1
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Rudani BA, Jakubowski A, Kriegs H, Wiegand S. Deciphering the guanidinium cation: Insights into thermal diffusion. J Chem Phys 2024; 160:214502. [PMID: 38828819 DOI: 10.1063/5.0215843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Accepted: 05/16/2024] [Indexed: 06/05/2024] Open
Abstract
Thermophoresis, or thermodiffusion, is becoming a more popular method for investigating the interactions between proteins and ligands due to its high sensitivity to the interactions between solutes and water. Despite its growing use, the intricate mechanisms behind thermodiffusion remain unclear. This gap in knowledge stems from the complexities of thermodiffusion in solvents that have specific interactions as well as the intricate nature of systems that include many components with both non-ionic and ionic groups. To deepen our understanding, we reduce complexity by conducting systematic studies on aqueous salt solutions. In this work, we focused on how guanidinium salt solutions behave in a temperature gradient, using thermal diffusion forced Rayleigh scattering experiments at temperatures ranging from 15 to 35 °C. We looked at the thermodiffusive behavior of four guanidinium salts (thiocyanate, iodide, chloride, and carbonate) in solutions with concentrations ranging from 1 to 3 mol/kg. The guanidinium cation is disk-shaped and is characterized by flat hydrophobic surfaces and three amine groups, which enable directional hydrogen bonding along the edges. We compare our results to the behavior of salts with spherical cations, such as sodium, potassium, and lithium. Our discussions are framed around how different salts are solvated, specifically in the context of the Hofmeister series, which ranks ions based on their effects on the solvation of proteins.
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Affiliation(s)
- Binny A Rudani
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Andre Jakubowski
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Hartmut Kriegs
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
| | - Simone Wiegand
- IBI-4:Biomacromolecular Systems and Processes, Forschungszentrum Jülich GmbH, D-52428 Jülich, Germany
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2
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Ertekin UE, Okur HI. Greasy Cations Bind to Neutral Macromolecules in Aqueous Solution. J Phys Chem Lett 2024:6151-6157. [PMID: 38835205 DOI: 10.1021/acs.jpclett.4c00925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
Ions influence the solution properties of macromolecules. Although much is known about anions, cationic effects are considered mostly in terms of weak interactions or exclusion from neutral interfaces. Herein, we have systematically studied the effect of quaternary tetraalkylammonium cations (NH4+, NMe4+, NEt4+, NPr4+, NBu4+) on the phase transition of poly(N-isopropylacrylamide) (PNIPAM) in aqueous solution. Solubility measurements were coupled to 1H NMR and ATR-FTIR spectroscopic measurements. The solubility and NMR measurements revealed a direct binding between the greasiest cations and the isopropyl group of the macromolecule, evidenced from the nonlinear, Langmuir-type chemical shift response only at the isopropyl NMR signals with increasing salt concentrations. The ATR-FTIR measurements focusing on the amide oxygen showed that it is not the main direct-binding site. Additionally, the salting-out effects of the greasier cations correlate with their hydration entropies. These results demonstrate that the most weakly hydrated cations can bind to macromolecules as strongly as the weakly hydrated Hofmeister anions.
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Affiliation(s)
- Umay Eren Ertekin
- Department of Chemistry, Faculty of Science, Bilkent University, 06800 Ankara, Turkey
| | - Halil Ibrahim Okur
- Department of Chemistry, Faculty of Science, Bilkent University, 06800 Ankara, Turkey
- National Nanotechnology Research Center (UNAM), Bilkent University, 06800 Ankara, Turkey
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3
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Zhu L, Pan Y, Hua Z, Liu Y, Zhang X. Ionic Effect on the Microenvironment of Biomolecular Condensates. J Am Chem Soc 2024; 146:14307-14317. [PMID: 38722189 DOI: 10.1021/jacs.4c04036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Biomolecules such as proteins and RNA could organize to form condensates with distinct microenvironments through liquid-liquid phase separation (LLPS). Recent works have demonstrated that the microenvironment of biomolecular condensates plays a crucial role in mediating biological activities, such as the partition of biomolecules, and the subphase organization of the multiphasic condensates. Ions could influence the phase transition point of LLPS, following the Hofmeister series. However, the ion-specific effect on the microenvironment of biomolecular condensates remains unknown. In this study, we utilized fluorescence lifetime imaging microscopy (FLIM), fluorescence recovery after photobleaching (FRAP), and microrheology techniques to investigate the ion effect on the microenvironment of condensates. We found that ions significantly affect the microenvironment of biomolecular condensates: salting-in ions increase micropolarity and reduce the microviscosity of the condensate, while salting-out ions induce opposing effects. Furthermore, we manipulate the miscibility and multilayering behavior of condensates through ion-specific effects. In summary, our work provides the first quantitative survey of the microenvironment of protein condensates in the presence of ions from the Hofmeister series, demonstrating how ions impact micropolarity, microviscosity, and viscoelasticity of condensates. Our results bear implications on how membrane-less organelles would exhibit varying microenvironments in the presence of continuously changing cellular conditions.
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Affiliation(s)
- Longchen Zhu
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
| | - Yifei Pan
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
| | - Ziyi Hua
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Xin Zhang
- Department of Chemistry, School of Science and Research Center for Industries of the Future, Westlake University, Hangzhou 310030, P. R. China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, P. R. China
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4
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Jordan J, Gibb CL, Tran T, Yao W, Rose A, Mague JT, Easson MW, Gibb BC. Anion Binding to Ammonium and Guanidinium Hosts: Implications for the Reverse Hofmeister Effects Induced by Lysine and Arginine Residues. J Org Chem 2024; 89:6877-6891. [PMID: 38662908 PMCID: PMC11110012 DOI: 10.1021/acs.joc.4c00242] [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: 01/27/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 05/18/2024]
Abstract
Anions have a profound effect on the properties of soluble proteins. Such Hofmeister effects have implications in biologics stability, protein aggregation, amyloidogenesis, and crystallization. However, the interplay between the important noncovalent interactions (NCIs) responsible for Hofmeister effects is poorly understood. To contribute to improving this state of affairs, we report on the NCIs between anions and ammonium and guanidinium hosts 1 and 2, and the consequences of these. Specifically, we investigate the properties of cavitands designed to mimic two prime residues for anion-protein NCIs─lysines and arginines─and the solubility consequences of complex formation. Thus, we report NMR and ITC affinity studies, X-ray analysis, MD simulations, and anion-induced critical precipitation concentrations. Our findings emphasize the multitude of NCIs that guanidiniums can form and how this repertoire qualitatively surpasses that of ammoniums. Additionally, our studies demonstrate the ease by which anions can dispense with a fraction of their hydration-shell waters, rearrange those that remain, and form direct NCIs with the hosts. This raises many questions concerning how solvent shell plasticity varies as a function of anion, how the energetics of this impact the different NCIs between anions and ammoniums/guanidiniums, and how this affects the aggregation of solutes at high anion concentrations.
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Affiliation(s)
- Jacobs
H. Jordan
- The
Southern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 1100 Allen Toussaint Blvd., New Orleans, Louisiana 70124, United States
| | - Corinne L.D. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Thien Tran
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Wei Yao
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Austin Rose
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Joel T. Mague
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Michael W. Easson
- The
Southern Regional Research Center, Agricultural Research Service, US Department of Agriculture, 1100 Allen Toussaint Blvd., New Orleans, Louisiana 70124, United States
| | - Bruce C. Gibb
- Department
of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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5
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Tan X, Wang Z, Cheung U, Hu Z, Liu Q, Wang L, Sullivan MA, Cozzolino D, Gilbert RG. Liver glycogen fragility in the presence of hydrogen-bond breakers. Int J Biol Macromol 2024; 268:131741. [PMID: 38649083 DOI: 10.1016/j.ijbiomac.2024.131741] [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: 10/27/2023] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Glycogen, a complex branched glucose polymer, is responsible for sugar storage in blood glucose homeostasis. It comprises small β particles bound together into composite α particles. In diabetic livers, α particles are fragile, breaking apart into smaller particles in dimethyl sulfoxide, DMSO; they are however stable in glycogen from healthy animals. We postulate that the bond between β particles in α particles involves hydrogen bonding. Liver-glycogen fragility in normal and db/db mice (an animal model for diabetes) is compared using various hydrogen-bond breakers (DMSO, guanidine and urea) at different temperatures. The results showed different degrees of α-particle disruption. Disrupted glycogen showed changes in the mid-infra-red spectrum that are related to hydrogen bonds. While glycogen α-particles are only fragile under harsh, non-physiological conditions, these results nevertheless imply that the bonding between β particles in α particles is different in diabetic livers compared to healthy, and is probably associated with hydrogen bonding.
