1
|
Panda SK, Karmakar S, Sen Gupta PS, Rana MK. Can Duvelisib and Eganelisib work for both cancer and COVID-19? Molecular-level insights from MD simulations and enhanced samplings. Phys Chem Chem Phys 2024; 26:10961-10973. [PMID: 38526354 DOI: 10.1039/d3cp05934k] [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: 03/26/2024]
Abstract
SARS-CoV-2 has caused severe illness and anxiety worldwide, evolving into more dreadful variants capable of evading the host's immunity. Cytokine storms, led by PI3Kγ, are common in cancer and SARS-CoV-2. Naturally, there is a yearning to see whether any drugs could alleviate cytokine storms for both. Upon investigation, we identified two anticancer drugs, Duvelisib and Eganelisib, that could also work against SARS-CoV-2. This report is the first to decipher their synergic therapeutic effectiveness against COVID-19 and cancer with molecular insights from atomistic simulations. In addition to PI3Kγ, these drugs exhibit specificity for the main protease among all SARS-CoV-2 targets, with significant negative binding free energies and small time-dependent conformational changes of the complexes. Complexation makes active sites and secondary structures highly mechanically stiff, with barely any deformation. Replica simulations estimated large pulling forces in enhanced sampling to dissociate the drugs from Mpro's active site. Furthermore, the radial distribution function (RDF) demonstrated that the therapeutic molecules were closest to the His41 and Cys145 catalytic dyad residues. Finally, analyses implied Duvelisib and Eganelisib as promising dual-purposed anti-COVID and anticancer drugs, potentially targeting Mpro and PI3Kγ to stop virus replication and cytokine storms concomitantly. We also distinguished hotspot residues imparting significant interactions.
Collapse
Affiliation(s)
- Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| | - Shaswata Karmakar
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| | - Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University, Akurdi, Pune, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India.
| |
Collapse
|
2
|
Kaynak BT, Dahmani ZL, Doruker P, Banerjee A, Yang SH, Gordon R, Itzhaki LS, Bahar I. Cooperative mechanics of PR65 scaffold underlies the allosteric regulation of the phosphatase PP2A. Structure 2023; 31:607-618.e3. [PMID: 36948205 PMCID: PMC10164121 DOI: 10.1016/j.str.2023.02.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 01/25/2023] [Accepted: 02/23/2023] [Indexed: 03/24/2023]
Abstract
PR65, a horseshoe-shaped scaffold composed of 15 HEAT (observed in Huntingtin, elongation factor 3, protein phosphatase 2A, and the yeast kinase TOR1) repeats, forms, together with catalytic and regulatory subunits, the heterotrimeric protein phosphatase PP2A. We examined the role of PR65 in enabling PP2A enzymatic activity with computations at various levels of complexity, including hybrid approaches that combine full-atomic and elastic network models. Our study points to the high flexibility of this scaffold allowing for end-to-end distance fluctuations of 40-50 Å between compact and extended conformations. Notably, the intrinsic dynamics of PR65 facilitates complexation with the catalytic subunit and is retained in the PP2A complex enabling PR65 to engage the two domains of the catalytic subunit and provide the mechanical framework for enzymatic activity, with support from the regulatory subunit. In particular, the intra-repeat coils at the C-terminal arm play an important role in allosterically mediating the collective dynamics of PP2A, pointing to target sites for modulating PR65 function.
