1
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Khaykelson D, Asor R, Zhao Z, Schlicksup CJ, Zlotnick A, Raviv U. Guanidine Hydrochloride-Induced Hepatitis B Virus Capsid Disassembly Hysteresis. Biochemistry 2024; 63:1543-1552. [PMID: 38787909 PMCID: PMC11191408 DOI: 10.1021/acs.biochem.4c00077] [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: 02/14/2024] [Revised: 04/20/2024] [Accepted: 04/25/2024] [Indexed: 05/26/2024]
Abstract
Hepatitis B virus (HBV) displays remarkable self-assembly capabilities that interest the scientific community and biotechnological industries as HBV is leading to an annual mortality of up to 1 million people worldwide (especially in Africa and Southeast Asia). When the ionic strength is increased, hepatitis B virus-like particles (VLPs) can assemble from dimers of the first 149 residues of the HBV capsid protein core assembly domain (Cp149). Using solution small-angle X-ray scattering, we investigated the disassembly of the VLPs by titrating guanidine hydrochloride (GuHCl). Measurements were performed with and without 1 M NaCl, added either before or after titrating GuHCl. Fitting the scattering curves to a linear combination of atomic models of Cp149 dimer (the subunit) and T = 3 and T = 4 icosahedral capsids revealed the mass fraction of the dimer in each structure in all the titration points. Based on the mass fractions, the variation in the dimer-dimer association standard free energy was calculated as a function of added GuHCl, showing a linear relation between the interaction strength and GuHCl concentration. Using the data, we estimated the energy barriers for assembly and disassembly and the critical nucleus size for all of the assembly reactions. Extrapolating the standard free energy to [GuHCl] = 0 showed an evident hysteresis in the assembly process, manifested by differences in the dimer-dimer association standard free energy obtained for the disassembly reactions compared with the equivalent assembly reactions. Similar hysteresis was observed in the energy barriers for assembly and disassembly and the critical nucleus size. The results suggest that above 1.5 M, GuHCl disassembled the capsids by attaching to the protein and adding steric repulsion, thereby weakening the hydrophobic attraction.
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Affiliation(s)
- Daniel Khaykelson
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Roi Asor
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
| | - Zhongchao Zhao
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Christopher John Schlicksup
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Adam Zlotnick
- Department
of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Uri Raviv
- Institute
of Chemistry and the Center for Nanoscience and Nanotechnology, the Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 9190401, Israel
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2
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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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3
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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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4
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Polverino G, Russo F, D’Andrea F. Bioactive Dressing: A New Algorithm in Wound Healing. J Clin Med 2024; 13:2488. [PMID: 38731023 PMCID: PMC11084389 DOI: 10.3390/jcm13092488] [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: 03/05/2024] [Revised: 04/03/2024] [Accepted: 04/20/2024] [Indexed: 05/13/2024] Open
Abstract
Wound management presents a significant global challenge, necessitating a comprehensive understanding of wound care products and clinical expertise in selecting dressings. Bioactive dressings (BD) represent a diverse category of dressings, capable of influencing wound healing through various mechanisms. These dressings, including honey, hyaluronic acid, collagen, alginates, and polymers enriched with polyhexamethylene biguanide, chitin, and chitosan derivatives, create a conducive environment for healing, promoting moisture balance, pH regulation, oxygen permeability, and fluid management. Interactive dressings further enhance targeted action by serving as substrates for bioactive agents. The continuous evolution of BDs, with new products introduced annually, underscores the need for updated knowledge in wound care. To facilitate dressing selection, a practical algorithm considers wound exudate, infection probability, and bleeding, guiding clinicians through the process. This algorithm aims to optimize wound care by ensuring the appropriate selection of BDs tailored to individual patient needs, ultimately improving outcomes in wound management.
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Affiliation(s)
- Gianmarco Polverino
- Correspondence: (G.P.); (F.R.); Tel.: +39-32-7449-3917 (G.P.); +39-33-3834-1531 (F.R.)
| | - Francesca Russo
- Correspondence: (G.P.); (F.R.); Tel.: +39-32-7449-3917 (G.P.); +39-33-3834-1531 (F.R.)
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5
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Azam S, Zhu J, Jiang J, Wang J, Zhao H. Photolysis of dinotefuran in aqueous solution: Kinetics, influencing factors and photodegradation mechanism. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 344:123352. [PMID: 38219898 DOI: 10.1016/j.envpol.2024.123352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024]
Abstract
The environmental behaviour of neonicotinoid insecticides (NNIs) is of momentous concern due to their frequent detection in aquatic environment and their biotoxicity for non-target organisms. Phototransformation is one of the most significant transformation processes, which is directly related to NNIs exposure and environmental risks. In this study, the photodegradation of dinotefuran (DIN, 1-Methyl-2-nitro-3-(tetrahydro-3-furanylmethyl)-guanidine), one of the most promising NNIs, was conducted under irritated light in the presence of Cl-, DOM along with the effect of pH and initial concentration. The findings demonstrated that in ultra-pure (UP) water, the photolysis rate constants (k) of DIN rose with increasing initial concentration. Whereas, in tap water, at varied pH levels, and in the presence of Cl-, the outcomes were reversed. At the same time, lower concentration of DOM promoted DIN photolysis processes due to the production of reactive oxygen species, while higher concentrations of DOM inhibited the photolysis by the predominance of light shielding effects. The singlet oxygen (1O2) was produced in the photolysis processes of DIN with Cl- and DOM, which was confirmed by electron spin resonance (EPR) analysis. Four main photolysis products and three intermediates were identified by UPLC-Q-Exactive Orbitrap MS analysis. The possible photodegradation pathways of DIN were proposed including the oxidation by 1O2, reduction and hydrolysis after the removal of nitro group from parent compounds. This study expanding our understanding of transformation behavior and fate of NNIs in the aquatic environment, which is essential for estimating their environmental risks.
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Affiliation(s)
- Shafiul Azam
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian, 116023, China
| | - Jie Zhu
- Institute of Environment and Sustainable Development in Agriculture, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingqiu Jiang
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 100012, Beijing, China.
| | - Jingyao Wang
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian, 116023, China
| | - Hongxia Zhao
- Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), School of Environmental Science and Technology, Dalian University of Technology, Linggong Road 2, Dalian, 116023, China
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6
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Vaz LM, Branco R, Morais PV, Guiomar AJ. Sterilized Polyhexanide-Releasing Chitosan Membranes with Potential for Use in Antimicrobial Wound Dressings. MEMBRANES 2023; 13:877. [PMID: 37999363 PMCID: PMC10673555 DOI: 10.3390/membranes13110877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/26/2023] [Accepted: 11/03/2023] [Indexed: 11/25/2023]
Abstract
Wound infection is a common complication of chronic wounds. It can impair healing, which may not occur without external help. Antimicrobial dressings (AMDs) are a type of external help to infected chronic wounds. In this study, highly porous membranes made of only chitosan and containing the antiseptic polyhexanide (poly(hexamethylene biguanide); PHMB) were prepared by cryogelation, aiming to be used in AMDs. These membranes exhibited a water swelling capacity of 748%, a water drop penetration time of 11 s in a dry membrane and a water vapor transmission rate of 34,400 g H2O/m2/24 h when in contact with water. The best drug loading method involved simultaneous loading by soaking in a PHMB solution and sterilization by autoclaving, resulting in sterilized, drug-loaded membranes. When these membranes and a commercial PHMB-releasing AMD were assayed under the same conditions, albeit far from the in vivo conditions, their drug release kinetics were comparable, releasing PHMB for ca. 6 and 4 h, respectively. These membranes exhibited high antibacterial activity against Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa, which are bacterial species commonly found in infected wounds and blood clotting activity. The obtained results suggest that these membranes may have potential for use in the development of AMDs.