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Affiliation(s)
- Xinle Tan
- Centre for Animal Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Ziyi Wang
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Ut Cheung
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia.
| | - Zhenxia Hu
- Department of Pharmacy, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
| | - Qinghua Liu
- State Key Laboratory of Quality Research in Chinese Medicines, Macau University of Science and Technology, Taipa, Macau SAR 999078, China
| | - Liang Wang
- Laboratory Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Mitchell A Sullivan
- Glycation and Diabetes Group, Mater Research Institute, The University of Queensland, Translational Research Institute, Brisbane, Queensland, 4012, Australia.
| | - Daniel Cozzolino
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia.
| | - Robert G Gilbert
- Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland 4072, Australia; Jiangsu Key Laboratory of Crop Genetics and Physiology/State Key Laboratory of Hybrid Rice, College of Agriculture, Yangzhou University, Yangzhou 225009, China; Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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6
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Zhu T, Sun J, Pang H, Wu B. Computational Enzyme Redesign Enhances Tolerance to Denaturants for Peptide C-Terminal Amidation. JACS AU 2024; 4:788-797. [PMID: 38425901 PMCID: PMC10900485 DOI: 10.1021/jacsau.3c00792] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 03/02/2024]
Abstract
The escalating demand for biocatalysts in pharmaceutical and biochemical applications underscores the critical imperative to enhance enzyme activity and durability under high denaturant concentrations. Nevertheless, the development of a practical computational redesign protocol for improving enzyme tolerance to denaturants is challenging due to the limitations of relying solely on model-driven approaches to adequately capture denaturant-enzyme interactions. In this study, we introduce an enzyme redesign strategy termed GRAPE_DA, which integrates multiple data-driven and model-driven computational methods to mitigate the sampling biases inherent in a single approach and comprehensively predict beneficial mutations on both the protein surface and backbone. To illustrate the methodology's effectiveness, we applied it to engineer a peptidylamidoglycolate lyase, resulting in a variant exhibiting up to a 24-fold increase in peptide C-terminal amidation activity under 2.5 M guanidine hydrochloride. We anticipate that this integrated engineering strategy will facilitate the development of enzymatic peptide synthesis and functionalization under denaturing conditions and highlight the role of engineering surface residues in governing protein stability.
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Affiliation(s)
- Tong Zhu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinyuan Sun
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Pang
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Bian Wu
- AIM Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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7
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Takács D, Adžić M, Omerović N, Vraneš M, Katona J, Pavlović M. Electrolyte-induced aggregation of zein protein nanoparticles in aqueous dispersions. J Colloid Interface Sci 2024; 656:457-465. [PMID: 38006868 DOI: 10.1016/j.jcis.2023.11.123] [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: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Ion specific effects on the charging and aggregation features of zein nanoparticles (ZNP) were studied in aqueous suspensions by electrophoretic and time-resolved dynamic light scattering techniques. The influence of mono- and multivalent counterions on the colloidal stability was investigated for positively and negatively charged particles at pH values below and above the isoelectric point, respectively. The sequence of the destabilization power of monovalent salts followed the prediction of the indirect Hofmeister series for positively charged particles, while the direct Hofmeister series for negatively charged ones assumed a hydrophobic character for their surface. The multivalent ions destabilized the oppositely charged ZNPs more effectively and the aggregation process followed the Schulze-Hardy rule. For some multivalent ions, strong adsorption led to charge reversal resulting in restabilization of the suspensions. The experimental critical coagulation concentrations (CCCs) could be well-predicted with the theory developed by Derjaguin, Landau, Verwey and Overbeek indicating that the aggregation processes were mainly driven by electrical double layer repulsion and van der Waals attraction. The ion specific dependence of the CCCs is owing to the modification of the surface charge through ion adsorption at different extents. These results are crucial for drug delivery applications, where inorganic electrolytes are present in ZNP samples.
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Affiliation(s)
- Dóra Takács
- MTA-SZTE Lendület Biocolloids Research Group, Department of Physical Chemistry and Materials Science, University of Szeged, 6720 Szeged, Hungary
| | - Maja Adžić
- Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Nejra Omerović
- BioSense Institute, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Milan Vraneš
- Department of Chemistry, Biochemistry and Environmental Protection, Faculty of Sciences, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Jaroslav Katona
- Department of Applied and Engineering Chemistry, Faculty of Technology Novi Sad, University of Novi Sad, 21000 Novi Sad, Serbia
| | - Marko Pavlović
- BioSense Institute, University of Novi Sad, 21000 Novi Sad, Serbia; Department of Physics and John A. Paulson School of Engineering and Applied Sciences, Harvard University, MA-02138 Cambridge, USA.
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8
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Pavlin N, Černigoj U, Bavčar M, Plesničar T, Mavri J, Zidar M, Bone M, Kralj Savič U, Sever T, Štrancar A. Analytical separation of plasmid DNA isoforms using anion exchanging chromatographic monoliths with 6 µm channels. Electrophoresis 2023; 44:1967-1977. [PMID: 37160710 DOI: 10.1002/elps.202300031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 04/10/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023]
Abstract
High-performance liquid chromatography (HPLC)-based analytical assays are used to effectively monitor purity and quantity of plasmid DNA (pDNA) throughout the purification process. However, the phenomenon of physical entrapment of open circular (OC) isoforms pDNA inside narrow channels of chromatographic support decreases its accuracy and precision and the effect increases with pDNA size. The purpose of the study was to develop a chromatographic method for accurate analytical separation between isoforms of <16 kbp pDNA using weak anion exchanging monolithic column with large (6 µm) convective channels. Purified samples of 4.7 and 15.4 kbp large pDNA with known isoform composition were prepared and their isoforms separated in ascending salt gradient. Both OC and supercoiled (SC) isoforms were baseline separated at a flow rate below 0.5 mL min-1 in a guanidinium chloride (GdnCl) gradient with a ≥95% OC pDNA elution recovery. However, these chromatographic conditions increased 2 times the peak width for linear (LIN) pDNA isoform compared to the results using monoliths with 1.4 µm channel size. If other chaotropic agents, such as urea or thiocyanate (SCN), were added to Gdn ions, the elution volume for LIN isoform decreased. Optimization of combined GdnCl/GdnSCN gradient for pDNA elution resulted in a simple and robust chromatographic method, where OC-LIN and LIN-SC pDNA (up to 15 kbp size) were separated with resolution above 1.0 and above 2.0, respectively. The accessibility and general acceptance of anion exchange chromatography for pDNA analytics give the newly developed method a great potential for in-process control monitoring of pDNA production processes.
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Affiliation(s)
- Nejc Pavlin
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | - Urh Černigoj
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | - Mojca Bavčar
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | | | - Jan Mavri
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | - Martin Zidar
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | - Matevž Bone
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | | | - Tadej Sever
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
| | - Aleš Štrancar
- Sartorius BIA Separations d.o.o., Ajdovscina, Slovenia
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9
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Zhao Y, Bharadwaj S, Myers RL, Okur HI, Bui PT, Cao M, Welsh LK, Yang T, Cremer PS, van der Vegt NFA. Solvation Behavior of Elastin-like Polypeptides in Divalent Metal Salt Solutions. J Phys Chem Lett 2023; 14:10113-10118. [PMID: 37921693 DOI: 10.1021/acs.jpclett.3c02476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
The effects of CaCl2 and MgCl2 on the cloud point temperature of two different elastin-like polypeptides (ELPs) were studied using a combination of cloud point measurements, molecular dynamics simulations, and infrared spectroscopy. Changes in the cloud point for the ELPs in aqueous divalent metal cation solutions were primarily governed by two competing interactions: the cation-amide oxygen electrostatic interaction and the hydration of the cation. In particular, Ca2+ cations can more readily shed their hydration shells and directly contact two amide oxygens by the formation of ion bridges. By contrast, Mg2+ cations were more strongly hydrated and preferred to partition toward the amide oxygens along with their hydration shells. In fact, although hydrophilic ELP V5A2G3 was salted-out at low concentrations of MgCl2, it was salted-in at higher salt concentrations. By contrast, CaCl2 salted the ELP sharply out of solution at higher salt concentrations because of the bridging effect.
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Affiliation(s)
- Yani Zhao
- Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Swaminath Bharadwaj
- Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
- Department of Chemical Engineering, Shiv Nadar Institution of Eminence, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Ryan L Myers
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Halil I Okur
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Pho T Bui
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Mengrui Cao
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Lauren K Welsh
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Tinglu Yang
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
| | - Paul S Cremer
- Department of Chemistry, Penn State University, University Park, Pennsylvania 16802, United States
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, Pennsylvania 16802, United States
| | - Nico F A van der Vegt
- Department of Chemistry, Technical University of Darmstadt, 64287 Darmstadt, Germany
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10
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Jesmer AH, Marple AST, Wylie RG. Controlled swelling of biomaterial devices for improved antifouling polymer coatings. Sci Rep 2023; 13:19950. [PMID: 37968497 PMCID: PMC10651925 DOI: 10.1038/s41598-023-47192-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/10/2023] [Indexed: 11/17/2023] Open
Abstract
Nonspecific interactions between cells and implantable elastomers often leads to failure modes for devices such as catheters, cosmetic and reconstructive implants, and sensors. To reduce these interactions, device surfaces can be coated with hydrophilic polymers, where greater polymer density enhances antifouling properties. Although graft-from coating techniques result in higher density polymer films and lower fouling in controlled settings, simpler graft-to methods show similar results on complex implanted devices, despite limited density. To address the need for improved graft-to methods, we developed Graft then shrink (GtS) where elastomeric materials are temporarily swollen during polymer grafting. Herein, we demonstrate a graft-to based method for poly(oligo(ethylene glycol) methyl ether methacrylate) (pOEGMA) on swollen silicone, GtS, that enhances grafted polymer content and fouling resistance. Total grafted polymer content of pOEGMA on toluene swollen silicone increased over ~ 13 × compared to non-swollen controls, dependent on the degree of silicone swelling. Increases in total grafted polymer within the top 200 µm of the material led to bacterial and mammalian cell adhesion reductions of 75% and 91% respectively, compared to Shrink then Graft (StG) antifouling polymer coated controls. GtS allows for the simple 3D coating of swellable elastomers (e.g., silicone medical devices) with improved antifouling pOEGMA coatings.
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Affiliation(s)
- Alexander H Jesmer
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada
| | - April S T Marple
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada
| | - Ryan G Wylie
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, L8S 4M1, Canada.
- School of Biomedical Engineering, McMaster University, Hamilton, ON, L8S 4M1, Canada.