Collapse
Affiliation(s)
- Burak T Kaynak
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Zakaria L Dahmani
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Pemra Doruker
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Anupam Banerjee
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA; Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Shang-Hua Yang
- Department of Electrical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Reuven Gordon
- Department of Electrical and Computer Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Laura S Itzhaki
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, UK
| | - Ivet Bahar
- Laufer Center for Physical and Quantitative Biology, and Department of Biochemistry and Cell Biology, School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA.
| |
Collapse
|
3
|
Chataigner LMP, Gogou C, den Boer MA, Frias CP, Thies-Weesie DME, Granneman JCM, Heck AJR, Meijer DH, Janssen BJC. Structural insights into the contactin 1 - neurofascin 155 adhesion complex. Nat Commun 2022; 13:6607. [PMID: 36329006 PMCID: PMC9633819 DOI: 10.1038/s41467-022-34302-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Cell-surface expressed contactin 1 and neurofascin 155 control wiring of the nervous system and interact across cells to form and maintain paranodal myelin-axon junctions. The molecular mechanism of contactin 1 - neurofascin 155 adhesion complex formation is unresolved. Crystallographic structures of complexed and individual contactin 1 and neurofascin 155 binding regions presented here, provide a rich picture of how competing and complementary interfaces, post-translational glycosylation, splice differences and structural plasticity enable formation of diverse adhesion sites. Structural, biophysical, and cell-clustering analysis reveal how conserved Ig1-2 interfaces form competing heterophilic contactin 1 - neurofascin 155 and homophilic neurofascin 155 complexes whereas contactin 1 forms low-affinity clusters through interfaces on Ig3-6. The structures explain how the heterophilic Ig1-Ig4 horseshoe's in the contactin 1 - neurofascin 155 complex define the 7.4 nm paranodal spacing and how the remaining six domains enable bridging of distinct intercellular distances.
Collapse
Affiliation(s)
- Lucas M. P. Chataigner
- grid.5477.10000000120346234Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Christos Gogou
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maurits A. den Boer
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cátia P. Frias
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Dominique M. E. Thies-Weesie
- grid.5477.10000000120346234Van’t Hoff Laboratory for Physical and Colloid Chemistry, Debye Institute of Nanomaterials Science, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Joke C. M. Granneman
- grid.5477.10000000120346234Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Albert J. R. Heck
- grid.5477.10000000120346234Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands ,Netherlands Proteomics Center, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dimphna H. Meijer
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Kavli Institute of Nanoscience, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Bert J. C. Janssen
- grid.5477.10000000120346234Structural Biochemistry, Bijvoet Center for Biomolecular Research, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| |
Collapse
|
4
|
Nanomechanical and Morphological AFM Mapping of Normal Tissues and Tumors on Live Brain Slices Using Specially Designed Embedding Matrix and Laser-Shaped Cantilevers. Biomedicines 2022; 10:biomedicines10071742. [PMID: 35885046 PMCID: PMC9313344 DOI: 10.3390/biomedicines10071742] [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: 05/18/2022] [Revised: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 12/02/2022] Open
Abstract
Cell and tissue nanomechanics has been intriguingly introduced into biomedical research, not only complementing traditional immunophenotyping and molecular analysis, but also bringing unexpected new insights for clinical diagnostics and bioengineering. However, despite the progress in the study of individual cells in culture by atomic force microscopy (AFM), its application for mapping live tissues has a number of technical limitations. Here, we elaborate a new technique to study live slices of normal brain tissue and tumors by combining morphological and nanomechanical AFM mapping in high throughput scanning mode, in contrast to the typically utilized force spectroscopy mode based on single-point probe application. This became possible due to the combined use of an appropriate embedding matrix for vibratomy and originally modified AFM probes. The embedding matrix composition was carefully developed by regulating the amounts of agar and collagen I to reach optimal viscoelastic properties for obtaining high-quality live slices that meet AFM requirements. AFM tips were rounded by irradiating them with focused nanosecond laser pulses, while the resulting tip morphology was verified by scanning electron microscopy. Live slices preparation and AFM investigation take only 55 min and could be combined with a vital cell tracer analysis or immunostaining, thus making it promising for biomedical research and clinical diagnostics.
