1
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Truong DT, Ho K, Pham DQH, Chwastyk M, Nguyen-Minh T, Nguyen MT. Treatment of flexibility of protein backbone in simulations of protein-ligand interactions using steered molecular dynamics. Sci Rep 2024; 14:10475. [PMID: 38714683 PMCID: PMC11076533 DOI: 10.1038/s41598-024-59899-3] [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: 02/11/2024] [Accepted: 04/16/2024] [Indexed: 05/10/2024] Open
Abstract
To ensure that an external force can break the interaction between a protein and a ligand, the steered molecular dynamics simulation requires a harmonic restrained potential applied to the protein backbone. A usual practice is that all or a certain number of protein's heavy atoms or Cα atoms are fixed, being restrained by a small force. This present study reveals that while fixing both either all heavy atoms and or all Cα atoms is not a good approach, while fixing a too small number of few atoms sometimes cannot prevent the protein from rotating under the influence of the bulk water layer, and the pulled molecule may smack into the wall of the active site. We found that restraining the Cα atoms under certain conditions is more relevant. Thus, we would propose an alternative solution in which only the Cα atoms of the protein at a distance larger than 1.2 nm from the ligand are restrained. A more flexible, but not too flexible, protein will be expected to lead to a more natural release of the ligand.
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Affiliation(s)
- Duc Toan Truong
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam
| | - Kiet Ho
- Institute for Computational Science and Technology (ICST), Quang Trung Software City, Ho Chi Minh City, 70000, Vietnam
| | | | - Mateusz Chwastyk
- Institute of Physics, Polish Academy of Sciences, Warsaw, Poland
| | - Thai Nguyen-Minh
- University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, 70000, Vietnam
| | - Minh Tho Nguyen
- Laboratory for Chemical Computation and Modeling, Institute for Computational Science and Artificial Intelligence, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
- Faculty of Applied Technology, School of Technology, Van Lang University, Ho Chi Minh City, 70000, Vietnam.
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2
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Fernandez M, Shkumatov AV, Liu Y, Stulemeijer C, Derclaye S, Efremov R, Hallet B, Alsteens D. AFM-based force spectroscopy unravels stepwise formation of the DNA transposition complex in the widespread Tn3 family mobile genetic elements. Nucleic Acids Res 2023; 51:4929-4941. [PMID: 37026471 PMCID: PMC10250215 DOI: 10.1093/nar/gkad241] [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: 12/21/2022] [Revised: 03/03/2023] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Transposon Tn4430 belongs to a widespread family of bacterial transposons, the Tn3 family, which plays a prevalent role in the dissemination of antibiotic resistance among pathogens. Despite recent data on the structural architecture of the transposition complex, the molecular mechanisms underlying the replicative transposition of these elements are still poorly understood. Here, we use force-distance curve-based atomic force microscopy to probe the binding of the TnpA transposase of Tn4430 to DNA molecules containing one or two transposon ends and to extract the thermodynamic and kinetic parameters of transposition complex assembly. Comparing wild-type TnpA with previously isolated deregulated TnpA mutants supports a stepwise pathway for transposition complex formation and activation during which TnpA first binds as a dimer to a single transposon end and then undergoes a structural transition that enables it to bind the second end cooperatively and to become activated for transposition catalysis, the latter step occurring at a much faster rate for the TnpA mutants. Our study thus provides an unprecedented approach to probe the dynamic of a complex DNA processing machinery at the single-particle level.