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11
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Guo Y, Liu S, Jing D, Liu N, Luo X. The construction of elastin-like polypeptides and their applications in drug delivery system and tissue repair. J Nanobiotechnology 2023; 21:418. [PMID: 37951928 PMCID: PMC10638729 DOI: 10.1186/s12951-023-02184-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/02/2023] [Indexed: 11/14/2023] Open
Abstract
Elastin-like polypeptides (ELPs) are thermally responsive biopolymers derived from natural elastin. These peptides have a low critical solution temperature phase behavior and can be used to prepare stimuli-responsive biomaterials. Through genetic engineering, biomaterials prepared from ELPs can have unique and customizable properties. By adjusting the amino acid sequence and length of ELPs, nanostructures, such as micelles and nanofibers, can be formed. Correspondingly, ELPs have been used for improving the stability and prolonging drug-release time. Furthermore, ELPs have widespread use in tissue repair due to their biocompatibility and biodegradability. Here, this review summarizes the basic property composition of ELPs and the methods for modulating their phase transition properties, discusses the application of drug delivery system and tissue repair and clarifies the current challenges and future directions of ELPs in applications.
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Affiliation(s)
- Yingshu Guo
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China.
| | - Shiwei Liu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Dan Jing
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Nianzu Liu
- School of Chemistry and Chemical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, China
| | - Xiliang Luo
- Key Laboratory of Optic-Electric Sensing and Analytical Chemistry for Life Science, MOE, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China.
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12
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Hanke M, Dornbusch D, Tomm E, Grundmeier G, Fahmy K, Keller A. Superstructure-dependent stability of DNA origami nanostructures in the presence of chaotropic denaturants. NANOSCALE 2023; 15:16590-16600. [PMID: 37747200 DOI: 10.1039/d3nr02045b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
The structural stability of DNA origami nanostructures in various chemical environments is an important factor in numerous applications, ranging from biomedicine and biophysics to analytical chemistry and materials synthesis. In this work, the stability of six different 2D and 3D DNA origami nanostructures is assessed in the presence of three different chaotropic salts, i.e., guanidinium sulfate (Gdm2SO4), guanidinium chloride (GdmCl), and tetrapropylammonium chloride (TPACl), which are widely employed denaturants. Using atomic force microscopy (AFM) to quantify nanostructural integrity, Gdm2SO4 is found to be the weakest and TPACl the strongest DNA origami denaturant, respectively. Despite different mechanisms of actions of the selected salts, DNA origami stability in each environment is observed to depend on DNA origami superstructure. This is especially pronounced for 3D DNA origami nanostructures, where mechanically more flexible designs show higher stability in both GdmCl and TPACl than more rigid ones. This is particularly remarkable as this general dependence has previously been observed under Mg2+-free conditions and may provide the possibility to optimize DNA origami design toward maximum stability in diverse chemical environments. Finally, it is demonstrated that melting temperature measurements may overestimate the stability of certain DNA origami nanostructures in certain chemical environments, so that such investigations should always be complemented by microscopic assessments of nanostructure integrity.
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Affiliation(s)
- Marcel Hanke
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Daniel Dornbusch
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, Dresden 01328, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
| | - Emilia Tomm
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Guido Grundmeier
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
| | - Karim Fahmy
- Helmholtz-Zentrum Dresden-Rossendorf, Institute of Resource Ecology, Bautzner Landstrasse 400, Dresden 01328, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden 01062, Germany
| | - Adrian Keller
- Paderborn University, Technical and Macromolecular Chemistry, Warburger Str. 100, 33098 Paderborn, Germany.
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13
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Zhu M, Wang X, Xie R, Wang Y, Xu X, Burger J, Gong S. Guanidinium-Rich Lipopeptide-Based Nanoparticle Enables Efficient Gene Editing in Skeletal Muscles. ACS APPLIED MATERIALS & INTERFACES 2023; 15:10464-10476. [PMID: 36800641 DOI: 10.1021/acsami.2c21683] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Genome editing mediated by the CRISPR-Cas system holds great promise for the treatment of genetic diseases. However, safe and efficient in vivo delivery of CRISPR genome editing machinery remains a challenge. Here, we report a lipopeptide-based nanoparticle (LNP) that can efficiently deliver the CRISPR Cas9/sgRNA ribonucleoprotein (RNP) and enable efficient genome editing both in vitro and in vivo. An artificial lipopeptide, GD-LP, was constructed by linking a hydrophilic guanidinium-rich head to an oleic acid-based hydrophobic tail via a disulfide bond. LNP formed by the self-assembly of GD-LP can easily form a complex with RNP with a loading content of up to 20 wt %. The resulting RNP-LNP nanocomplex led to 72.6% gene editing efficiency in GFP-HEK cells with negligible cytotoxicity. The LNP also showed significantly higher transfection efficiencies than Lipofectamine 2000 for the delivery of mRNA in NIH 3T3 and RAW 264.7 and the delivery of plasmid DNA in B78 cells. In vivo studies showed that intramuscular injection of the RNP-LNP nanocomplex in Ai14 mice induced efficient gene editing in muscular tissues. Moreover, the delivery of Cas9 RNP and donor DNA by LNP (i.e., RNP/ssODN-LNP nanocomplex) restored dystrophin expression, reduced skeletal muscle fibrosis, and significantly improved muscle strength in a Duchenne muscular dystrophy (DMD) mouse model.
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Affiliation(s)
- Min Zhu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xiuxiu Wang
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Ruosen Xie
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yuyuan Wang
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Xianghui Xu
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jacobus Burger
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Shaoqin Gong
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715, United States
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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14
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Separation of phosphorothioate oligonucleotide impurities by WAX HPLC under high organic content elution conditions. Anal Biochem 2022; 659:114956. [PMID: 36270331 DOI: 10.1016/j.ab.2022.114956] [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: 06/28/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 12/14/2022]
Abstract
The separation of impurities in phosphorothioate diester (PS) oligonucleotides is complicated by (1) the presence of a very large number of diastereoisomers, e.g., 219 for a 20-mer oligonucleotide, (2) peak broadening due to the hydrophobic character of the sulfur atom, and (3) the chemical similarity of the impurities to the parent oligonucleotide and each other. Further difficulties arise due to the chemical nature of oligonucleotides, which display a complex mixture of ionic, hydrophobic, H-bonding, and other functionalities. To minimize hydrophobic interactions and peak broadening due to the PS modification, we have developed a novel method that combines a weak anion exchange (WAX) column with a mobile phase elution system designed to maximize separation by a single ionic/electrostatic interaction. We found that although chaotropes are helpful, the most significant beneficial effect of the hydrophilic WAX column is that high-organic, low-salt mobile phase is required for product elution. Separations are also benefitted by pH gradient effects on stationary phase electrostatic potential and analyte ionization. An extraordinary degree of separation is achieved by the new WAX method in comparison to SAX (strong anion exchange) chromatography. For the first time, the extent of deamination of PS oligonucleotides is directly determined by a chromatography-only method. The approach, representative results, and the mechanisms of separation are discussed.
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15
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Hanke M, Hansen N, Tomm E, Grundmeier G, Keller A. Time-Dependent DNA Origami Denaturation by Guanidinium Chloride, Guanidinium Sulfate, and Guanidinium Thiocyanate. Int J Mol Sci 2022; 23:ijms23158547. [PMID: 35955680 PMCID: PMC9368935 DOI: 10.3390/ijms23158547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/29/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Guanidinium (Gdm) undergoes interactions with both hydrophilic and hydrophobic groups and, thus, is a highly potent denaturant of biomolecular structure. However, our molecular understanding of the interaction of Gdm with proteins and DNA is still rather limited. Here, we investigated the denaturation of DNA origami nanostructures by three Gdm salts, i.e., guanidinium chloride (GdmCl), guanidinium sulfate (Gdm2SO4), and guanidinium thiocyanate (GdmSCN), at different temperatures and in dependence of incubation time. Using DNA origami nanostructures as sensors that translate small molecular transitions into nanostructural changes, the denaturing effects of the Gdm salts were directly visualized by atomic force microscopy. GdmSCN was the most potent DNA denaturant, which caused complete DNA origami denaturation at 50 °C already at a concentration of 2 M. Under such harsh conditions, denaturation occurred within the first 15 min of Gdm exposure, whereas much slower kinetics were observed for the more weakly denaturing salt Gdm2SO4 at 25 °C. Lastly, we observed a novel non-monotonous temperature dependence of DNA origami denaturation in Gdm2SO4 with the fraction of intact nanostructures having an intermediate minimum at about 40 °C. Our results, thus, provide further insights into the highly complex Gdm–DNA interaction and underscore the importance of the counteranion species.
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16
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Haris L, Biehl R, Dulle M, Radulescu A, Holderer O, Hoffmann I, Stadler AM. Variation of Structural and Dynamical Flexibility of Myelin Basic Protein in Response to Guanidinium Chloride. Int J Mol Sci 2022; 23:ijms23136969. [PMID: 35805997 PMCID: PMC9266411 DOI: 10.3390/ijms23136969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/18/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
Myelin basic protein (MBP) is intrinsically disordered in solution and is considered as a conformationally flexible biomacromolecule. Here, we present a study on perturbation of MBP structure and dynamics by the denaturant guanidinium chloride (GndCl) using small-angle scattering and neutron spin–echo spectroscopy (NSE). A concentration of 0.2 M GndCl causes charge screening in MBP resulting in a compact, but still disordered protein conformation, while GndCl concentrations above 1 M lead to structural expansion and swelling of MBP. NSE data of MBP were analyzed using the Zimm model with internal friction (ZIF) and normal mode (NM) analysis. A significant contribution of internal friction was found in compact states of MBP that approaches a non-vanishing internal friction relaxation time of approximately 40 ns at high GndCl concentrations. NM analysis demonstrates that the relaxation rates of internal modes of MBP remain unaffected by GndCl, while structural expansion due to GndCl results in increased amplitudes of internal motions. Within the model of the Brownian oscillator our observations can be rationalized by a loss of friction within the protein due to structural expansion. Our study highlights the intimate coupling of structural and dynamical plasticity of MBP, and its fundamental difference to the behavior of ideal polymers in solution.