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Affiliation(s)
- Luís M. Vaz
- Chemical Process Engineering and Forest Products Research Centre, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal;
| | - Rita Branco
- Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (R.B.); (P.V.M.)
| | - Paula V. Morais
- Centre for Mechanical Engineering, Materials and Processes, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal; (R.B.); (P.V.M.)
| | - António Jorge Guiomar
- Chemical Process Engineering and Forest Products Research Centre, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal;
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7
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Eskandari S, Rezayof A, Asghari SM, Hashemizadeh S. Neurobiochemical characteristics of arginine-rich peptides explain their potential therapeutic efficacy in neurodegenerative diseases. Neuropeptides 2023; 101:102356. [PMID: 37390744 DOI: 10.1016/j.npep.2023.102356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/02/2023]
Abstract
Neurodegenerative diseases, including Alzheimer̕ s disease (AD), Parkinson̕ s disease (PD), Huntington̕ s disease (HD), and Amyotrophic Lateral Sclerosis (ALS) require special attention to find new potential treatment methods. This review aims to summarize the current knowledge of the relationship between the biochemical properties of arginine-rich peptides (ARPs) and their neuroprotective effects to deal with the harmful effects of risk factors. It seems that ARPs have portrayed a promising and fantastic landscape for treating neurodegeneration-associated disorders. With multimodal mechanisms of action, ARPs play various unprecedented roles, including as the novel delivery platforms for entering the central nervous system (CNS), the potent antagonists for calcium influx, the invader molecules for targeting mitochondria, and the protein stabilizers. Interestingly, these peptides inhibit the proteolytic enzymes and block protein aggregation to induce pro-survival signaling pathways. ARPs also serve as the scavengers of toxic molecules and the reducers of oxidative stress agents. They also have anti-inflammatory, antimicrobial, and anti-cancer properties. Moreover, by providing an efficient nucleic acid delivery system, ARPs can play an essential role in developing various fields, including gene vaccines, gene therapy, gene editing, and imaging. ARP agents and ARP/cargo therapeutics can be raised as an emergent class of neurotherapeutics for neurodegeneration. Part of the aim of this review is to present recent advances in treating neurodegenerative diseases using ARPs as an emerging and powerful therapeutic tool. The applications and progress of ARPs-based nucleic acid delivery systems have also been discussed to highlight their usefulness as a broad-acting class of drugs.
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Affiliation(s)
- Sedigheh Eskandari
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran; Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran
| | - Ameneh Rezayof
- Department of Animal Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
| | - S Mohsen Asghari
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
| | - Shiva Hashemizadeh
- School of Cognitive Sciences, Institute for Research in Fundamental Sciences, IPM, Tehran, Iran
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8
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Burgos MI, Dassie SA, Fidelio GD. The effect of denaturants on protein thermal stability analyzed through a theoretical model considering multiple binding sites. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140920. [PMID: 37207817 DOI: 10.1016/j.bbapap.2023.140920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/02/2023] [Accepted: 05/05/2023] [Indexed: 05/21/2023]
Abstract
A novel mathematical development applied to protein ligand binding thermodynamics is proposed, which allows the simulation, and therefore the analysis of the effects of multiple and independent binding sites to the Native and/or Unfolded protein conformations, with different binding constant values. Protein stability is affected when it binds to a small number of high affinity ligands or to a high number of low affinity ligands. Differential scanning calorimetry (DSC) measures released or absorbed energy of thermally induced structural transitions of biomolecules. This paper presents the general theoretical development for the analysis of thermograms of proteins obtained for n-ligands bound to the native protein and m-ligands bound to their unfolded form. In particular, the effect of ligands with low affinity and with a high number of binding sites (n and/or m > 50) is analyzed. If the interaction with the native form of the protein is the one that predominates, they are considered stabilizers and if the binding with the unfolded species predominates, it is expected a destabilizing effect. The formalism presented here can be adapted to fitting routines in order to simultaneously obtain the unfolding energy and ligand binding energy of the protein. The effect of guanidinium chloride on bovine serum albumin thermal stability, was successfully analyzed with the model considering low number of middle affinity binding sites to the native state and a high number of weak binding sites to the unfolded state.
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Affiliation(s)
- M Ines Burgos
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Ciudad Universitaria, X5000HUA Córdoba, Argentina.
| | - Sergio A Dassie
- Departamento de Fisicoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), CONICET, Ciudad Universitaria, X5000HUA Córdoba, Argentina
| | - Gerardo D Fidelio
- Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, X5000HUA Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Ciudad Universitaria, X5000HUA Córdoba, Argentina
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9
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Paladino A, Vitagliano L, Graziano G. The Action of Chemical Denaturants: From Globular to Intrinsically Disordered Proteins. BIOLOGY 2023; 12:biology12050754. [PMID: 37237566 DOI: 10.3390/biology12050754] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Proteins perform their many functions by adopting either a minimal number of strictly similar conformations, the native state, or a vast ensemble of highly flexible conformations. In both cases, their structural features are highly influenced by the chemical environment. Even though a plethora of experimental studies have demonstrated the impact of chemical denaturants on protein structure, the molecular mechanism underlying their action is still debated. In the present review, after a brief recapitulation of the main experimental data on protein denaturants, we survey both classical and more recent interpretations of the molecular basis of their action. In particular, we highlight the differences and similarities of the impact that denaturants have on different structural classes of proteins, i.e., globular, intrinsically disordered (IDP), and amyloid-like assemblies. Particular attention has been given to the IDPs, as recent studies are unraveling their fundamental importance in many physiological processes. The role that computation techniques are expected to play in the near future is illustrated.
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Affiliation(s)
- Antonella Paladino
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Luigi Vitagliano
- Institute of Biostructures and Bioimaging, CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giuseppe Graziano
- Department of Science and Technology, University of Sannio, via Francesco de Sanctis snc, 82100 Benevento, Italy
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10
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Khan A, Nayeem SM. Stability of the Aβ42 Peptide in Mixed Solutions of Denaturants and Proline. J Phys Chem B 2023; 127:1572-1585. [PMID: 36786778 DOI: 10.1021/acs.jpcb.2c08505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Amyloid β-peptide (Aβ) is responsible for the neuronal damage and death of a patient with Alzheimer's disease (AD). Aβ42 oligomeric forms are dominant neurotoxins and are related to neurodegeneration. Their different forms are related to various pathological conditions in the brain. We investigated Aβ42 peptides in different environments of proline, urea, and GdmCl solutions (in pure and mixed binary forms) through atomistic molecular dynamics simulations. Preferential exclusion from the protein surface and facile formation of a large number of weak molecular interactions are the driving forces for the osmolyte's action. We have focused on these interactions between peptide monomers and pure/mixed osmolytes and denaturants. Urea, as usual, denatures the peptide strongly compared to the GdmCl by accumulation around the peptide. GdmCl shows lesser build-up around protein in contrast to urea but is involved in destabilizing the salt bridge formation of Asp23 and Lys28. Proline as an osmolyte protects the peptide from aggregation when mixed with urea and GdmCl solutions. In mixed solutions of two denaturants and osmolyte plus denaturant, the peptide shows enhanced stability as compared to pure denaturant urea solution. The enhanced stability of peptides in proline may be attributed to its exclusion from the peptide surface and favoring salt bridge formation.
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Affiliation(s)
- Ashma Khan
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India
| | - Shahid M Nayeem
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, UP, India
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11
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El Harrar T, Gohlke H. Cumulative Millisecond-Long Sampling for a Comprehensive Energetic Evaluation of Aqueous Ionic Liquid Effects on Amino Acid Interactions. J Chem Inf Model 2023; 63:281-298. [PMID: 36520535 DOI: 10.1021/acs.jcim.2c01123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The interactions of amino acid side-chains confer diverse energetic contributions and physical properties to a protein's stability and function. Various computational tools estimate the effect of changing a given amino acid on the protein's stability based on parametrized (free) energy functions. When parametrized for the prediction of protein stability in water, such energy functions can lead to suboptimal results for other solvents, such as ionic liquids (IL), aqueous ionic liquids (aIL), or salt solutions. However, to our knowledge, no comprehensive data are available describing the energetic effects of aIL on intramolecular protein interactions. Here, we present the most comprehensive set of potential of mean force (PMF) profiles of pairwise protein-residue interactions to date, covering 50 relevant interactions in water, the two biotechnologically relevant aIL [BMIM/Cl] and [BMIM/TfO], and [Na/Cl]. These results are based on a cumulated simulation time of >1 ms. aIL and salt ions can weaken, but also strengthen, specific residue interactions by more than 3 kcal mol-1, depending on the residue pair, residue-residue configuration, participating ions, and concentration, necessitating considering such interactions specifically. These changes originate from a complex interplay of competitive or cooperative noncovalent ion-residue interactions, changes in solvent structural dynamics, or unspecific charge screening effects and occur at the contact distance but also at larger, solvent-separated distances. This data provide explanations at the atomistic and energetic levels for complex IL effects on protein stability and should help improve the prediction accuracies of computational tools that estimate protein stability based on (free) energy functions.