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Affiliation(s)
- Maricruz Fernandez
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Alexander V Shkumatov
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Yun Liu
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Claire Stulemeijer
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Sylvie Derclaye
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Rouslan G Efremov
- Center for Structural Biology, Vlaams Instituut voor Biotechnologie, Brussels, Belgium
- Structural Biology Brussels, Department of Bioengineering Sciences, Vrije Universiteit Brussel, Brussels, Belgium
| | - Bernard Hallet
- Biochemistry and Genetics of Microorganisms, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
| | - David Alsteens
- NanoBioPhysics lab, Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve, Belgium
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3
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Viljoen A, Vercellone A, Chimen M, Gaibelet G, Mazères S, Nigou J, Dufrêne YF. Nanoscale clustering of mycobacterial ligands and DC-SIGN host receptors are key determinants for pathogen recognition. SCIENCE ADVANCES 2023; 9:eadf9498. [PMID: 37205764 PMCID: PMC10198640 DOI: 10.1126/sciadv.adf9498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 04/14/2023] [Indexed: 05/21/2023]
Abstract
The bacterial pathogen Mycobacterium tuberculosis binds to the C-type lectin DC-SIGN (dendritic cell-specific intercellular adhesion molecule 3-grabbing nonintegrin) on dendritic cells to evade the immune system. While DC-SIGN glycoconjugate ligands are ubiquitous among mycobacterial species, the receptor selectively binds pathogenic species from the M. tuberculosis complex (MTBC). Here, we unravel the molecular mechanism behind this intriguing selective recognition by means of a multidisciplinary approach combining single-molecule atomic force microscopy with Förster resonance energy transfer and bioassays. Molecular recognition imaging of mycobacteria demonstrates that the distribution of DC-SIGN ligands markedly differs between Mycobacterium bovis Bacille Calmette-Guérin (BCG) (model MTBC species) and Mycobacterium smegmatis (non-MTBC species), the ligands being concentrated into dense nanodomains on M. bovis BCG. Upon bacteria-host cell adhesion, ligand nanodomains induce the recruitment and clustering of DC-SIGN. Our study highlights the key role of clustering of both ligands on MTBC species and DC-SIGN host receptors in pathogen recognition, a mechanism that might be widespread in host-pathogen interactions.
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Affiliation(s)
- Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07., B-1348 Louvain-la-Neuve, Belgium
| | - Alain Vercellone
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Myriam Chimen
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Gérald Gaibelet
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Serge Mazères
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Jérôme Nigou
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, Université Toulouse III - Paul Sabatier (UPS), Toulouse, France
| | - Yves F. Dufrêne
- Louvain Institute of Biomolecular Science and Technology, UCLouvain, Croix du Sud, 4-5, bte L7.07.07., B-1348 Louvain-la-Neuve, Belgium
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4
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Dumitru AC, Koehler M. Recent advances in the application of atomic force microscopy to structural biology. J Struct Biol 2023; 215:107963. [PMID: 37044358 DOI: 10.1016/j.jsb.2023.107963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/21/2023] [Accepted: 04/07/2023] [Indexed: 04/14/2023]
Abstract
The application of atomic force microscopy (AFM) for (functional) imaging and manipulating biomolecules at all levels of organization has enabled great progress in the structural biology field over the last decades, contributing to the discovery of novel structural entities of biological significance across many disciplines ranging from biochemistry, biomedicine and biophysics to molecular and cell biology, up to food systems and beyond. AFM has the capability to generate high-resolution topographic images spanning from the submolecular to the (sub)cellular range and can probe biochemical and biophysical sample properties in close to native conditions with excellent temporal resolution. Instrumental developments in the past decade enable dynamical structural and conformational studies of single biomolecules and new techniques for structural and chemical modification of the AFM probe have converted the cantilever into a versatile tool to study different biological phenomena, such as the mechanical stability of biomolecular complexes or the force induced dynamic changes of mechanically stressed proteins at the nanoscopic level. To improve the functionality of AFM and approach dynamic processes of complex biological systems ex vivo, AFM is combined with complementary microscopy, nanoscopy and spectroscopy tools. These multimethodological approaches provide unprecedented possibilities of probing physical, chemical and biological properties of complex cellular systems with high spatio-temporal resolution, leading to novel applications that correlate structural results with functional biochemical, biophysical, immunological, or genetic data on the system under study.
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Affiliation(s)
- Andra C Dumitru
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid 28029, Spain.
| | - Melanie Koehler
- Leibniz Institute for Food Systems Biology at the Technical University Munich, Freising, Germany.
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5
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Byvalov AA, Belozerov VS, Ananchenko BA, Konyshev IV. Specific and Nonspecific Interactions of Yersinia pseudotuberculosis Lipopolysaccharide with Monoclonal Antibodies Assessed by Atomic Force Microscopy. Biophysics (Nagoya-shi) 2022. [DOI: 10.1134/s0006350922060033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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6
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Lo Giudice C, Yang J, Poncin MA, Adumeau L, Delguste M, Koehler M, Evers K, Dumitru AC, Dawson KA, Alsteens D. Nanophysical Mapping of Inflammasome Activation by Nanoparticles via Specific Cell Surface Recognition Events. ACS NANO 2022; 16:306-316. [PMID: 34957816 DOI: 10.1021/acsnano.1c06301] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Silica nanoparticles (SiNP) trigger a range of innate immune responses in relevant essential organs, such as the liver and the lungs. Inflammatory reactions, including NLRP3 inflammasome activation, have been linked to particulate materials; however, the molecular mechanisms and key actors remain elusive. Although many receptors, including several scavenger receptors, were suggested to participate in SiNP cellular uptake, mechanistic evidence of their role on innate immunity is lacking. Here we present an atomic force microscopy-based approach to physico-mechanically map the specific interaction occurring between nanoparticles and scavenger receptor A1 (SRA1) in vitro on living lung epithelial cells. We find that SiNP recognition by SRA1 on human macrophages plays a key role in mediating NLRP3 inflammasome activation, and we identify cellular mechanical changes as clear indicators of inflammasome activation in human macrophages, greatly advancing our knowledge on the interplay among nanomaterials and innate immunity.