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Affiliation(s)
- Luman Haris
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (L.H.); (R.B.); (M.D.)
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
| | - Ralf Biehl
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (L.H.); (R.B.); (M.D.)
| | - Martin Dulle
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (L.H.); (R.B.); (M.D.)
| | - Aurel Radulescu
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungzentrum Jülich GmbH, 85747 Garching, Germany; (A.R.); (O.H.)
| | - Olaf Holderer
- Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungzentrum Jülich GmbH, 85747 Garching, Germany; (A.R.); (O.H.)
| | - Ingo Hoffmann
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, CEDEX 9, 38042 Grenoble, France;
| | - Andreas M. Stadler
- Jülich Centre for Neutron Science (JCNS-1) and Institute of Biological Information Processing (IBI-8), Forschungszentrum Jülich GmbH, 52425 Jülich, Germany; (L.H.); (R.B.); (M.D.)
- Institute of Physical Chemistry, RWTH Aachen University, Landoltweg 2, 52056 Aachen, Germany
- Correspondence:
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17
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Wei W, Chen X, Wang X. Nanopore Sensing Technique for Studying the Hofmeister Effect. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2200921. [PMID: 35484475 DOI: 10.1002/smll.202200921] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/22/2022] [Indexed: 06/14/2023]
Abstract
The nanopore sensing technique is an emerging method of detecting single molecules, and extensive research has gone into various fields, including nanopore sequencing and other applications of single-molecule studies. Recently, several researchers have explored the specific ion effects in nanopore channels, enabling a unique understanding of the Hofmeister effect at the single-molecule level. Herein, the recent advances of using nanopore sensing techniques are reviewed to study the Hofmeister effect and the physicochemical mechanism of this process is attempted. The challenges and goals are also discussed for the future in this field.
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Affiliation(s)
- Weichen Wei
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xiaojuan Chen
- Department of Nanoengineering, University of California San Diego, La Jolla, CA, 92093, USA
| | - Xuejiao Wang
- Fujian Provincial University Engineering Research Center of Industrial Biocatalysis, College of Chemistry and Materials Science, Fujian Normal University, Fuzhou, 350007, China
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18
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Sun L, Gong J, Xu B, Wang Y, Ding X, Zhang Y, Liu C, Zhao L, Xu B. Ion-Specific Effects on Vesicle-to-Micelle Transitions of an Amino Acid Surfactant Probed by Chemical Trapping. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:6295-6304. [PMID: 35476409 DOI: 10.1021/acs.langmuir.1c03415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Ion-specific effects widely exist in biological and chemical systems and cannot be explained by classical theories. The complexity of ion-specific effects in protein systems at the molecular level necessitates the use of mimetic models involving smaller molecules, such as amino acids, oligopeptides, and other organic molecules bearing amide bonds. Therefore, it is of theoretical value to determine the effect of additional salts on the aggregation transitions of acyl amino acid surfactants. Herein, the effects of specific tetraalkylammonium ions (TAA+) on sodium lauroyl glycinate (SLG) aggregation were studied by dynamic light scattering (DLS) and transmission electron microscopy. Although previous studies have shown that the kosmotropic TAA+ ions tend to induce micellar growth or micelle-to-vesicle transitions of some anionic surfactants, TAA+ addition in the present study induced partial vesicle-to-micelle transitions in SLG solutions. The chemical trapping (CT) method was employed to estimate changes in the interfacial molarities of water, amide bonds, and carboxylate groups during such transitions. The vesicle-to-micelle transitions were accompanied by a marked rise in interfacial water molarity and a decline in interfacial amide bonds molarity, suggesting that the hydrated TAA+ entered the interfacial region and disrupted hydrogen bonding, thus preventing the SLG monomers from packing tightly. Molecular dynamic simulation was also performed to demonstrate the salt-induced cleavage of amide-amide bonds between SLG headgroups. Furthermore, both CT and DLS results show that the ability of tetraalkylammonium cations to induce such transitions increased with increasing size and hydrophobicity of the cation, which follows the Hofmeister series. The current study offers critical molecular-level evidence for understanding the specific effects of tetraalkylammonium ions on the aggregation transitions of an acyl amino acid surfactant.
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Affiliation(s)
- Lijie Sun
- Department of Daily Chemical Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, Beijing 100048, People's Republic of China
| | - Jiani Gong
- Department of Daily Chemical Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, Beijing 100048, People's Republic of China
| | - Bo Xu
- McIntire School of Commerce, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Yuzhao Wang
- Department of Daily Chemical Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, Beijing 100048, People's Republic of China
| | - Xiaoxuan Ding
- Department of Daily Chemical Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, Beijing 100048, People's Republic of China
| | - Yongliang Zhang
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, 610 Taylor Road, Piscataway, New Jersey 08854, United States
| | - Changyao Liu
- Department of Daily Chemical Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, Beijing 100048, People's Republic of China
| | - Li Zhao
- Department of Daily Chemical Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, Beijing 100048, People's Republic of China
| | - Baocai Xu
- Department of Daily Chemical Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, Beijing 100048, People's Republic of China
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19
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Hanke M, Dornbusch D, Hadlich C, Rossberg A, Hansen N, Grundmeier G, Tsushima S, Keller A, Fahmy K. Anion-specific structure and stability of guanidinium-bound DNA origami. Comput Struct Biotechnol J 2022; 20:2611-2623. [PMID: 35685373 PMCID: PMC9163702 DOI: 10.1016/j.csbj.2022.05.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 05/19/2022] [Accepted: 05/19/2022] [Indexed: 12/13/2022] Open
Abstract
While the folding of DNA into rationally designed DNA origami nanostructures has been studied extensively with the aim of increasing structural diversity and introducing functionality, the fundamental physical and chemical properties of these nanostructures remain largely elusive. Here, we investigate the correlation between atomistic, molecular, nanoscopic, and thermodynamic properties of DNA origami triangles. Using guanidinium (Gdm) as a DNA-stabilizing but potentially also denaturing cation, we explore the dependence of DNA origami stability on the identity of the accompanying anions. The statistical analyses of atomic force microscopy (AFM) images and circular dichroism (CD) spectra reveals that sulfate and chloride exert stabilizing and destabilizing effects, respectively, already below the global melting temperature of the DNA origami triangles. We identify structural transitions during thermal denaturation and show that heat capacity changes ΔCp determine the temperature sensitivity of structural damage. The different hydration shells of the anions and their potential to form Gdm+ ion pairs in concentrated salt solutions modulate ΔCp by altered wetting properties of hydrophobic DNA surface regions as shown by molecular dynamics simulations. The underlying structural changes on the molecular scale become amplified by the large number of structurally coupled DNA segments and thereby find nanoscopic correlations in AFM images.
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20
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Tripathy M, Bharadwaj S, van der Vegt NFA. Solvation shell thermodynamics of extended hydrophobic solutes in mixed solvents. J Chem Phys 2022; 156:164901. [DOI: 10.1063/5.0090646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The ability of various cosolutes and cosolvents to enhance or quench solvent density fluctuations at solute–water interfaces has crucial implications on the conformational equilibrium of macromolecules such as polymers and proteins. Herein, we use an extended hydrophobic solute as a model system to study the effect of urea and methanol on the density fluctuations in the solute’s solvation shell and the resulting thermodynamics. On strengthening the solute–water/cosolute repulsive interaction, we observe distinct trends in the mutual affinities between various species in, and the thermodynamic properties of, the solvation shell. These trends strongly follow the respective trends in the preferential adsorption of urea and methanol: solute–water/cosolute repulsion strengthens, urea accumulation decreases, and methanol accumulation increases. Preferential accumulation of urea is found to quench the density fluctuations around the extended solute, leading to a decrease in the compressibility of the solvation shell. In contrast, methanol accumulation enhances the density fluctuations, leading to an increase in the compressibility. The mode of action of urea and methanol seems to be strongly coupled to their hydration behavior. The observations from this simple model is discussed in relation to urea driven swelling and methanol induced collapse of some well-known thermo-responsive polymers.
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Affiliation(s)
- Madhusmita Tripathy
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Swaminath Bharadwaj
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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21
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Bharadwaj S, Niebuur BJ, Nothdurft K, Richtering W, van der Vegt NFA, Papadakis CM. Cononsolvency of thermoresponsive polymers: where we are now and where we are going. SOFT MATTER 2022; 18:2884-2909. [PMID: 35311857 DOI: 10.1039/d2sm00146b] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Cononsolvency is an intriguing phenomenon where a polymer collapses in a mixture of good solvents. This cosolvent-induced modulation of the polymer solubility has been observed in solutions of several polymers and biomacromolecules, and finds application in areas such as hydrogel actuators, drug delivery, compound detection and catalysis. In the past decade, there has been a renewed interest in understanding the molecular mechanisms which drive cononsolvency with a predominant emphasis on its connection to the preferential adsorption of the cosolvent. Significant efforts have also been made to understand cononsolvency in complex systems such as micelles, block copolymers and thin films. In this review, we will discuss some of the recent developments from the experimental, simulation and theoretical fronts, and provide an outlook on the problems and challenges which are yet to be addressed.
