1
|
Guo Q, Liu B, Guo X, Yan P, Cao B, Liu R, Liu X. Characterization and application of LysSGF2 and HolSGF2 as potential biocontrol agents against planktonic and biofilm cells of common pathogenic bacteria. Int J Food Microbiol 2024; 425:110848. [PMID: 39208563 DOI: 10.1016/j.ijfoodmicro.2024.110848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
Antimicrobial resistance represents a global health emergency, necessitating the introduction of novel antimicrobial agents. In the present study, lysozyme and holin from Shigella flexneri 1.1868 phage SGF2, named LysSGF2 and HolSGF2, respectively, were cloned, expressed, and characterized. LysSGF2 and HolSGF2 showed lytic activities against S. flexneri 1.1868 cells at 4-55 °C and pH 3.1-10.3. LysSGF2 exhibited antimicrobial activity against five gram-negative and two gram-positive bacteria. HolSGF2 showed antimicrobial activity against four gram-negative and one gram-positive species. The antibacterial activities of LysSGF2 and HolSGF2 were determined in liquid beverages, including bottled water and milk. The relative lytic activity of LysSGF2 combined with HolSGF2 against the tested bacteria was approximately 46-77 % in water. Furthermore, the combination markedly decreased the viable counts of tested bacteria by approximately 3-5 log CFU/mL. LysSGF2 and HolSGF2 could efficiently remove biofilms on polystyrene, glass, and stainless-steel. The efficacy of the LysSGF2 and HolSGF2 combination against the tested bacteria on polystyrene was 58-71 %. Combination treatment effectively killed biofilm cells formed on stainless-steel and glass by 1-4 log CFU/mL. ese results indicate that LysSGF2 and HolSGF2 can successfully control both the planktonic and biofilm cells of common pathogenic bacteria, suggesting that the combined or single use of LysSGF2 and HolSGF2 may be of great value in food processing.
Collapse
Affiliation(s)
- Qiucui Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Bingxin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Xiaoxiao Guo
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Peihan Yan
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Bing Cao
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Ruyin Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, China.
| | - Xinchun Liu
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 101408, China.
| |
Collapse
|
2
|
Carpenter KA, Altman RB. Databases of ligand-binding pockets and protein-ligand interactions. Comput Struct Biotechnol J 2024; 23:1320-1338. [PMID: 38585646 PMCID: PMC10997877 DOI: 10.1016/j.csbj.2024.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/16/2024] [Accepted: 03/17/2024] [Indexed: 04/09/2024] Open
Abstract
Many research groups and institutions have created a variety of databases curating experimental and predicted data related to protein-ligand binding. The landscape of available databases is dynamic, with new databases emerging and established databases becoming defunct. Here, we review the current state of databases that contain binding pockets and protein-ligand binding interactions. We have compiled a list of such databases, fifty-three of which are currently available for use. We discuss variation in how binding pockets are defined and summarize pocket-finding methods. We organize the fifty-three databases into subgroups based on goals and contents, and describe standard use cases. We also illustrate that pockets within the same protein are characterized differently across different databases. Finally, we assess critical issues of sustainability, accessibility and redundancy.
Collapse
Affiliation(s)
- Kristy A. Carpenter
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Russ B. Altman
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
3
|
Wen S, Zhao Y, Qi X, Cai M, Huang K, Liu H, Kong DX. Conformational plasticity of SpyCas9 induced by AcrIIA4 and AcrIIA2: Insights from molecular dynamics simulation. Comput Struct Biotechnol J 2024; 23:537-548. [PMID: 38235361 PMCID: PMC10791570 DOI: 10.1016/j.csbj.2023.12.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 12/06/2023] [Accepted: 12/22/2023] [Indexed: 01/19/2024] Open
Abstract
CRISPR-Cas9 systems constitute bacterial adaptive immune systems that protect against phage infections. Bacteriophages encode anti-CRISPR proteins (Acrs) that mitigate the bacterial immune response. However, the structural basis for their inhibitory actions from a molecular perspective remains elusive. In this study, through microsecond atomistic molecular dynamics simulations, we demonstrated the remarkable flexibility of Streptococcus pyogenes Cas9 (SpyCas9) and its conformational adaptability during interactions with AcrIIA4 and AcrIIA2. Specifically, we demonstrated that the binding of AcrIIA4 and AcrIIA2 to SpyCas9 induces a conformational rearrangement that causes spatial separation between the nuclease and cleavage sites, thus making the endonuclease inactive. This separation disrupts the transmission of signals between the protospacer adjacent motif recognition and nuclease domains, thereby impeding the efficient processing of double-stranded DNA. The simulation also reveals that AcrIIA4 and AcrIIA2 cause different structural variations of SpyCas9. Our research illuminates the precise mechanisms underlying the suppression of SpyCas9 by AcrIIA4 and AcrIIA2, thus presenting new possibilities for controlling genome editing with higher accuracy.
Collapse
Affiliation(s)
- Shuixiu Wen
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Yuxin Zhao
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Xinyu Qi
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Mingzhu Cai
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Kaisheng Huang
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - Hui Liu
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| | - De-Xin Kong
- National Key Laboratory of Agricultural Microbiology, Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan, PR China
| |
Collapse
|
4
|
Mi Y, Marcu SB, Tabirca S, Yallapragada VV. PS-GO parametric protein search engine. Comput Struct Biotechnol J 2024; 23:1499-1509. [PMID: 38633387 PMCID: PMC11021831 DOI: 10.1016/j.csbj.2024.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 04/01/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024] Open
Abstract
With the explosive growth of protein-related data, we are confronted with a critical scientific inquiry: How can we effectively retrieve, compare, and profoundly comprehend these protein structures to maximize the utilization of such data resources? PS-GO, a parametric protein search engine, has been specifically designed and developed to maximize the utilization of the rapidly growing volume of protein-related data. This innovative tool addresses the critical need for effective retrieval, comparison, and deep understanding of protein structures. By integrating computational biology, bioinformatics, and data science, PS-GO is capable of managing large-scale data and accurately predicting and comparing protein structures and functions. The engine is built upon the concept of parametric protein design, a computer-aided method that adjusts and optimizes protein structures and sequences to achieve desired biological functions and structural stability. PS-GO utilizes key parameters such as amino acid sequence, side chain angle, and solvent accessibility, which have a significant influence on protein structure and function. Additionally, PS-GO leverages computable parameters, derived computationally, which are crucial for understanding and predicting protein behavior. The development of PS-GO underscores the potential of parametric protein design in a variety of applications, including enhancing enzyme activity, improving antibody affinity, and designing novel functional proteins. This advancement not only provides a robust theoretical foundation for the field of protein engineering and biotechnology but also offers practical guidelines for future progress in this domain.
Collapse
Affiliation(s)
- Yanlin Mi
- School of Computer Science and Information Technology, University College Cork, Cork, Ireland
- SFI Centre for Research Training in Artificial Intelligence, University College Cork, Cork, Ireland
| | - Stefan-Bogdan Marcu
- School of Computer Science and Information Technology, University College Cork, Cork, Ireland
| | - Sabin Tabirca
- School of Computer Science and Information Technology, University College Cork, Cork, Ireland
- Faculty of Mathematics and Informatics, Transylvania University of Brasov, Brasov, Romania
| | - Venkata V.B. Yallapragada
- Centre for Advanced Photonics and Process Analytics, Munster Technological University, Cork, Ireland
| |
Collapse
|
5
|
Joiret M, Kerff F, Rapino F, Close P, Geris L. Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel. Comput Struct Biotechnol J 2024; 23:2453-2464. [PMID: 38882677 PMCID: PMC11179572 DOI: 10.1016/j.csbj.2024.05.045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/10/2024] [Accepted: 05/27/2024] [Indexed: 06/18/2024] Open
Abstract
The kinetics of the protein elongation cycle by the ribosome depends on intertwined factors. One of these factors is the electrostatic interaction of the nascent protein with the ribosome exit tunnel. In this computational biology theoretical study, we focus on the rate of the peptide bond formation and its dependence on the ribosome exit tunnel electrostatic potential profile. We quantitatively predict how oligopeptides of variable lengths can affect the peptide bond formation rate. We applied the Michaelis-Menten model as previously extended to incorporate the mechano-biochemical effects of forces on the rate of reaction at the catalytic site of the ribosome. For a given pair of carboxy-terminal amino acid substrate at the P- and an aminoacyl-tRNA at the A-sites, the relative time courses of the peptide bond formation reaction can be reversed depending on the oligopeptide sequence embedded in the tunnel and their variable lengths from the P-site. The reversal is predicted to occur from a shift in positions of charged amino acids upstream in the oligopeptidyl-tRNA at the P-site. The position shift must be adjusted by clever design of the oligopeptide probes using the electrostatic potential profile along the exit tunnel axial path. These predicted quantitative results bring strong evidence of the importance and relative contribution of the electrostatic interaction of the ribosome exit tunnel with the nascent peptide chain during elongation.
Collapse
Affiliation(s)
- Marc Joiret
- Biomechanics Research Unit, GIGA In Silico Medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
| | - Frederic Kerff
- UR InBios Centre d'Ingénierie des Protéines, Liège University, Bât B6a, Allèe du 6 Août, 19, B-4000 Liège, Belgium
| | - Francesca Rapino
- Cancer Signaling, GIGA Stem Cells, Liège University, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Pierre Close
- Cancer Signaling, GIGA Stem Cells, Liège University, CHU-B34(+2) 1 Avenue de l'Hôpital, B-4000 Liège, Belgium
| | - Liesbet Geris
- Biomechanics Research Unit, GIGA In Silico Medicine, Liège University, CHU-B34(+5) 1 Avenue de l'Hôpital, 4000 Liège, Belgium
- Skeletal Biology & Engineering Research Center, KU Leuven, ON I Herestraat 49 - Box 813, 3000 Leuven, Belgium
- Biomechanics Section, KU Leuven, Celestijnenlaan 300C - Box 2419, B-3001 Heverlee, Belgium
| |
Collapse
|
6
|
Ni L, Shen R, Luo H, Li X, Zhang X, Huang L, Deng Y, Liao X, Wu Y, Duan C, Xie X. GlmS plays a key role in the virulence factor expression and biofilm formation ability of Staphylococcus aureus promoted by advanced glycation end products. Virulence 2024; 15:2352476. [PMID: 38741276 PMCID: PMC11095574 DOI: 10.1080/21505594.2024.2352476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 05/03/2024] [Indexed: 05/16/2024] Open
Abstract
Staphylococcus aureus (S. aureus) is well known for its biofilm formation ability and is responsible for serious, chronic refractory infections worldwide. We previously demonstrated that advanced glycation end products (AGEs), a hallmark of chronic hyperglycaemia in diabetic tissues, enhanced biofilm formation by promoting eDNA release via sigB upregulation in S. aureus, contributing to the high morbidity and mortality of patients presenting a diabetic foot ulcer infection. However, the exact regulatory network has not been completely described. Here, we used pull-down assay and LC-MS/MS to identify the GlmS as a candidate regulator of sigB in S. aureus stimulated by AGEs. Dual-luciferase assays and electrophoretic mobility shift assays (EMSAs) revealed that GlmS directly upregulated the transcriptional activity of sigB. We constructed NCTC 8325 ∆glmS for further validation. qRT-PCR analysis revealed that AGEs promoted both glmS and sigB expression in the NCTC 8325 strain but had no effect on NCTC 8325 ∆glmS. NCTC 8325 ∆glmS showed a significant attenuation in biofilm formation and virulence factor expression, accompanied by a decrease in sigB expression, even under AGE stimulation. All of the changes, including pigment deficiency, decreased haemolysis ability, downregulation of hla and hld expression, and less and sparser biofilms, indicated that sigB and biofilm formation ability no longer responded to AGEs in NCTC 8325 ∆glmS. Our data extend the understanding of GlmS in the global regulatory network of S. aureus and demonstrate a new mechanism by which AGEs can upregulate GlmS, which directly regulates sigB and plays a significant role in mediating biofilm formation and virulence factor expression.
Collapse
Affiliation(s)
- Lijia Ni
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Rui Shen
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hua Luo
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xuexue Li
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaofan Zhang
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Lisi Huang
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yawen Deng
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoyan Liao
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yonglin Wu
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chaohui Duan
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xiaoying Xie
- Department of Clinical Laboratory, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
- Institution of Antibiotic, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| |
Collapse
|
7
|
Fagnani E, Bonì F, Seneci P, Gornati D, Muzio L, Mastrangelo E, Milani M. Stabilization of the retromer complex: Analysis of novel binding sites of bis-1,3-phenyl guanylhydrazone 2a to the VPS29/VPS35 interface. Comput Struct Biotechnol J 2024; 23:1088-1093. [PMID: 38487369 PMCID: PMC10937258 DOI: 10.1016/j.csbj.2024.02.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
The stabilization of the retromer protein complex can be effective in the treatment of different neurological disorders. Following the identification of bis-1,3-phenyl guanylhydrazone 2a as an effective new compound for the treatment of amyotrophic lateral sclerosis, in this work we analyze the possible binding sites of this molecule to the VPS35/VPS29 dimer of the retromer complex. Our results show that the affinity for different sites of the protein assembly depends on compound charge and therefore slight changes in the cell microenvironment could promote different binding states. Finally, we describe a novel binding site located in a deep cleft between VPS29 and VPS35 that should be further explored to select novel molecular chaperones for the stabilization of the retromer complex.