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Affiliation(s)
- Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
- Max Planck Institute for Medical Research, Heidelberg D-69120, Germany
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Mégane A Poncin
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Laurent Adumeau
- Centre for BioNano Interactions, School of Chemistry, University College Dublin, Dublin D04 N2E5, Ireland
| | - Martin Delguste
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Melanie Koehler
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Koen Evers
- Centre for BioNano Interactions, School of Chemistry, University College Dublin, Dublin D04 N2E5, Ireland
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
| | - Kenneth A Dawson
- Centre for BioNano Interactions, School of Chemistry, University College Dublin, Dublin D04 N2E5, Ireland
- Guangdong Provincial Education Department Key Laboratory of Nano-Immunoregulation Tumour Microenvironment, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510261, China
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université catholique de Louvain, Louvain-la-Neuve 1348, Belgium
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7
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Li S, Pang X, Zhao J, Zhang Q, Shan Y. Evaluating the single-molecule interactions between targeted peptides and the receptors on living cell membrane. NANOSCALE 2021; 13:17318-17324. [PMID: 34642724 DOI: 10.1039/d1nr05547j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
As potential ligands, targeted peptides have become an important part in the construction of intelligent drug delivery systems (DDSs). The targeting interaction of peptides with receptors is a key point affecting the efficacy of targeted nano-drugs. Herein, three common peptides (HAIYPRH (T7), YHWYGYTPQNVI (GE11), and RGD) that have been widely used in cancer targeted therapy and tumor diagnostics, targeting the corresponding receptors (transferrin receptor (TfR), epidermal growth factor receptor (EGFR), and ανβ3 integrin receptor), were selected as examples to study the targeting interacton on living cell surface at the single-molecule level by using single-molecule force spectroscopy (SMFS) based on atomic force microscopy (AFM). The dissociation activation energy in the absence of an external force (ΔGβ,0) of T7-TfR, GE11-EGFR, and RGD-ανβ3 integrin is evaluated at single-molecule level. Among these three peptide-receptor pairs, the T7-TfR bond is the most stable with a smaller dissociation kinetic rate constant at zero force (Koff), larger kinetic on-rate constant (Kon), and shorter interaction time (τ). Furthermore, T7 can target TfR even more effectively on A549 cell membrane after treatment with drugs. Our methodology can also be applicable to the study of other ligand targeted DDSs.
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Affiliation(s)
- Siying Li
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
- School of Chemical Engineering, Changchun University of Technology, Changchun 130012, China
| | - Xuelei Pang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Jing Zhao
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Qingrong Zhang
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
| | - Yuping Shan
- School of Chemistry and Life Science, Advanced Institute of Materials Science, Changchun University of Technology, Changchun 130012, China
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8
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Cheng H, Yu J, Wang Z, Ma P, Guo C, Wang B, Zhong W, Xu B. Details of Single-Molecule Force Spectroscopy Data Decoded by a Network-Based Automatic Clustering Algorithm. J Phys Chem B 2021; 125:9660-9667. [PMID: 34425052 DOI: 10.1021/acs.jpcb.1c03552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomic force microscopy-single-molecule force spectroscopy (AFM-SMFS) is a powerful methodology to probe intermolecular and intramolecular interactions in biological systems because of its operability in physiological conditions, facile and rapid sample preparation, versatile molecular manipulation, and combined functionality with high-resolution imaging. Since a huge number of AFM-SMFS force-distance curves are collected to avoid human bias and errors and to save time, numerous algorithms have been developed to analyze the AFM-SMFS curves. Nevertheless, there is still a need to develop new algorithms for the analysis of AFM-SMFS data since the current algorithms cannot specify an unbinding force to a corresponding/each binding site due to the lack of networking functionality to model the relationship between the unbinding forces. To address this challenge, herein, we develop an unsupervised method, i.e., a network-based automatic clustering algorithm (NASA), to decode the details of specific molecules, e.g., the unbinding force of each binding site, given the input of AFM-SMFS curves. Using the interaction of heparan sulfate (HS)-antithrombin (AT) on different endothelial cell surfaces as a model system, we demonstrate that NASA is able to automatically detect the peak and calculate the unbinding force. More importantly, NASA successfully identifies three unbinding force clusters, which could belong to three different binding sites, for both Ext1f/f and Ndst1f/f cell lines. NASA has great potential to be applied either readily or slightly modified to other AFM-based SMFS measurements that result in "saw-tooth"-shaped force-distance curves showing jumps related to the force unbinding, such as antibody-antigen interaction and DNA-protein interaction.