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Affiliation(s)
- Swaminath Bharadwaj
- Technical University of Darmstadt, Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Computational Physical Chemistry Group, 64287 Darmstadt, Germany.
| | - Bart-Jan Niebuur
- Technical University of Munich, Physics Department, Soft Matter Physics Group, James-Franck-Str. 1, 85748 Garching, Germany
| | - Katja Nothdurft
- RWTH Aachen University, Institut für Physikalische Chemie, Landoltweg 2, 52056 Aachen, Germany, European Union
| | - Walter Richtering
- RWTH Aachen University, Institut für Physikalische Chemie, Landoltweg 2, 52056 Aachen, Germany, European Union
| | - Nico F A van der Vegt
- Technical University of Darmstadt, Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Computational Physical Chemistry Group, 64287 Darmstadt, Germany.
| | - Christine M Papadakis
- Technical University of Munich, Physics Department, Soft Matter Physics Group, James-Franck-Str. 1, 85748 Garching, Germany
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22
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Barrios A, Estrada M, Moon JH. Carbamoylated Guanidine-Containing Polymers for Non-Covalent Functional Protein Delivery in Serum-Containing Media. Angew Chem Int Ed Engl 2022; 61:e202116722. [PMID: 34995405 DOI: 10.1002/anie.202116722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 11/08/2022]
Abstract
Despite the high potential of controlling cellular processes and treating various diseases by intracellularly delivered proteins, current delivery systems exhibit poor efficiency due to poor serum stability, cellular entry, and cytosolic availability of proteins. Here, we report a novel functional group, phenyl carbamoylated guanidine (Ph-CG), that greatly enhances the delivery efficiency to various types of cells. Owing to the substantially lowered pKa , the hydrophobic Ph-CG offers optimized inter-macromolecular interactions via enhanced hydrogen-bonding and hydrophobic interactions. The coplanarity of Ph-CG also leads to the better intracellular entry of protein complexes. Intracellularly delivered apoptosis-inducing enzymes and antibodies significantly induce cell viability inhibitions in a serum-containing medium. The newly developed Ph-CG can be introduced to various existing carriers, leading to the realization of future therapeutic protein delivery.
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Affiliation(s)
- Alfonso Barrios
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institutes, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - Marilen Estrada
- Department of Natural and Applied Sciences, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
| | - Joong Ho Moon
- Department of Chemistry and Biochemistry, Biomolecular Sciences Institutes, Florida International University, 11200 SW 8th St., Miami, FL 33199, USA
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23
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The Effect of Electrolytes and Urea on the Ethyl Lauroyl Arginate and Cellulose Nanocrystals Foam Stability. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12062797] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Carboxylated cellulose nanocrystals (cCNC) are highly dispersible particles useful in many industries. In particular, they can be applied to form Pickering emulsions and foams for “green” applications in the cosmetics, pharmaceutical industry or food processing. We demonstrated that carboxylated cellulose nanocrystals enhance foamability and foam stability when mixed with cationic surfactant ethyl lauroyl arginate (LAE), having superior properties over sulfated cellulose nanocrystals (sCNC) concerning surfactant concentration range and foam volume. Mixtures of LAE and cCNC were characterized for their hydrodynamic diameter, zeta potential, surface tension and surface rheological properties. The influence of electrolytes, namely, sodium chloride, guanidine hydrochloride and sodium salicylate, and the addition of concentrated urea to LAE-cCNC mixtures on foamability and foam stability were investigated. Electrolytes in the concentration of 5 mM showed a moderate effect on foam stability. In contrast, spectacular foam collapse was detected after adding concentrated urea. The preliminary rheological data from the pendant drop oscillations revealed low elastic modulus upon urea addition and the loss modulus that increased with the frequency, which suggested a viscous interfacial layer.
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24
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Paladino A, Balasco N, Graziano G, Vitagliano L. A Protein Data Bank survey of multimodal binding of thiocyanate to proteins: Evidence for thiocyanate promiscuity. Int J Biol Macromol 2022; 208:29-36. [PMID: 35259436 DOI: 10.1016/j.ijbiomac.2022.03.012] [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: 12/21/2021] [Revised: 02/16/2022] [Accepted: 03/02/2022] [Indexed: 11/28/2022]
Abstract
Over the last one and half century, a myriad of studies has demonstrated that Hofmeister ions have a major impact on protein stability and solubility. Nevertheless, the definition of the physico-chemical basis of their activity has proved to be highly challenging and controversial. Here, by exploiting the enormous information content of the Protein Data Bank, we explored the binding to proteins of thiocyanate, the anion of the series exerting the highest solubilization/destabilization effects. The survey, which led to the identification and characterization of 712 thiocyanate binding sites, provides a comprehensive and atomic-level view of the varied interactions that the ion forms with proteins. The inspection of these sites highlights a limited tendency of thiocyanate to interact with structured water molecules, in line with the reported poor hydration of the ion. On the other hand, the thiocyanate makes interactions with protein nonpolar moieties, especially with the backbone Cα atom. In as many as 104 cases, the ion exclusively makes nonpolar contacts. In conclusion, these findings suggest that the ability of thiocyanate to bind all types of protein exposed patches may lead to the formation of a negatively charged electrostatic barrier that could prevent protein-protein aggregation and promote protein solubility. Moreover, the denaturing action of thiocyanate may be ascribed to its ability to establish multiple attractive interactions with protein surfaces.
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Affiliation(s)
- Antonella Paladino
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, Benevento 82100, Italy.
| | - Nicole Balasco
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, Benevento 82100, Italy.
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
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25
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Zhou J, Zlotnick A, Jacobson SC. Disassembly of Single Virus Capsids Monitored in Real Time with Multicycle Resistive-Pulse Sensing. Anal Chem 2022; 94:985-992. [PMID: 34932317 PMCID: PMC8784147 DOI: 10.1021/acs.analchem.1c03855] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Virus assembly and disassembly are critical steps in the virus lifecycle; however, virus disassembly is much less well understood than assembly. For hepatitis B virus (HBV) capsids, disassembly of the virus capsid in the presence of guanidine hydrochloride (GuHCl) exhibits strong hysteresis that requires additional chemical energy to initiate disassembly and disrupt the capsid structure. To study disassembly of HBV capsids, we mixed T = 4 HBV capsids with 1.0-3.0 M GuHCl, monitored the reaction over time by randomly selecting particles, and measured their size with resistive-pulse sensing. Particles were cycled forward and backward multiple times to increase the observation time and likelihood of observing a disassembly event. The four-pore device used for resistive-pulse sensing produces four current pulses for each particle during translocation that improves tracking and identification of single particles and increases the precision of particle-size measurements when pulses are averaged. We studied disassembly at GuHCl concentrations below and above denaturing conditions of the dimer, the fundamental unit of HBV capsid assembly. As expected, capsids showed little disassembly at low GuHCl concentrations (e.g., 1.0 M GuHCl), whereas at higher GuHCl concentrations (≥1.5 M), capsids exhibited disassembly, sometimes as a complex series of events. In all cases, disassembly was an accelerating process, where capsids catastrophically disassembled within a few 100 ms of reaching critical stability; disassembly rates reached tens of dimers per second just before capsids fell apart. Some disassembly events exhibited metastable intermediates that appeared to lose one or more trimers of dimers in a stepwise fashion.
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Affiliation(s)
- Jinsheng Zhou
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, U.S.A
| | - Adam Zlotnick
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405-7003, U.S.A
| | - Stephen C. Jacobson
- Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, U.S.A,Corresponding author.
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Barrios A, Estrada M, Moon JH. Carbamoylated Guanidine‐Containing Polymers for Non‐Covalent Functional Protein Delivery in Serum‐Containing Media. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202116722] [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]
Affiliation(s)
- Alfonso Barrios
- Florida International University chemistry and biochemistry UNITED STATES
| | - Marilen Estrada
- Florida International University Natural and Applied Sciences UNITED STATES
| | - Joong Ho Moon
- Florida International University Chemistry and Biochemistry 11200 SW 8th St.MMC CP311 33199 Miami UNITED STATES
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27
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Zhao Y, Bharadwaj S, van der Vegt N. Nonadditive ion effects on the coil-globule equilibrium of PNIPAM: A computer simulation study. Phys Chem Chem Phys 2022; 24:10346-10355. [DOI: 10.1039/d2cp00057a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The combined effect of a weakly hydrated and a strongly hydrated anion on the lower critical solution temperature (LCST) of poly(N-isopropylacrylamide)(PNIPAM) is nonadditive (Bruce et al. J. Am. Chem. Soc....
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28
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Gregory KP, Wanless EJ, Webber GB, Craig VSJ, Page AJ. The electrostatic origins of specific ion effects: quantifying the Hofmeister series for anions. Chem Sci 2021; 12:15007-15015. [PMID: 34976339 PMCID: PMC8612401 DOI: 10.1039/d1sc03568a] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/15/2021] [Indexed: 12/23/2022] Open
Abstract
Life as we know it is dependent upon water, or more specifically salty water. Without dissolved ions, the interactions between biological molecules are insufficiently complex to support life. This complexity is intimately tied to the variation in properties induced by the presence of different ions. These specific ion effects, widely known as Hofmeister effects, have been known for more than 100 years. They are ubiquitous throughout the chemical, biological and physical sciences. The origin of these effects and their relative strengths is still hotly debated. Here we reconsider the origins of specific ion effects through the lens of Coulomb interactions and establish a foundation for anion effects in aqueous and non-aqueous environments. We show that, for anions, the Hofmeister series can be explained and quantified by consideration of site-specific electrostatic interactions. This can simply be approximated by the radial charge density of the anion, which we have calculated for commonly reported ions. This broadly quantifies previously unpredictable specific ion effects, including those known to influence solution properties, virus activities and reaction rates. Furthermore, in non-aqueous solvents, the relative magnitude of the anion series is dependent on the Lewis acidity of the solvent, as measured by the Gutmann Acceptor Number. Analogous SIEs for cations bear limited correlation with their radial charge density, highlighting a fundamental asymmetry in the origins of specific ion effects for anions and cations, due to competing non-Coulombic phenomena.