Collapse
Affiliation(s)
- Elisa Fagnani
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Francesco Bonì
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Pierfausto Seneci
- Department of Chemistry, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Davide Gornati
- Department of Chemistry, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Luca Muzio
- INSPE—Institute of Experimental Neurology, San Raffaele Scientific Institute, Via Olgettina 60, I–20132 Milano, Italy
| | - Eloise Mastrangelo
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| | - Mario Milani
- Biophysics Institute, CNR-IBF, Via Corti 12, I-20133 Milano, Italy
- Department of Bioscience, University of Milan, Via Celoria 26, I-20133 Milano, Italy
| |
Collapse
|
8
|
Wei L, Fan C, Sun X, Wang X, Yu H. Hereditary coagulation factor VII deficiency caused by novel compound heterozygous mutations c.572-1G>A and c.1037A>C in a Chinese pedigree. Gene 2024; 928:148788. [PMID: 39047958 DOI: 10.1016/j.gene.2024.148788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Revised: 06/29/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
Abstract
Hereditary coagulation factor VII (FVII) deficiency is a rare autosomal recessive bleeding disorder. The aims of this study were to identify and verify the pathogenic mutation sites in a family with hereditary coagulation FVII deficiency, and preliminarily explore the underlying mechanisms. We identified a novel combination of compound heterozygous mutations, c.572-1G>A and c.1037A>C in F7 gene, associated with FVII deficiency. The splice site mutation c.572-1G>A led to a truncation, resulting in the loss of the essential catalytic domain of the FVII protein. The c.1037A>C missense mutation has not been previously reported. Our study revealed that this mutation leads to steric hindrance between residues, causing significant changes in the energy and structure of the FVII protein, ultimately affecting its function. These changes disrupt the normal function of the FVII protein, accelerating the development of inherited FVII deficiency. Moreover, the mRNA expression of the F7 gene and the protein expression of the FVII antigen (FVII: Ag) were significantly lower in the proband, as well as in the proband's parents, compared to the healthy control (P<0.05). Our findings not only elucidate the genetic underpinning of FVII deficiency in the family studied but also contribute a new mutation to the known disease spectrum, potentially assisting in future diagnostic and therapeutic approaches.
Collapse
Affiliation(s)
- Lindan Wei
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Guizhou, China
| | - Chenxi Fan
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Guizhou, China
| | - Xin Sun
- School of Basic Medical Sciences, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Guizhou, China
| | - Xin Wang
- School of Basic Medical Sciences, Special Key Laboratory of Ocular Diseases of Guizhou Province, Zunyi Medical University, Guizhou, China.
| | - Hongsong Yu
- Department of Immunology, Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi Medical University, Guizhou, China.
| |
Collapse
|
9
|
Dahlström C, Duan R, Eivazi A, Magalhães S, Alves L, Engholm M, Svanedal I, Edlund H, Medronho B, Norgren M. Stacking self-gluing cellulose II films: A facile strategy for the formation of novel all-cellulose laminates. Carbohydr Polym 2024; 344:122523. [PMID: 39218546 DOI: 10.1016/j.carbpol.2024.122523] [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: 02/09/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 09/04/2024]
Abstract
Cellulose laminates represent a remarkable convergence of natural materials and modern engineering, offering a wide range of versatile applications in sustainable packaging, construction, and advanced materials. In this study, novel all-cellulose laminates are developed using an environmentally friendly approach, where freshly regenerated cellulose II films are stacked without the need for solvents (for impregnation and/or partial dissolution), chemical modifications, or resins. The structural and mechanical properties of these all-cellulose laminates were thoroughly investigated. This simple and scalable procedure results in transparent laminates with exceptional mechanical properties comparable to or even superior to common plastics, with E-modulus higher than 9 GPa for a single layer and 7 GPa for the laminates. These laminates are malleable and can be easily patterned. Depending on the number of layers, they can be thin and flexible (with just one layer) or thick and rigid (with three layers). Laminates were also doped with 10 wt% undissolved fibers without compromising their characteristics. These innovative all-cellulose laminates present a robust, eco-friendly alternative to traditional synthetic materials, thus bridging the gap between environmental responsibility and high-performance functionality.
Collapse
Affiliation(s)
- Christina Dahlström
- Surface and Colloid Engineering, FSCN Research Centre, Mid Sweden University, Holmgatan 10, SE-851 70 Sundsvall, Sweden.
| | - Ran Duan
- Surface and Colloid Engineering, FSCN Research Centre, Mid Sweden University, Holmgatan 10, SE-851 70 Sundsvall, Sweden; Tetra Pak, Ruben Rausings gata, SE-221 00 Lund, Sweden
| | - Alireza Eivazi
- Surface and Colloid Engineering, FSCN Research Centre, Mid Sweden University, Holmgatan 10, SE-851 70 Sundsvall, Sweden
| | - Solange Magalhães
- University of Coimbra, CERES, Department of Chemical Engineering, 3030-790 Coimbra, Portugal
| | - Luís Alves
- University of Coimbra, CERES, Department of Chemical Engineering, 3030-790 Coimbra, Portugal
| | - Magnus Engholm
- Advanced Materials and Processes, FSCN Research Centre, Mid Sweden University, Holmgatan 10, SE-851 70 Sundsvall, Sweden
| | - Ida Svanedal
- Surface and Colloid Engineering, FSCN Research Centre, Mid Sweden University, Holmgatan 10, SE-851 70 Sundsvall, Sweden
| | - Håkan Edlund
- Surface and Colloid Engineering, FSCN Research Centre, Mid Sweden University, Holmgatan 10, SE-851 70 Sundsvall, Sweden
| | - Bruno Medronho
- Surface and Colloid Engineering, FSCN Research Centre, Mid Sweden University, Holmgatan 10, SE-851 70 Sundsvall, Sweden; MED-Mediterranean Institute for Agriculture, Environment and Development, CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, Ed. 8, 8005-139 Faro, Portugal
| | - Magnus Norgren
- Surface and Colloid Engineering, FSCN Research Centre, Mid Sweden University, Holmgatan 10, SE-851 70 Sundsvall, Sweden
| |
Collapse
|
10
|
Ceballos-Ávila D, Vázquez-Sandoval I, Ferrusca-Martínez F, Jiménez-Sánchez A. Conceptually innovative fluorophores for functional bioimaging. Biosens Bioelectron 2024; 264:116638. [PMID: 39153261 DOI: 10.1016/j.bios.2024.116638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2024] [Revised: 07/30/2024] [Accepted: 08/06/2024] [Indexed: 08/19/2024]
Abstract
Fluorophore chemistry is at the forefront of bioimaging, revolutionizing the visualization of biological processes with unparalleled precision. From the serendipitous discovery of mauveine in 1856 to cutting-edge fluorophore engineering, this field has undergone transformative evolution. Today, the synergy of chemistry, biology, and imaging technologies has produced diverse, specialized fluorophores that enhance brightness, photostability, and targeting capabilities. This review delves into the history and innovation of fluorescent probes, showcasing their pivotal role in advancing our understanding of cellular dynamics and disease mechanisms. We highlight groundbreaking molecules and their applications, envisioning future breakthroughs that promise to redefine biomedical research and diagnostics.
Collapse
Affiliation(s)
- Daniela Ceballos-Ávila
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n. Coyoacán, 04510, Ciudad de México, Mexico
| | - Ixsoyen Vázquez-Sandoval
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n. Coyoacán, 04510, Ciudad de México, Mexico
| | - Fernanda Ferrusca-Martínez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n. Coyoacán, 04510, Ciudad de México, Mexico
| | - Arturo Jiménez-Sánchez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n. Coyoacán, 04510, Ciudad de México, Mexico.
| |
Collapse
|
11
|
Sanchez HA, Kraujaliene L, Verselis VK. A pore locus in the E1 domain differentially regulates Cx26 and Cx30 hemichannel function. J Gen Physiol 2024; 156:e202313502. [PMID: 39302316 DOI: 10.1085/jgp.202313502] [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: 10/26/2023] [Revised: 05/06/2024] [Accepted: 08/28/2024] [Indexed: 09/22/2024] Open
Abstract
Connexins (Cxs) function as gap junction (GJ) channels and hemichannels that mediate intercellular and transmembrane signaling, respectively. Here, we investigated the proximal segment of the first extracellular loop, E1, of two closely related Cxs, Cx26 and Cx30, that share widespread expression in the cochlea. Computational studies of Cx26 proposed that this segment of E1 contains a parahelix and functions in gating. The sequence of the parahelix is identical between Cx26 and Cx30 except for an Ala/Glu difference at position 49. We show through cysteine-scanning and mutational analyses that position 49 is pore-lining and interacts with the adjacent Asp50 residue to impact hemichannel functionality. When both positions 49 and 50 are charged, as occurs naturally in Cx30, the hemichannel function is dampened. Co-expression of Cx30 with Cx26(D50N), the most common mutation associated with keratitis-ichthyosis-deafness syndrome, results in robust hemichannel currents indicating that position 49-50 interactions are relevant in heteromerically assembled hemichannels. Cysteine substitution at position 49 in either Cx26 or Cx30 results in tonic inhibition of hemichannels, both through disulfide formation and high-affinity metal coordination, suggestive of a flexible region of the pore that can narrow substantially. These effects are absent in GJ channels, which exhibit wild-type functionality. Examination of postnatal cochlear explants suggests that Cx30 expression is associated with reduced propagation of Ca2+ waves. Overall, these data identify a pore locus in E1 of Cx26 and Cx30 that impacts hemichannel functionality and provide new considerations for understanding the roles of these connexins in cochlear function.
Collapse
Affiliation(s)
- Helmuth A Sanchez
- Centro Interdisciplinario de Neurociencia de Valparaíso, Facultad de Ciencias, Universidad de Valparaíso , Valparaíso, Chile
| | - Lina Kraujaliene
- Institute of Cardiology, Lithuanian University of Health Sciences , Kaunas, Lithuania
| | - Vytas K Verselis
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA
| |
Collapse
|
12
|
Li J, Eagles DA, Tucker IJ, Pereira Schmidt AC, Deplazes E. Secondary structure propensities of the Ebola delta peptide E40 in solution and model membrane environments. Biophys Chem 2024; 314:107318. [PMID: 39226875 DOI: 10.1016/j.bpc.2024.107318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 08/27/2024] [Accepted: 08/27/2024] [Indexed: 09/05/2024]
Abstract
The Ebola delta peptide is an amphipathic, 40-residue peptide encoded by the Ebola virus, referred to as E40. The membrane-permeabilising activity of the E40 delta peptide has been demonstrated in cells and lipid vesicles suggesting the E40 delta peptide likely acts as a viroporin. The lytic activity of the peptide increases in the presence of anionic lipids and a disulphide bond in the C-terminal part of the peptide. Previous in silico work predicts the peptide to show a partially helical structure, but there is no experimental information on the structure of E40. Here, we use circular dichroism spectroscopy to report the secondary structure propensities of the reduced and oxidised forms of the E40 peptide in water, detergent micelles, and lipid vesicles composed of neutral and anionic lipids (POPC and POPG, respectively). Results indicate that the peptide is predominately a random coil in solution, and the disulphide bond has a small but measurable effect on peptide conformation. Secondary structure analysis shows large uncertainties and dependence on the reference data set and, in our system, cannot be used to accurately determine the secondary structure motifs of the peptide in membrane environments. Nevertheless, the spectra can be used to assess the relative changes in secondary structure propensities of the peptide depending on the solvent environment and disulphide bond. In POPC-POPG vesicles, the peptide transitions from a random coil towards a more structured conformation, which is even more pronounced in negatively charged SDS micelles. In vesicles, the effect depends on the peptide-lipid ratio, likely resulting from vesicle surface saturation. Further experiments with zwitterionic POPC vesicles and DPC micelles show that both curvature and negatively charged lipids can induce a change in conformation, with the two effects being cumulative. Electrostatic screening from Na+ ions reduced this effect. The oxidised form of the peptide shows a slightly lower propensity for secondary structure and retains a more random coil conformation even in the presence of PG-PC vesicles.
Collapse
Affiliation(s)
- Jiayu Li
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Australia
| | - David A Eagles
- Institute of Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Isaac J Tucker
- Institute of Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | | | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Australia.
| |
Collapse
|
13
|
Kalinin V, Padnya P, Stoikov I. Romanowsky staining: history, recent advances and future prospects from a chemistry perspective. Biotech Histochem 2024; 99:1-20. [PMID: 37929609 DOI: 10.1080/10520295.2023.2273860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Abstract
Romanowsky staining was an important methodological breakthrough in diagnostic hematology and cytopathology during the late 19th and early 20th centuries; it has facilitated for decades the work of biologists, hematologists and pathologists working with blood cells. Despite more than a century of studying Romanowsky staining, no systematic review has been published that explains the chemical processes that produce the "Romanowsky effect" or "Romanowsky-Giemsa effect" (RGE), i.e., a purple coloration arising from the interaction of an azure dye with eosin and not due merely to their simultaneous presence. Our review is an attempt to build a bridge between chemists and biomedical scientists and to summarize the available data on methylene blue (MB) demethylation as well as the related reduction and decomposition of MB to simpler compounds by both light and enzyme systems and microorganisms. To do this, we analyze modern data on the mechanisms of MB demethylation both in the presence of acids and bases and by disproportionation due to the action of light. We also offer an explanation for why the RGE occurs only when azure B, or to a lesser extent, azure A is present by applying experimental and calculated physicochemical parameters including dye-DNA binding constants and electron density distributions in the molecules of these ligands. Finally, we discuss modern techniques for obtaining new varieties of Romanowsky dyes by modifying previously known ones. We hope that our critical literature study will help scientists understand better the chemical and physicochemical processes and mechanisms of cell staining with such dyes.