Collapse
|
5
|
Bauer J, Žoldák G. Interpretation of Single-Molecule Force Experiments on Proteins Using Normal Mode Analysis. NANOMATERIALS 2021; 11:nano11112795. [PMID: 34835560 PMCID: PMC8624234 DOI: 10.3390/nano11112795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 11/25/2022]
Abstract
Single-molecule force spectroscopy experiments allow protein folding and unfolding to be explored using mechanical force. Probably the most informative technique for interpreting the results of these experiments at the structural level makes use of steered molecular dynamics (MD) simulations, which can explicitly model the protein under load. Unfortunately, this technique is computationally expensive for many of the most interesting biological molecules. Here, we find that normal mode analysis (NMA), a significantly cheaper technique from a computational perspective, allows at least some of the insights provided by MD simulation to be gathered. We apply this technique to three non-homologous proteins that were previously studied by force spectroscopy: T4 lysozyme (T4L), Hsp70 and the glucocorticoid receptor domain (GCR). The NMA results for T4L and Hsp70 are compared with steered MD simulations conducted previously, and we find that we can recover the main results. For the GCR, which did not undergo MD simulation, our approach identifies substructures that correlate with experimentally identified unfolding intermediates. Overall, we find that NMA can make a valuable addition to the analysis toolkit for the structural analysis of single-molecule force experiments on proteins.
Collapse
Affiliation(s)
- Jacob Bauer
- Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 845 51 Bratislava, Slovakia
- Correspondence: (J.B.); (G.Ž.); Tel.: +421-55-234-2242 (G.Ž.)
| | - Gabriel Žoldák
- Center for Interdisciplinary Biosciences, P. J. Šafárik University, Technology and Innovation Park, Trieda SNP 1, 041 54 Košice, Slovakia
- Correspondence: (J.B.); (G.Ž.); Tel.: +421-55-234-2242 (G.Ž.)
| |
Collapse
|
6
|
Khairallah A, Ross CJ, Tastan Bishop Ö. GTP Cyclohydrolase I as a Potential Drug Target: New Insights into Its Allosteric Modulation via Normal Mode Analysis. J Chem Inf Model 2021; 61:4701-4719. [PMID: 34450011 DOI: 10.1021/acs.jcim.1c00898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) catalyzes the conversion of GTP into dihydroneopterin triphosphate (DHNP). DHNP is the first intermediate of the folate de novo biosynthesis pathway in prokaryotic and lower eukaryotic microorganisms and the tetrahydrobiopterin (BH4) biosynthesis pathway in higher eukaryotes. The de novo folate biosynthesis provides essential cofactors for DNA replication, cell division, and synthesis of key amino acids in rapidly replicating pathogen cells, such as Plasmodium falciparum (P. falciparum), a causative agent of malaria. In eukaryotes, the product of the BH4 biosynthesis pathway is essential for the production of nitric oxide and several neurotransmitter precursors. An increased copy number of the malaria parasite P. falciparum GCH1 gene has been reported to influence antimalarial antifolate drug resistance evolution, whereas mutations in the human GCH1 are associated with neuropathic and inflammatory pain disorders. Thus, GCH1 stands as an important and attractive drug target for developing therapeutics. The GCH1 intrinsic dynamics that modulate its activity remains unclear, and key sites that exert allosteric effects across the structure are yet to be elucidated. This study employed the anisotropic network model to analyze the intrinsic motions of the GCH1 structure alone and in complex with its regulatory partner protein. We showed that the GCH1 tunnel-gating mechanism is regulated by a global shear motion and an outward expansion of the central five-helix bundle. We further identified hotspot residues within sites of structural significance for the GCH1 intrinsic allosteric modulation. The obtained results can provide a solid starting point to design novel antineuropathic treatments for humans and novel antimalarial drugs against the malaria parasite P. falciparum GCH1 enzyme.