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Affiliation(s)
- Huimin Cheng
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Jun Yu
- School of Mathematics and Statistics, Beijing Institute of Technology, Beijing 100081, P. R. China
| | - Zhen Wang
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Ping Ma
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Cunlan Guo
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, P. R. China.,Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Bin Wang
- Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
| | - Wenxuan Zhong
- Big Data Analytics Lab, Department of Statistics, University of Georgia, Athens, Georgia 30602, United States
| | - Bingqian Xu
- Single Molecule Study Laboratory, College of Engineering, University of Georgia, Athens, Georgia 30602, United States
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9
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Targosz-Korecka M, Kubisiak A, Kloska D, Kopacz A, Grochot-Przeczek A, Szymonski M. Endothelial glycocalyx shields the interaction of SARS-CoV-2 spike protein with ACE2 receptors. Sci Rep 2021; 11:12157. [PMID: 34108510 PMCID: PMC8190434 DOI: 10.1038/s41598-021-91231-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 05/21/2021] [Indexed: 12/23/2022] Open
Abstract
Endothelial cells (ECs) play a crucial role in the development and propagation of the severe COVID-19 stage as well as multiorgan dysfunction. It remains, however, controversial whether COVID-19-induced endothelial injury is caused directly by the infection of ECs with SARS-CoV-2 or via indirect mechanisms. One of the major concerns is raised by the contradictory data supporting or denying the presence of ACE2, the SARS-CoV-2 binding receptor, on the EC surface. Here, we show that primary human pulmonary artery ECs possess ACE2 capable of interaction with the viral Spike protein (S-protein) and demonstrate the crucial role of the endothelial glycocalyx in the regulation of the S-protein binding to ACE2 on ECs. Using force spectroscopy method, we directly measured ACE2- and glycocalyx-dependent adhesive forces between S-protein and ECs and characterized the nanomechanical parameters of the cells exposed to S-protein. We revealed that the intact glycocalyx strongly binds S-protein but screens its interaction with ACE2. Reduction of glycocalyx layer exposes ACE2 receptors and promotes their interaction with S-protein. These results indicate that the susceptibility of ECs to COVID-19 infection may depend on the glycocalyx condition.
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Affiliation(s)
- Marta Targosz-Korecka
- Department of Physics of Nanostructures and Nanotechnology, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Kraków, Poland.
| | - Agata Kubisiak
- Department of Physics of Nanostructures and Nanotechnology, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Kraków, Poland
| | - Damian Kloska
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Aleksandra Kopacz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Anna Grochot-Przeczek
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Marek Szymonski
- Department of Physics of Nanostructures and Nanotechnology, Faculty of Physics, Astronomy and Applied Computer Science, Jagiellonian University, Kraków, Poland
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10
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Dufrêne YF, Viljoen A, Mignolet J, Mathelié-Guinlet M. AFM in cellular and molecular microbiology. Cell Microbiol 2021; 23:e13324. [PMID: 33710716 DOI: 10.1111/cmi.13324] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/14/2022]
Abstract
The unique capabilities of the atomic force microscope (AFM), including super-resolution imaging, piconewton force-sensitivity, nanomanipulation and ability to work under physiological conditions, have offered exciting avenues for cellular and molecular biology research. AFM imaging has helped unravel the fine architectures of microbial cell envelopes at the nanoscale, and how these are altered by antimicrobial treatment. Nanomechanical measurements have shed new light on the elasticity, tensile strength and turgor pressure of single cells. Single-molecule and single-cell force spectroscopy experiments have revealed the forces and dynamics of receptor-ligand interactions, the nanoscale distribution of receptors on the cell surface and the elasticity and adhesiveness of bacterial pili. Importantly, recent force spectroscopy studies have demonstrated that extremely stable bonds are formed between bacterial adhesins and their cognate ligands, originating from a catch bond behaviour allowing the pathogen to reinforce adhesion under shear or tensile stress. Here, we survey how the versatility of AFM has enabled addressing crucial questions in microbiology, with emphasis on bacterial pathogens. TAKE AWAYS: AFM topographic imaging unravels the ultrastructure of bacterial envelopes. Nanomechanical mapping shows what makes cell envelopes stiff and resistant to drugs. Force spectroscopy characterises the molecular forces in pathogen adhesion. Stretching pili reveals a wealth of mechanical and adhesive responses.