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Affiliation(s)
- Till El Harrar
- Institute of Biotechnology, RWTH Aachen University, 52074 Aachen, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany
| | - Holger Gohlke
- John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry), and Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich GmbH, 52428 Jülich, Germany.,Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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12
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Guiomar AJ, Urbano AM. Polyhexanide-Releasing Membranes for Antimicrobial Wound Dressings: A Critical Review. MEMBRANES 2022; 12:1281. [PMID: 36557188 PMCID: PMC9781366 DOI: 10.3390/membranes12121281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
The prevalence of chronic, non-healing skin wounds in the general population, most notably diabetic foot ulcers, venous leg ulcers and pressure ulcers, is approximately 2% and is expected to increase, driven mostly by the aging population and the steady rise in obesity and diabetes. Non-healing wounds often become infected, increasing the risk of life-threatening complications, which poses a significant socioeconomic burden. Aiming at the improved management of infected wounds, a variety of wound dressings that incorporate antimicrobials (AMDs), namely polyhexanide (poly(hexamethylene biguanide); PHMB), have been introduced in the wound-care market. However, many wound-care professionals agree that none of these wound dressings show comprehensive or optimal antimicrobial activity. This manuscript summarizes and discusses studies on PHMB-releasing membranes (PRMs) for wound dressings, detailing their preparation, physical properties that are relevant to the context of AMDs, drug loading and release, antibacterial activity, biocompatibility, wound-healing capacity, and clinical trials conducted. Some of these PRMs were able to improve wound healing in in vivo models, with no associated cytotoxicity, but significant differences in study design make it difficult to compare overall efficacies. It is hoped that this review, which includes, whenever available, international standards for testing AMDs, will provide a framework for future studies.
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Affiliation(s)
- António Jorge Guiomar
- Chemical Process Engineering and Forest Products Research Centre, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Ana M. Urbano
- Molecular Physical-Chemistry R&D Unit, Center of Investigation in Environment, Genetics and Oncobiology-CIMAGO, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
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13
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Ausserwöger H, Schneider MM, Herling TW, Arosio P, Invernizzi G, Knowles TPJ, Lorenzen N. Non-specificity as the sticky problem in therapeutic antibody development. Nat Rev Chem 2022; 6:844-861. [PMID: 37117703 DOI: 10.1038/s41570-022-00438-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2022] [Indexed: 11/16/2022]
Abstract
Antibodies are highly potent therapeutic scaffolds with more than a hundred different products approved on the market. Successful development of antibody-based drugs requires a trade-off between high target specificity and target binding affinity. In order to better understand this problem, we here review non-specific interactions and explore their fundamental physicochemical origins. We discuss the role of surface patches - clusters of surface-exposed amino acid residues with similar physicochemical properties - as inducers of non-specific interactions. These patches collectively drive interactions including dipole-dipole, π-stacking and hydrophobic interactions to complementary moieties. We elucidate links between these supramolecular assembly processes and macroscopic development issues, such as decreased physical stability and poor in vivo half-life. Finally, we highlight challenges and opportunities for optimizing protein binding specificity and minimizing non-specificity for future generations of therapeutics.
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14
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Kim S, Lee WB, de Souza NR, Choi SH. QENS study on local segmental dynamics of polyelectrolytes in complex coacervates. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.125525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Panda DP, Swain D, Chaudhary M, Mishra S, Bhutani G, De AK, Waghmare UV, Sundaresan A. Electron-Phonon Coupling Mediated Self-Trapped-Exciton Emission and Internal Quantum Confinement in Highly Luminescent Zero-Dimensional (Guanidinium) 6Mn 3X 12 (X = Cl and Br). Inorg Chem 2022; 61:17026-17036. [PMID: 36242586 DOI: 10.1021/acs.inorgchem.2c01581] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report a large Stokes shift and broad emission band in a Mn-based organic-inorganic hybrid halide, (guanidinium)6Mn3Br12 [GuMBr], consisting of trimeric units of distorted MnBr6 octahedra representing a zero-dimensional compound with a liquid like crystalline lattice. Analysis of the photoluminescence (PL) line width and Raman spectra reveals the effects of electron-phonon coupling, suggestive of the formation of Frenkel-like bound excitons. These bound excitons, regarded as the self-trapped excitons (STEs), account for the large Stokes shift and broad emission band. The excited-state dynamics was studied using femtosecond transient absorption spectroscopy, which confirms the STE emission. Further, this compound is highly emissive with a PL quantum yield of ∼50%. With chloride ion incorporation, we observe enhancement of the emissive properties and attribute it to the effects of intrinsic quantum confinement. Localized electronic states in flat bands lining the gap and their strong coupling with phonons are confirmed with first-principles calculations.
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Affiliation(s)
- Debendra Prasad Panda
- School of Advanced Materials and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore560064, India
| | - Diptikanta Swain
- Institute of Chemical Technology, IndianOil Odisha Campus, Bhubaneswar751013, India
| | - Mohit Chaudhary
- Theoretical Sciences Unit, School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore560064, India
| | - Samita Mishra
- Condensed Phase Dynamics Group, Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab140306, India
| | - Garima Bhutani
- Condensed Phase Dynamics Group, Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab140306, India
| | - Arijit K De
- Condensed Phase Dynamics Group, Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Mohali, Punjab140306, India
| | - Umesh V Waghmare
- Theoretical Sciences Unit, School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore560064, India
| | - A Sundaresan
- School of Advanced Materials and Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore560064, India
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16
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Dey A, Yadav M, Kumar D, Dey AK, Samal S, Tanwar S, Sarkar D, Pramanik SK, Chaudhuri S, Das A. A combination therapy strategy for treating antibiotic resistant biofilm infection using a guanidinium derivative and nanoparticulate Ag(0) derived hybrid gel conjugate. Chem Sci 2022; 13:10103-10118. [PMID: 36128224 PMCID: PMC9430544 DOI: 10.1039/d2sc02980d] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022] Open
Abstract
Bacteria organized in biofilms show significant tolerance to conventional antibiotics compared to their planktonic counterparts and form the basis for chronic infections. Biofilms are composites of different types of extracellular polymeric substances that help in resisting several host-defense measures, including phagocytosis. These are increasingly being recognized as a passive virulence factor that enables many infectious diseases to proliferate and an essential contributing facet to anti-microbial resistance. Thus, inhibition and dispersion of biofilms are linked to addressing the issues associated with therapeutic challenges imposed by biofilms. This report is to address this complex issue using a self-assembled guanidinium-Ag(0) nanoparticle (AD-L@Ag(0)) hybrid gel composite for executing a combination therapy strategy for six difficult to treat biofilm-forming and multidrug-resistant bacteria. Improved efficacy was achieved primarily through effective biofilm inhibition and dispersion by the cationic guanidinium ion derivative, while Ag(0) contributes to the subsequent bactericidal activity on planktonic bacteria. Minimum Inhibitory Concentration (MIC) of the AD-L@Ag(0) formulation was tested against Acinetobacter baumannii (25 μg mL-1), Pseudomonas aeruginosa (0.78 μg mL-1), Staphylococcus aureus (0.19 μg mL-1), Klebsiella pneumoniae (0.78 μg mL-1), Escherichia coli (clinical isolate (6.25 μg mL-1)), Klebsiella pneumoniae (clinical isolate (50 μg mL-1)), Shigella flexneri (clinical isolate (0.39 μg mL-1)) and Streptococcus pneumoniae (6.25 μg mL-1). Minimum bactericidal concentration, and MBIC50 and MBIC90 (Minimum Biofilm Inhibitory Concentration at 50% and 90% reduction, respectively) were evaluated for these pathogens. All these results confirmed the efficacy of the formulation AD-L@Ag(0). Minimum Biofilm Eradication Concentration (MBEC) for the respective pathogens was examined by following the exopolysaccharide quantification method to establish its potency in inhibition of biofilm formation, as well as eradication of mature biofilms. These effects were attributed to the bactericidal effect of AD-L@Ag(0) on biofilm mass-associated bacteria. The observed efficacy of this non-cytotoxic therapeutic combination (AD-L@Ag(0)) was found to be better than that reported in the existing literature for treating extremely drug-resistant bacterial strains, as well as for reducing the bacterial infection load at a surgical site in a small animal BALB/c model. Thus, AD-L@Ag(0) could be a promising candidate for anti-microbial coatings on surgical instruments, wound dressing, tissue engineering, and medical implants.