Collapse
Affiliation(s)
- Afrah Khairallah
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Caroline J Ross
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| |
Collapse
|
7
|
Alegre-Cebollada J. Protein nanomechanics in biological context. Biophys Rev 2021; 13:435-454. [PMID: 34466164 PMCID: PMC8355295 DOI: 10.1007/s12551-021-00822-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022] Open
Abstract
How proteins respond to pulling forces, or protein nanomechanics, is a key contributor to the form and function of biological systems. Indeed, the conventional view that proteins are able to diffuse in solution does not apply to the many polypeptides that are anchored to rigid supramolecular structures. These tethered proteins typically have important mechanical roles that enable cells to generate, sense, and transduce mechanical forces. To fully comprehend the interplay between mechanical forces and biology, we must understand how protein nanomechanics emerge in living matter. This endeavor is definitely challenging and only recently has it started to appear tractable. Here, I introduce the main in vitro single-molecule biophysics methods that have been instrumental to investigate protein nanomechanics over the last 2 decades. Then, I present the contemporary view on how mechanical force shapes the free energy of tethered proteins, as well as the effect of biological factors such as post-translational modifications and mutations. To illustrate the contribution of protein nanomechanics to biological function, I review current knowledge on the mechanobiology of selected muscle and cell adhesion proteins including titin, talin, and bacterial pilins. Finally, I discuss emerging methods to modulate protein nanomechanics in living matter, for instance by inducing specific mechanical loss-of-function (mLOF). By interrogating biological systems in a causative manner, these new tools can contribute to further place protein nanomechanics in a biological context.
Collapse
|
8
|
Abdollahiyan P, Oroojalian F, Baradaran B, de la Guardia M, Mokhtarzadeh A. Advanced mechanotherapy: Biotensegrity for governing metastatic tumor cell fate via modulating the extracellular matrix. J Control Release 2021; 335:596-618. [PMID: 34097925 DOI: 10.1016/j.jconrel.2021.06.002] [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: 05/03/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/19/2022]
Abstract
Mechano-transduction is the procedure of mechanical stimulus translation via cells, among substrate shear flow, topography, and stiffness into a biochemical answer. TAZ and YAP are transcriptional coactivators which are recognized as relay proteins that promote mechano-transduction within the Hippo pathway. With regard to healthy cells in homeostasis, mechano-transduction regularly restricts proliferation, and TAZ and YAP are totally inactive. During cancer development a YAP/TAZ - stimulating positive response loop is formed between the growing tumor and the stiffening ECM. As tumor developments, local stromal and cancerous cells take advantage of mechanotransduction to enhance proliferation, induce their migratory into remote tissues, and promote chemotherapeutic resistance. As a newly progresses paradigm, nanoparticle-conjunctions (such as magnetic nanoparticles, and graphene derivatives nanoparticles) hold significant promises for remote regulation of cells and their relevant events at molecular scale. Despite outstanding developments in employing nanoparticles for drug targeting studies, the role of nanoparticles on cellular behaviors (proliferation, migration, and differentiation) has still required more evaluations in the field of mechanotherapy. In this paper, the in-depth contribution of mechano-transduction is discussed during tumor progression, and how these consequences can be evaluated in vitro.
Collapse
Affiliation(s)
| | - Fatemeh Oroojalian
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd, Iran; Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, Iran.
| | - Behzad Baradaran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
9
|
Mikulska-Ruminska K, Anthonymuthu TS, Levkina A, Shrivastava IH, Kapralov AA, Bayır H, Kagan VE, Bahar I. NO ● Represses the Oxygenation of Arachidonoyl PE by 15LOX/PEBP1: Mechanism and Role in Ferroptosis. Int J Mol Sci 2021; 22:ijms22105253. [PMID: 34067535 PMCID: PMC8156958 DOI: 10.3390/ijms22105253] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
We recently discovered an anti-ferroptotic mechanism inherent to M1 macrophages whereby high levels of NO● suppressed ferroptosis via inhibition of hydroperoxy-eicosatetraenoyl-phosphatidylethanolamine (HpETE-PE) production by 15-lipoxygenase (15LOX) complexed with PE-binding protein 1 (PEBP1). However, the mechanism of NO● interference with 15LOX/PEBP1 activity remained unclear. Here, we use a biochemical model of recombinant 15LOX-2 complexed with PEBP1, LC-MS redox lipidomics, and structure-based modeling and simulations to uncover the mechanism through which NO● suppresses ETE-PE oxidation. Our study reveals that O2 and NO● use the same entry pores and channels connecting to 15LOX-2 catalytic site, resulting in a competition for the catalytic site. We identified residues that direct O2 and NO● to the catalytic site, as well as those stabilizing the esterified ETE-PE phospholipid tail. The functional significance of these residues is supported by in silico saturation mutagenesis. We detected nitrosylated PE species in a biochemical system consisting of 15LOX-2/PEBP1 and NO● donor and in RAW264.7 M2 macrophages treated with ferroptosis-inducer RSL3 in the presence of NO●, in further support of the ability of NO● to diffuse to, and react at, the 15LOX-2 catalytic site. The results provide first insights into the molecular mechanism of repression of the ferroptotic Hp-ETE-PE production by NO●.