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Affiliation(s)
- Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Albertus Viljoen
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Johann Mignolet
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Marion Mathelié-Guinlet
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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11
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Li M, Xi N, Wang YC, Liu LQ. Atomic force microscopy for revealing micro/nanoscale mechanics in tumor metastasis: from single cells to microenvironmental cues. Acta Pharmacol Sin 2021; 42:323-339. [PMID: 32807839 PMCID: PMC8027022 DOI: 10.1038/s41401-020-0494-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 07/27/2020] [Indexed: 02/06/2023] Open
Abstract
Mechanics are intrinsic properties which appears throughout the formation, development, and aging processes of biological systems. Mechanics have been shown to play important roles in regulating the development and metastasis of tumors, and understanding tumor mechanics has emerged as a promising way to reveal the underlying mechanisms guiding tumor behaviors. In particular, tumors are highly complex diseases associated with multifaceted factors, including alterations in cancerous cells, tissues, and organs as well as microenvironmental cues, indicating that investigating tumor mechanics on multiple levels is significantly helpful for comprehensively understanding the effects of mechanics on tumor progression. Recently, diverse techniques have been developed for probing the mechanics of tumors, among which atomic force microscopy (AFM) has appeared as an excellent platform enabling simultaneously characterizing the structures and mechanical properties of living biological systems ranging from individual molecules and cells to tissue samples with unprecedented spatiotemporal resolution, offering novel possibilities for understanding tumor physics and contributing much to the studies of cancer. In this review, we survey the recent progress that has been achieved with the use of AFM for revealing micro/nanoscale mechanics in tumor development and metastasis. Challenges and future progress are also discussed.
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Affiliation(s)
- Mi Li
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110169, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Ning Xi
- Department of Industrial and Manufacturing Systems Engineering, The University of Hong Kong, Hong Kong, China
| | - Yue-Chao Wang
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110169, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lian-Qing Liu
- State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences, Shenyang, 110016, China.
- Institutes for Robotics and Intelligent Manufacturing, Chinese Academy of Sciences, Shenyang, 110169, China.
- University of Chinese Academy of Sciences, Beijing 100049, China.
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12
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Investigating virus-host cell interactions: Comparative binding forces between hepatitis C virus-like particles and host cell receptors in 2D and 3D cell culture models. J Colloid Interface Sci 2021; 592:371-384. [PMID: 33677197 DOI: 10.1016/j.jcis.2021.02.067] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 02/13/2021] [Accepted: 02/15/2021] [Indexed: 12/25/2022]
Abstract
Cell cultures have been successfully used to study hepatitis C virus (HCV) for many years. However, most work has been done using traditional, 2-dimensional (2D) cell cultures (cells grown as a monolayer in growth flasks or dishes). Studies have shown that when cells are grown suspended in an extra-cellular-matrix-like material, they develop into spherical, 'organoid' arrangements of cells (3D growth) that display distinct differences in morphological and functional characteristics compared to 2D cell cultures. In liver organoids, one key difference is the development of clearly differentiated apical and basolateral surfaces separated and maintained by cellular tight junctions. This phenomenon, termed polarity, is vital to normal barrier function of hepatocytes in vivo. It has also been shown that viruses, and virus-like particles, interact very differently with cells derived from 2D as compared to 3D cell cultures, bringing into question the usefulness of 2D cell cultures to study virus-host cell interactions. Here, we investigate differences in cellular architecture as a function of cell culture system, using confocal scanning laser microscopy, and determine differences in binding interactions between HCV virus-like particles (VLPs) and their cognate receptors in the different cell culture systems using atomic force microscopy (AFM). We generated organoid cultures that were polarized, as determined by localization of key apical and basolateral markers. We found that, while uptake of HCV VLPs by both 2D and 3D Huh7 cells was observed by flow cytometry, binding interactions between HCV VLPs and cells were measurable by AFM only on polarized cells. The work presented here adds to the growing body of research suggesting that polarized cell systems are more suitable for the study of HCV infection and dynamics than non-polarized systems.