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Affiliation(s)
- Ananta Dey
- CSIR - Central Salt and Marine Chemical Research Institute Bhavnagar Gujarat India
- Indian Institute of Science Education and Research Kolkata Mohanpur 741246 West Bengal India
| | - Manisha Yadav
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Deepak Kumar
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Anik Kumar Dey
- CSIR - Central Salt and Marine Chemical Research Institute Bhavnagar Gujarat India
| | - Sweety Samal
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Subhash Tanwar
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Debrupa Sarkar
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Sumit Kumar Pramanik
- CSIR - Central Salt and Marine Chemical Research Institute Bhavnagar Gujarat India
| | - Susmita Chaudhuri
- Translational Health Science and Technology Institute (THSTI) Faridabad 121001 Haryana India
| | - Amitava Das
- Indian Institute of Science Education and Research Kolkata Mohanpur 741246 West Bengal India
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17
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Kim S, Kim JM, Wood K, Choi SH. Ionic group-dependent structure of complex coacervate hydrogels formed by ABA triblock copolymers. SOFT MATTER 2022; 18:4146-4155. [PMID: 35583260 DOI: 10.1039/d2sm00255h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study investigates the nanostructure of complex coacervate core hydrogels (C3Gs) with varying compositions of cationic charged groups (i.e., ammonium and guanidinium) using small-angle X-ray/neutron scattering (SAX/NS). C3Gs were prepared by stoichiometric mixing of two oppositely charged ABA triblock copolymers in aqueous solvents, in which A end-blocks were functionalized with either sulfonate groups or a mixture of ammonium and guanidinium groups. Comprehensive small-angle X-ray/neutron scattering (SAX/NS) analysis elucidated the dependence of C3Gs structures on the fraction of guanidinium groups in the cationic end-block (x) and salt concentration (cs). As x increases, the polymer volume fraction in the cores, and interfacial tension (γcore) and salt resistance (c*) of the coacervate cores increase, which is attributed to the greater hydrophobicity and non-electrostatic association. Furthermore, we observed that the salt dependence of the interfacial tension follows γcore ∼ (1 - cs/c*)3/2 in all series of x. The results show that the variation of the ionic group provides a powerful method to control the salt-responsiveness of C3Gs as stimuli-responsive materials.
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Affiliation(s)
- Seyoung Kim
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea.
| | - Jung-Min Kim
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea.
| | - Kathleen Wood
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia
| | - Soo-Hyung Choi
- Department of Chemical Engineering, Hongik University, Seoul 04066, Republic of Korea.
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18
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Cobalt and nickel coordinated guanidinium-based two-dimensional covalent organic framework nanosheets for efficient photocatalytic CO2 reduction. Catal Today 2022. [DOI: 10.1016/j.cattod.2022.03.039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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19
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Das N, Yadav S, Negi KS, Tariff E, Sen P. Microsecond Active-Site Dynamics Primarily control Proteolytic Activity of Bromelain: A Single Molecular Level Study with a Denaturant, a Stabilizer and a Macromolecular Crowder. BBA ADVANCES 2022; 2:100041. [PMID: 37082607 PMCID: PMC10074955 DOI: 10.1016/j.bbadva.2022.100041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/13/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022] Open
Abstract
Proteins are dynamic entity with various molecular motions at different timescale and length scale. Molecular motions are crucial for the optimal function of an enzyme. It seems intuitive that these motions are crucial for optimal enzyme activity. However, it is not easy to directly correlate an enzyme's dynamics and activity due to biosystems' enormous complexity. amongst many factors, structure and dynamics are two prime aspects that combinedly control the activity. Therefore, having a direct correlation between protein dynamics and activity is not straightforward. Herein, we observed and correlated the structural, functional, and dynamical responses of an industrially crucial proteolytic enzyme, bromelain with three versatile classes of chemicals: GnHCl (protein denaturant), sucrose (protein stabilizer), and Ficoll-70 (macromolecular crowder). The only free cysteine (Cys-25 at the active-site) of bromelain has been tagged with a cysteine-specific dye to unveil the structural and dynamical changes through various spectroscopic studies both at bulk and at the single molecular level. Proteolytic activity is carried out using casein as the substrate. GnHCl and sucrose shows remarkable structure-dynamics-activity relationships. Interestingly, with Ficoll-70, structure and activity are not correlated. However, microsecond dynamics and activity are beautifully correlated in this case also. Overall, our result demonstrates that bromelain dynamics in the microsecond timescale around the active-site is probably a key factor in controlling its proteolytic activity.
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20
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Mamsa SSA, Meloni BP. Arginine and Arginine-Rich Peptides as Modulators of Protein Aggregation and Cytotoxicity Associated With Alzheimer's Disease. Front Mol Neurosci 2021; 14:759729. [PMID: 34776866 PMCID: PMC8581540 DOI: 10.3389/fnmol.2021.759729] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/29/2021] [Indexed: 01/10/2023] Open
Abstract
A substantial body of evidence indicates cationic, arginine-rich peptides (CARPs) are effective therapeutic compounds for a range of neurodegenerative pathologies, with beneficial effects including the reduction of excitotoxic cell death and mitochondrial dysfunction. CARPs, therefore, represent an emergent class of promising neurotherapeutics with multimodal mechanisms of action. Arginine itself is a known chaotrope, able to prevent misfolding and aggregation of proteins. The putative role of proteopathies in chronic neurodegenerative diseases such as Alzheimer's disease (AD) warrants investigation into whether CARPs could also prevent the aggregation and cytotoxicity of amyloidogenic proteins, particularly amyloid-beta and tau. While monomeric arginine is well-established as an inhibitor of protein aggregation in solution, no studies have comprehensively discussed the anti-aggregatory properties of arginine and CARPs on proteins associated with neurodegenerative disease. Here, we review the structural, physicochemical, and self-associative properties of arginine and the guanidinium moiety, to explore the mechanisms underlying the modulation of protein aggregation by monomeric and multimeric arginine molecules. Arginine-rich peptide-based inhibitors of amyloid-beta and tau aggregation are discussed, as well as further modulatory roles which could reduce proteopathic cytotoxicity, in the context of therapeutic development for AD.
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Affiliation(s)
- Somayra S A Mamsa
- School of Molecular Sciences, Faculty of Science, The University of Western Australia, Perth, WA, Australia.,Perron Institute for Neurological and Translational Science, QEII Medical Centre, Perth, WA, Australia
| | - Bruno P Meloni
- Perron Institute for Neurological and Translational Science, QEII Medical Centre, Perth, WA, Australia.,Centre for Neuromuscular and Neurological Disorders, The University of Western Australia, Crawley, WA, Australia.,Department of Neurology, Sir Charles Gairdner Hospital, QEII Medical Centre, Perth, WA, Australia
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21
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Parray ZA, Naqvi AAT, Ahmad F, Hassan MI, Islam A. Characterization of different intermediate states in myoglobin induced by polyethylene glycol: A process of spontaneous molecular self-organization foresees the energy landscape theory via in vitro and in silico approaches. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Photophysical Properties of BADAN Revealed in the Study of GGBP Structural Transitions. Int J Mol Sci 2021; 22:ijms222011113. [PMID: 34681772 PMCID: PMC8540541 DOI: 10.3390/ijms222011113] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 01/14/2023] Open
Abstract
The fluorescent dye BADAN (6-bromoacetyl-2-dimetylaminonaphtalene) is widely used in various fields of life sciences, however, the photophysical properties of BADAN are not fully understood. The study of the spectral properties of BADAN attached to a number of mutant forms of GGBP, as well as changes in its spectral characteristics during structural changes in proteins, allowed to shed light on the photophysical properties of BADAN. It was shown that spectral properties of BADAN are determined by at least one non-fluorescent and two fluorescent isomers with overlapping absorbing bands. It was found that BADAN fluorescence is determined by the unsolvated "PICT" (planar intramolecular charge transfer state) and solvated "TICT" (twisted intramolecular charge transfer state) excited states. While "TICT" state can be formed both as a result of the "PICT" state solvation and as a result of light absorption by the solvated ground state of the dye. BADAN fluorescence linked to GGBP/H152C apoform is quenched by Trp 183, but this effect is inhibited by glucose intercalation. New details of the changes in the spectral characteristics of BADAN during the unfolding of the protein apo and holoforms have been obtained.