Collapse
Affiliation(s)
- Karolina Mikulska-Ruminska
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA;
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University in Toruń, Grudziadzka 5, 87-100 Toruń, Poland
- Correspondence: (K.M.-R.); (V.E.K.); (I.B.)
| | - Tamil S. Anthonymuthu
- Department of Critical Care Medicine, Safar Center for Resuscitation Research, Children’s Neuroscience Institute, Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15260, USA; (T.S.A.); (H.B.)
| | - Anastasia Levkina
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15260, USA; (A.L.); (A.A.K.)
- Institute of Translational Medicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia
| | - Indira H. Shrivastava
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA;
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15260, USA; (A.L.); (A.A.K.)
| | - Alexandr A. Kapralov
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15260, USA; (A.L.); (A.A.K.)
| | - Hülya Bayır
- Department of Critical Care Medicine, Safar Center for Resuscitation Research, Children’s Neuroscience Institute, Children’s Hospital of Pittsburgh, University of Pittsburgh, Pittsburgh, PA 15260, USA; (T.S.A.); (H.B.)
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15260, USA; (A.L.); (A.A.K.)
| | - Valerian E. Kagan
- Department of Environmental and Occupational Health and Center for Free Radical and Antioxidant Health, University of Pittsburgh, Pittsburgh, PA 15260, USA; (A.L.); (A.A.K.)
- Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Institute of Regenerative Medicine, IM Sechenov Moscow State Medical University, 119048 Moscow, Russia
- Correspondence: (K.M.-R.); (V.E.K.); (I.B.)
| | - Ivet Bahar
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA;
- Correspondence: (K.M.-R.); (V.E.K.); (I.B.)
| |
Collapse
|
10
|
Shinde A, Illath K, Gupta P, Shinde P, Lim KT, Nagai M, Santra TS. A Review of Single-Cell Adhesion Force Kinetics and Applications. Cells 2021; 10:577. [PMID: 33808043 PMCID: PMC8000588 DOI: 10.3390/cells10030577] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/01/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Cells exert, sense, and respond to the different physical forces through diverse mechanisms and translating them into biochemical signals. The adhesion of cells is crucial in various developmental functions, such as to maintain tissue morphogenesis and homeostasis and activate critical signaling pathways regulating survival, migration, gene expression, and differentiation. More importantly, any mutations of adhesion receptors can lead to developmental disorders and diseases. Thus, it is essential to understand the regulation of cell adhesion during development and its contribution to various conditions with the help of quantitative methods. The techniques involved in offering different functionalities such as surface imaging to detect forces present at the cell-matrix and deliver quantitative parameters will help characterize the changes for various diseases. Here, we have briefly reviewed single-cell mechanical properties for mechanotransduction studies using standard and recently developed techniques. This is used to functionalize from the measurement of cellular deformability to the quantification of the interaction forces generated by a cell and exerted on its surroundings at single-cell with attachment and detachment events. The adhesive force measurement for single-cell microorganisms and single-molecules is emphasized as well. This focused review should be useful in laying out experiments which would bring the method to a broader range of research in the future.