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13
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Müller DJ, Dumitru AC, Lo Giudice C, Gaub HE, Hinterdorfer P, Hummer G, De Yoreo JJ, Dufrêne YF, Alsteens D. Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems. Chem Rev 2020; 121:11701-11725. [PMID: 33166471 DOI: 10.1021/acs.chemrev.0c00617] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into a nanoscopic laboratory to directly observe and chemically characterize molecular and cell biological systems under physiological conditions. Here, we review key technological improvements that have established AFM as an analytical tool to observe and quantify native biological systems from the micro- to the nanoscale. Native biological systems include living tissues, cells, and cellular components such as single or complexed proteins, nucleic acids, lipids, or sugars. We showcase the procedures to customize nanoscopic chemical laboratories by functionalizing AFM tips and outline the advantages and limitations in applying different AFM modes to chemically image, sense, and manipulate biosystems at (sub)nanometer spatial and millisecond temporal resolution. We further discuss theoretical approaches to extract the kinetic and thermodynamic parameters of specific biomolecular interactions detected by AFM for single bonds and extend the discussion to multiple bonds. Finally, we highlight the potential of combining AFM with optical microscopy and spectroscopy to address the full complexity of biological systems and to tackle fundamental challenges in life sciences.
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Affiliation(s)
- Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, Mattenstrasse 28, 4056 Basel, Switzerland
| | - Andra C Dumitru
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - Hermann E Gaub
- Applied Physics, Ludwig-Maximilians-Universität Munich, Amalienstrasse 54, 80799 München, Germany
| | - Peter Hinterdorfer
- Institute of Biophysics, Johannes Kepler University of Linz, Gruberstrasse 40, 4020 Linz, Austria
| | - Gerhard Hummer
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics and Department of Physics, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.,Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Yves F Dufrêne
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain (UCLouvain), Croix du Sud, 4-5, bte L7.07.07, B-1348 Louvain-la-Neuve, Belgium
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14
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Dumitru AC, Mohammed D, Maja M, Yang J, Verstraeten S, del Campo A, Mingeot‐Leclercq M, Tyteca D, Alsteens D. Label-Free Imaging of Cholesterol Assemblies Reveals Hidden Nanomechanics of Breast Cancer Cells. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2002643. [PMID: 33240781 PMCID: PMC7675049 DOI: 10.1002/advs.202002643] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/24/2020] [Indexed: 05/13/2023]
Abstract
Tumor cells present profound alterations in their composition, structural organization, and functional properties. A landmark of cancer cells is an overall altered mechanical phenotype, which so far are linked to changes in their cytoskeletal regulation and organization. Evidence exists that the plasma membrane (PM) of cancer cells also shows drastic changes in its composition and organization. However, biomechanical characterization of PM remains limited mainly due to the difficulties encountered to investigate it in a quantitative and label-free manner. Here, the biomechanical properties of PM of a series of MCF10 cell lines, used as a model of breast cancer progression, are investigated. Notably, a strong correlation between the cell PM elasticity and oncogenesis is observed. The altered membrane composition under cancer progression, as emphasized by the PM-associated cholesterol levels, leads to a stiffening of the PM that is uncoupled from the elastic cytoskeletal properties. Conversely, cholesterol depletion of metastatic cells leads to a softening of their PM, restoring biomechanical properties similar to benign cells. As novel therapies based on targeting membrane lipids in cancer cells represent a promising approach in the field of anticancer drug development, this method contributes to deciphering the functional link between PM lipid content and disease.