Collapse
Affiliation(s)
- Valeriy Kalinin
- A.M. Butlerov' Chemistry Institute, Kazan Federal University, Kazan, Russia
| | - Pavel Padnya
- A.M. Butlerov' Chemistry Institute, Kazan Federal University, Kazan, Russia
| | - Ivan Stoikov
- A.M. Butlerov' Chemistry Institute, Kazan Federal University, Kazan, Russia
| |
Collapse
|
14
|
Saga Y, Sasamoto Y, Inada K, Wang-Otomo ZY, Kimura Y. Spectral modulation of B850 bacteriochlorophyll a in light-harvesting complex 2 from purple photosynthetic bacterium Thermochromatium tepidum by detergents and calcium ions. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2024; 1865:149503. [PMID: 39153589 DOI: 10.1016/j.bbabio.2024.149503] [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: 07/22/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 08/19/2024]
Abstract
Spectral variations of light-harvesting (LH) proteins of purple photosynthetic bacteria provide insight into the molecular mechanisms underlying spectral tuning of circular bacteriochlorophyll (BChl) arrays, which play crucial roles in photoenergy conversion in these organisms. Here we investigate spectral changes of the Qy band of B850 BChl a in LH2 protein from purple sulfur bacterium Thermochromatium tepidum (tepidum-LH2) by detergents and Ca2+. The tepidum-LH2 solubilized with lauryl dimethylamine N-oxide and n-octyl-β-D-glucoside (LH2LDAO and LH2OG, respectively) exhibited blue-shift of the B850 Qy band with hypochromism compared with the tepidum-LH2 solubilized with n-dodecyl-β-D-maltoside (LH2DDM), resulting in the LH3-like spectral features. Resonance Raman spectroscopy indicated that this blue-shift was ascribable to the loss of hydrogen-bonding between the C3-acetyl group in B850 BChl a and the LH2 polypeptides. Ca2+ produced red-shift of the B850 Qy band in LH2LDAO by forming hydrogen-bond for the C3-acetyl group in B850 BChl a, probably due to a change in the microenvironmental structure around B850. Ca2+-induced red-shift was also observed in LH2OG although the B850 acetyl group is still free from hydrogen-bonding. Therefore, the Ca2+-induced B850 red-shift in LH2OG would originate from an electrostatic effect of Ca2+. The current results suggest that the B850 Qy band in tepidum-LH2 is primarily tuned by two mechanisms, namely the hydrogen-bonding of the B850 acetyl group and the electrostatic effect.
Collapse
Affiliation(s)
- Yoshitaka Saga
- Faculty of Science and Engineering, Kindai University, Higashi-Osaka, Osaka 577-8502, Japan.
| | - Yuhi Sasamoto
- Faculty of Science and Engineering, Kindai University, Higashi-Osaka, Osaka 577-8502, Japan
| | - Kazuki Inada
- Graduate School of Agriculture, Kobe University, Kobe 657-8501, Japan
| | | | - Yukihiro Kimura
- Graduate School of Agriculture, Kobe University, Kobe 657-8501, Japan
| |
Collapse
|
15
|
Wei Y, Liang Y, Qi K, Gu Z, Yan B, Xie H. Exploring the application of piezoelectric ceramics in bone regeneration. J Biomater Appl 2024; 39:409-420. [PMID: 39152927 DOI: 10.1177/08853282241274528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2024]
Abstract
Piezoelectric ceramics are piezoelectric materials with polycrystalline structure and have been widely used in many fields such as medical imaging and sound sensors. As knowledge about this kind of material develops, researchers find piezoelectric ceramics possess favorable piezoelectricity, biocompatibility, mechanical properties, porous structure and antibacterial effect and endeavor to apply piezoelectric ceramics to the field of bone tissue engineering. However, clinically no piezoelectric ceramics have been exercised so far. Therefore, in this paper we present a comprehensive review of the research and development of various piezoelectric ceramics including barium titanate, potassium sodium niobate and zinc oxide ceramics and aims to explore the application of piezoelectric ceramics in bone regeneration by providing a detailed overview of the current knowledge and research of piezoelectric ceramics in bone tissue regeneration.
Collapse
Affiliation(s)
- Yige Wei
- State Key Laboratory of Oral Diseases, National Center for Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yaxian Liang
- State Key Laboratory of Oral Diseases, National Center for Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Kailong Qi
- State Key Laboratory of Oral Diseases, National Center for Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Zhipeng Gu
- College of Polymer Science and Engineering, State Key Laboratory of Polymer Materials Engineering, Sichuan University, Chengdu, China
| | - Bing Yan
- State Key Laboratory of Oral Diseases, National Center for Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Huixu Xie
- State Key Laboratory of Oral Diseases, National Center for Oral Diseases, National Clinical Research Center for Oral Diseases, Department of Head and Neck Oncology Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| |
Collapse
|
16
|
Tong Y, Childs-Disney JL, Disney MD. Targeting RNA with small molecules, from RNA structures to precision medicines: IUPHAR review: 40. Br J Pharmacol 2024; 181:4152-4173. [PMID: 39224931 DOI: 10.1111/bph.17308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/10/2024] [Accepted: 07/09/2024] [Indexed: 09/04/2024] Open
Abstract
RNA plays important roles in regulating both health and disease biology in all kingdoms of life. Notably, RNA can form intricate three-dimensional structures, and their biological functions are dependent on these structures. Targeting the structured regions of RNA with small molecules has gained increasing attention over the past decade, because it provides both chemical probes to study fundamental biology processes and lead medicines for diseases with unmet medical needs. Recent advances in RNA structure prediction and determination and RNA biology have accelerated the rational design and development of RNA-targeted small molecules to modulate disease pathology. However, challenges remain in advancing RNA-targeted small molecules towards clinical applications. This review summarizes strategies to study RNA structures, to identify small molecules recognizing these structures, and to augment the functionality of RNA-binding small molecules. We focus on recent advances in developing RNA-targeted small molecules as potential therapeutics in a variety of diseases, encompassing different modes of actions and targeting strategies. Furthermore, we present the current gaps between early-stage discovery of RNA-binding small molecules and their clinical applications, as well as a roadmap to overcome these challenges in the near future.
Collapse
Affiliation(s)
- Yuquan Tong
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Jessica L Childs-Disney
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, Florida, USA
- Department of Chemistry, The Herbert Wertheim UF Scripps Institute for Biomedical Innovation & Technology, Jupiter, Florida, USA
| |
Collapse
|
17
|
Kim YJ, Shin DM, Oh EJ, Chun YG, Shin JK, Choi YS, Kim BK. Mechanisms underlying the changes in the structural, physicochemical, and emulsification properties of porcine myofibrillar proteins induced by prolonged pulsed electric field treatment. Food Chem 2024; 456:140024. [PMID: 38870818 DOI: 10.1016/j.foodchem.2024.140024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/19/2024] [Accepted: 06/06/2024] [Indexed: 06/15/2024]
Abstract
This study aimed to explore how pulsed electric field (PEF) treatment affects the structural, physicochemical, and emulsification properties of porcine-derived myofibrillar proteins (MPs). Increasing PEF treatment induced partial polarization and protein unfolding, resulting in notable denaturation that affected both the secondary and tertiary structures. PEF treatment also improved the solubility and emulsification ability of MPs by reducing their pH and surface hydrophobicity. Confocal laser scanning microscopy confirmed the effective adsorption of MPs and PEF-treated MPs at the oil/water interface, resulting in well-fabricated Pickering emulsions. A weak particle network increased the apparent viscosity in short-term PEF-treated Pickering emulsions. Conversely, in emulsions with long-term PEF-treated MP, rheological variables decreased, and dispersion stability increased. These results endorse the potential application of PEF-treated porcine-derived MPs as efficient Pickering stabilizers, offering valuable insights into the creative use of PEF for enhancing high-quality meat products, meeting the increasing demand for clean-label choices.
Collapse
Affiliation(s)
- Yun Jeong Kim
- Research Group of Food Processing, Korea Food Research Institute, Wanju 55365, Republic of Korea.; Department of Food Biotechnology, Korea National University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Dong-Min Shin
- Food Science and Technology, Keimyung University, Daegu 42601, Republic of Korea
| | - Eun-Jae Oh
- Research Group of Food Processing, Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Yong Gi Chun
- Research Group of Food Processing, Korea Food Research Institute, Wanju 55365, Republic of Korea
| | - Jung-Kue Shin
- Department of Korean Cuisine, Jeonju University, Jeonju 55069, Republic of Korea
| | - Yun-Sang Choi
- Research Group of Food Processing, Korea Food Research Institute, Wanju 55365, Republic of Korea..
| | - Bum-Keun Kim
- Research Group of Food Processing, Korea Food Research Institute, Wanju 55365, Republic of Korea.; Department of Food Biotechnology, Korea National University of Science and Technology, Daejeon 34113, Republic of Korea..
| |
Collapse
|
18
|
Shreesha L, Levin M. Stress sharing as cognitive glue for collective intelligences: A computational model of stress as a coordinator for morphogenesis. Biochem Biophys Res Commun 2024; 731:150396. [PMID: 39018974 PMCID: PMC11356093 DOI: 10.1016/j.bbrc.2024.150396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 07/03/2024] [Accepted: 07/11/2024] [Indexed: 07/19/2024]
Abstract
Individual cells have numerous competencies in physiological and metabolic spaces. However, multicellular collectives can reliably navigate anatomical morphospace towards much larger, reliable endpoints. Understanding the robustness and control properties of this process is critical for evolutionary developmental biology, bioengineering, and regenerative medicine. One mechanism that has been proposed for enabling individual cells to coordinate toward specific morphological outcomes is the sharing of stress (where stress is a physiological parameter that reflects the current amount of error in the context of a homeostatic loop). Here, we construct and analyze a multiscale agent-based model of morphogenesis in which we quantitatively examine the impact of stress sharing on the ability to reach target morphology. We found that stress sharing improves the morphogenetic efficiency of multicellular collectives; populations with stress sharing reached anatomical targets faster. Moreover, stress sharing influenced the future fate of distant cells in the multi-cellular collective, enhancing cells' movement and their radius of influence, consistent with the hypothesis that stress sharing works to increase cohesiveness of collectives. During development, anatomical goal states could not be inferred from observation of stress states, revealing the limitations of knowledge of goals by an extern observer outside the system itself. Taken together, our analyses support an important role for stress sharing in natural and engineered systems that seek robust large-scale behaviors to emerge from the activity of their competent components.
Collapse
Affiliation(s)
| | - Michael Levin
- Department of Biology, Tufts University, Medford, MA, 02155, USA; Allen Discovery Center at Tufts University, Medford, MA, 02155, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
| |
Collapse
|
19
|
Lu Z, Gui L, Sun X, Wang K, Lan Y, Deng Y, Cao S, Xu K. Unveiling the impact of low-frequency electrical stimulation on network synchronization and learning behavior in cultured hippocampal neural networks. Biochem Biophys Res Commun 2024; 731:150363. [PMID: 39018969 DOI: 10.1016/j.bbrc.2024.150363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 06/14/2024] [Accepted: 07/04/2024] [Indexed: 07/19/2024]
Abstract
Understanding the dynamics of neural networks and their response to external stimuli is crucial for unraveling the mechanisms associated with learning processes. In this study, we hypothesized that electrical stimulation (ES) would lead to significant alterations in the activity patterns of hippocampal neuronal networks and investigated the effects of low-frequency ES on hippocampal neuronal populations using the microelectrode arrays (MEAs). Our findings revealed significant alterations in the activity of hippocampal neuronal networks following low-frequency ES trainings. Post-stimulation, the neural activity exhibited an organized burst firing pattern characterized by increased spike and burst firings, increased synchronization, and enhanced learning behaviors. Analysis of peri-stimulus time histograms (PSTHs) further revealed that low-frequency ES (1Hz) significantly enhanced neural plasticity, thereby facilitating the learning process of cultured neurons, whereas high-frequency ES (>10Hz) impeded this process. Moreover, we observed a substantial increase in correlations and connectivity within neuronal networks following ES trainings. These alterations in network properties indicated enhanced synaptic plasticity and emphasized the positive impact of low-frequency ES on hippocampal neural activities, contributing to the brain's capacity for learning and memory.
