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Chakravarti A, Joseph JA. Accurate prediction of thermoresponsive phase behavior of disordered proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.04.641540. [PMID: 40093057 PMCID: PMC11908177 DOI: 10.1101/2025.03.04.641540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2025]
Abstract
Protein responses to environmental stress, particularly temperature fluctuations, have long been a subject of investigation, with a focus on how proteins maintain homeostasis and exhibit thermoresponsive properties. While UCST-type (upper critical solution temperature) phase behavior has been studied extensively and can now be predicted reliably using computational models, LCST-type (lower critical solution temperature) phase transitions remain less explored, with a lack of computational models capable of accurate prediction. This gap limits our ability to probe fully how proteins undergo phase transitions in response to temperature changes. Here, we introduce Mpipi-T, a residue-level coarse-grained model designed to predict LCST-type phase behavior of proteins. Parametrized using both atomistic simulations and experimental data, Mpipi-T accounts for entropically driven protein phase separation that occurs upon heating. Accordingly, Mpipi-T predicts temperature-driven protein behavior quantitatively in both single- and multi-chain systems. Beyond its predictive capabilities, we demonstrate that Mpipi-T provides a framework for uncovering the molecular mechanisms underlying heat stress responses, offering new insights into how proteins sense and adapt to thermal changes in biological systems.
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Affiliation(s)
- Ananya Chakravarti
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Omenn–Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA
| | - Jerelle A. Joseph
- Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA
- Omenn–Darling Bioengineering Institute, Princeton University, Princeton, NJ 08544, USA
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Urmi R, Banerjee P, Singh M, Singh R, Chhillar S, Sharma N, Chandra A, Singh N, Qamar I. Revolutionizing biomedicine: Aptamer-based nanomaterials and nanodevices for therapeutic applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 42:e00843. [PMID: 38881649 PMCID: PMC11179248 DOI: 10.1016/j.btre.2024.e00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/28/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024]
Abstract
With the progress in two distinct areas of nanotechnology and aptamer identification technologies, the two fields have merged to what is known as aptamer nanotechnology. Aptamers have varying properties in the biomedical field include their small size, non-toxicity, ease of manufacturing, negligible immunogenicity, ability to identify a wide range of targets, and high immobilizing capacity. Nevertheless, aptamers can utilize the distinct characteristics offered by nanomaterials like optical, magnetic, thermal, electronic properties to become more versatile and function as a novel device in diagnostics and therapeutics. This engineered aptamer conjugated nanomaterials, in turn provides a potentially new and unique properties apart from the pre-existing characteristics of aptamer and nanomaterials, where they act to offer wide array of applications in the biomedical field ranging from drug targeting, delivery of drugs, biosensing, bioimaging. This review gives comprehensive insight of the different aptamer conjugated nanomaterials and their utilization in biomedical field. Firstly, it introduces on the aptamer selection methods and roles of nanomaterials offered. Further, different conjugation strategies are explored in addition, the class of aptamer conjugated nanodevices being discussed. Typical biomedical examples and studies specifically, related to drug delivery, biosensing, bioimaging have been presented.
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Affiliation(s)
- Rajkumari Urmi
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Pallabi Banerjee
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Manisha Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Risha Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Sonam Chhillar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Neha Sharma
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Anshuman Chandra
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
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Niu X, Fu Y, Feng L, Xie M, Li B, Que L, You Z. Upper-critical solution temperature (UCST) polymer functionalized nanomedicine for controlled drug release and hypoxia alleviation in hepatocellular carcinoma therapy. PLoS One 2023; 18:e0290237. [PMID: 37624853 PMCID: PMC10456220 DOI: 10.1371/journal.pone.0290237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Recently, bioinspired material such as nanoparticle has been successfully applied in the cancer therapy. However, how to precisely control the drug release from nanomedicine in tumor tissue and overcome the hypoxic microenvironment of tumor tissue is still an important challenge in the development of nanomedicine. In this work, a new type of drug-loaded nanoparticles P(AAm-co-AN)-AuNRs@CeO2-DOX (PA-DOX) was prepared by combining high-efficiency photothermal reagents, critical up-conversion temperature polymer layer and anti-cancer drug doxorubicin (DOX) for the treatment of hepatocellular carcinoma (HCC). In this system, CeO2 can decompose hydrogen peroxide to H2O and O2 alleviate the anaerobic microenvironment of liver cancer cells. As a photothermal reagent, AuNRs@CeO2 can convert near-infrared light into heat energy to achieve local heat to kill cancer cells and ablate solid tumors. In addition, the elevated temperature would enable the polymer layer to undergo a phase transition to release more DOX to achieve a controlled release mechanism, which will open up a new horizon for clinical cancer treatment.