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Affiliation(s)
- Andra C. Dumitru
- Louvain Institute of Biomolecular Science and Technology (LIBST)Université catholique de LouvainLouvain‐la‐Neuve1348Belgium
| | - Danahe Mohammed
- Louvain Institute of Biomolecular Science and Technology (LIBST)Université catholique de LouvainLouvain‐la‐Neuve1348Belgium
| | - Mauriane Maja
- Cell Biology (CELL) Unit de Duve InstituteUniversité catholique de LouvainBrussels1200Belgium
| | - Jinsung Yang
- Louvain Institute of Biomolecular Science and Technology (LIBST)Université catholique de LouvainLouvain‐la‐Neuve1348Belgium
| | - Sandrine Verstraeten
- Cellular and Molecular Pharmacology Unit (FACM)Louvain Drug Research InstituteUniversité catholique de LouvainBrussels1200Belgium
| | - Aranzazu del Campo
- INM – Leibniz‐Institut für Neue Materialien gGmbHCampus D2 2Saarbrücken66123Germany
| | - Marie‐Paule Mingeot‐Leclercq
- Cellular and Molecular Pharmacology Unit (FACM)Louvain Drug Research InstituteUniversité catholique de LouvainBrussels1200Belgium
| | - Donatienne Tyteca
- Cell Biology (CELL) Unit de Duve InstituteUniversité catholique de LouvainBrussels1200Belgium
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology (LIBST)Université catholique de LouvainLouvain‐la‐Neuve1348Belgium
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15
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Ananchenko B, Belozerov V, Byvalov A, Konyshev I, Korzhavina A, Dudina L. Evaluation of intermolecular forces between lipopolysaccharides and monoclonal antibodies using atomic force microscopy. Int J Biol Macromol 2020; 156:841-850. [PMID: 32305368 DOI: 10.1016/j.ijbiomac.2020.04.055] [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: 12/27/2019] [Revised: 03/20/2020] [Accepted: 04/06/2020] [Indexed: 11/19/2022]
Abstract
Understanding of interactions between a bacterium and an immune or non-immune host organism at the cellular and subcellular level is important in order to improve new and existing immunobiological tools for the treatment of bacterial infections (including pseudotuberculosis). The aim of this work was to quantify the interaction force between Yersinia pseudotuberculosis and monoclonal antibodies (mAbs) in the model system "lipopolysaccharide (LPS) - mAbs" by atomic force microscopy (AFM). Our research findings provided the methodical approaches to force measurements between an AFM probe, which was functionalized with Y. pseudotuberculosis LPS, and mica coated by different mAbs. Based on the criteria for force estimation there was shown a greater binding force in the system "LPS - complementary mAbs" than in the system "LPS - heterologous mAbs". In both cases binding force increase followed by increase a contact time between the functionalized AFM probe and mica from 1 to 5 s. It has been shown that single bonds between LPS and complementary mAbs molecules also included a clearly defined non-specific component along with immunochemically specific one. The evidence suggests a significant proportion of applied force exerted to unfolding of high-molecular aggregates whose length may attain many hundreds of nanometers.
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Affiliation(s)
| | - Vladislav Belozerov
- The Institute of Physiology of the Коmi Science Centre of the Ural Branch of the Russian Academy of Sciences, FRC Komi SC UB RAS, Syktyvkar, Komi Republic 167982, Russian Federation; Vyatka State University, Kirov 610000, Russian Federation
| | - Andrey Byvalov
- The Institute of Physiology of the Коmi Science Centre of the Ural Branch of the Russian Academy of Sciences, FRC Komi SC UB RAS, Syktyvkar, Komi Republic 167982, Russian Federation; Vyatka State University, Kirov 610000, Russian Federation.
| | - Ilya Konyshev
- The Institute of Physiology of the Коmi Science Centre of the Ural Branch of the Russian Academy of Sciences, FRC Komi SC UB RAS, Syktyvkar, Komi Republic 167982, Russian Federation; Vyatka State University, Kirov 610000, Russian Federation
| | | | - Lyubov Dudina
- The Institute of Physiology of the Коmi Science Centre of the Ural Branch of the Russian Academy of Sciences, FRC Komi SC UB RAS, Syktyvkar, Komi Republic 167982, Russian Federation; Vyatka State University, Kirov 610000, Russian Federation
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16
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Vorselen D, Piontek MC, Roos WH, Wuite GJL. Mechanical Characterization of Liposomes and Extracellular Vesicles, a Protocol. Front Mol Biosci 2020; 7:139. [PMID: 32850949 PMCID: PMC7396484 DOI: 10.3389/fmolb.2020.00139] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/09/2020] [Indexed: 12/26/2022] Open
Abstract
Both natural as well as artificial vesicles are of tremendous interest in biology and nanomedicine. Small vesicles (<200 nm) perform essential functions in cell biology and artificial vesicles (liposomes) are used as drug delivery vehicles. Atomic Force Microscopy (AFM) is a powerful technique to study the structural properties of these vesicles. AFM is a well-established technique for imaging at nanometer resolution and for mechanical measurements under physiological conditions. Here, we describe the procedure of AFM imaging and force spectroscopy on small vesicles. We discuss how to image vesicles with minimal structural disturbance, and how to analyze the data for accurate size and shape measurements. In addition, we describe the procedure for performing nanoindentations on vesicles and the subsequent data analysis including mechanical models used for data interpretation.