Collapse
Affiliation(s)
- Zeying Lu
- State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing, PR China
| | - Lili Gui
- State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing, PR China.
| | - Xiaojuan Sun
- State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing, PR China; School of Science, Beijing University of Posts and Telecommunications, PR China
| | - Ke Wang
- State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing, PR China
| | - Yueheng Lan
- State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing, PR China; School of Science, Beijing University of Posts and Telecommunications, PR China
| | - Yin Deng
- State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing, PR China
| | - Shiyang Cao
- State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing, PR China
| | - Kun Xu
- State Key Laboratory of Information Photonics and Optical Communications, Beijing University of Posts and Telecommunications, Beijing, PR China
| |
Collapse
|
20
|
Parlow J, Rodler A, Gråsjö J, Sjögren H, Hansson P. FRAP analysis of peptide diffusion in extracellular matrix mimetic hydrogels as an in vitro model for subcutaneous injection. Int J Pharm 2024; 664:124628. [PMID: 39179009 DOI: 10.1016/j.ijpharm.2024.124628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 08/20/2024] [Accepted: 08/20/2024] [Indexed: 08/26/2024]
Abstract
Subcutaneous (SC) injection is a common route of administration for drug compounds with poor oral bioavailability. However, bioavailability is often variable and incomplete, and there is as yet no standard accepted medium for simulation of the human SC environment. In this work we evaluate a FRAP based method for quantitative determination of local self-diffusion coefficients within extracellular matrix (ECM) mimetic hydrogels, potentially useful as in vitro models for drug transport in the ECM after SC injection. Gels were made consisting of either agarose, cross-linked collagen (COL) and hyaluronic acid (HA) or cross-linked HA. The diffusivities of uncharged FITC-dextran (FD4), the highly charged poly-lysine (PLK20) and poly-glutamic acid (PLE20) as well as the GLP-1 analogue exenatide were determined within the gels using FRAP. The diffusion coefficients in uncharged agarose gels were in the range of free diffusion in PBS. The diffusivity of cationic PLK20 in gels containing anionic HA was substantially decreased due to strong electrostatic interactions. Peptide aggregation could be observed as immobile fractions in experiments with exenatide. We conclude that the FRAP method provides useful information of peptides' interactions and transport properties in hydrogel networks, giving insight into the mechanisms affecting absorption of drug compounds after subcutaneous injection.
Collapse
Affiliation(s)
- Julia Parlow
- Department of Medicinal Chemistry, Uppsala University, SE-75123 Uppsala, Sweden
| | - Agnes Rodler
- Department of Medicinal Chemistry, Uppsala University, SE-75123 Uppsala, Sweden
| | - Johan Gråsjö
- Department of Medicinal Chemistry, Uppsala University, SE-75123 Uppsala, Sweden
| | - Helen Sjögren
- Ferring Pharmaceuticals A/S, Amager Strandvej 405, DK-2770 Kastrup, Denmark
| | - Per Hansson
- Department of Medicinal Chemistry, Uppsala University, SE-75123 Uppsala, Sweden.
| |
Collapse
|
21
|
Stepanyan V, Badasyan A, Morozov V, Mamasakhlisov Y, Podgornik R. Sequence disorder-induced first order phase transition in confined polyelectrolytes. J Chem Phys 2024; 161:134906. [PMID: 39356068 DOI: 10.1063/5.0228162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Accepted: 09/18/2024] [Indexed: 10/03/2024] Open
Abstract
We consider a statistical mechanical model of a generic flexible polyelectrolyte, comprised of identically charged monomers with long-range electrostatic interactions and short-range interactions quantified by a disorder field along the polymer contour sequence, which is randomly quenched. The free energy and the monomer density profile of the system for no electrolyte screening are calculated in the case of a system composed of two infinite planar bounding surfaces with an intervening oppositely charged polyelectrolyte chain. We show that the effect of the contour sequence disorder, mediated by short-range interactions, leads to an enhanced localization of the polyelectrolyte chain and a first order phase transition at a critical value of the inter-surface spacing. This phase transition results in an abrupt change of the pressure from negative to positive values, effectively eliminating polyelectrolyte mediated bridging attraction.
Collapse
Affiliation(s)
| | - A Badasyan
- University of Nova Gorica, Nova Gorica, Slovenia
| | - V Morozov
- Institute of Applied Problems of Physics, Yerevan, Armenia
| | - Y Mamasakhlisov
- Yerevan State University, Yerevan, Armenia
- Institute of Applied Problems of Physics, Yerevan, Armenia
| | - R Podgornik
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
- Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou, Zhejiang 325011, China
- Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, 1000 Ljubljana, Slovenia
| |
Collapse
|
22
|
Nishio T, Schiessel H. Coalescence of liquid or gel-like DNA-encapsulating microdroplets. J Chem Phys 2024; 161:134904. [PMID: 39356067 DOI: 10.1063/5.0223951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Accepted: 09/19/2024] [Indexed: 10/03/2024] Open
Abstract
Liquid-liquid phase separation plays a prominent role in the physics of life, providing the cells with various membrane-less compartments. These structures exhibit a range of material properties that, in many cases, change over time. Inspired by this, we investigate here an aqueous two-phase system formed by mixing polyethylene glycol with dextran. We modulate the material properties of the resulting dextran droplets by adding DNA that readily enters the droplets. We find a non-monotonic dependence of the physical properties of the droplets under the imposed ionic conditions.
Collapse
Affiliation(s)
- Takashi Nishio
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, 01307 Dresden, Germany
| | - Helmut Schiessel
- Cluster of Excellence Physics of Life, TUD Dresden University of Technology, 01307 Dresden, Germany
- Institut für Theoretische Physik, TUD Dresden University of Technology, 01062 Dresden, Germany
| |
Collapse
|
23
|
Altıntop MD, Ertorun İ, Akalın Çiftçi G, Özdemir A. Design, synthesis and biological evaluation of a new series of imidazothiazole-hydrazone hybrids as dual EGFR and Akt inhibitors for NSCLC therapy. Eur J Med Chem 2024; 276:116698. [PMID: 39047611 DOI: 10.1016/j.ejmech.2024.116698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/24/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
In search of small molecules for targeted therapy of non-small cell lung carcinoma (NSCLC), an efficient four-step synthetic route was followed for the synthesis of new imidazothiazole-hydrazone hybrids, which were assessed for their cytotoxic effects on human lung adenocarcinoma (A549) and human lung fibroblast (CCD-19Lu) cells. Among them, compounds 4, 6, 13, 16, 17 and 21 exhibited selective cytotoxic activity against A549 cell line. In vitro mechanistic studies were performed to assess their effects on apoptosis, caspase-3, cell cycle, EGFR and Akt in A549 cells. Compounds 6, 16, 17 and 21 promoted apoptotic cell death more than erlotinib. According to the in vitro data, it is quite clear that compound 6 promotes apoptosis through caspase-3 activation and arrests the cell cycle at the G0/G1 phase in A549 cells. Compounds 16 and 17 arrested the cell cycle at the S phase, whereas compounds 4, 13 and 21 caused the cell cycle arrest at the G2/M phase. The most effective EGFR inhibitor in this series was found as compound 13, followed by compounds 17 and 16. Furthermore, Akt inhibitory effects of compounds 16 and 17 in A549 cells were close to that of GSK690693. In particular, it can be concluded that the cytotoxic and apoptotic effects of compounds 16 and 17 are associated with their inhibitory effects on both EGFR and Akt. Molecular docking studies suggest that compounds 16 and 17 interact with crucial amino acid residues in the binding sites of human EGFR (PDB ID: 1M17) and Akt2 (PDB ID: 3D0E). Based on the in silico data, both compounds are predicted to possess favorable oral bioavailability and drug-likeness. Further studies are required to benefit from these compounds as anticancer agents for targeted therapy of NSCLC.
Collapse
Affiliation(s)
- Mehlika Dilek Altıntop
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470, Eskişehir, Turkey
| | - İpek Ertorun
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, 26470, Eskişehir, Turkey
| | - Gülşen Akalın Çiftçi
- Department of Biochemistry, Faculty of Pharmacy, Anadolu University, 26470, Eskişehir, Turkey
| | - Ahmet Özdemir
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Anadolu University, 26470, Eskişehir, Turkey.
| |
Collapse
|
24
|
Zhang D, Feng F, Chen Y, Sui J, Ding L. The potential of marine natural products and their synthetic derivatives as drugs targeting ion channels. Eur J Med Chem 2024; 276:116644. [PMID: 38971051 DOI: 10.1016/j.ejmech.2024.116644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/20/2024] [Accepted: 06/29/2024] [Indexed: 07/08/2024]
Abstract
Ion channels are a type of protein channel that play a vital role in numerous physiological functions by facilitating the passage of ions through cell membranes, thereby enabling ion and electrical signal transmission. As a crucial target for drug action, ion channels have been implicated in various diseases. Many natural products from marine organisms, such as fungi, algae, sponges, and sea cucumber, etc. have been found to have activities related to ion channels for decades. These interesting natural product molecules undoubtedly bring good news for the treatment of neurological and cardiovascular diseases. In this review, 92 marine natural products and their synthetic derivatives with ion channel-related activities that were identified during the period 2000-2024 were systematically reviewed. The synthesis and mechanisms of action of selected compounds were also discussed, aiming to offer insights for the development of drugs targeting ion channels.
Collapse
Affiliation(s)
- Dashuai Zhang
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, School of Pharmacy, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Fangjian Feng
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, School of Pharmacy, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Yaoyao Chen
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, School of Pharmacy, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Jingyao Sui
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, School of Pharmacy, Health Science Center, Ningbo University, Ningbo, 315211, China
| | - Lijian Ding
- Li Dak Sum Yip Yio Chin Kenneth Li Marine Biopharmaceutical Research Center, School of Pharmacy, Health Science Center, Ningbo University, Ningbo, 315211, China.
| |
Collapse
|
25
|
Crescenzi O, Graziano G. The interaction of thiocyanate with peptides-A computational study. J Comput Chem 2024; 45:2214-2231. [PMID: 38795315 DOI: 10.1002/jcc.27440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 05/07/2024] [Accepted: 05/14/2024] [Indexed: 05/27/2024]
Abstract
According to the Hofmeister series, thiocyanate is the strongest "salting in" anion. In fact, it has a strong denaturant activity against the native state of globular proteins. A molecular level rationalization of the Hofmeister series is still missing, and therefore the denaturant activity of thiocyanate also awaits a robust explanation. In the last years, different types of experimental studies have shown that thiocyanate is capable to directly interact with both polar and nonpolar groups of polypeptide chains. This finding has been scrutinized via a careful computational procedure based on density functional theory approaches. The results indicate that thiocyanate is able to make H-bonds via both the nitrogen and sulfur atom, and to make strong van der Waals interactions with almost all the groups of polypeptide chains, regardless of their polarity.
Collapse
Affiliation(s)
- Orlando Crescenzi
- Dipartimento di Scienze Chimiche, Università di Napoli Federico II, Naples, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Benevento, Italy
| |
Collapse
|
26
|
Galindo AV, Raj M. Solvent-Dependent Chemoselectivity Switch to Arg-Lys Imidazole Cross-Links. Org Lett 2024; 26:8356-8360. [PMID: 39303223 DOI: 10.1021/acs.orglett.4c03101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Herein, we report a trifluoroethanol-mediated, chemoselective method for the formation of Arg-Lys imidazole cross-links with methylglyoxal and its application in the selective macrocyclization of peptides between Lys and Arg and the late-stage diversification of Lys-containing peptides with guanidine. Our findings highlight the critical role of solvent choice in controlling chemoselectivity, providing valuable insights into solvent-dependent peptide modification.
Collapse
Affiliation(s)
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
27
|
Yasuda T, Nakajima N, Ogi T, Yanaka T, Tanaka I, Gotoh T, Kagawa W, Sugasawa K, Tajima K. Heavy water inhibits DNA double-strand break repairs and disturbs cellular transcription, presumably via quantum-level mechanisms of kinetic isotope effects on hydrolytic enzyme reactions. PLoS One 2024; 19:e0309689. [PMID: 39361575 DOI: 10.1371/journal.pone.0309689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Accepted: 08/16/2024] [Indexed: 10/05/2024] Open
Abstract
Heavy water, containing the heavy hydrogen isotope, is toxic to cells, although the underlying mechanism remains incompletely understood. In addition, certain enzymatic proton transfer reactions exhibit kinetic isotope effects attributed to hydrogen isotopes and their temperature dependencies, indicative of quantum tunneling phenomena. However, the correlation between the biological effects of heavy water and the kinetic isotope effects mediated by hydrogen isotopes remains elusive. In this study, we elucidated the kinetic isotope effects arising from hydrogen isotopes of water and their temperature dependencies in vitro, focusing on deacetylation, DNA cleavage, and protein cleavage, which are crucial enzymatic reactions mediated by hydrolysis. Intriguingly, the intracellular isotope effects of heavy water, related to the in vitro kinetic isotope effects, significantly impeded multiple DNA double-strand break repair mechanisms crucial for cell survival. Additionally, heavy water exposure enhanced histone acetylation and associated transcriptional activation in cells, consistent with the in vitro kinetic isotope effects observed in histone deacetylation reactions. Moreover, as observed for the in vitro kinetic isotope effects, the cytotoxic effect on cell proliferation induced by heavy water exhibited temperature-dependency. These findings reveal the substantial impact of heavy water-induced isotope effects on cellular functions governed by hydrolytic enzymatic reactions, potentially mediated by quantum-level mechanisms underlying kinetic isotope effects.