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23
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Kruchinin SE, Fedotova MV. Ion Pairing of the Neurotransmitters Acetylcholine and Glutamate in Aqueous Solutions. J Phys Chem B 2021; 125:11219-11231. [PMID: 34597044 DOI: 10.1021/acs.jpcb.1c05117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Neurotransmitters (NTs) play an important role in neural communication, regulating a variety of functions such as motivation, learning, memory, and muscle contraction. Their intermolecular interactions in biological media are an important factor affecting their biological activity. However, the available information on the features of these interactions is scarce and contradictory, especially, in an estimation of possible ion binding. In this paper, we present the results of a study for two well-known NTs, acetylcholine (ACh) and glutamate (Glu), with relation to the NT-inorganic ion and the NT-NT binding in a water environment. The features of NT pairing are investigated in aqueous AChCl and NaGlu solutions over a wide concentration range using the integral equation method in 1D- and 3D- reference interaction site model (RISM) approaches. The data for ACh are given for its two bioactive TG (trans, gauche) and TT (trans, trans) conformers. As was found, for both NTs, the results indicate the NT-inorganic counterion contact pair to be the predominant associate type in the concentrated solutions. In this case, the counterions occupy the vacated "water" space in the hydration shell of the onium moiety (ACh) or carboxylate groups (Glu). For ACh, the "unfolded" TT conformer demonstrates a slightly greater possibility for counterion pairing in comparison with the "folded" TG conformer. For Glu, the probability of its binding with a counterion is slightly stronger for the "side-chain" carboxylate group than for the "backbone" group. The obtained results also revealed an insignificant probability of Glu--Glu- pairing. Namely, the RISM data indicate Glu--Glu- binding by NH3+-COO- interactions. A link between the ion binding of NTs and their biological activity is discussed. This contribution adds new knowledge to our understanding of the interactions between the NTs and their molecular environment, providing further insights into the behavior of these compounds in biological media.
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Affiliation(s)
- Sergey E Kruchinin
- G.A. Krestov Institute of Solution Chemistry, the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia
| | - Marina V Fedotova
- G.A. Krestov Institute of Solution Chemistry, the Russian Academy of Sciences, Akademicheskaya Street 1, Ivanovo 153045, Russia
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24
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Effects of hydrophobic solute on water normal modes. Chem Phys 2021. [DOI: 10.1016/j.chemphys.2021.111303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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25
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Wang C, Biok NA, Nayani K, Wang X, Yeon H, Derek Ma CK, Gellman SH, Abbott NL. Cationic Side Chain Identity Directs the Hydrophobically Driven Self-Assembly of Amphiphilic β-Peptides in Aqueous Solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3288-3298. [PMID: 33683138 DOI: 10.1021/acs.langmuir.0c03255] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Hydrophobic interactions mediated by nonpolar molecular fragments in water are influenced by local chemical and physical contexts in ways that are not yet fully understood. Here, we use globally amphiphilic (GA) β-peptides (GA-Lys and GA-Arg) with stable conformations to explore if replacement of β3-homolysine (βLys) with β3-homoarginine (βArg) influences the hydrophobically driven assembly of these peptides in bulk aqueous solution. The studies were conducted in 10 mM triethanolamine buffer at pH 7, where both βLys (ammonium) and βArg (guanidinium) side chains are substantially protonated. Comparisons of light scattering measurements and cryo-electron micrographs before and after the addition of 60 vol% MeOH indicate very different outcomes of the hydrophobically driven assembly of AcY-GA-Lys versus AcY-GA-Arg (AcY denotes an N-acetylated-β3-homotyrosine (βTyr) at each N-terminus). Nuclear magnetic resonance and analytical ultracentrifugation confirm that AcY-GA-Lys assembles into large aggregates in aqueous buffer, whereas AcY-GA-Arg at comparable concentrations forms only small oligomers. Titration of AcY-GA-Arg into aqueous solutions of AcY-GA-Lys reveals that the driving force for AcY-GA-Lys association is far stronger than that for AcY-GA-Arg association. We discuss these results in the light of past experimental observations involving single molecule force measurements with GA β-peptides and hydrophobically driven dimerization of conventional peptides that form a GA α-helix upon dimerization (but do not display the Lys versus Arg trend predicted by extrapolating from the earlier AFM studies with β-peptides). Overall, our results establish that the identity of proximal cationic groups, ammonium versus guanidinium, profoundly modulates the hydrophobically driven self-assembly of conformationally stable β-peptides in bulk aqueous solution.
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Affiliation(s)
- Chenxuan Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
- Department of Biophysics and Structural Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing100005, China
| | - Naomi A Biok
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
| | - Karthik Nayani
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca14853, New York, United States
| | - Xiaoguang Wang
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Hongseung Yeon
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Chi-Kuen Derek Ma
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison53706, Wisconsin, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison53706, Wisconsin, United States
| | - Nicholas L Abbott
- Smith School of Chemical and Biomolecular Engineering, Cornell University, 1 Ho Plaza, Ithaca14853, New York, United States
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26
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Abstract
Aqueous cosolvent systems (ACoSs) are mixtures of small polar molecules such as amides, alcohols, dimethyl sulfoxide, or ions in water. These liquids have been the focus of fundamental studies due to their complex intermolecular interactions as well as their broad applications in chemistry, medicine, and materials science. ACoSs are fully miscible at the macroscopic level but exhibit nanometer-scale spatial heterogeneity. ACoSs have recently received renewed attention within the chemical physics community as model systems to explore the relationship between intermolecular interactions and microscopic liquid-liquid phase separation. In this perspective, we provide an overview of ACoS spatial segregation, dynamic heterogeneity, and multiscale relaxation dynamics. We describe emerging approaches to characterize liquid microstructure, H-bond networks, and dynamics using modern experimental tools combined with molecular dynamics simulations and network-based analysis techniques.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry, University of Texas at Austin, Austin, Texas 19104, USA
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, Texas 19104, USA
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27
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Moritsugu N, Nara T, Koda SI, Tominaga K, Saito S. Molecular Mechanism of Acceleration and Retardation of Collective Orientation Relaxation of Water Molecules in Aqueous Solutions. J Phys Chem B 2020; 124:11730-11737. [PMID: 33320675 DOI: 10.1021/acs.jpcb.0c10036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The collective orientation relaxation (COR) of water molecules in aqueous solutions is faster or slower with an increase in the concentration of the solutions than that in pure water; for example, acceleration (deceleration) of the COR is observed in a solution of sodium chloride (tetramethylammonium chloride) with increasing concentration. However, the molecular mechanism of the solution and concentration dependence of the relaxation time of the COR has not yet been clarified. We theoretically investigate the concentration dependence of the COR of water molecules in solutions of tetramethylammonium chloride (TMACl), guanidinium chloride (GdmCl), and sodium chloride (NaCl). Based on the Mori-Zwanzig equation, we identify two opposing factors that determine the COR of water molecules in any aqueous solution: the correlation of dipole moments and the single-molecule orientation relaxation. We reveal the molecular mechanism of the concentration dependence of the relaxation time of the COR in the TMACl, GdmCl, and NaCl solutions in terms of these two factors.
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Affiliation(s)
- Norifumi Moritsugu
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Takafumi Nara
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Shin-Ichi Koda
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
| | - Keisuke Tominaga
- Graduate School of Science, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan.,Molecular Photoscience Research Center, Kobe University, Rokkodai-cho 1-1, Nada, Kobe 657-8501, Japan
| | - Shinji Saito
- The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan.,Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan
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28
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Garajová K, Sedláková D, Berta M, Gazova Z, Sedlák E. Destabilization effect of imidazolium cation-Hofmeister anion salts on cytochrome c. Int J Biol Macromol 2020; 164:3808-3813. [DOI: 10.1016/j.ijbiomac.2020.09.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 08/24/2020] [Accepted: 09/02/2020] [Indexed: 01/15/2023]
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29
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Kim BS, Naito M, Chaya H, Hori M, Hayashi K, Min HS, Yi Y, Kim HJ, Nagata T, Anraku Y, Kishimura A, Kataoka K, Miyata K. Noncovalent Stabilization of Vesicular Polyion Complexes with Chemically Modified/Single-Stranded Oligonucleotides and PEG- b-guanidinylated Polypeptides for Intracavity Encapsulation of Effector Enzymes Aimed at Cooperative Gene Knockdown. Biomacromolecules 2020; 21:4365-4376. [PMID: 32924444 DOI: 10.1021/acs.biomac.0c01192] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
For the simultaneous delivery of antisense oligonucleotides and their effector enzymes into cells, nanosized vesicular polyion complexes (PICs) were fabricated from oppositely charged polyion pairs of oligonucleotides and poly(ethylene glycol) (PEG)-b-polypeptides. First, the polyion component structures were carefully designed to facilitate a multimolecular (or secondary) association of unit PICs for noncovalent (or chemical cross-linking-free) stabilization of vesicular PICs. Chemically modified, single-stranded oligonucleotides (SSOs) dramatically stabilized the multimolecular associates under physiological conditions, compared to control SSOs without chemical modifications and duplex oligonucleotides. In addition, a high degree of guanidino groups in the polypeptide segment was also crucial for the high stability of multimolecular associates. Dynamic light scattering and transmission electron microscopy revealed the stabilized multimolecular associates to have a 100 nm sized vesicular architecture with a narrow size distribution. The loading number of SSOs per nanovesicle was determined to be ∼2500 using fluorescence correlation spectroscopic analyses with fluorescently labeled SSOs. Furthermore, the nanovesicle stably encapsulated ribonuclease H (RNase H) as an effector enzyme at ∼10 per nanovesicle through simple vortex-mixing with preformed nanovesicles. Ultimately, the RNase H-encapsulated nanovesicle efficiently delivered SSOs with RNase H into cultured cancer cells, thereby eliciting the significantly higher gene knockdown compared with empty nanovesicles (without RNase H) or a mixture of nanovesicles with RNase H without encapsulation. These results demonstrate the great potential of noncovalently stabilized nanovesicles for the codelivery of two varying bio-macromolecule payloads for ensuring their cooperative biological activity.