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Affiliation(s)
- Daan Vorselen
- Fysica Van Levende Systemen and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Melissa C. Piontek
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Wouter H. Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, Netherlands
| | - Gijs J. L. Wuite
- Fysica Van Levende Systemen and LaserLab, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
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17
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Lo Giudice C, Zhang H, Wu B, Alsteens D. Mechanochemical Activation of Class-B G-Protein-Coupled Receptor upon Peptide-Ligand Binding. NANO LETTERS 2020; 20:5575-5582. [PMID: 32578992 DOI: 10.1021/acs.nanolett.0c02333] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Glucagon binding to the class-B G-protein-coupled glucagon receptor (GCGR) triggers the release of glucose from the liver during fasting. Recently, GCGR crystal structures have highlighted the conformation and molecular details of inactive and active receptor states. However, the dynamics of the conformational changes accompanying GCGR activation remains unclear. Here, we use multiplex force-distance curve-based atomic force microscopy (FD-based AFM) to probe in situ glucagon binding to individual GCGRs and monitor dynamically the transition to the active conformer. After a "dock" step, in which glucagon is partially bound to the GCGR extracellular domain, further interactions of the N-terminus with the transmembrane domain trigger an increase in the stiffness of the complex, adopting a highly stable and rigid "lock" conformer. This mechanotransduction is key for G-protein recruitment.
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Affiliation(s)
- Cristina Lo Giudice
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Haonan Zhang
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Beili Wu
- CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - David Alsteens
- Louvain Institute of Biomolecular Science and Technology, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
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18
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Koehler M, Lo Giudice C, Vogl P, Ebner A, Hinterdorfer P, Gruber HJ, Alsteens D. Control of Ligand-Binding Specificity Using Photocleavable Linkers in AFM Force Spectroscopy. NANO LETTERS 2020; 20:4038-4042. [PMID: 32320256 PMCID: PMC7252943 DOI: 10.1021/acs.nanolett.0c01426] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 04/21/2020] [Indexed: 05/26/2023]
Abstract
In recent decades, atomic force microscopy (AFM), in particular the force spectroscopy mode, has become a method of choice to study biomolecular interactions at the single-molecule level. However, grafting procedures as well as determining binding specificity remain challenging. We report here an innovative approach based on a photocleavable group that enables in situ release of the ligands bound to the AFM tip and thus allows direct assessment of the binding specificity. Applicable to a wide variety of molecules, the strategy presented here provides new opportunities to study specific interactions and deliver single molecules with high spatiotemporal resolution in a wide range of applications, including AFM-based cell biology.
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Affiliation(s)
- Melanie Koehler
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Cristina Lo Giudice
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Philipp Vogl
- Institute
of Biophysics, Johannes Kepler University, 4020 Linz, Austria
| | - Andreas Ebner
- Institute
of Biophysics, Johannes Kepler University, 4020 Linz, Austria
| | | | - Hermann J. Gruber
- Institute
of Biophysics, Johannes Kepler University, 4020 Linz, Austria
| | - David Alsteens
- Louvain
Institute of Biomolecular Science and Technology, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
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19
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Lansakara TI, Morris HS, Singh P, Kohen A, Tivanski AV. Rigid Double-Stranded DNA Linkers for Single Molecule Enzyme-Drug Interaction Measurements Using Molecular Recognition Force Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:4174-4183. [PMID: 32233509 DOI: 10.1021/acs.langmuir.9b03495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Single-molecule studies can reveal the distribution of states and interactions between ligand-enzyme complexes not accessible for most studies that measure a large ensemble average response of many molecules. Furthermore, in some biological applications, the information regarding the outliers, not the average of measured properties, can be more important. The high spatial and force resolution provided by atomic force microscopy (AFM) under physiological conditions has been utilized in this study to quantify the force-distance relations of enzyme-drug interactions. Different immobilization techniques of the protein to a surface and the drug to AFM tip were quantitatively compared to improve the accuracy and precision of the measurement. Protein that is directly bound to the surface, forming a monolayer, was compared to enzyme molecules bound to the surface with rigid double-stranded (ds) DNA spacers. These surfaces immobilization techniques were studied with the drug bound directly to the AFM tip and drug bound via flexible poly(ethylene glycol) and rigid dsDNA linkers. The activity of the enzyme was found to be not significantly altered by immobilization methods relative to its activity in solution. The findings indicate that the approach for studying drug-enzyme interaction based on rigid dsDNA linker on the surface and either flexible or rigid linker on the tip affords straightforward, highly specific, reproducible, and accurate force measurements with a potential for single-molecule level studies. The method could facilitate in-depth examination of a broad spectrum of biological targets and potential drugs.
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Affiliation(s)
| | - Holly S Morris
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Priyanka Singh
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Amnon Kohen
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Alexei V Tivanski
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
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