Collapse
Affiliation(s)
- Ashwini Shinde
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Kavitha Illath
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Pallavi Gupta
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Pallavi Shinde
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| | - Ki-Taek Lim
- Department of Biosystems Engineering, Kangwon National University, Chuncheon-Si, Gangwon-Do 24341, Korea;
| | - Moeto Nagai
- Department of Mechanical Engineering, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi 441-8580, Japan;
| | - Tuhin Subhra Santra
- Department of Engineering Design, Indian Institute of Technology Madras, Chennai 600036, Tamil Nadu, India; (A.S.); (K.I.); (P.G.); (P.S.)
| |
Collapse
|
11
|
Wang J, Zhang X, Li H, Wang C, Li H, Keller S, Mishra UK, Nener BD, Parish G, Atkin R. pH-Dependent surface charge at the interfaces between aluminum gallium nitride (AlGaN) and aqueous solution revealed by surfactant adsorption. J Colloid Interface Sci 2021; 583:331-339. [DOI: 10.1016/j.jcis.2020.09.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 12/16/2022]
|
12
|
Kurus NN, Dultsev FN, Golyshev VM, Nekrasov DV, Pyshnyi DV, Lomzov AA. A QCM-based rupture event scanning technique as a simple and reliable approach to study the kinetics of DNA duplex dissociation. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:3771-3777. [PMID: 32716423 DOI: 10.1039/d0ay00613k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Rupture Event Scanning (REVS) is applied for the first time within an approach based on dynamic force spectroscopy. Using model DNA duplexes containing 20 pairs of oligonucleotides including those containing single mismatches, we demonstrated the possibility of reliable determination of the kinetic parameters of dissociation of biomolecular complexes: barrier positions, the rate constants of dissociation, and the lifetime of complexes. Within this approach, mechanical dissociation of DNA duplexes occurs according to a mechanism similar to unzipping. It is shown that this process takes place by overcoming a single energy barrier. In the case where a mismatch is located at the farthest duplex end from the QCM surface, a substantial decrease in the position of the barrier between the bound and unbound states is observed. We suppose that this is due to the formation of an initiation complex containing 3-4 pairs of bases, and this is sufficient for starting duplex unzipping.
Collapse
Affiliation(s)
- N N Kurus
- Rzhanov Institute of Semiconductor Physics SB, RAS, 630090, Russia.
| | | | | | | | | | | |
Collapse
|
13
|
Dąbrowski J, Nowak W, Ptak A. How strong are hydrogen bonds in the peptide model? Phys Chem Chem Phys 2020; 22:1392-1399. [DOI: 10.1039/c9cp05564a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We provide a methodology based on the steered molecular dynamics simulations and dynamic force spectroscopy calculations to determine the kinetic and energetic characteristics of hydrogen bonds.
Collapse
Affiliation(s)
- Jakub Dąbrowski
- Institute of Physics
- Faculty of Technical Physics
- Poznan University of Technology
- PL-60965 Poznan
- Poland
| | - Wiesław Nowak
- Institute of Physics
- Faculty of Physics
- Astronomy and Informatics
- Nicolaus Copernicus University
- PL-87100 Torun
| | - Arkadiusz Ptak
- Institute of Physics
- Faculty of Technical Physics
- Poznan University of Technology
- PL-60965 Poznan
- Poland
| |
Collapse
|
14
|
Mikulska-Ruminska K, Strzelecki J, Nowak W. Dynamics, nanomechanics and signal transduction in reelin repeats. Sci Rep 2019; 9:18974. [PMID: 31831824 PMCID: PMC6908669 DOI: 10.1038/s41598-019-55461-8] [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: 08/09/2019] [Accepted: 11/27/2019] [Indexed: 12/04/2022] Open
Abstract
Reelin is a large glycoprotein controlling brain development and cell adhesion. It regulates the positioning of neurons, as well as neurotransmission and memory formation. Perturbations in reelin signaling are linked to psychiatric disorders. Reelin participates in signal transduction by binding to the lipoprotein receptors VLDLR and ApoER2 through its central region. This part is rich in repeating BNR-EGF-BNR modules. We used standard molecular dynamics, steered molecular dynamics, and perturbation response scanning computational methods to characterize unique dynamical properties of reelin modules involved in signaling. Each module has specific sensors and effectors arranged in a similar topology. In the modules studied, disulfide bridges play a protective role, probably making both selective binding and protease activity of reelin possible. Results of single reelin molecule stretching by atomic force microscopy provide the first data on the mechanical stability of individual reelin domains. The forces required for partial unfolding of the modules studied are below 60 pN.