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Affiliation(s)
- Xiaoya Niu
- Department of General Surgery, Division of Biliary Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yi Fu
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Peking University, Beijing, 100191, China
| | - Lei Feng
- Department of General Surgery, Division of Biliary Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Maodi Xie
- West Chia-Washington Mitochondria and Metabolism Center, West China Hospital of Sichuan University, Chengdu, 610041, Sichuan, China
| | - Bei Li
- Department of General Surgery, Division of Biliary Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Lin Que
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
- State Key Laboratory of Oral Diseases, West China College of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Zhen You
- Department of General Surgery, Division of Biliary Surgery, West China Hospital, Sichuan University, Chengdu, 610041, China
- Research Center for Biliary Diseases, West China Hospital, Sichuan University, Chengdu, 610041, China
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Light, Water, and Melatonin: The Synergistic Regulation of Phase Separation in Dementia. Int J Mol Sci 2023; 24:ijms24065835. [PMID: 36982909 PMCID: PMC10054283 DOI: 10.3390/ijms24065835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 03/17/2023] [Indexed: 03/22/2023] Open
Abstract
The swift rise in acceptance of molecular principles defining phase separation by a broad array of scientific disciplines is shadowed by increasing discoveries linking phase separation to pathological aggregations associated with numerous neurodegenerative disorders, including Alzheimer’s disease, that contribute to dementia. Phase separation is powered by multivalent macromolecular interactions. Importantly, the release of water molecules from protein hydration shells into bulk creates entropic gains that promote phase separation and the subsequent generation of insoluble cytotoxic aggregates that drive healthy brain cells into diseased states. Higher viscosity in interfacial waters and limited hydration in interiors of biomolecular condensates facilitate phase separation. Light, water, and melatonin constitute an ancient synergy that ensures adequate protein hydration to prevent aberrant phase separation. The 670 nm visible red wavelength found in sunlight and employed in photobiomodulation reduces interfacial and mitochondrial matrix viscosity to enhance ATP production via increasing ATP synthase motor efficiency. Melatonin is a potent antioxidant that lowers viscosity to increase ATP by scavenging excess reactive oxygen species and free radicals. Reduced viscosity by light and melatonin elevates the availability of free water molecules that allow melatonin to adopt favorable conformations that enhance intrinsic features, including binding interactions with adenosine that reinforces the adenosine moiety effect of ATP responsible for preventing water removal that causes hydrophobic collapse and aggregation in phase separation. Precise recalibration of interspecies melatonin dosages that account for differences in metabolic rates and bioavailability will ensure the efficacious reinstatement of the once-powerful ancient synergy between light, water, and melatonin in a modern world.
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A review on structural aspects and applications of PAMAM dendrimers in analytical chemistry: Frontiers from separation sciences to chemical sensor technologies. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Kojima C, Fu Y, Tamaki M. Control of Stimuli Sensitivity in pH-Switchable LCST/UCST-Type Thermosensitive Dendrimers by Changing the Dendrimer Structure. Polymers (Basel) 2022; 14:polym14122426. [PMID: 35746002 PMCID: PMC9227611 DOI: 10.3390/polym14122426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 02/01/2023] Open
Abstract
Stimuli-sensitive materials, such as pH- and temperature-responsive polymers, are useful as smart materials. Phenylalanine (Phe)-modified polyamidoamine (PAMAM) dendrimers with succinic acid termini, PAMAM-Phe-Suc, have been reported as unique pH-switchable lower critical solution temperature (LCST)-/upper critical solution temperature (UCST)-type thermosensitive polymers. Regulating the phase transition behavior of dendrimers is important for their applications. This study investigated the relationship between the dendrimer structure and stimuli sensitivity. Phe-modified PAMAM dendrimers with cyclohexanedicarboxylate termini (PAMAM-Phe-CHex) and sulfonate termini (PAMAM-Phe-SO3Na) were synthesized. The temperature-dependent transmittance of these aqueous dendrimer solutions was examined at various pH values. PAMAM-Phe-CHex with Phe at all termini (PAMAM-Phe64-CHex) demonstrated a broad UCST-like phase transition at pH 7.0 but lacked an LCST-type phase transition. PAMAM-Phe-CHex with ≤ 27 Phe residues showed both LCST- and UCST-like phase transitions at different pH values, but the phase transition was broad. PAMAM-Phe-SO3Na showed both LCST- and UCST-type phase transitions at different pH values, and the transition temperature increased as the bound Phe number decreased. Thus, the phase transition behavior of PAMAM-Phe-SO3Na dendrimers can be regulated by varying the Phe/PAMAM ratios.