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Affiliation(s)
- Beob Soo Kim
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mitsuru Naito
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroyuki Chaya
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mao Hori
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kotaro Hayashi
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| | - Hyun Su Min
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yu Yi
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hyun Jin Kim
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Tetsuya Nagata
- Department of Neurology and Neurological Science, Graduate School, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
| | - Yasutaka Anraku
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akihiro Kishimura
- Department of Applied Chemistry, Faculty of Engineering, Kyushu University, 744 Moto-oka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine, Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan.,Institute for Future Initiatives, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kanjiro Miyata
- Department of Materials Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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30
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Reddy KD, Biswas R. Theoretical spectroscopy of isotopically dilute water and hydrophobicity. J Chem Phys 2020; 153:094501. [DOI: 10.1063/5.0018401] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Kambham Devendra Reddy
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
| | - Rajib Biswas
- Department of Chemistry and Center for Atomic, Molecular and Optical Sciences & Technologies, Indian Institute of Technology Tirupati, Yerpedu 517619, Andhra Pradesh, India
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31
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Curland S, Allolio C, Javitt L, Dishon Ben-Ami S, Weissbuch I, Ehre D, Harries D, Lahav M, Lubomirsky I. Heterogeneous Electrofreezing of Super-Cooled Water on Surfaces of Pyroelectric Crystals is Triggered by Trigonal Planar Ions. Angew Chem Int Ed Engl 2020; 59:15575-15579. [PMID: 32627307 DOI: 10.1002/anie.202006435] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Indexed: 11/11/2022]
Abstract
Electrofreezing experiments of super-cooled water (SCW) with different ions, performed directly on the charged hemihedral faces of pyroelectric LiTaO3 and AgI crystals, in the presence and in the absence of pyroelectric charge are reported. It is demonstrated that bicarbonate (HCO3 - ) ions elevate the icing temperature near the positively charged faces. In contrast, the hydronium (H3 O+ ) slightly reduces the icing temperature. Molecular dynamics simulations suggest that the hydrated trigonal planar HCO3 - ions self-assemble with water molecules near the surface of the AgI crystal as clusters of slightly different configuration from those of the ice-like hexagons. These clusters, however, have a tendency to serve as embryonic nuclei for ice crystallization. Consequently, we predicted and experimentally confirmed that the trigonal planar ions of NO3 - and guanidinium (Gdm+ ), at appropriate concentrations, elevate the icing temperature near the positive and negative charged surfaces, respectively. On the other hand, the Cl- and SO4 2- ions of different configurations reduce the icing temperature.
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Affiliation(s)
- Sofia Curland
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-, Rehovot, Israel
| | - Christoph Allolio
- Institute of Chemistry and the Fritz Haber Research Centre, The Hebrew University, 91904, Jerusalem, Israel.,Faculty of Mathematics and Physics, Charles University, Sokolovská 83, 18675, Praha 8, Czech Republic
| | - Leah Javitt
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-, Rehovot, Israel
| | - Shiri Dishon Ben-Ami
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-, Rehovot, Israel
| | - Isabelle Weissbuch
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-, Rehovot, Israel
| | - David Ehre
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-, Rehovot, Israel
| | - Daniel Harries
- Institute of Chemistry and the Fritz Haber Research Centre, The Hebrew University, 91904, Jerusalem, Israel
| | - Meir Lahav
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-, Rehovot, Israel
| | - Igor Lubomirsky
- Department of Materials and Interfaces, The Weizmann Institute of Science, 76100-, Rehovot, Israel
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32
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Curland S, Allolio C, Javitt L, Dishon Ben‐Ami S, Weissbuch I, Ehre D, Harries D, Lahav M, Lubomirsky I. Heterogeneous Electrofreezing of Super‐Cooled Water on Surfaces of Pyroelectric Crystals is Triggered by Trigonal Planar Ions. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Sofia Curland
- Department of Materials and Interfaces The Weizmann Institute of Science 76100- Rehovot Israel
| | - Christoph Allolio
- Institute of Chemistry and the Fritz Haber Research Centre The Hebrew University 91904 Jerusalem Israel
- Faculty of Mathematics and Physics Charles University Sokolovská 83 18675 Praha 8 Czech Republic
| | - Leah Javitt
- Department of Materials and Interfaces The Weizmann Institute of Science 76100- Rehovot Israel
| | - Shiri Dishon Ben‐Ami
- Department of Materials and Interfaces The Weizmann Institute of Science 76100- Rehovot Israel
| | - Isabelle Weissbuch
- Department of Materials and Interfaces The Weizmann Institute of Science 76100- Rehovot Israel
| | - David Ehre
- Department of Materials and Interfaces The Weizmann Institute of Science 76100- Rehovot Israel
| | - Daniel Harries
- Institute of Chemistry and the Fritz Haber Research Centre The Hebrew University 91904 Jerusalem Israel
| | - Meir Lahav
- Department of Materials and Interfaces The Weizmann Institute of Science 76100- Rehovot Israel
| | - Igor Lubomirsky
- Department of Materials and Interfaces The Weizmann Institute of Science 76100- Rehovot Israel
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33
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Sowlati-Hashjin S, Carbone P, Karttunen M. Insights into the Polyhexamethylene Biguanide (PHMB) Mechanism of Action on Bacterial Membrane and DNA: A Molecular Dynamics Study. J Phys Chem B 2020; 124:4487-4497. [DOI: 10.1021/acs.jpcb.0c02609] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shahin Sowlati-Hashjin
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Paola Carbone
- Department of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester M13 9PL, United Kingdom
| | - Mikko Karttunen
- Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- The Centre of Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
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34
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Dasari S, Mallik BS. Solubility and solvation free energy of a cardiovascular drug, LASSBio-294, in ionic liquids: A computational study. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112449] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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35
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Raghunathan S, Jaganade T, Priyakumar UD. Urea-aromatic interactions in biology. Biophys Rev 2020; 12:65-84. [PMID: 32067192 PMCID: PMC7040157 DOI: 10.1007/s12551-020-00620-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 01/08/2020] [Indexed: 02/06/2023] Open
Abstract
Noncovalent interactions are key determinants in both chemical and biological processes. Among such processes, the hydrophobic interactions play an eminent role in folding of proteins, nucleic acids, formation of membranes, protein-ligand recognition, etc.. Though this interaction is mediated through the aqueous solvent, the stability of the above biomolecules can be highly sensitive to any small external perturbations, such as temperature, pressure, pH, or even cosolvent additives, like, urea-a highly soluble small organic molecule utilized by various living organisms to regulate osmotic pressure. A plethora of detailed studies exist covering both experimental and theoretical regimes, to understand how urea modulates the stability of biological macromolecules. While experimentalists have been primarily focusing on the thermodynamic and kinetic aspects, theoretical modeling predominantly involves mechanistic information at the molecular level, calculating atomistic details applying the force field approach to the high level electronic details using the quantum mechanical methods. The review focuses mainly on examples with biological relevance, such as (1) urea-assisted protein unfolding, (2) urea-assisted RNA unfolding, (3) urea lesion interaction within damaged DNA, (4) urea conduction through membrane proteins, and (5) protein-ligand interactions those explicitly address the vitality of hydrophobic interactions involving exclusively the urea-aromatic moiety.
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Affiliation(s)
- Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Tanashree Jaganade
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.