Collapse
Affiliation(s)
- Takeshi Yasuda
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Nakako Nakajima
- QST Hospital, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Tomoo Ogi
- Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Tomoko Yanaka
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Izumi Tanaka
- Institute for Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Takaya Gotoh
- Department of Health Science, Daito Bunka University, Saitama, Japan
| | - Wataru Kagawa
- Department of Interdisciplinary Science and Engineering, Program in Chemistry and Life Science, School of Science and Engineering, Meisei University, Tokyo, Japan
| | - Kaoru Sugasawa
- Biosignal Research Center, and Graduate School of Science, Kobe University, Kobe, Japan
| | - Katsushi Tajima
- Department of Hematology, Yamagata Prefectural Central Hospital, Yamagata, Japan
| |
Collapse
|
28
|
Dolai S, Pal S, Deepa S, Garai K. Quantitative Assessment of Conformational Heterogeneity in Apolipoprotein E4 Using Hydrogen-Deuterium Exchange Mass Spectrometry. J Phys Chem B 2024. [PMID: 39360975 DOI: 10.1021/acs.jpcb.4c04738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2024]
Abstract
Apolipoprotein E4 (apoE4) is the strongest genetic risk factor for Alzheimer's disease (AD). However, structural differences between apoE4 and the AD-neutral isoform, apoE3, still remain unclear. Recent studies suggest that apoE4 harbors intermediates. However, the biophysical properties and isoform specificity of these intermediates are not known. Here, we use the kinetics of hydrogen-deuterium exchange by mass spectrometry (HDX-MS) to examine the conformational heterogeneities in apoE3 and apoE4. First, we use numerical simulations to compute the HDX-mass spectra of a protein following mixed EX1/EX2 kinetics. The results indicate that in the presence of EX1 kinetics, which is an indicator of conformational heterogeneity, time evolution of the standard deviation (σ(t)) of the spectra exhibits a clear peak, which is dependent on the number of residues (NEX1) and the rate constant of EX1 kinetics (kEX1). Then, we performed experiments with several variants of the apoE proteins and compared them with simulation to estimate NEX1 and kEX1. Kinetics of the mean deuteration is found to be faster for apoE4, consistent with its poorer stability than apoE3. Importantly, in the case of apoE4, σ(t) exhibits a clear peak at t ∼ 60 s, but apoE3 shows only a small peak at 1800 s. Therefore, both NEX1 and kEX1 are larger for apoE4, indicating greater conformational heterogeneity. Notably, the partial EX1 kinetics is observed in both the isolated N-terminal fragment and the full-length form of apoE4, although it is more pronounced in the full-length protein. Moreover, it is enhanced at higher pH and in the presence of bis-ANS. Mutations such as R61T and R112I diminish the EX1 kinetics, making apoE4 behave more like apoE3. Thus, the amino acid substitution at position 112 alters the structural dynamics of the N-terminal domain of apoE4; the changes are further propagated and amplified in the full-length protein. We conclude that HDX-MS is a label-free and robust methodology to characterize structural heterogeneities of proteins even under native conditions. This opens opportunities for screening of the "structure corrector" drug molecules that could convert apoE4 to apoE3-like.
Collapse
Affiliation(s)
- Subhrajyoti Dolai
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Sudip Pal
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - S Deepa
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| | - Kanchan Garai
- Tata Institute of Fundamental Research, 36/P, Gopanpally Village, Serilingampally Mandal, Hyderabad 500046, India
| |
Collapse
|
29
|
Tan P, Liu T, Yang Y, Chen Y, Guan Y, Li Z, Yu S, Yang X, Xiang X, Zhao X, Li Y, Ding H, Wu X, Fink Z, Gao S, Hou X, Jiao X, Zhu J, Fan F, Yang S, Russell TP, Liu X, Hu Q, Long S. Flexible Soft X-Ray Image Sensors based on Metal Halide Perovskites With High Quantum Efficiency. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024:e2407244. [PMID: 39363637 DOI: 10.1002/adma.202407244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/02/2024] [Indexed: 10/05/2024]
Abstract
Soft X-ray imaging is a powerful tool to explore the structure of cells, probe material with nanometer resolution, and investigate the energetic phenomena in the universe. Conventional soft X-ray image sensors are by and large Si-based charge coupled devices that suffer from low frame rates, complex fabrication processes, mechanical inflexibility, and required cooling below -60 °C. Here, a soft X-ray photodiode is reported based on low-cost metal halide perovskite with comparable performance to commercial Si-based device. Nanothrough network electrode minimized the optical loss due to the shadowing of insensitive layers, while a multidimensional perovskite heterojunction is generated to reduce the photo-generated carrier loss. This strategy promoted a record quantum efficiency of 8 × 103% without cooling, several orders of magnitude greater than the previously achieved. Flexible and curved soft X-ray imaging arrays are fabricated based on this high-performance device structure, demonstrating stable soft X-ray response and sharp imaging capabilities. This work highlights the low-cost and efficient perovskite photodiode as a strong candidate for the next-generation soft X-ray image sensors.
Collapse
Affiliation(s)
- Pengju Tan
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| | - Tianyu Liu
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| | - Yuqian Yang
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| | - Yuangan Chen
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| | - Yong Guan
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, China
| | - Zidu Li
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Shunjie Yu
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| | - Xunyong Yang
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| | - Xueqiang Xiang
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| | - Xiaolong Zhao
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| | - Yu Li
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, China
| | - Honghe Ding
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, China
| | - Xuefei Wu
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Zachary Fink
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, MA, 01003, USA
- Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Shuang Gao
- Key Laboratory of Precision and Intelligent Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Department of Materials Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Xiaohu Hou
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| | - Xuechen Jiao
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, China
| | - Junfa Zhu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, China
| | - Fengjia Fan
- CAS Key Laboratory of Microscale Magnetic Resonance and School of Physical Sciences, University of Science and Technology of China, Hefei, 230026, China
| | - Shangfeng Yang
- Key Laboratory of Precision and Intelligent Chemistry, Collaborative Innovation Center of Chemistry for Energy Materials (iChEM), Department of Materials Science and Engineering, University of Science and Technology of China, Hefei, 230026, China
| | - Thomas P Russell
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Polymer Science and Engineering Department, University of Massachusetts, Amherst, MA, 01003, USA
| | - Xiaosong Liu
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230029, China
| | - Qin Hu
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| | - Shibing Long
- School of Microelectronics, University of Science and Technology of China, Hefei, 230026, China
| |
Collapse
|
30
|
Rossi E, Kundu A, Ferrarini A, Elsaesser T, Sulpizi M. Structure and Dynamics of ATP and the ATP-Zn 2+ Complex in Solution. J Phys Chem Lett 2024; 15:10039-10045. [PMID: 39323317 DOI: 10.1021/acs.jpclett.4c02296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Despite the crucial role of ATP in life and artificial life-like applications, fundamental aspects relevant to its function, such as its conformational properties and its interaction with water and ions, remain unclear. Here, by integrating linear and two-dimensional infrared spectroscopy with ab initio molecular dynamics, we provide a detailed characterization of the vibrational spectra of the phosphate groups in ATP and in its complex with Zn2+ in water. Our study highlights the role of conformational disorder and solvation dynamics, beyond the harmonic normal-mode analysis, and reveals a complex scenario in which electronic and environmental effects tune the coupling between phosphate vibrations. We identify βγ-bidentate and αβγ-tridentate modes as the preferential coordination modes of Zn2+, as was proposed in the literature for Mg2+, although this conclusion is reached by a different spectral interpretation.
Collapse
Affiliation(s)
- Emma Rossi
- Università degli Studi di Padova, Department of Chemical Sciences, 35131 Padova, Italy
- Ruhr-Universität Bochum, Department of Physics and Astronomy, 44801 Bochum, Germany
| | - Achintya Kundu
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Alberta Ferrarini
- Università degli Studi di Padova, Department of Chemical Sciences, 35131 Padova, Italy
| | - Thomas Elsaesser
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, 12489 Berlin, Germany
| | - Marialore Sulpizi
- Ruhr-Universität Bochum, Department of Physics and Astronomy, 44801 Bochum, Germany
| |
Collapse
|
31
|
Xu C, Käser T, Xia Y, Kumar N, Zenobi R. Probing Deuteration-Induced Phase Separation in Supported Lipid Monolayers using Hyperspectral TERS Imaging. J Phys Chem Lett 2024:10237-10243. [PMID: 39356968 DOI: 10.1021/acs.jpclett.4c01994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
In this study, we investigate the impact of deuteration on the formation of phase-separated domains in supported lipid monolayers using hyperspectral Tip-Enhanced Raman Spectroscopy (TERS) imaging. The intricate organization of biological membranes plays a crucial role in cellular functions. Various factors that influence domain formation have been identified in previous studies such as lipid tail length and cholesterol concentration. Deuterium labeling of lipids has proven useful for probing cellular structures and dynamics, but its impact on lipid phase separation remains underexplored. By examining 1:1 mixed monolayers of dipalmitoylphosphatidylcholine (DPPC) and deuterated DPPC on Au(111) surfaces, we reveal partial segregation of domains rich in deuterated and nondeuterated lipids. This study addresses a gap in knowledge by examining the impact of deuteration on lipid tail behavior, offering new insights into how even subtle structural modifications can influence phase behavior. Furthermore, it demonstrates that TERS can be a powerful, nondestructive, and label-free nanoanalytical tool for analyzing lipid membranes and advance the field of membrane biophysics.
Collapse
Affiliation(s)
- Chengcheng Xu
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Timon Käser
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Yuanzhi Xia
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Naresh Kumar
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| | - Renato Zenobi
- Department of Chemistry and Applied Biosciences, ETH Zurich, 8093 Zurich, Switzerland
| |
Collapse
|
32
|
Xue L, Chen W, Zheng P, Geng J, Zhang F, Li X, Zhang Z, Hu X. Catalyst-Free Oxidation of Styrene to Styrene Oxide Using Circulating Microdroplets in an Oxygen Atmosphere. J Am Chem Soc 2024; 146:26909-26915. [PMID: 39300790 DOI: 10.1021/jacs.4c08018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Water microdroplets possess unique interfacial properties that enable chemical reactions to occur spontaneously and increase the reaction rate by orders of magnitude. In this study, water containing styrene (SY) was cyclically sprayed into the air to form microdroplets with an average diameter of 6.7 μm. These microdroplets allowed SY to be oxidized into styrene oxide (SO) without catalysts. No oxidation products of SY were observed in the bulk solution under the same conditions, while in microdroplet reactions 4.2% conversion of SY with approximately 3.1 mM SO was detected. Compared with the traditional spraying microdroplet method, the oxidation product concentration was enhanced by 1000 times. Experiments proved that an aerobic environment boosts SY oxidation, leading to a proposed dual-path hydrogen peroxide (H2O2) oxidation mechanism at the droplet interface. This was confirmed by density functional theory calculations (DFT). Furthermore, in the presence of additional ultrasound, the SY oxidation process initiated by water droplets can be further enhanced, and 7.0% conversion of SY with approximately 5.2 mM SO was detected. The cyclic spraying method greatly enhanced the oxidation product concentration, showing the potential for large scale chemical production using microdroplets.
Collapse
Affiliation(s)
- Lian Xue
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Weida Chen
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Peng Zheng
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Jiao Geng
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Feng Zhang
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Xinyao Li
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Zhibing Zhang
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| | - Xingbang Hu
- Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, PR China
| |
Collapse
|
33
|
Posey AE, Bremer A, Erkamp NA, Pant A, Knowles TPJ, Dai Y, Mittag T, Pappu RV. Biomolecular Condensates are Characterized by Interphase Electric Potentials. J Am Chem Soc 2024. [PMID: 39356108 DOI: 10.1021/jacs.4c08946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2024]
Abstract
Biomolecular condensates form via processes that combine phase separation and reversible associations of multivalent macromolecules. Condensates can be two- or multiphase systems defined by coexisting dense and dilute phases. Here, we show that solution ions partition asymmetrically across coexisting phases defined by condensates formed by intrinsically disordered proteins or homopolymeric RNA molecules. Our findings were enabled by direct measurements of the activities of cations and anions within coexisting phases of protein and RNA condensates. Asymmetries in ion partitioning between coexisting phases vary with protein sequence, macromolecular composition, salt concentration, and ion type. The Donnan equilibrium set up by the asymmetrical partitioning of solution ions generates interphase electric potentials known as Donnan and Nernst potentials. Our measurements show that the interphase potentials of condensates are of the same order of magnitude as membrane potentials of membrane-bound organelles. Interphase potentials quantify the degree to which microenvironments of coexisting phases are different from one another. Importantly, and based on condensate-specific interphase electric potentials, we reason that condensates are akin to capacitors that store charge. Interphase potentials should lead to electric double layers at condensate interfaces, thereby explaining recent observations of condensate interfaces being electrochemically active.
