environments have brought to light violations of the Szilard rule, whereby molecules assemble into ordered or disordered precursors that then host and promote nucleation or contribute to fast crystal growth. Nonclassical crystallization has risen to a default mode presumed to operate in the majority of the inspected crystallizing systems. In some cases, the existence of precursors in the growth media is admitted as proof for their role in nucleation and growth. With the example of olanzapine, a marketed drug for schizophrenia and bipolar disorder, we demonstrate that molecular assemblies in the solution selectively participate in crystal nucleation and growth. In aqueous and organic solutions, olanzapine assembles into both mesoscopic solute-rich clusters and dimers. The clusters facilitate nucleation of crystals and crystal form transformations. During growth, however, the clusters land on the crystal surface and transform into defects, but do not support step growth. The dimers are present at low concentrations in the supersaturated solution, yet the crystals grow by the association of dimers, and not of the majority monomers. The observations with olanzapine emphasize that detailed studies of the crystal and solution structures and the dynamics of molecular association may empower classical and nonclassical models that advance the understanding of natural crystallization, and support the design and manufacture of promising functional materials.
Collapse
|
8
|
Glass-like protein condensate for the long-term storage of proteins. Int J Biol Macromol 2021; 182:162-167. [PMID: 33836199 DOI: 10.1016/j.ijbiomac.2021.04.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 03/31/2021] [Accepted: 04/03/2021] [Indexed: 11/21/2022]
Abstract
Long-term storage of proteins at ambient temperature is required for applications in pharmaceutics and biotechnology. Lyophilization is a versatile approach for stabilizing proteins at ambient temperature, although its freezing and drying processes negatively affect the protein structure. In this study, we show a glass-like protein condensate (GLPC) as a new method for protein stabilization at ambient temperature. Various protein types, including immunoglobulin G, gamma globulin, albumin, and chymotrypsin, formed a glassy state during ultracentrifugation and natural drying, while proteins that tend to crystalize, such as hen egg-white lysozyme, did not. The GLPCs were characterized by a transparent solid state, similar to a dry glass ball. Importantly, the GLPCs were dissolved easily in saline solution at a physiological concentration, thereby retaining their native structures and functions. The GLPCs preserved their native structures even after 1 year of incubation at ambient temperature. These results provide a framework for the development of protein preservation methods at ambient temperature other than lyophilization.
Collapse
|
9
|
Yang DS, Saeedi A, Davtyan A, Fathi M, Sherman MB, Safari MS, Klindziuk A, Barton MC, Varadarajan N, Kolomeisky AB, Vekilov PG. Mesoscopic protein-rich clusters host the nucleation of mutant p53 amyloid fibrils. Proc Natl Acad Sci U S A 2021; 118:e2015618118. [PMID: 33653952 PMCID: PMC7958401 DOI: 10.1073/pnas.2015618118] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The protein p53 is a crucial tumor suppressor, often called "the guardian of the genome"; however, mutations transform p53 into a powerful cancer promoter. The oncogenic capacity of mutant p53 has been ascribed to enhanced propensity to fibrillize and recruit other cancer fighting proteins in the fibrils, yet the pathways of fibril nucleation and growth remain obscure. Here, we combine immunofluorescence three-dimensional confocal microscopy of human breast cancer cells with light scattering and transmission electron microscopy of solutions of the purified protein and molecular simulations to illuminate the mechanisms of phase transformations across multiple length scales, from cellular to molecular. We report that the p53 mutant R248Q (R, arginine; Q, glutamine) forms, both in cancer cells and in solutions, a condensate with unique properties, mesoscopic protein-rich clusters. The clusters dramatically diverge from other protein condensates. The cluster sizes are decoupled from the total cluster population volume and independent of the p53 concentration and the solution concentration at equilibrium with the clusters varies. We demonstrate that the clusters carry out a crucial biological function: they host and facilitate the nucleation of amyloid fibrils. We demonstrate that the p53 clusters are driven by structural destabilization of the core domain and not by interactions of its extensive unstructured region, in contradistinction to the dense liquids typical of disordered and partially disordered proteins. Two-step nucleation of mutant p53 amyloids suggests means to control fibrillization and the associated pathologies through modifying the cluster characteristics. Our findings exemplify interactions between distinct protein phases that activate complex physicochemical mechanisms operating in biological systems.