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36
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37
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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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38
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Kumari A, Somvanshi P, Grover A. Ameliorating amyloid aggregation through osmolytes as a probable therapeutic molecule against Alzheimer's disease and type 2 diabetes. RSC Adv 2020; 10:12166-12182. [PMID: 35497581 PMCID: PMC9050657 DOI: 10.1039/d0ra00429d] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/16/2020] [Indexed: 01/31/2023] Open
Abstract
Large numbers of neurological and metabolic disorders occurring in humans are induced by the aberrant growth of aggregated or misfolded proteins.
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Affiliation(s)
- Anchala Kumari
- Department of Biotechnology
- Teri School of Advanced Studies
- New Delhi-110070
- India
- School of Biotechnology
| | - Pallavi Somvanshi
- Department of Biotechnology
- Teri School of Advanced Studies
- New Delhi-110070
- India
| | - Abhinav Grover
- School of Biotechnology
- Jawaharlal Nehru University
- New Delhi-110067
- India
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39
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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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40
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Parui S, Jana B. Relative Solvent Exposure of the Alpha-Helix and Beta-Sheet in Water Determines the Initial Stages of Urea and Guanidinium Chloride-Induced Denaturation of Alpha/Beta Proteins. J Phys Chem B 2019; 123:8889-8900. [DOI: 10.1021/acs.jpcb.9b06859] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Sridip Parui
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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41
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AbouGhaly MHH, Du J, Patel SM, Topp EM. Effects of ionic interactions on protein stability prediction using solid-state hydrogen deuterium exchange with mass spectrometry (ssHDX-MS). Int J Pharm 2019; 568:118512. [PMID: 31301464 DOI: 10.1016/j.ijpharm.2019.118512] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/07/2019] [Accepted: 07/09/2019] [Indexed: 12/13/2022]
Abstract
Deuterium incorporation in solid-state hydrogen deuterium exchange with mass spectrometry (ssHDX-MS) has been correlated with protein aggregation on storage in sugar-based solid matrices. Here, the effects of sucrose, arginine and histidine buffer on the rate of aggregation of a lyophilized monoclonal antibody (mAb) were assessed using design of experiments (DoE) and response surface methodology. Lyophilized formulations were characterized using ssHDX-MS and Fourier transform infrared spectroscopy (ssFTIR) to assess potential correlation with stability in solid state. The samples were subjected to storage stability at 5 °C and stressed stability at 40 °C/75% RH for 6 months, and the aggregation rate was measured using size exclusion chromatography (SEC). Different levels of arginine had no significant effect on deuterium uptake in ssHDX-MS, although stability studies showed that aggregation rate decreased with increasing arginine concentration. Similarly, when histidine buffer was replaced with phosphate buffer at the same pH and molarity, ssHDX-MS showed no differences in deuterium uptake, but storage stability studies showed a significant increase in aggregation rate. The results suggest that proteins can be stabilized in amorphous solids by ionic interactions which ssHDX-MS does not detect, an important indication of the limitations of the method.
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Affiliation(s)
- Mohamed H H AbouGhaly
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA; Department of Pharmaceutics and Industrial Pharmacy, Faculty of Pharmacy, Cairo University, Cairo 11562, Egypt.
| | - Jiali Du
- Dosage Form Design & Development, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Sajal M Patel
- Dosage Form Design & Development, AstraZeneca, Gaithersburg, MD 20878, USA
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, IN 47907, USA
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42
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Rabia LA, Zhang Y, Ludwig SD, Julian MC, Tessier PM. Net charge of antibody complementarity-determining regions is a key predictor of specificity. Protein Eng Des Sel 2019; 31:409-418. [PMID: 30770934 DOI: 10.1093/protein/gzz002] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 12/23/2018] [Accepted: 01/18/2019] [Indexed: 11/14/2022] Open
Abstract
Specificity is one of the most important and complex properties that is central to both natural antibody function and therapeutic antibody efficacy. However, it has proven extremely challenging to define robust guidelines for predicting antibody specificity. Here we evaluated the physicochemical determinants of antibody specificity for multiple panels of antibodies, including >100 clinical-stage antibodies. Surprisingly, we find that the theoretical net charge of the complementarity-determining regions (CDRs) is a strong predictor of antibody specificity. Antibodies with positively charged CDRs have a much higher risk of low specificity than antibodies with negatively charged CDRs. Moreover, the charge of the entire set of six CDRs is a much better predictor of antibody specificity than the charge of individual CDRs, variable domains (VH or VL) or the entire variable fragment (Fv). The best indicators of antibody specificity in terms of CDR amino acid composition are reduced levels of arginine and lysine and increased levels of aspartic and glutamic acid. Interestingly, clinical-stage antibodies with negatively charged CDRs also have a lower risk for poor biophysical properties in general, including a reduced risk for high levels of self-association. These findings provide powerful guidelines for predicting antibody specificity and for identifying safe and potent antibody therapeutics.
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Affiliation(s)
- Lilia A Rabia
- Isermann Department of Chemical & Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.,Department of Pharmaceutical Sciences.,Department of Chemical Engineering
| | | | - Seth D Ludwig
- Isermann Department of Chemical & Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Mark C Julian
- Isermann Department of Chemical & Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Peter M Tessier
- Isermann Department of Chemical & Biological Engineering, Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA.,Department of Pharmaceutical Sciences.,Department of Chemical Engineering.,Department of Biomedical Engineering, Biointerfaces Institute, University of Michigan, Ann Arbor, MI, USA
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43
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Hirano A, Iwashita K, Ura T, Sakuraba S, Shiraki K, Arakawa T, Kameda T. The binding affinity of uncharged aromatic solutes for negatively charged resins is enhanced by cations via cation–π interactions: The case of sodium ion and arginine. J Chromatogr A 2019; 1595:97-107. [DOI: 10.1016/j.chroma.2019.02.043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Revised: 02/15/2019] [Accepted: 02/19/2019] [Indexed: 01/01/2023]
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44
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Prather LJ, Weerasekare GM, Sima M, Quinn C, Stewart RJ. Aqueous Liquid-Liquid Phase Separation of Natural and Synthetic Polyguanidiniums. Polymers (Basel) 2019; 11:polym11040649. [PMID: 30970637 PMCID: PMC6523547 DOI: 10.3390/polym11040649] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/29/2019] [Accepted: 04/04/2019] [Indexed: 12/21/2022] Open
Abstract
Protamines are natural polyguanidiniums, arginine(R)-rich proteins involved in the compaction of chromatin during vertebrate spermatogenesis. Salmine, a protamine isolated from salmon sperm, contains 65 mol% R residues, with positively charged guanidino (Gdm+) sidechains, and no other amino acids with ionizable or aromatic sidechains. Salmine sulfate solutions undergo liquid-liquid phase separation (LLPS) with a concentration-dependent upper critical solution temperature (UCST). The condensed liquid phase comprises 50 wt % water and >600 mg·mL−1 salmine with a constant 1:2 ratio of sulfate (SO42−) to Gdm+. Isothermal titration calorimetry, titrating Na2SO4 into salmine chloride above and below the UCST, allowed isolation of exothermic sulfate binding to salmine chloride from subsequent endothermic condensation and exothermic phase separation events. Synthetic random polyacrylate analogs of salmine, with 3-guanidinopropyl sidechains, displayed similar counterion dependent phase behavior, demonstrating that the LLPS of polyguanidiniums does not depend upon subunit sequence or polymer backbone chirality, and was due entirely to Gdm+ sidechain interactions. The results provide experimental evidence for like-charge pairing of Gdm+ sidechains, and an experimental approach for further characterizing these interactions.
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Affiliation(s)
- Leland J. Prather
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA; (L.J.P.); (G.M.W.); (M.S.)
| | - G. Mahika Weerasekare
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA; (L.J.P.); (G.M.W.); (M.S.)
| | - Monika Sima
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA; (L.J.P.); (G.M.W.); (M.S.)
| | - Colette Quinn
- TA Instruments, 890 W 410 N St, Lindon, UT 84042, USA;
| | - Russell J. Stewart
- Department of Biomedical Engineering, University of Utah, Salt Lake City, UT 84112, USA; (L.J.P.); (G.M.W.); (M.S.)