Collapse
Affiliation(s)
- Ammon E Posey
- Department of Biomedical Engineering, Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899, United States
| | - Anne Bremer
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38103, United States
| | - Nadia A Erkamp
- Department of Biomedical Engineering, Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899, United States
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Avnika Pant
- Department of Biomedical Engineering, Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899, United States
| | - Tuomas P J Knowles
- Yusuf Hamied Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
- Cavendish Laboratory, Department of Physics, University of Cambridge, J. J. Thomson Ave, Cambridge CB3 0HE, U.K
| | - Yifan Dai
- Department of Biomedical Engineering, Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899, United States
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38103, United States
| | - Rohit V Pappu
- Department of Biomedical Engineering, Center for Biomolecular Condensates, James McKelvey School of Engineering, Washington University in St. Louis, St. Louis, Missouri 63130-4899, United States
| |
Collapse
|
34
|
Zhao M, Cho SH, Wu X, Mao J, Vogt BD, Zacharia NS. Covalently crosslinked coacervates: immobilization and stabilization of proteins with enhanced enzymatic activity. SOFT MATTER 2024; 20:7623-7633. [PMID: 39291470 DOI: 10.1039/d4sm00765d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2024]
Abstract
Coacervates represent models for membrane-free protocells and thus provide a simple route to synthetic cellular-like systems that provide selective encapsulation of solutes. Here, we demonstrate a simple and versatile post-coacervation crosslink method using the thiol-ene click reaction in aqueous media to prepare covalently crosslinked coacervates. The crosslinking of the coacervate enables stability at extreme pH where the uncrosslinked coacervate fully disassembles. The crosslinking also enhances the hydrophobicity within the coacervate environment to increase the encapsulation efficiency of bovine serum albumin (BSA), as compared to the uncrosslinked coacervate. Additionally, the crosslinked coacervate increases the stabilization of BSA at low pH. These crosslinked coacervates can act as carriers for enzymes. The enzymatic activity of alkaline phosphatase (ALP) is enhanced within the crosslinked coacervate compared to the ALP in aqueous solution. The post-coacervation crosslink approach allows the utilization of coacervates for encapsulation of biologicals under conditions where the coacervate would generally disassemble. We demonstrate that these crosslinked coacervates enable the protection of encapsulated protein against denaturation at extreme pH and enhance the enzymatic activity with encapsulation. This click approach to stabilization of coacervates should be broadly applicable to other systems for a variety of biologics and environmentally sensitive molecules.
Collapse
Affiliation(s)
- Mengmeng Zhao
- Department of Polymer Engineering, University of Akron, Akron OH 44325, USA
| | - Szu-Hao Cho
- Department of Polymer Engineering, University of Akron, Akron OH 44325, USA
| | - Xinchi Wu
- Department of Polymer Engineering, University of Akron, Akron OH 44325, USA
| | - Jingyi Mao
- Department of Polymer Engineering, University of Akron, Akron OH 44325, USA
| | - Bryan D Vogt
- Department of Polymer Engineering, University of Akron, Akron OH 44325, USA
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA 16802, USA.
| | - Nicole S Zacharia
- Department of Polymer Engineering, University of Akron, Akron OH 44325, USA
| |
Collapse
|
35
|
Xu X, Poggetto GD, McCoy M, Reibarkh M, Trigo-Mourino P. Rapid Characterization of Structural and Behavioral Changes of Therapeutic Proteins by Relaxation and Diffusion 1H-SOFAST NMR Experiments. Anal Chem 2024. [PMID: 39356572 DOI: 10.1021/acs.analchem.4c03479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
Abstract
Biologic drugs have emerged as a rapidly expanding and important modality, offering promising therapeutic solutions by interacting with previously "undruggable" targets, thus significantly expanding the range of modern pharmaceutical applications. However, the inherent complexity of these drugs also introduces liabilities and poses challenges in their development, necessitating efficient screening methods to evaluate the structural stability and behavior. Although nuclear magnetic resonance (NMR) spectroscopy is well-suited for detecting weak interactions, changes in dynamics, high-order structure, and association states of macromolecules in fully formulated samples, the inherent low sensitivity limits its utility as a fast screening and characterization tool. In this study, we present two fast pulsing NMR experiments, namely the band-Selective Optimized Flip-Angle Internally encoded Relaxation (SOFAIR) and the band-Selective Optimized Flip-angle Internally encoded Translational diffusion (SOFIT)), which enable rapid and reliable measurements of transverse relaxation rates and diffusion coefficients with more than 10-fold higher sensitivity compared to commonly used methods, like Carr-Purcell-Meiboom-Gill and diffusion-ordered spectroscopy, allowing the rapid assessment of biologics even at low concentrations. We demonstrated the effectiveness and versatility of these experiments by evaluating several examples, including thermally stressed proteins, proteins at different concentrations, and a therapeutic protein in various formulations. We anticipate that these novel approaches will greatly facilitate the analysis and characterization of biologics during drug discovery.
Collapse
Affiliation(s)
- Xingjian Xu
- Analytical Research & Development, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Guilherme Dal Poggetto
- Analytical Research & Development, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mark McCoy
- Quantitative Biosciences, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Mikhail Reibarkh
- Analytical Research & Development, MRL, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Pablo Trigo-Mourino
- Analytical Research & Development, MRL, Merck & Co., Inc., Boston, Massachusetts 02115, United States
| |
Collapse
|
36
|
Ito K, Tayama T, Uemura S, Iizuka R. Isolation of novel fluorogenic RNA aptamers via in vitro compartmentalization using microbead-display libraries. Talanta 2024; 278:126488. [PMID: 38955098 DOI: 10.1016/j.talanta.2024.126488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 06/12/2024] [Accepted: 06/28/2024] [Indexed: 07/04/2024]
Abstract
Fluorogenic RNA aptamers, which specifically bind to fluorogens and dramatically enhance their fluorescence, are valuable for imaging and detecting RNAs and metabolites in living cells. Most fluorogenic RNA aptamers have been identified and engineered through iterative rounds of in vitro selection based on their binding to target fluorogens. While such selection is an efficient approach for generating RNA aptamers, it is less efficient for isolating fluorogenic aptamers because it does not directly screen for fluorogenic properties. In this study, we combined a fluorescence-based in vitro selection technique using water-in-oil microdroplets with an affinity-based selection technique to obtain fluorogenic RNA aptamers. This approach allowed us to identify novel fluorogenic aptamers for a biotin-modified thiazole orange derivative. Our results demonstrate that our approach can expand the diversity of fluorogenic RNA aptamers, thus leading to new applications for the imaging and detection of biomolecules.
Collapse
Affiliation(s)
- Keisuke Ito
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Tomotaka Tayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Sotaro Uemura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Chiyoda-ku, Tokyo, 102-0075, Japan.
| | - Ryo Iizuka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
| |
Collapse
|
37
|
Kämäräinen T, Nakayama Y, Uchiyama H, Tozuka Y, Kadota K. Amyloid Nanofibril-Assisted Spray Drying of Crumpled Supraparticles. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2309645. [PMID: 38716922 DOI: 10.1002/smll.202309645] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/19/2024] [Indexed: 10/04/2024]
Abstract
Nanofibrils are known to improve the cohesion of supraparticle (SP) assemblies. However, tailoring the morphology of SPs using nanofibrillar additives is not well developed. Herein, β-lactoglobulin amyloid nanofibrils (ANFs) are investigated as means to impart morphological control over the assembly process of spray-dried SPs composed of 10-100 nm silica nanoparticles (SiNPs). Phytoglycogen (PG) and silver nanowires (AgNWs) are used to assess the influence of building block softness and aspect ratio, respectively. The results demonstrate that ANFs promote the onset of structural arrest during the particle consolidation enabling the preparation of corrugated SP morphologies. The critical ANF loading required to induce SP corrugation increases by roughly 1 vol% for every 10-nm increase in SiNP diameter, while the ensuing ANF network density decreases with SiNP volume fraction and increases with SiNP diameter. Results imply that ANF length starts to become influential when it approaches the SiNP diameter. ANFs display a reduced effectiveness in altering soft PG SP morphology compared with hard SiNPs of comparable size. In SiNP-AgNW SPs, ANFs induce a toroid-to-corrugated morphology transformation for sufficiently large SPs and small SiNPs. The results illustrate that ANFs are effective additives for the morphological engineering of spray-dried SPs important for numerous applications.
Collapse
Affiliation(s)
- Tero Kämäräinen
- Department of Formulation Design and Pharmaceutical Technology, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Yuzuki Nakayama
- Department of Formulation Design and Pharmaceutical Technology, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Hiromasa Uchiyama
- Department of Formulation Design and Pharmaceutical Technology, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Yuichi Tozuka
- Department of Formulation Design and Pharmaceutical Technology, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Kazunori Kadota
- Department of Formulation Design and Pharmaceutical Technology, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| |
Collapse
|
38
|
Abrusán G, Zelezniak A. Cellular location shapes quaternary structure of enzymes. Nat Commun 2024; 15:8505. [PMID: 39353940 PMCID: PMC11445431 DOI: 10.1038/s41467-024-52662-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Accepted: 09/18/2024] [Indexed: 10/03/2024] Open
Abstract
The main forces driving protein complex evolution are currently not well understood, especially in homomers, where quaternary structure might frequently evolve neutrally. Here we examine the factors determining oligomerisation by analysing the evolution of enzymes in circumstances where homomers rarely evolve. We show that 1) In extracellular environments, most enzymes with known structure are monomers, while in the cytoplasm homomers, indicating that the evolution of oligomers is cellular environment dependent; 2) The evolution of quaternary structure within protein orthogroups is more consistent with the predictions of constructive neutral evolution than an adaptive process: quaternary structure is gained easier than it is lost, and most extracellular monomers evolved from proteins that were monomers also in their ancestral state, without the loss of interfaces. Our results indicate that oligomerisation is context-dependent, and even when adaptive, in many cases it is probably not driven by the intrinsic properties of enzymes, like their biochemical function, but rather the properties of the environment where the enzyme is active. These factors might be macromolecular crowding and excluded volume effects facilitating the evolution of interfaces, and the maintenance of cellular homeostasis through shaping cytoplasm fluidity, protein degradation, or diffusion rates.
Collapse
Affiliation(s)
- György Abrusán
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, New Hunt's House, London, UK.
| | - Aleksej Zelezniak
- Randall Centre for Cell and Molecular Biophysics, School of Basic and Medical Biosciences, King's College London, New Hunt's House, London, UK
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Institute of Biotechnology, Life Sciences Centre, Vilnius University, Vilnius, Lithuania
| |
Collapse
|
39
|
Kurakin S, Ivankov O, Dushanov E, Murugova T, Ermakova E, Efimov S, Mukhametzyanov T, Smerdova S, Klochkov V, Kuklin A, Kučerka N. Calcium ions do not influence the Aβ(25-35) triggered morphological changes of lipid membranes. Biophys Chem 2024; 313:107292. [PMID: 39018778 DOI: 10.1016/j.bpc.2024.107292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024]
Abstract
We have studied the effect of calcium ions (Ca2+) at various concentrations on the structure of lipid vesicles in the presence of amyloid-beta peptide Aβ(25-35). In particular, we have investigated the influence of calcium ions on the formation of recently documented bicelle-like structures (BLSs) emerged as a result of Aβ(25-35) triggered membrane disintegration. First, we have shown by using small-angle X-ray and neutron scattering that peptide molecules rigidify the lipid bilayer of gel phase DPPC unilamellar vesicles (ULVs), while addition of the calcium ions to the system hinders this effect of Aβ(25-35). Secondly, the Aβ(25-35) demonstrates a critical peptide concentration at which the BLSs reorganize from ULVs due to heating and cooling the samples through the lipid main phase transition temperature (Tm). However, addition of calcium ions does not affect noticeably the Aβ-induced formation of BLSs and their structural parameters, though the changes in peptide's secondary structure, e.g. the increased α-helix fraction, has been registered by circular dichroism spectroscopy. Finally, according to 31P nuclear magnetic resonance (NMR) measurements, calcium ions do not affect the lipid-peptide arrangement in BLSs and their ability to align in the magnetic field of NMR spectrometer. The influences of various concentrations of calcium ions on the lipid-peptide interactions may prove biologically important because their local concentrations vary widely in in-vivo conditions. In the present work, calcium ions were investigated as a possible tool aimed at regulating the lipid-peptide interactions that demonstrated the disruptive effect of Aβ(25-35) on lipid membranes.
Collapse
Affiliation(s)
- Sergei Kurakin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia.
| | - Oleksandr Ivankov
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Ermuhammad Dushanov
- Laboratory of Radiation Biology, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Department of Biophysics, Dubna State University, Universitetskaya 19, Dubna, Moscow Region 141982, Russia
| | - Tatiana Murugova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Elena Ermakova
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia
| | - Sergey Efimov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Timur Mukhametzyanov
- Butlerov Chemistry Institute, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Svetlana Smerdova
- Kazan National Research Technological University, Karl Marx 68, Kazan 420015, Russia
| | - Vladimir Klochkov
- Institute of Physics, Kazan Federal University, Kremlevskaya 18, Kazan 420008, Russia
| | - Alexander Kuklin
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Moscow Institute of Physics and Technology, Instytutskiy Pereulok 9, Dolgoprudny, Moscow Region 141701, Russia
| | - Norbert Kučerka
- Frank Laboratory of Neutron Physics, Joint Institute for Nuclear Research, Joliot-Curie 6, Dubna, Moscow Region 141980, Russia; Department of Physical Chemistry of Drugs, Faculty of Pharmacy, Comenius University Bratislava, Odbojárov 10, Bratislava 832 32, Slovakia.
| |
Collapse
|
40
|
Schweitzer-Stenner R. Probing the versatility of cytochrome c by spectroscopic means: A Laudatio on resonance Raman spectroscopy. J Inorg Biochem 2024; 259:112641. [PMID: 38901065 DOI: 10.1016/j.jinorgbio.2024.112641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Over the last 50 years resonance Raman spectroscopy has become an invaluable tool for the exploration of chromophores in biological macromolecules. Among them, heme proteins and metal complexes have attracted considerable attention. This interest results from the fact that resonance Raman spectroscopy probes the vibrational dynamics of these chromophores without direct interference from the surrounding. However, the indirect influence via through-bond and through-space chromophore-protein interactions can be conveniently probed and analyzed. This review article illustrates this point by focusing on class 1 cytochrome c, a comparatively simple heme protein generally known as electron carrier in mitochondria. The article demonstrates how through selective excitation of resonance Raman active modes information about the ligation, the redox state and the spin state of the heme iron can be obtained from band positions in the Raman spectra. The investigation of intensities and depolarization ratios emerged as tools for the analysis of in-plane and out-of-plane deformations of the heme macrocycle. The article further shows how resonance Raman spectroscopy was used to characterize partially unfolded states of oxidized cytochrome c. Finally, it describes its use for exploring structural changes due to the protein's binding to anionic surfaces like cardiolipin containing membranes.