Collapse
Affiliation(s)
- David S Yang
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Arash Saeedi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Aram Davtyan
- Department of Chemistry, Rice University, Houston, TX 77251
| | - Mohsen Fathi
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Michael B Sherman
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555
| | - Mohammad S Safari
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544
| | | | - Michelle C Barton
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX 77030
| | - Navin Varadarajan
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204
| | - Anatoly B Kolomeisky
- Department of Chemistry, Rice University, Houston, TX 77251
- Center for Theoretical Biological Physics, Rice University, Houston, TX 77251
| | - Peter G Vekilov
- William A. Brookshire Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204;
- Department of Chemistry, University of Houston, Houston, TX 77204
| |
Collapse
|
10
|
Nikfarjam S, Jouravleva EV, Anisimov MA, Woehl TJ. Effects of Protein Unfolding on Aggregation and Gelation in Lysozyme Solutions. Biomolecules 2020; 10:biom10091262. [PMID: 32887233 PMCID: PMC7563771 DOI: 10.3390/biom10091262] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 08/29/2020] [Indexed: 12/15/2022] Open
Abstract
In this work, we investigate the role of folding/unfolding equilibrium in protein aggregation and formation of a gel network. Near the neutral pH and at a low buffer ionic strength, the formation of the gel network around unfolding conditions prevents investigations of protein aggregation. In this study, by deploying the fact that in lysozyme solutions the time of folding/unfolding is much shorter than the characteristic time of gelation, we have prevented gelation by rapidly heating the solution up to the unfolding temperature (~80 °C) for a short time (~30 min.) followed by fast cooling to the room temperature. Dynamic light scattering measurements show that if the gelation is prevented, nanosized irreversible aggregates (about 10–15 nm radius) form over a time scale of 10 days. These small aggregates persist and aggregate further into larger aggregates over several weeks. If gelation is not prevented, the nanosized aggregates become the building blocks for the gel network and define its mesh length scale. These results support our previously published conclusion on the nature of mesoscopic aggregates commonly observed in solutions of lysozyme, namely that aggregates do not form from lysozyme monomers in their native folded state. Only with the emergence of a small fraction of unfolded proteins molecules will the aggregates start to appear and grow.
Collapse
Affiliation(s)
- Shakiba Nikfarjam
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; (S.N.); (T.J.W.)
| | - Elena V. Jouravleva
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA;
| | - Mikhail A. Anisimov
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; (S.N.); (T.J.W.)
- Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA;
- Correspondence:
| | - Taylor J. Woehl
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD 20742, USA; (S.N.); (T.J.W.)
| |
Collapse
|
11
|
Affiliation(s)
- Peter G. Vekilov
- Department of Chemical and Biomolecular Engineering and Department of Chemistry, University of Houston, Houston, Texas 77204, United States
| |
Collapse
|
12
|
Nikfarjam S, Ghorbani M, Adhikari S, Karlsson AJ, Jouravleva EV, Woehl TJ, Anisimov MA. Irreversible Nature of Mesoscopic Aggregates in Lysozyme Solutions. COLLOID JOURNAL 2019. [DOI: 10.1134/s1061933x19050090] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
13
|
Abstract
The aggregation of amyloid fibrils can lead to various diseases including Alzheimer's, Parkinson's disease, and transmissible spongiform encephalopathy. Amyloid fibrils can develop from a variety of proteins in the body as they misfold into a primarily β-sheet structure and aggregate. Human lysozyme has been shown to have far reaching effects in the human health-a homologous enzyme, hen egg-white lysozyme, has been shown to denature to a primarily β-sheet structure at low pH and high alcohol content solution. We have studied these systems in atomic-level detail with a combination of constant pH and microsecond long molecular dynamics simulation in explicit solvent, which cumulatively total over 10 μs of simulation time. These studies have allowed us to determine two potential unfolding pathways depending on the protonation state of a key glutamic acid residue as well as the effect of solution dynamics and pH on the unfolding process.