Collapse
Affiliation(s)
- Karolina Mikulska-Ruminska
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland.
| | - Janusz Strzelecki
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland
| | - Wieslaw Nowak
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100, Torun, Poland.
| |
Collapse
|
15
|
Mikulska-Ruminska K, Shrivastava I, Krieger J, Zhang S, Li H, Bayır H, Wenzel SE, VanDemark AP, Kagan VE, Bahar I. Characterization of Differential Dynamics, Specificity, and Allostery of Lipoxygenase Family Members. J Chem Inf Model 2019; 59:2496-2508. [PMID: 30762363 PMCID: PMC6541894 DOI: 10.1021/acs.jcim.9b00006] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Accurate modeling of structural dynamics of proteins and their differentiation across different species can help us understand generic mechanisms of function shared by family members and the molecular basis of the specificity of individual members. We focused here on the family of lipoxygenases, enzymes that catalyze lipid oxidation, the mammalian and bacterial structures of which have been elucidated. We present a systematic method of approach for characterizing the sequence, structure, dynamics, and allosteric signaling properties of these enzymes using a combination of structure-based models and methods and bioinformatics tools applied to a data set of 88 structures. The analysis elucidates the signature dynamics of the lipoxygenase family and its differentiation among members, as well as key sites that enable its adaptation to specific substrate binding and allosteric activity.
Collapse
Affiliation(s)
- Karolina Mikulska-Ruminska
- Institute of Physics, Department of Biophysics and Medical Physics , Nicolaus Copernicus University , 87-100 Torun , Poland
| | | | | | | | | | | | | | | | - Valerian E Kagan
- Laboratory of Navigational Redox Lipidomics , I M Sechenov Moscow State Medical University , Moskva 119146 , Russia
| | - Ivet Bahar
- Mol & Cell Cancer Biology , UPMC Hillman Cancer Center , Pittsburgh , Pennsylvania 15232 , United States
| |
Collapse
|
16
|
Atomic force microscopy for imaging and nanomechanical characterisation of live nematode epicuticle: A comparative Caenorhabditis elegans and Turbatrix aceti study. Ultramicroscopy 2018; 194:40-47. [PMID: 30071372 DOI: 10.1016/j.ultramic.2018.07.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 06/28/2018] [Accepted: 07/22/2018] [Indexed: 11/24/2022]
Abstract
Atomic force microscopy (AFM), a powerful tool in interdisciplinary biomedical research, has been applied here to investigate the surface of live nematodes epicuticle. We have used AFM in PeakForce Tapping non-resonant imaging and nanomechanical characterisation mode to investigate and compare the surface features of epicuticle of two free-living microscopic nematodes, Caenorhabditis elegans and Turbatrix aceti. We have successfully immobilised live anesthetized adult nematodes on glass supports using either layer-by-layer-deposited polyelectrolyte films or bioadhesive coatings, which allowed for imaging the living nematodes in native environment. We have obtained AFM images and corresponding nanomechanical maps of annular rings and furrows, demonstrating the differences in topography and structure between the species. Our results demonstrate that AFM in PeakForce Tapping mode can be used to image and characterise surfaces of relatively-large live immobilised multicellular organisms, which can be further applied to a number of invertebrates.
Collapse
|