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Affiliation(s)
- Kasimir P Gregory
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle Callaghan New South Wales 2308 Australia
| | - Erica J Wanless
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle Callaghan New South Wales 2308 Australia
| | - Grant B Webber
- School of Engineering, The University of Newcastle Callaghan New South Wales 2308 Australia
| | - Vincent S J Craig
- Department of Applied Mathematics, Research School of Physics, Australian National University Canberra ACT 0200 Australia
| | - Alister J Page
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle Callaghan New South Wales 2308 Australia
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29
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30
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Hao LT, Park S, Choy S, Kim YM, Lee SW, Ok YS, Koo JM, Hwang SY, Hwang DS, Park J, Oh DX. Strong, Multifaceted Guanidinium-Based Adhesion of Bioorganic Nanoparticles to Wet Biological Tissue. JACS AU 2021; 1:1399-1411. [PMID: 34604850 PMCID: PMC8479763 DOI: 10.1021/jacsau.1c00193] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Indexed: 06/13/2023]
Abstract
Gluing dynamic, wet biological tissue is important in injury treatment yet difficult to achieve. Polymeric adhesives are inconvenient to handle due to rapid cross-linking and can raise biocompatibility concerns. Inorganic nanoparticles adhere weakly to wet surfaces. Herein, an aqueous suspension of guanidinium-functionalized chitin nanoparticles as a biomedical adhesive with biocompatible, hemostatic, and antibacterial properties is developed. It glues porcine skin up to 3000-fold more strongly (30 kPa) than inorganic nanoparticles at the same concentration and adheres at neutral pH, which is unachievable with mussel-inspired adhesives alone. The glue exhibits an instant adhesion (2 min) to fully wet surfaces, and the glued assembly endures one-week underwater immersion. The suspension is lowly viscous and stable, hence sprayable and convenient to store. A nanomechanic study reveals that guanidinium moieties are chaotropic, creating strong, multifaceted noncovalent bonds with proteins: salt bridges comprising ionic attraction and bidentate hydrogen bonding with acidic moieties, cation-π interactions with aromatic moieties, and hydrophobic interactions. The adhesion mechanism provides a blueprint for advanced tissue adhesives.
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Affiliation(s)
- Lam Tan Hao
- Research
Center for Bio-based Chemistry, Korea Research
Institute of Chemical Technology (KRICT), Ulsan 44429, Republic
of Korea
- Advanced
Materials and Chemical Engineering, University
of Science and Technology (UST), Daejeon 34113, Republic
of Korea
| | - Sohee Park
- Division
of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Seunghwan Choy
- Biomedical
Institute for Convergence, Sungkyunkwan
University, Suwon 16419, Republic of Korea
| | - Young-Min Kim
- Division
of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Seung-Woo Lee
- Division
of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- Department
of Life Sciences, Pohang University of Science
and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Yong Sik Ok
- Korea
Biochar Research Center, APRU Sustainable Waste Management Program,
Division of Environmental Science and Ecological Engineering, Korea University, Seoul 02841, Republic
of Korea
| | - Jun Mo Koo
- Research
Center for Bio-based Chemistry, Korea Research
Institute of Chemical Technology (KRICT), Ulsan 44429, Republic
of Korea
| | - Sung Yeon Hwang
- Research
Center for Bio-based Chemistry, Korea Research
Institute of Chemical Technology (KRICT), Ulsan 44429, Republic
of Korea
- Advanced
Materials and Chemical Engineering, University
of Science and Technology (UST), Daejeon 34113, Republic
of Korea
| | - Dong Soo Hwang
- Division
of Environmental Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Jeyoung Park
- Research
Center for Bio-based Chemistry, Korea Research
Institute of Chemical Technology (KRICT), Ulsan 44429, Republic
of Korea
- Advanced
Materials and Chemical Engineering, University
of Science and Technology (UST), Daejeon 34113, Republic
of Korea
| | - Dongyeop X. Oh
- Research
Center for Bio-based Chemistry, Korea Research
Institute of Chemical Technology (KRICT), Ulsan 44429, Republic
of Korea
- Advanced
Materials and Chemical Engineering, University
of Science and Technology (UST), Daejeon 34113, Republic
of Korea
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31
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A guanidine-degrading enzyme controls genomic stability of ethylene-producing cyanobacteria. Nat Commun 2021; 12:5150. [PMID: 34446715 PMCID: PMC8390497 DOI: 10.1038/s41467-021-25369-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 08/05/2021] [Indexed: 11/17/2022] Open
Abstract
Recent studies have revealed the prevalence and biological significance of guanidine metabolism in nature. However, the metabolic pathways used by microbes to degrade guanidine or mitigate its toxicity have not been widely studied. Here, via comparative proteomics and subsequent experimental validation, we demonstrate that Sll1077, previously annotated as an agmatinase enzyme in the model cyanobacterium Synechocystis sp. PCC 6803, is more likely a guanidinase as it can break down guanidine rather than agmatine into urea and ammonium. The model cyanobacterium Synechococcus elongatus PCC 7942 strain engineered to express the bacterial ethylene-forming enzyme (EFE) exhibits unstable ethylene production due to toxicity and genomic instability induced by accumulation of the EFE-byproduct guanidine. Co-expression of EFE and Sll1077 significantly enhances genomic stability and enables the resulting strain to achieve sustained high-level ethylene production. These findings expand our knowledge of natural guanidine degradation pathways and demonstrate their biotechnological application to support ethylene bioproduction. The metabolic pathways used by microbes to degrade guanidine or mitigate its toxicity remain unclear. Here, the authors report a guanidine degrading enzyme that controls genomic stability of ethylene producing cyanobacterial strains.
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32
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The Anion Binding Affinity Determines the Strength of Anion Specificities of Thermosensitive Polymers. CHINESE JOURNAL OF POLYMER SCIENCE 2021. [DOI: 10.1007/s10118-021-2633-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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33
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Nguyen KDQ, Vigers M, Sefah E, Seppälä S, Hoover JP, Schonenbach NS, Mertz B, O'Malley MA, Han S. Homo-oligomerization of the human adenosine A 2A receptor is driven by the intrinsically disordered C-terminus. eLife 2021; 10:e66662. [PMID: 34269678 PMCID: PMC8328514 DOI: 10.7554/elife.66662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/15/2021] [Indexed: 11/27/2022] Open
Abstract
G protein-coupled receptors (GPCRs) have long been shown to exist as oligomers with functional properties distinct from those of the monomeric counterparts, but the driving factors of oligomerization remain relatively unexplored. Herein, we focus on the human adenosine A2A receptor (A2AR), a model GPCR that forms oligomers both in vitro and in vivo. Combining experimental and computational approaches, we discover that the intrinsically disordered C-terminus of A2AR drives receptor homo-oligomerization. The formation of A2AR oligomers declines progressively with the shortening of the C-terminus. Multiple interaction types are responsible for A2AR oligomerization, including disulfide linkages, hydrogen bonds, electrostatic interactions, and hydrophobic interactions. These interactions are enhanced by depletion interactions, giving rise to a tunable network of bonds that allow A2AR oligomers to adopt multiple interfaces. This study uncovers the disordered C-terminus as a prominent driving factor for the oligomerization of a GPCR, offering important insight into the effect of C-terminus modification on receptor oligomerization of A2AR and other GPCRs reconstituted in vitro for biophysical studies.
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Affiliation(s)
- Khanh Dinh Quoc Nguyen
- Department of Chemistry and Biochemistry, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Michael Vigers
- Department of Chemical Engineering, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Eric Sefah
- C. Eugene Bennett Department of Chemistry, West Virginia UniversityMorgantownUnited States
| | - Susanna Seppälä
- Department of Chemical Engineering, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Jennifer Paige Hoover
- Department of Chemistry and Biochemistry, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Nicole Star Schonenbach
- Department of Chemical Engineering, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Blake Mertz
- C. Eugene Bennett Department of Chemistry, West Virginia UniversityMorgantownUnited States
| | - Michelle Ann O'Malley
- Department of Chemical Engineering, University of California, Santa BarbaraSanta BarbaraUnited States
| | - Songi Han
- Department of Chemistry and Biochemistry, University of California, Santa BarbaraSanta BarbaraUnited States
- Department of Chemical Engineering, University of California, Santa BarbaraSanta BarbaraUnited States
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34
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Sahu R, Nayar D. Crowding effects on water-mediated hydrophobic interactions. J Chem Phys 2021; 155:024903. [PMID: 34266250 DOI: 10.1063/5.0054410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Understanding the fundamental forces such as hydrophobic interactions in a crowded intracellular environment is necessary to comprehensively decipher the mechanisms of protein folding and biomolecular self-assemblies. The widely accepted entropic depletion view of crowding effects primarily attributes biomolecular compaction to the solvent excluded volume effects exerted by the "inert" crowders, neglecting their soft interactions with the biomolecule. In this study, we examine the effects of chemical nature and soft attractive energy of crowders on the water-mediated hydrophobic interaction between two non-polar neopentane solutes using molecular dynamics simulations. The crowded environment is modeled using dipeptides composed of polar and non-polar amino acids of varying sizes. The results show that amongst the non-polar crowders, Leu2 strengthens the hydrophobic interactions significantly, whereas the polar and small-sized non-polar crowders do not show significant strengthening. Distinct underlying thermodynamic driving forces are illustrated where the small-sized crowders drive hydrophobic interaction via a classic entropic depletion effect and the bulky crowders strengthen it by preferential interaction with the solute. A crossover from energy-stabilized solvent-separated pair to entropy-stabilized contact pair state is observed in the case of bulky non-polar (Leu2) and polar (Lys2) crowders. The influence of solute-crowder energy in affecting the dehydration energy penalty is found to be crucial for determining the neopentane association. The findings demonstrate that along with the entropic (size) effects, the energetic effects also play a crucial role in determining hydrophobic association. The results can be extended and have implications in understanding the impact of protein crowding with varying chemistry in modulating the protein free energy landscapes.