Collapse
Affiliation(s)
- Alice R. Walker
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
| | - Nikhil Baddam
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - G. Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, TX 76201, USA
| |
Collapse
|
14
|
Anomalous Dense Liquid Condensates Host the Nucleation of Tumor Suppressor p53 Fibrils. iScience 2019; 12:342-355. [PMID: 30739016 PMCID: PMC6369220 DOI: 10.1016/j.isci.2019.01.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 01/03/2019] [Accepted: 01/16/2019] [Indexed: 01/09/2023] Open
Abstract
About half of human cancers are associated with mutations of the tumor suppressor p53. Gained oncogenic functions of the mutants have been related to aggregation behaviors of wild-type and mutant p53. The thermodynamic and kinetic mechanisms of p53 aggregation are poorly understood. Here we find that wild-type p53 forms an anomalous liquid phase. The liquid condensates exhibit several behaviors beyond the scope of classical phase transition theories: their size, ca. 100 nm, is independent of the p53 concentration and decoupled from the protein mass held in the liquid phase. Furthermore, the liquid phase lacks constant solubility. The nucleation of p53 fibrils deviates from the accepted mechanism of sequential association of single solute molecules. We find that the liquid condensates serve as pre-assembled precursors of high p53 concentration that facilitate fibril assembly. Fibril nucleation hosted by precursors represents a novel biological pathway, which opens avenues to suppress protein fibrillation in aggregation diseases.
Collapse
|
15
|
Zheng X, Anisimov MA, Sengers JV, He M. Mesoscopic Diffusion of Poly(ethylene oxide) in Pure and Mixed Solvents. J Phys Chem B 2017; 122:3454-3464. [PMID: 29131952 DOI: 10.1021/acs.jpcb.7b10420] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present results from an experimental dynamic light-scattering study of poly(ethylene oxide) (PEO) in both a pure solvent (water) and a mixed solvent (tert-butanol + water). The concentration dependence of the diffusive relaxation of the PEO molecules is found to be typical of polymers in a good solvent. However, the mesoscopic diffusive behavior of PEO in the mixed solvent is very different, indicating an initial collapse and subsequent reswelling of PEO caused by co-nonsolvency. Furthermore, in the solutions of PEO with very large molecular weights, we found additional hydrodynamic modes indicating the presence of PEO clusters and aggregates similar to those found by some other investigators.
Collapse
Affiliation(s)
- Xiong Zheng
- Institute for Physical Science and Technology and Department of Chemical and Biomolecular Engineering , University of Maryland , College Park , Maryland 20742 , United States.,Key Laboratory of Thermo-Fluid Science and Engineering , Ministry of Education, Xi'an Jiaotong University , Xi'an , Shaanxi Province 710049 , People's Republic of China
| | - Mikhail A Anisimov
- Institute for Physical Science and Technology and Department of Chemical and Biomolecular Engineering , University of Maryland , College Park , Maryland 20742 , United States.,Oil and Gas Research Institute of the Russian Academy of Sciences , Moscow 117333 , Russia
| | - Jan V Sengers
- Institute for Physical Science and Technology and Department of Chemical and Biomolecular Engineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Maogang He
- Key Laboratory of Thermo-Fluid Science and Engineering , Ministry of Education, Xi'an Jiaotong University , Xi'an , Shaanxi Province 710049 , People's Republic of China
| |
Collapse
|