Collapse
|
41
|
Nishijima M, Kobayashi K, Masuda-Endo M, Yoda H, Koike-Takeshita A. Regioselective photocyclodimerization of 2-anthracenecarboxylic acid through ATP hydrolysis-driven conformational change using simulation prediction-designed GroEL mutant. J Biosci Bioeng 2024; 138:283-289. [PMID: 39097441 DOI: 10.1016/j.jbiosc.2024.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 08/05/2024]
Abstract
GroEL, a chaperone protein responsible for peptide and denatured protein folding, undergoes substantial conformational changes driven by ATP binding and hydrolysis during folding. Utilizing these conformational changes, we demonstrated the GroEL-mediated regioselective photocyclodimerization of 2-anthracenecarboxylic acid (AC) using ATP hydrolysis as an external stimulus. We designed and prepared an optimal GroEL mutant to employ in a docking simulation that has been actively used in recent years. Based on the large difference in the motif of hydrogen bonds between AC and GroEL mutant compared with the wild-type, we predicted that GroELMEL, in which the 307‒309th amino acid residues were mutated to Ala, could alter the orientation of bound AC in GroEL. The GroELMEL-mediated photocyclodimerization of AC can be used for regioselective inversion upon ATP addition to a moderate extent.
Collapse
Affiliation(s)
- Masaki Nishijima
- National Institute of Technology (KOSEN), Wakayama College, 77 Noshima, Gobo, Wakayama 644-0023, Japan.
| | - Kota Kobayashi
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan
| | - Megumi Masuda-Endo
- Biomedical Research Center, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan
| | - Hiromi Yoda
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan; Biomedical Research Center, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan
| | - Ayumi Koike-Takeshita
- Department of Applied Chemistry and Bioscience, Graduate School of Engineering, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan; Biomedical Research Center, Kanagawa Institute of Technology, 1030 Shimo-ogino, Atsugi, Kanagawa 243-0292, Japan
| |
Collapse
|
42
|
Javed A, Johnson OT, Balana AT, Volk RF, Langen A, Ahn BS, Zaro BW, Gestwicki JE, Pratt MR. O-GlcNAc modification of HSP27 alters its protein interactions and promotes refolding of proteins through the BAG3/HSP70 co-chaperone. Protein Sci 2024; 33:e5173. [PMID: 39291732 PMCID: PMC11409196 DOI: 10.1002/pro.5173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 08/05/2024] [Accepted: 08/28/2024] [Indexed: 09/19/2024]
Abstract
Almost all types of cellular stress induce post-translational O-GlcNAc modifications of proteins, and this increase promotes cell survival. We previously demonstrated that O-GlcNAc on certain small heat shock proteins (sHSPs), including HSP27, directly increases their chaperone activity as one potential protective mechanism. Here, we furthered our use of synthetic proteins to prepare biotinylated sHSPs and show that O-GlcNAc modification of HSP27 also changes how it interacts within the sHSP system and the broader HSP network. Specifically, we show that O-GlcNAc modified HSP27 binds more strongly to the co-chaperone protein BAG3, which then promotes refolding of a model substrate by HSP70. We use proteomics to identify other potential HSP27 interactions that are changed by O-GlcNAc, including one that we confirm with another sHSP, αB-crystallin. These findings add additional evidence for O-GlcNAc as a switch for regulating protein-protein interactions and for modifications of chaperones as one mechanism by which O-GlcNAc protects against protein aggregation.
Collapse
Affiliation(s)
- Afraah Javed
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Oleta T. Johnson
- Department of ChemistryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
| | - Aaron T. Balana
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Regan F. Volk
- Department of Pharmaceutical Chemistry and Cardiovascular Research InstituteUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Andreas Langen
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Benjamin S. Ahn
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| | - Balyn W. Zaro
- Department of Pharmaceutical Chemistry and Cardiovascular Research InstituteUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Jason E. Gestwicki
- Department of Pharmaceutical Chemistry, Institute for Neurodegenerative DiseaseUniversity of California at San FranciscoSan FranciscoCaliforniaUSA
| | - Matthew R. Pratt
- Department of ChemistryUniversity of Southern CaliforniaLos AngelesCaliforniaUSA
| |
Collapse
|
43
|
Wu Y, Yu Q, Zhou X, Ding W, Li X, Zhou P, Qiao Y, Huang Z, Wang S, Zhang J, Yang L, Zhang L, Sun D. MXene-coated piezoelectric poly-L-lactic acid membrane accelerates wound healing by biomimicking low-voltage electrical pulses. Int J Biol Macromol 2024; 278:134971. [PMID: 39182879 DOI: 10.1016/j.ijbiomac.2024.134971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 08/16/2024] [Accepted: 08/20/2024] [Indexed: 08/27/2024]
Abstract
Electrical stimulation therapy is effective in promoting wound healing by rescuing the decreased endogenous electrical field, where self-powered and miniaturized devices such as nanogenerators become the emerging trends. While high-voltage and unidirectional electric field may pose thermal effect and damage to the skin, nanogenerators with lower voltages, pulsed or bidirectional currents, and less invasive electrodes are preferred. Herein, we construct a polydopamine (PDA)-modified poly-L-lactic acid (PLLA) /MXene (PDMP/MXene) nanofibrous composite membrane that generates piezoelectric voltages matching the transepithelial potential (TEP) to accelerate wound healing. PDA coating not only enhances the piezoelectricity of PLLA by dipole attraction and alignment, but also increases its hydrophilicity and facilitates subsequent MXene adhesion for electrical conductivity and stability in physiological environment. When applied as wound dressings in mice, the PDMP/MXene membranes act as a nanogenerators with reduced internal resistances and satisfactory piezoelectric performances that resemble bioelectric potentials (~10 mV) responding to physical activities. The membrane significantly accelerates wound closure by facilitating fibroblast migration, collagen deposition and angiogenesis, and suppressing the expression of inflammatory responses. This piezoelectric fibrous membrane therefore provides a convenient solution for speeding up wound healing by sustained low voltage mimicking bioelectricity, better cell affinity.
Collapse
Affiliation(s)
- Yixuan Wu
- Institute of Chemicobiology and Functional Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Qingqing Yu
- Institute of Chemicobiology and Functional Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xuyue Zhou
- Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing 210042, China
| | - Weixiao Ding
- Institute of Chemicobiology and Functional Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Xinmeng Li
- Institute of Chemicobiology and Functional Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Peng Zhou
- Institute of Chemicobiology and Functional Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Yalei Qiao
- Institute of Chemicobiology and Functional Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Zhen Huang
- Institute of Chemicobiology and Functional Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Shujun Wang
- Department of Blood Transfusion, Jinling Hospital, Nanjing University School of Medicine, Nanjing 210002, China
| | - Jiaan Zhang
- Institute of Dermatology, Chinese Academy of Medical Science and Peking Union Medical College, Nanjing 210042, China
| | - Luyu Yang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
| | - Lei Zhang
- Institute of Chemicobiology and Functional Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| | - Dongping Sun
- Institute of Chemicobiology and Functional Materials, School of Chemistry and Chemical Engineering, Nanjing University of Science and Technology, Nanjing 210094, China.
| |
Collapse
|
44
|
Heritz JA, Backe SJ, Mollapour M. Molecular chaperones: Guardians of tumor suppressor stability and function. Oncotarget 2024; 15:679-696. [PMID: 39352796 DOI: 10.18632/oncotarget.28653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2024] Open
Abstract
The term 'tumor suppressor' describes a widely diverse set of genes that are generally involved in the suppression of metastasis, but lead to tumorigenesis upon loss-of-function mutations. Despite the protein products of tumor suppressors exhibiting drastically different structures and functions, many share a common regulatory mechanism-they are molecular chaperone 'clients'. Clients of molecular chaperones depend on an intracellular network of chaperones and co-chaperones to maintain stability. Mutations of tumor suppressors that disrupt proper chaperoning prevent the cell from maintaining sufficient protein levels for physiological function. This review discusses the role of the molecular chaperones Hsp70 and Hsp90 in maintaining the stability and functional integrity of tumor suppressors. The contribution of cochaperones prefoldin, HOP, Aha1, p23, FNIP1/2 and Tsc1 as well as the chaperonin TRiC to tumor suppressor stability is also discussed. Genes implicated in renal cell carcinoma development-VHL, TSC1/2, and FLCN-will be used as examples to explore this concept, as well as how pathogenic mutations of tumor suppressors cause disease by disrupting protein chaperoning, maturation, and function.
Collapse
Affiliation(s)
- Jennifer A Heritz
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Sarah J Backe
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
| | - Mehdi Mollapour
- Department of Urology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Upstate Cancer Center, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Department of Biochemistry and Molecular Biology, SUNY Upstate Medical University, Syracuse, NY 13210, USA
- Syracuse VA Medical Center, New York VA Health Care, Syracuse, NY 13210, USA
| |
Collapse
|
45
|
Valdivia Pérez JA, Nocelli NE, Bustos J, Antonio ML, Smania A, Vico RV, Fanani ML. Membrane-targeted mechanism for amphiphilic vitamin C compounds as methicillin-resistant Staphylococcus aureus biofilm eradicating agents. Chem Phys Lipids 2024; 264:105423. [PMID: 39097132 DOI: 10.1016/j.chemphyslip.2024.105423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 07/30/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Staphylococcus aureus infections and its biofilm removal is an important concern in health care management. Methicillin-resistant S. aureus is responsible for severe morbidity and mortality worldwide. The extensive use of disinfectants against biofilms has led to negative environmental impacts. Developing new and more potent biofilm eradication agents with minimal detrimental effects on human and environmental health is currently on the agenda. The alkyl esters of L-ascorbic acid (ASCn) are antioxidant amphiphiles, which show antimicrobial capacity against methicillin-sensitive and resistant S. aureus strains. ASC12 and ASC14 formulations are able to kill the persister cells of the deepest layers of the biofilm. We tested the hypothesis that the antimicrobial and antibiofilm capacity found for the ASCn emerges from a combined effect of its amphiphilic and their redox capacity. This mechanism appears related to: I) a larger diffusion capacity of the ASC12 micelles than ASC14 and ASC16 microstructures; II) the neutralization of the ASCn acid hydroxyl when the amphiphile reaches the surface of an anionic surface, followed by a rapid insertion; III) the disruption of cell membrane by alteration of membrane tension and structure and IV) ASCn accumulation in the cell membrane or biofilm extracellular matrix surfaces, reducing functional chemical groups and affecting its biological function.
Collapse
Affiliation(s)
- Jessica A Valdivia Pérez
- Depto. de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC) CONICET, Córdoba, Argentina
| | - Natalia E Nocelli
- Depto. de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC) CONICET, Córdoba, Argentina
| | - Jeremías Bustos
- Depto. de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - María Laura Antonio
- Depto. de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Andrea Smania
- Depto. de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC) CONICET, Córdoba, Argentina
| | - Raquel V Vico
- Departamento de Química Orgánica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; Instituto de Investigaciones en Físico-Química de Córdoba (INFIQC), CONICET, Córdoba, Argentina
| | - María Laura Fanani
- Depto. de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC) CONICET, Córdoba, Argentina.
| |
Collapse
|
46
|
King ONF, Levik KE, Sandy J, Basham M. CHiMP: deep-learning tools trained on protein crystallization micrographs to enable automation of experiments. Acta Crystallogr D Struct Biol 2024; 80:744-764. [PMID: 39361357 DOI: 10.1107/s2059798324009276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Accepted: 09/22/2024] [Indexed: 10/05/2024] Open
Abstract
A group of three deep-learning tools, referred to collectively as CHiMP (Crystal Hits in My Plate), were created for analysis of micrographs of protein crystallization experiments at the Diamond Light Source (DLS) synchrotron, UK. The first tool, a classification network, assigns images into categories relating to experimental outcomes. The other two tools are networks that perform both object detection and instance segmentation, resulting in masks of individual crystals in the first case and masks of crystallization droplets in addition to crystals in the second case, allowing the positions and sizes of these entities to be recorded. The creation of these tools used transfer learning, where weights from a pre-trained deep-learning network were used as a starting point and repurposed by further training on a relatively small set of data. Two of the tools are now integrated at the VMXi macromolecular crystallography beamline at DLS, where they have the potential to absolve the need for any user input, both for monitoring crystallization experiments and for triggering in situ data collections. The third is being integrated into the XChem fragment-based drug-discovery screening platform, also at DLS, to allow the automatic targeting of acoustic compound dispensing into crystallization droplets.