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Affiliation(s)
- Rahul Sahu
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
| | - Divya Nayar
- Centre for Computational and Data Sciences, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302, India
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35
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Bharadwaj S, Nayar D, Dalgicdir C, van der Vegt NFA. An interplay of excluded-volume and polymer-(co)solvent attractive interactions regulates polymer collapse in mixed solvents. J Chem Phys 2021; 154:134903. [PMID: 33832270 DOI: 10.1063/5.0046746] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Cosolvent effects on the coil-globule transitions in aqueous polymer solutions are not well understood, especially in the case of amphiphilic cosolvents that preferentially adsorb on the polymer and lead to both polymer swelling and collapse. Although a predominant focus in the literature has been placed on the role of polymer-cosolvent attractive interactions, our recent work has shown that excluded-volume interactions (repulsive interactions) can drive both preferential adsorption of the cosolvent and polymer collapse via a surfactant-like mechanism. Here, we further study the role of polymer-(co)solvent attractive interactions in two kinds of polymer solutions, namely, good solvent (water)-good cosolvent (alcohol) (GSGC) and poor solvent-good cosolvent (PSGC) solutions, both of which exhibit preferential adsorption of the cosolvent and a non-monotonic change in the polymer radius of gyration with the addition of the cosolvent. Interestingly, at low concentrations, the polymer-(co)solvent energetic interactions oppose polymer collapse in the GSGC solutions and contrarily support polymer collapse in the PSGC solutions, indicating the importance of the underlying polymer chemistry. Even though the alcohol molecules are preferentially adsorbed on the polymer, the trends of the energetic interactions at low cosolvent concentrations are dominated by the polymer-water energetic interactions in both the cases. Therefore, polymer-(co)solvent energetic interactions can either reinforce or compensate the surfactant-like mechanism, and it is this interplay that drives coil-to-globule transitions in polymer solutions. These results have implications for rationalizing the cononsolvency transitions in real systems such as polyacrylamides in aqueous alcohol solutions where the understanding of microscopic driving forces is still debatable.
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Affiliation(s)
- Swaminath Bharadwaj
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Divya Nayar
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Cahit Dalgicdir
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Nico F A van der Vegt
- Eduard-Zintl-Institut für Anorganische und Physikalische Chemie, Technische Universität Darmstadt, 64287 Darmstadt, Germany
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36
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Lian L, Liu L, Ding Y, Hua Z, Liu G. Specific Anion Effects on Charged-Neutral Random Copolymers: Interplay between Different Anion-Polymer Interactions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1697-1706. [PMID: 33499598 DOI: 10.1021/acs.langmuir.0c02907] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The study of ion specificities of charged-neutral random copolymers is of great importance for understanding specific ion effects on natural macromolecules. In the present work, we have investigated the specific anion effects on the thermoresponsive behavior of poly([2-(methacryloyloxy)ethyl trimethylammonium chloride]-co-N-isopropylacrylamide) [P(METAC-co-NIPAM)] random copolymers. Our study demonstrates that the anion specificities of the P(METAC-co-NIPAM) copolymers are dependent on their chemical compositions. The specific anion effects on the copolymers with high mole fractions of poly(N-isopropylacrylamide) (PNIPAM) are similar to those on the PNIPAM homopolymer. As the mole fraction of PNIPAM decreases to a certain value, a V-shaped anion series can be observed in terms of the anion-specific cloud point temperature of the copolymer, as induced by the interplay between different anion-polymer interactions. Our study also suggests that both the direct and the indirect anion-polymer interactions contribute to the anion specificities of the copolymers. This work would improve our understanding of the relationship between the ion specificities and the ion-macromolecule interactions for naturally occurring macromolecules.
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Affiliation(s)
- Leilei Lian
- Hefei National Laboratory for Physical Sciences at the Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Lvdan Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Yanwei Ding
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, P. R. China
| | - Zan Hua
- Biomass Molecular Engineering Center, Department of Materials Science and Engineering, Anhui Agricultural University, Hefei 230036, P. R. China
| | - Guangming Liu
- Hefei National Laboratory for Physical Sciences at the Microscale, Key Laboratory of Surface and Interface Chemistry and Energy Catalysis of Anhui Higher Education Institutes, Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, P. R. China
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37
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Chen J, Yang H, Zhang M, Chen H, Liu J, Yin K, Chen S, Shao A. Electrochemical-induced regioselective C-3 thiocyanation of imidazoheterocycles with hydrogen evolution. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2020.152755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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38
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Lteif S, Abou Shaheen S, Schlenoff JB. The Thiouronium Group for Ultrastrong Pairing Interactions between Polyelectrolytes. J Phys Chem B 2020; 124:10832-10840. [PMID: 33174752 DOI: 10.1021/acs.jpcb.0c07456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Various charged groups may be used as a repeat unit in polyelectrolytes to provide physical interactions between oppositely charged polymers leading to phase separation. The materials formed thus are termed polyelectrolyte complexes or coacervates (PECs). The strength of pairing between positive, Pol+, and negative, Pol-, repeat units depends on the specific identity of the monomer repeat unit. In this work, the pairing strength of the thiouronium group, a cation closely related to guanidinium, is evaluated using a polythiouronium polyelectrolyte. Polymers containing guanidinium, notably polyarginine, a peptide, are known for their unusual behavior, such as the formation of like-charge ion pairs and hydrogen bonding. It is shown here that some of this behavior is carried over to polythiouroniums, which results in exceptionally strong interactions with polyanions such as polysulfonates and polycarboxylates. The resilience of the polythiouronium/Pol- interaction was evaluated using the buildup of polyelectrolyte multilayers at various salt concentrations and by breaking up preformed PECs with high concentrations of added salt. The thiouronium group even interacts strongly enough with polymeric zwitterions to enable complexation with this nominally weakly interacting, net-neutral polymer.
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Affiliation(s)
- Sandrine Lteif
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, United States
| | - Samir Abou Shaheen
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, United States
| | - Joseph B Schlenoff
- Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, United States
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39
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A cosolvent surfactant mechanism affects polymer collapse in miscible good solvents. Commun Chem 2020; 3:165. [PMID: 36703319 PMCID: PMC9814688 DOI: 10.1038/s42004-020-00405-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/14/2020] [Indexed: 01/29/2023] Open
Abstract
The coil-globule transition of aqueous polymers is of profound significance in understanding the structure and function of responsive soft matter. In particular, the remarkable effect of amphiphilic cosolvents (e.g., alcohols) that leads to both swelling and collapse of stimuli-responsive polymers has been hotly debated in the literature, often with contradictory mechanisms proposed. Using molecular dynamics simulations, we herein demonstrate that alcohols reduce the free energy cost of creating a repulsive polymer-solvent interface via a surfactant-like mechanism which surprisingly drives polymer collapse at low alcohol concentrations. This hitherto neglected role of interfacial solvation thermodynamics is common to all coil-globule transitions, and rationalizes the experimentally observed effects of higher alcohols and polymer molecular weight on the coil-to-globule transition of thermoresponsive polymers. Polymer-(co)solvent attractive interactions reinforce or compensate this mechanism and it is this interplay which drives polymer swelling or collapse.
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40
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Bogunia M, Makowski M. Influence of Ionic Strength on Hydrophobic Interactions in Water: Dependence on Solute Size and Shape. J Phys Chem B 2020; 124:10326-10336. [PMID: 33147018 PMCID: PMC7681779 DOI: 10.1021/acs.jpcb.0c06399] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
Hydrophobicity is a phenomenon of
great importance in biology,
chemistry, and biochemistry. It is defined as the interaction between
nonpolar molecules or groups in water and their low solubility. Hydrophobic
interactions affect many processes in water, for example, complexation,
surfactant aggregation, and coagulation. These interactions play a
pivotal role in the formation and stability of proteins or biological
membranes. In the present study, we assessed the effect of ionic strength,
solute size, and shape on hydrophobic interactions between pairs of
nonpolar particles. Pairs of methane, neopentane, adamantane, fullerene,
ethane, propane, butane, hexane, octane, and decane were simulated
by molecular dynamics in AMBER 16.0 force field. As a solvent, TIP3P
and TIP4PEW water models were used. Potential of mean force (PMF)
plots of these dimers were determined at four values of ionic strength,
0, 0.04, 0.08, and 0.40 mol/dm3, to observe its impact
on hydrophobic interactions. The characteristic shape of PMFs with
three extrema (contact minimum, solvent-separated minimum, and desolvation
maximum) was observed for most of the compounds for hydrophobic interactions.
Ionic strength affected hydrophobic interactions. We observed a tendency
to deepen contact minima with an increase in ionic strength value
in the case of spherical and spheroidal molecules. Additionally, two-dimensional
distribution functions describing water density and average number
of hydrogen bonds between water molecules were calculated in both
water models for adamantane and hexane. It was observed that the density
of water did not significantly change with the increase in ionic strength,
but the average number of hydrogen bonds changed. The latter tendency
strongly depends on the water model used for simulations.