- Correspondence: ; Tel.: +1-(801)-581-8581
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45
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Hebert MJ, Russell DH. Hydration of Guanidinium Ions: An Experimental Search for Like-Charged Ion Pairs. J Phys Chem Lett 2019; 10:1349-1354. [PMID: 30840463 DOI: 10.1021/acs.jpclett.9b00268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Guanidinium ions (GdmH+) are reported to form stable complexes (GdmH+/GdmH+) in aqueous solution despite strong repulsive interactions between the like-charged centers. These complexes are thought to play important roles in protein folding, membrane penetration, and formation of protein dimers. Although GdmH+ ions are weakly hydrated, semiempirical calculations provide evidence that these like-charged complexes are stabilized by water molecules, which serve important structural and energetic roles. Specifically, water molecules bridge between the GdmH+ ions of GdmH+/GdmH+ complexes as well as complexes involving the guanidinium side chains of arginine. Potential biological significances of like-charged complexes have been largely confirmed by ab initio molecular dynamics simulations and indirect experimental evidence. We report cryo-ion mobility-mass spectrometry results for the GdmH+/GdmH+ ion pair confined in a nanodroplet- the first direct experimental observation of this like-charged complex. A second like-charged complex, described as a water-mediated complex involving GdmH+ and H3O+, was also observed.
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Affiliation(s)
- Michael J Hebert
- Department of Chemistry Texas A&M University College Station , Texas 77843 , United States
| | - David H Russell
- Department of Chemistry Texas A&M University College Station , Texas 77843 , United States
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46
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Balamurugan K, Prakash M, Subramanian V. Theoretical Insights into the Role of Water Molecules in the Guanidinium-Based Protein Denaturation Process in Specific to Aromatic Amino Acids. J Phys Chem B 2019; 123:2191-2202. [PMID: 30672268 DOI: 10.1021/acs.jpcb.8b08968] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Noncovalent interactions between the guanidinium cation (Gdm+) and aromatic amino acids (AAs) in the water molecules have been studied using quantum chemical calculation and molecular dynamics (MD) simulations. Our studies show that there are two different modes of interactions between Gdm+ and AAs with and without water molecules. It is observed that nonhydrated Gdm+ interacts with AAs through N-H···π interactions, whereas hydrated clusters of Gdm+ are stabilized by stacking interactions with the help of the water-mediated hydrogen bond. Thus, different hydration patterns have significant effects on the predominant cation···π interactions in AAs-Gdm+ complexes. Findings from MD simulation elicit that the interaction pattern of Gdm+ with AAs varies as Phe < Tyr < Trp. Both the QM and MD calculations show a similar trend in the interaction of AAs with Gdm+. Moreover, the interaction of AAs with Gdm+ depends on the spatial orientation of AAs in the protein and the concomitant local structure, that is, the AAs present in the unstructured region of protein such as coils and bends exhibit higher binding for Gdm+ when compared to the AAs present in the structured region of the protein such as the α-helix and the β-sheet. Our study clearly reveals that H-bonded water molecules and the hydration pattern of Gdm+ as well as the positional presence of these AAs in the protein structure context play determining roles in the denaturation of protein by the Gdm+ cation.
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Affiliation(s)
- Kanagasabai Balamurugan
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India
| | - Muthuramalingam Prakash
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India
| | - Venkatesan Subramanian
- Chemical Laboratory , CSIR-Central Leather Research Institute , Adyar, Chennai 600 020 , India.,Academy of Scientific and Innovative Research (AcSIR) , CSIR-CLRI Campus , Chennai 600 020 , India
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Xia K, Anand DV, Shikhar S, Mu Y. Persistent homology analysis of osmolyte molecular aggregation and their hydrogen-bonding networks. Phys Chem Chem Phys 2019; 21:21038-21048. [DOI: 10.1039/c9cp03009c] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dramatically different patterns can be observed in the topological fingerprints for hydrogen-bonding networks from two types of osmolyte systems.
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Affiliation(s)
- Kelin Xia
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - D. Vijay Anand
- Division of Mathematical Sciences
- School of Physical and Mathematical Sciences
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Saxena Shikhar
- School of Biological Sciences
- Nanyang Technological University
- Singapore
| | - Yuguang Mu
- School of Biological Sciences
- Nanyang Technological University
- Singapore
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Aqueous thermogalvanic cells with a high Seebeck coefficient for low-grade heat harvest. Nat Commun 2018; 9:5146. [PMID: 30514952 PMCID: PMC6279834 DOI: 10.1038/s41467-018-07625-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/12/2018] [Indexed: 12/03/2022] Open
Abstract
Thermogalvanic cells offer a cheap, flexible and scalable route for directly converting heat into electricity. However, achieving a high output voltage and power performance simultaneously from low-grade thermal energy remains challenging. Here, we introduce strong chaotropic cations (guanidinium) and highly soluble amide derivatives (urea) into aqueous ferri/ferrocyanide ([Fe(CN)6]4−/[Fe(CN)6]3−) electrolytes to significantly boost their thermopowers. The corresponding Seebeck coefficient and temperature-insensitive power density simultaneously increase from 1.4 to 4.2 mV K−1 and from 0.4 to 1.1 mW K−2 m−2, respectively. The results reveal that guanidinium and urea synergistically enlarge the entropy difference of the redox couple and significantly increase the Seebeck effect. As a demonstration, we design a prototype module that generates a high open-circuit voltage of 3.4 V at a small temperature difference of 18 K. This thermogalvanic cell system, which features high Seebeck coefficient and low cost, holds promise for the efficient harvest of low-grade thermal energy. Achieving high thermopower in liquid-state thermogalvanic cells is vital to realize a low-cost technology solution for thermal-to-electrical energy conversion. Here, the authors present aqueous thermogalvanic cells based on modified electrolyte with enhanced Seebeck coefficient and thermopower.
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Vazdar M, Heyda J, Mason PE, Tesei G, Allolio C, Lund M, Jungwirth P. Arginine "Magic": Guanidinium Like-Charge Ion Pairing from Aqueous Salts to Cell Penetrating Peptides. Acc Chem Res 2018; 51:1455-1464. [PMID: 29799185 DOI: 10.1021/acs.accounts.8b00098] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
It is a textbook knowledge that charges of the same polarity repel each other. For two monovalent ions in the gas phase at a close contact this repulsive interaction amounts to hundreds of kilojoules per mole. In aqueous solutions, however, this Coulomb repulsion is strongly attenuated by a factor equal to the dielectric constant of the medium. The residual repulsion, which now amounts only to units of kilojoules per mole, may be in principle offset by attractive interactions. Probably the smallest cationic pair, where a combination of dispersion and cavitation forces overwhelms the Coulomb repulsion, consists of two guanidinium ions in water. Indeed, by a combination of molecular dynamics with electronic structure calculations and electrophoretic, as well as spectroscopic, experiments, we have demonstrated that aqueous guanidinium cations form (weakly) thermodynamically stable like-charge ion pairs. The importance of pairing of guanidinium cations in aqueous solutions goes beyond a mere physical curiosity, since it has significant biochemical implications. Guanidinium chloride is known to be an efficient and flexible protein denaturant. This is due to the ability of the orientationally amphiphilic guanidinium cations to disrupt various secondary structural motifs of proteins by pairing promiscuously with both hydrophobic and hydrophilic groups, including guanidinium-containing side chains of arginines. The fact that the cationic guanidinium moiety forms the dominant part of the arginine side chain implies that the like-charge ion pairing may also play a role for interactions between peptides and proteins. Indeed, arginine-arginine pairing has been frequently found in structural protein databases. In particular, when strengthened by a presence of negatively charged glutamate, aspartate, or C-terminal carboxylic groups, this binding motif helps to stabilize peptide or protein dimers and is also found in or near active sites of several enzymes. The like-charge pairing of the guanidinium side-chain groups may also hold the key to the understanding of the arginine "magic", that is, the extraordinary ability of arginine-rich polypeptides to passively penetrate across cellular membranes. Unlike polylysines, which are also highly cationic but lack the ease in crossing membranes, polyarginines do not exhibit mutual repulsion. Instead, they accumulate at the membrane, weaken it, and might eventually cross in a concerted, "train-like" manner. This behavior of arginine-rich cell penetrating peptides can be exploited when devising smart strategies how to deliver in a targeted way molecular cargos into the cell.
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Affiliation(s)
- Mario Vazdar
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, Bijenička 54, HR-10000 Zagreb, Croatia
| | - Jan Heyda
- Department of Physical Chemistry, University of Chemistry and Technology, Prague, Technicka 5, 16628 Prague, Czech Republic
| | - Philip E. Mason
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
| | - Giulio Tesei
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Christoph Allolio
- Institute of Chemistry and The Fritz Haber Research Center, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Giv’at Ram, Jerusalem 9190401, Israel
| | - Mikael Lund
- Division of Theoretical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 166 10 Prague, Czech Republic
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