Collapse
Affiliation(s)
- Oliver N F King
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Karl E Levik
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - James Sandy
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| | - Mark Basham
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, United Kingdom
| |
Collapse
|
47
|
Sabry NM, Badry R, Abdel-Gawad FK, Elhaes H, Ibrahim MA. Electronic structure, global reactivity descriptors and nonlinear optical properties of glycine interacted with ZnO, MgO and CaO for bacterial detection. Sci Rep 2024; 14:22801. [PMID: 39353963 PMCID: PMC11445471 DOI: 10.1038/s41598-024-72846-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2024] [Accepted: 09/11/2024] [Indexed: 10/03/2024] Open
Abstract
Modern laboratory medicine relies on analytical instruments for bacterial detection, focusing on biosensors and optical sensors for early disease diagnosis and treatment. Thus, Density Functional Theory (DFT) was utilized to study the reactivity of glycine interacted with metal oxides (ZnO, MgO, and CaO) for bacterial detection. Total dipole moment (TDM), frontier molecular orbitals (FMOs), FTIR spectroscopic data, electronic transition states, chemical reactivity descriptors, nonlinear optical (NLO) characteristics, and molecular electrostatic potential (MESP) were all investigated at the B3LYP/6-31G(d, p) level using DFT and Time-Dependent DFT (TD-DFT). The Coulomb-attenuating approach (CAM-B3LYP) was utilized to obtain theoretical electronic absorption spectra with the 6-31G(d, p) basis set to be more accurate than alternative quantum chemical calculation approaches, showing good agreement with the experimental data. The TDM and FMO investigation showed that glycine/CaO model has the highest TDM (10.129Debye) and lowest band gap (1.643 eV). The DFT computed IR and the experimental FTIR are consistent. The calculated UV-vis spectra showed a red shift with an increase in polarity following an increase in the absorption wavelength due to the interaction with ZnO, MgO, and CaO. Among the five solvents of water, methanol, ethanol, DMSO and acetone, the water and DMSO enhances the UV-Vis absorption. Glycine/CaO model showed high linear polarizability (14.629 × 10-24esu) and first hyperpolarizability (23.117 × 10-30esu), indicating its potential for nonlinear optical applications. The results showed that all model molecules, particularly glycine/CaO, contribute significantly to the development of materials with potential NLO features for sensor and optoelectronic applications. Additionally, MESP confirmed the increased electronegativity of the studied structures. Additionally, glycine/ZnO nanocomposite was synthesized and characterized using IR and UV-visible spectroscopy to determine their structural and spectroscopic features. It was discovered that there was good agreement between the DFT computed findings and the related experimental data. The antibacterial activity of glycine/ZnO nanocomposites against Staphylococcus aureus (S. aureus) and Pseudomonas aeruginosa were studied in terms of concentration and time. The results showed that increasing the concentration of glycine/ZnO nanocomposite significantly enhanced its antibacterial efficacy by lowering optical density. Notably, Pseudomonas aeruginosa exhibited lower susceptibility to the nanocomposite compared to S. aureus, requiring higher concentrations for effective bactericidal action. In summary, this study contributes novel insights into the dual functionality of glycine-metal oxide complexes, with significant implications as optical biosensor for microbial detection.
Collapse
Affiliation(s)
- Noha M Sabry
- Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, 33 El-Bohouth St., Dokki, Giza, 12622, Egypt
- Center of Excellence for Research and Applied Studies on Climate Change and Sustainable Development, National Research Centre (NRC), 33 El Bohouth St. Dokki, Giza, 12622, Egypt
| | - Rania Badry
- Physics Department, Faculty of Women for Arts, Science and Education, Ain Shams University, 11757, Cairo, Egypt
| | - Fagr Kh Abdel-Gawad
- Water Pollution Research Department, Environment and Climate Change Research Institute, National Research Centre, 33 El-Bohouth St., Dokki, Giza, 12622, Egypt
- Center of Excellence for Research and Applied Studies on Climate Change and Sustainable Development, National Research Centre (NRC), 33 El Bohouth St. Dokki, Giza, 12622, Egypt
| | - Hanan Elhaes
- Physics Department, Faculty of Women for Arts, Science and Education, Ain Shams University, 11757, Cairo, Egypt
| | - Medhat A Ibrahim
- Spectroscopy Department, National Research Centre, 33 El-Bohouth St., 12622, Dokki, Giza, Egypt.
- Molecular Modeling and Spectroscopy Laboratory, Centre of Excellence for Advanced Science, National Research Centre, 33 El-Bohouth St., 12622, Dokki, Giza, Egypt.
| |
Collapse
|
48
|
Lin Y, Shen C, Zhao J, Wang C, Obara M, Maung AT, Morita M, Abdelaziz MNS, Masuda Y, Honjoh KI, Miyamoto T. Antibacterial effect and mechanism of theaflavin against Listeria monocytogenes and its application on apple skins. J Food Sci 2024; 89:6653-6663. [PMID: 39289799 DOI: 10.1111/1750-3841.17321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/21/2024] [Accepted: 08/01/2024] [Indexed: 09/19/2024]
Abstract
Theaflavin 3,3'-digallate (TF3), a major polyphenolic component of black tea, exhibits antibacterial effects against many foodborne pathogens. However, the antibacterial mechanisms of TF3 against Listeria monocytogenes remain unclear. In this study, we investigated the effects of TF3 on viability, biofilm, and membrane function of L. monocytogenes by the conventional plating method, crystal violet staining, and microscopy using fluorescent dyes JC-1 and Laurdan, respectively. It was found that TF3 showed excellent antibacterial activity against L. monocytogenes with the minimum inhibitory concentration of 62.5 mg/L. The viable count determined on TSA decreased by 3 log after the treatment for 2 h with TF3 at 62.5 mg/L. The viable count determined on TSA containing 4% NaCl decreased by more than 4 log after the treatment for 30 min with TF3 at the same concentration, suggesting that TF3 gave damage on the cells, enhancing the antibacterial action of 4% NaCl, but the damage was recoverable in the absence of 4% NaCl. To explore the antibacterial mechanisms of TF3, the effects of TF3 on membrane potential and membrane fluidity were investigated. TF3 reduced both membrane potential and fluidity of L. monocytogenes at 62.5 mg/L, suggesting that TF3 damaged the structural integrity of the cell membrane. TF3 reduced biofilm mass of mature biofilm of L. monocytogenes. Moreover, THEAFLAVIN TF40, a commercially available Camellia sinensis leaf extract containing TF3, reduced viable count of L. monocytogenes by 2 log on apple skin. These results suggest the potential of theaflavins as a natural anti-Listeria disinfectant.
Collapse
Affiliation(s)
- Yunzhi Lin
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Bioenvironmental Science, Kyushu University, Nishi-ku, Fukuoka, Japan
| | - Cunkuan Shen
- College of Biological and Environmental Science, Zhejiang Wanli University, Ningbo, Zhejiang, China
| | - Junxin Zhao
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Bioenvironmental Science, Kyushu University, Nishi-ku, Fukuoka, Japan
- Food and Pharmacy College, Xuchang University, Xuchang, China
| | - Chen Wang
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Bioenvironmental Science, Kyushu University, Nishi-ku, Fukuoka, Japan
| | - Manami Obara
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Bioenvironmental Science, Kyushu University, Nishi-ku, Fukuoka, Japan
| | - Aye Thida Maung
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Bioenvironmental Science, Kyushu University, Nishi-ku, Fukuoka, Japan
| | - Miho Morita
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Bioenvironmental Science, Kyushu University, Nishi-ku, Fukuoka, Japan
| | - Marwa Nabil Sayed Abdelaziz
- Department of Bioscience and Biotechnology, Graduate School of Bioscience and Bioenvironmental Science, Kyushu University, Nishi-ku, Fukuoka, Japan
| | - Yoshimitsu Masuda
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Nishi-ku, Fukuoka, Japan
| | - Ken-Ichi Honjoh
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Nishi-ku, Fukuoka, Japan
| | - Takahisa Miyamoto
- Department of Bioscience and Biotechnology, Faculty of Agriculture, Graduate School, Kyushu University, Nishi-ku, Fukuoka, Japan
| |
Collapse
|
49
|
Paula S, Floruta S, Pajazetovic K, Sobota S, Almahmodi D. The molecular determinants of calcium ATPase inhibition by curcuminoids. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2024; 1866:184367. [PMID: 38969202 DOI: 10.1016/j.bbamem.2024.184367] [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: 02/01/2024] [Revised: 06/04/2024] [Accepted: 07/01/2024] [Indexed: 07/07/2024]
Abstract
The natural product curcumin and some of its analogs are known inhibitors of the transmembrane enzyme sarco/endoplasmic reticulum calcium ATPase (SERCA). Despite their widespread use, the curcuminoids' binding site in SERCA and their relevant interactions with the enzyme remain elusive. This lack of knowledge has prevented the development of curcuminoids into valuable experimental tools or into agents of therapeutic value. We used the crystal structures of SERCA in its E1 conformation in conjunction with computational tools such as docking and surface screens to determine the most likely curcumin binding site, along with key enzyme/inhibitor interactions. Additionally, we determined the inhibitory potencies and binding affinities for a small set of curcumin analogs. The predicted curcumin binding site is a narrow cleft in the transmembrane section of SERCA, close to the transmembrane/cytosol interface. In addition to pronounced complementarity in shape and hydrophobicity profiles between curcumin and the binding pocket, several hydrogen bonds were observed that were spread over the entire curcumin scaffold, involving residues on several transmembrane helices. Docking-predicted interactions were compatible with experimental observations for inhibitory potencies and binding affinities. Based on these findings, we propose an inhibition mechanism that assumes that the presence of a curcuminoid in the binding site arrests the catalytic cycle of SERCA by preventing it from converting from the E1 to the E2 conformation. This blockage of conformational change is accomplished by a combination of steric hinderance and hydrogen-bond-based cross-linking of transmembrane helices that require flexibility throughout the catalytic cycle.
Collapse
Affiliation(s)
- Stefan Paula
- Department of Chemistry, California State University Sacramento, 6000 J Street, Sacramento, CA 95819, USA.
| | - Sergiu Floruta
- Department of Chemistry, California State University Sacramento, 6000 J Street, Sacramento, CA 95819, USA
| | - Karim Pajazetovic
- Department of Chemistry, California State University Sacramento, 6000 J Street, Sacramento, CA 95819, USA
| | - Sydni Sobota
- Department of Chemistry, California State University Sacramento, 6000 J Street, Sacramento, CA 95819, USA
| | - Dina Almahmodi
- Department of Chemistry, California State University Sacramento, 6000 J Street, Sacramento, CA 95819, USA
| |
Collapse
|
50
|
Tomar R, Ghodke PP, Patra A, Smyth E, Pontarelli A, Copp W, Guengerich FP, Chaput JC, Wilds CJ, Stone MP, Egli M. DNA Replication across α-l-(3'-2')-Threofuranosyl Nucleotides Mediated by Human DNA Polymerase η. Biochemistry 2024; 63:2425-2439. [PMID: 39259676 DOI: 10.1021/acs.biochem.4c00387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
Abstract
α-l-(3'-2')-Threofuranosyl nucleic acid (TNA) pairs with itself, cross-pairs with DNA and RNA, and shows promise as a tool in synthetic genetics, diagnostics, and oligonucleotide therapeutics. We studied in vitro primer insertion and extension reactions catalyzed by human trans-lesion synthesis (TLS) DNA polymerase η (hPol η) opposite a TNA-modified template strand without and in combination with O4-alkyl thymine lesions. Across TNA-T (tT), hPol η inserted mostly dAMP and dGMP, dTMP and dCMP with lower efficiencies, followed by extension of the primer to a full-length product. hPol η inserted dAMP opposite O4-methyl and -ethyl analogs of tT, albeit with reduced efficiencies relative to tT. Crystal structures of ternary hPol η complexes with template tT and O4-methyl tT at the insertion and extension stages demonstrated that the shorter backbone and different connectivity of TNA compared to DNA (3' → 2' versus 5' → 3', respectively) result in local differences in sugar orientations, adjacent phosphate spacings, and directions of glycosidic bonds. The 3'-OH of the primer's terminal thymine was positioned at 3.4 Å on average from the α-phosphate of the incoming dNTP, consistent with insertion opposite and extension past the TNA residue by hPol η. Conversely, the crystal structure of a ternary hPol η·DNA·tTTP complex revealed that the primer's terminal 3'-OH was too distant from the tTTP α-phosphate, consistent with the inability of the polymerase to incorporate TNA. Overall, our study provides a better understanding of the tolerance of a TLS DNA polymerase vis-à-vis unnatural nucleotides in the template and as the incoming nucleoside triphosphate.
Collapse
Affiliation(s)
- Rachana Tomar
- Department of Chemistry, Vanderbilt Ingram Cancer Center, and Vanderbilt Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Pratibha P Ghodke
- Department of Biochemistry, School of Medicine, Vanderbilt Ingram Cancer Center, and Vanderbilt Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Amritraj Patra
- Department of Biochemistry, School of Medicine, Vanderbilt Ingram Cancer Center, and Vanderbilt Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Elizabeth Smyth
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Alexander Pontarelli
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - William Copp
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - F Peter Guengerich
- Department of Biochemistry, School of Medicine, Vanderbilt Ingram Cancer Center, and Vanderbilt Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - John C Chaput
- Department of Pharmaceutical Sciences, University of California, Irvine, California 92697, United States
| | - Christopher J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Michael P Stone
- Department of Chemistry, Vanderbilt Ingram Cancer Center, and Vanderbilt Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Martin Egli
- Department of Biochemistry, School of Medicine, Vanderbilt Ingram Cancer Center, and Vanderbilt Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37232, United States
| |
Collapse
|