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Affiliation(s)
- Małgorzata Bogunia
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Mariusz Makowski
- Faculty of Chemistry, University of Gdańsk, ul. Wita Stwosza 63, 80-308 Gdańsk, Poland
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41
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Taylor PA, Huang H, Kiick KL, Jayaraman A. Placement of Tyrosine Residues as a Design Element for Tuning the Phase Transition of Elastin-peptide-containing Conjugates: Experiments and Simulations. MOLECULAR SYSTEMS DESIGN & ENGINEERING 2020; 5:1239-1254. [PMID: 33796336 PMCID: PMC8009313 DOI: 10.1039/d0me00051e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Elastin-like polypeptides (ELP) have been widely used in the biomaterials community due to their controllable, thermoresponsive properties and biocompatibility. Motivated by our previous work on the effect of tryptophan (W) substitutions on the LCST-like transitions of short ELPs, we studied a series of short ELPs containing tyrosine (Y) and/or phenylalanine (F) guest residues with only 5 or 6 pentapeptide repeat units. A combination of experiments and molecular dynamics (MD) simulations illustrated that the substitution of F with Y guest residues impacted the transition temperature (Tt) of short ELPs when conjugated to collagen-like-peptides (CLP), with a reduction in the transition temperature observed only after substitution of at least two residues. Placement of the Y residues near the N-terminal end of the ELP, away from the tethering point to the CLP, resulted in a lower Tt than that observed for peptides with the Y residues near the tethering point. Atomistic and coarse-grained MD simulations indicated an increase in intra- and inter- peptide hydrogen bonds in systems containing Y guest residues that are suggested to enhance the ability of the peptides to coacervate, with a concomitantly lower Tt. Simulations also revealed that the placement of Y-containing pentads near the N-terminus (i.e., away from CLP tethering point) versus C-terminus of the ELP led to more π-π stacking interactions at low temperatures, in agreement with our experimental observations of a lower Tt. Overall, this study provides mechanistic insights into the driving forces for the LCST-like transitions of ELPs and offers additional means for tuning the Tt of short ELPs for biomedical applications such as on-demand drug delivery and tissue engineering.
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Affiliation(s)
- Phillip A. Taylor
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716 USA
| | - Haofu Huang
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716 USA
| | - Kristi L. Kiick
- Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716 USA
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716 USA
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Huang J, Zhong Y, Zhang L, Cai J. Distinctive Viewpoint on the Rapid Dissolution Mechanism of α-Chitin in Aqueous Potassium Hydroxide–Urea Solution at Low Temperatures. Macromolecules 2020. [DOI: 10.1021/acs.macromol.0c00945] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Junchao Huang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Yi Zhong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Lina Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Hubei Engineering Center of Natural Polymer-Based Medical Materials, Wuhan University, Wuhan 430072, China
| | - Jie Cai
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- Hubei Engineering Center of Natural Polymer-Based Medical Materials, Wuhan University, Wuhan 430072, China
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43
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Hsu DJ, Leshchev D, Kosheleva I, Kohlstedt KL, Chen LX. Integrating solvation shell structure in experimentally driven molecular dynamics using x-ray solution scattering data. J Chem Phys 2020; 152:204115. [PMID: 32486681 DOI: 10.1063/5.0007158] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
In the past few decades, prediction of macromolecular structures beyond the native conformation has been aided by the development of molecular dynamics (MD) protocols aimed at exploration of the energetic landscape of proteins. Yet, the computed structures do not always agree with experimental observables, calling for further development of the MD strategies to bring the computations and experiments closer together. Here, we report a scalable, efficient MD simulation approach that incorporates an x-ray solution scattering signal as a driving force for the conformational search of stable structural configurations outside of the native basin. We further demonstrate the importance of inclusion of the hydration layer effect for a precise description of the processes involving large changes in the solvent exposed area, such as unfolding. Utilization of the graphics processing unit allows for an efficient all-atom calculation of scattering patterns on-the-fly, even for large biomolecules, resulting in a speed-up of the calculation of the associated driving force. The utility of the methodology is demonstrated on two model protein systems, the structural transition of lysine-, arginine-, ornithine-binding protein and the folding of deca-alanine. We discuss how the present approach will aid in the interpretation of dynamical scattering experiments on protein folding and association.
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Affiliation(s)
- Darren J Hsu
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Denis Leshchev
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Irina Kosheleva
- Center for Advanced Radiation Sources, The University of Chicago, Chicago, Illinois 60637, USA
| | - Kevin L Kohlstedt
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
| | - Lin X Chen
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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44
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Matějíček P. Erratic ions: self-assembly and coassembly of ions of nanometer size and of irregular structure. Curr Opin Colloid Interface Sci 2020. [DOI: 10.1016/j.cocis.2019.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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45
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Transition between protein-like and polymer-like dynamic behavior: Internal friction in unfolded apomyoglobin depends on denaturing conditions. Sci Rep 2020; 10:1570. [PMID: 32005832 PMCID: PMC6994677 DOI: 10.1038/s41598-020-57775-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/06/2020] [Indexed: 11/22/2022] Open
Abstract
Equilibrium dynamics of different folding intermediates and denatured states is strongly connected to the exploration of the conformational space on the nanosecond time scale and might have implications in understanding protein folding. For the first time, the same protein system apomyoglobin has been investigated using neutron spin-echo spectroscopy in different states: native-like, partially folded (molten globule) and completely unfolded, following two different unfolding paths: using acid or guanidinium chloride (GdmCl). While the internal dynamics of the native-like state can be understood using normal mode analysis based on high resolution structural information of myoglobin, for the unfolded and even for the molten globule states, models from polymer science are employed. The Zimm model accurately describes the slowly-relaxing, expanded GdmCl-denaturated state, ignoring the individuality of the different aminoacid side chain. The dynamics of the acid unfolded and molten globule state are similar in the framework of the Zimm model with internal friction, where the chains still interact and hinder each other: the first Zimm relaxation time is as large as the internal friction time. Transient formation of secondary structure elements in the acid unfolded and presence of α-helices in the molten globule state lead to internal friction to a similar extent.
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46
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Palanisamy K, Prakash M, Rajapandian V. Combined DFT and MD simulation studies of protein stability on imidazolium–water (ImH+Wn) clusters with aromatic amino acids. NEW J CHEM 2020. [DOI: 10.1039/d0nj03085f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The hydrated clusters of protonated imidazole (ImH+) can induce protein denaturation through various kinds of monovalent interactions such as cation···π (stacking), N–H⋯π (T-shaped) and water-mediated O–H⋯O H-bonds.
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Affiliation(s)
- Kandhan Palanisamy
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar
- Kattankulathur-603203
- India
| | - Muthuramalingam Prakash
- Department of Chemistry, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar
- Kattankulathur-603203
- India
| | - Varatharaj Rajapandian
- Department of Chemistry, Sri Ramakrishna Mission Vidyalaya College of Arts and Science
- Coimbatore-641020
- India
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47
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Ganguly P, Shea JE. Distinct and Nonadditive Effects of Urea and Guanidinium Chloride on Peptide Solvation. J Phys Chem Lett 2019; 10:7406-7413. [PMID: 31721587 DOI: 10.1021/acs.jpclett.9b03004] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Using enhanced-sampling replica exchange fully atomistic molecular dynamics simulations, we show that, individually, urea and guanidinium chloride (GdmCl) denature the Trpcage protein, but remarkably, the helical segment 1NLYIQWL7 of the protein is stabilized in mixed denaturant solutions. GdmCl induces protein denaturation via a combination of direct and indirect effects involving dehydration of the protein and destabilization of stabilizing salt bridges. In contrast, urea denatures the protein through favorable protein-urea preferential interactions, with peptide-specific indirect effects of urea on the water structure around the protein. In the case of the helical segment of Trpcage, urea "oversolvates" the peptide backbone by reorganizing water molecules from the peptide side chains to the peptide backbone. An intricate nonadditive thermodynamic balance between GdmCl-induced dehydration of the peptide and the urea-induced changes in solvation structure triggers partial counteraction to urea denaturation and stabilization of the helix.
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Affiliation(s)
- Pritam Ganguly
- Department of Chemistry and Biochemistry , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
- Department of Physics , University of California at Santa Barbara , Santa Barbara , California 93106 , United States
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48
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Muttathukattil AN, Srinivasan S, Halder A, Reddy G. Role of Guanidinium-Carboxylate Ion Interaction in Enzyme Inhibition with Implications for Drug Design. J Phys Chem B 2019; 123:9302-9311. [DOI: 10.1021/acs.jpcb.9b06130] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Aswathy N. Muttathukattil
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sriraksha Srinivasan
- Department of Chemistry, St. Joseph’s College, Bangalore, Karnataka 560027, India
| | - Antarip Halder
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Govardhan Reddy
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore, Karnataka 560012, India
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49
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The Hofmeister series: Specific ion effects in aqueous polymer solutions. J Colloid Interface Sci 2019; 555:615-635. [PMID: 31408761 DOI: 10.1016/j.jcis.2019.07.067] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 07/23/2019] [Accepted: 07/24/2019] [Indexed: 12/21/2022]
Abstract
Specific ion effects in aqueous polymer solutions have been under active investigation over the past few decades. The current state-of-the-art research is primarily focused on the understanding of the mechanisms through which ions interact with macromolecules and affect their solution stability. Hence, we herein first present the current opinion on the sources of ion-specific effects and review the relevant studies. This includes a summary of the molecular mechanisms through which ions can interact with polymers, quantification of the affinity of ions for the polymer surface, a thermodynamic description of the effects of salts on polymer stability, as well as a discussion on the different forces that contribute to ion-polymer interplay. Finally, we also highlight future research issues that call for further scrutiny. These include fundamental questions on the mechanisms of ion-specific effects and their correlation with polymer properties as well as a discussion on the specific ion effects in more complex systems such as mixed electrolyte solutions.
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50
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Bruce EE, van der Vegt NFA. Molecular Scale Solvation in Complex Solutions. J Am Chem Soc 2019; 141:12948-12956. [DOI: 10.1021/jacs.9b03469] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Ellen E. Bruce
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
| | - Nico F. A. van der Vegt
- Eduard-Zintl-Institut für Anorganische und
Physikalische Chemie, Technische Universität Darmstadt, D-64287 Darmstadt, Germany
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