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Shiba H, Nishio M, Sawada M, Tamaki M, Michigami M, Nakai S, Nakase I, Fujii I, Matsumoto A, Kojima C. Carboxy-terminal dendrimers with phenylalanine for a pH-sensitive delivery system into immune cells including T cells. J Mater Chem B 2021; 10:2463-2470. [PMID: 34935852 DOI: 10.1039/d1tb01980e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Although T cells play important roles in various immune reactions, there are only a few reports on delivery systems into T cells. Our previous study showed that carboxy-terminal phenylalanine (Phe)-modified polyamidoamine (PAMAM) dendrimers have both temperature- and pH-sensitive properties, which are affected by the chemical structure. The self-assembled structures of Phe, observed in phenylketonuria, enhance the protein aggregation, the association with the cell membrane and the membrane permeability. In this study, we applied the Phe-modified dendrimers to a pH-sensitive drug delivery system into T cells. Dendrimers with different amino acids and acid anhydrides were synthesized, and their pH-responsive association with T cells and their subsets was investigated. The dendrimers modified with Phe and cyclohexanedicarboxylic acid (CHex) showed higher uptake into various cells, including Jurkat cells, CD3+ T cells, CD3 + CD4+ helper T cells and CD3 + CD8+ killer T cells. These dendrimers were internalized into T cells via endocytosis, and their cellular uptake was enhanced under weak acidic conditions (pH 6.5). Our results showed that Phe- and CHex-modified dendrimers have a delivery potential to T cells and their subsets, which may be useful for cancer immunotherapy.
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Affiliation(s)
- Hiroya Shiba
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Misaki Nishio
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Mei Sawada
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Mamiko Tamaki
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Masataka Michigami
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Shinya Nakai
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Ikuhiko Nakase
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Ikuo Fujii
- Department of Biological Science, Graduate School of Science, Osaka Prefecture University, 1-1, Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan
| | - Akikazu Matsumoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
| | - Chie Kojima
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.
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Aflori M. Smart Nanomaterials for Biomedical Applications-A Review. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:396. [PMID: 33557177 PMCID: PMC7913901 DOI: 10.3390/nano11020396] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 12/12/2022]
Abstract
Recent advances in nanotechnology have forced the obtaining of new materials with multiple functionalities. Due to their reduced dimensions, nanomaterials exhibit outstanding physio-chemical functionalities: increased absorption and reactivity, higher surface area, molar extinction coefficients, tunable plasmonic properties, quantum effects, and magnetic and photo properties. However, in the biomedical field, it is still difficult to use tools made of nanomaterials for better therapeutics due to their limitations (including non-biocompatible, poor photostabilities, low targeting capacity, rapid renal clearance, side effects on other organs, insufficient cellular uptake, and small blood retention), so other types with controlled abilities must be developed, called "smart" nanomaterials. In this context, the modern scientific community developed a kind of nanomaterial which undergoes large reversible changes in its physical, chemical, or biological properties as a consequence of small environmental variations. This systematic mini-review is intended to provide an overview of the newest research on nanosized materials responding to various stimuli, including their up-to-date application in the biomedical field.
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Affiliation(s)
- Magdalena Aflori
- Petru Poni Institute of Macromolecular Chemistry, 41A Grigore Ghica Voda Alley, 700487 Iasi, Romania
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Kim B, Kwon M, Mohanty AK, Cho HY, Paik H. LCST and UCST Transition of Poly(DMAEMA‐
b
‐MEO
2
MA) Copolymer in KHP Buffer. MACROMOL CHEM PHYS 2020. [DOI: 10.1002/macp.202000330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Byoungjae Kim
- Department of Polymer Science and Engineering Pusan National University Busan 46214 Korea
| | - Minho Kwon
- Department of Polymer Science and Engineering Pusan National University Busan 46214 Korea
| | - Aruna Kumar Mohanty
- Department of Polymer Science and Engineering Pusan National University Busan 46214 Korea
| | - Hong Y. Cho
- Department of Polymer Science and Engineering Pusan National University Busan 46214 Korea
| | - Hyun‐jong Paik
- Department of Polymer Science and Engineering Pusan National University Busan 46214 Korea
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