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Świątek A, Kuczera K, Szoszkiewicz R. Effects of Proline on Internal Friction in Simulated Folding Dynamics of Several Alanine-Based α-Helical Peptides. J Phys Chem B 2024; 128:3856-3869. [PMID: 38606880 PMCID: PMC11056985 DOI: 10.1021/acs.jpcb.4c00623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/13/2024]
Abstract
We have studied in silico the effect of proline, a model cosolvent, on local and global friction coefficients in (un)folding of several typical alanine-based α-helical peptides. Local friction is related to dwell times of a single, ensemble-averaged hydrogen bond (HB) within each peptide. Global friction is related to energy dissipated in a series of configurational changes of each peptide experienced by increasing the number of HBs during folding. Both of these approaches are important in relation to future atomic force microscopic-based measurements of internal friction via force-clamp single-molecule force spectroscopy. Molecular dynamics (MD) simulations for six peptides, namely, ALA5, ALA8, ALA15, ALA21, (AAQAA)3, and H2N-GN(AAQAA)2G-COONH2, have been conducted at 2 and 5 M proline solutions in water. Using previously obtained MD data for these peptides in pure water as well as upgraded theoretical models, we obtained variations of local and global internal friction coefficients as a function of solution viscosity. The results showed the substantial role of proline in stabilizing the folded state and slowing the overall folding dynamics. Consequently, larger friction coefficients were obtained at larger viscosities. The local and global internal friction, i.e., respective, friction coefficients approximated to zero viscosity, was also obtained. The evolution of friction coefficients with viscosity was weakly dependent on the number of concurrent folding pathways but was rather dominated by a stabilizing effect of proline on the folded states. Obtained values of local and global internal friction showed qualitatively similar results and a clear dependency on the structure of the studied peptide.
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Affiliation(s)
- Adam Świątek
- Faculty of Chemistry,
Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Krzysztof Kuczera
- Department
of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Molecular Biosciences, The
University of Kansas, Lawrence, Kansas 66045, United States
| | - Robert Szoszkiewicz
- Faculty of Chemistry,
Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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Hu Q, Bian Q, Rong D, Wang L, Song J, Huang HS, Zeng J, Mei J, Wang PY. JAK/STAT pathway: Extracellular signals, diseases, immunity, and therapeutic regimens. Front Bioeng Biotechnol 2023; 11:1110765. [PMID: 36911202 PMCID: PMC9995824 DOI: 10.3389/fbioe.2023.1110765] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 02/13/2023] [Indexed: 02/25/2023] Open
Abstract
Janus kinase/signal transduction and transcription activation (JAK/STAT) pathways were originally thought to be intracellular signaling pathways that mediate cytokine signals in mammals. Existing studies show that the JAK/STAT pathway regulates the downstream signaling of numerous membrane proteins such as such as G-protein-associated receptors, integrins and so on. Mounting evidence shows that the JAK/STAT pathways play an important role in human disease pathology and pharmacological mechanism. The JAK/STAT pathways are related to aspects of all aspects of the immune system function, such as fighting infection, maintaining immune tolerance, strengthening barrier function, and cancer prevention, which are all important factors involved in immune response. In addition, the JAK/STAT pathways play an important role in extracellular mechanistic signaling and might be an important mediator of mechanistic signals that influence disease progression, immune environment. Therefore, it is important to understand the mechanism of the JAK/STAT pathways, which provides ideas for us to design more drugs targeting diseases based on the JAK/STAT pathway. In this review, we discuss the role of the JAK/STAT pathway in mechanistic signaling, disease progression, immune environment, and therapeutic targets.
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Affiliation(s)
- Qian Hu
- Department of Pharmacy, School of Medicine, Sir Run Run Shaw Hospital, Zhejiang University, Hangzhou, China.,Oujiang Laboratory, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Qihui Bian
- Oujiang Laboratory, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
| | - Dingchao Rong
- Department of Orthopaedic Surgery, The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Leiyun Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China.,Department of Pharmacy, Wuhan First Hospital, Wuhan, China
| | - Jianan Song
- Oujiang Laboratory, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
| | - Hsuan-Shun Huang
- Department of Research, Center for Prevention and Therapy of Gynecological Cancers, Buddhist Tzu Chi General Hospital, Hualien, Taiwan
| | - Jun Zeng
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Jie Mei
- Oujiang Laboratory, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China.,Hunan Key Laboratory of Pharmacogenetics, Institute of Clinical Pharmacology, Central South University, Changsha, China
| | - Peng-Yuan Wang
- Oujiang Laboratory, Key Laboratory of Alzheimer's Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
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Manokawinchoke J, Pavasant P, Limjeerajarus CN, Limjeerajarus N, Osathanon T, Egusa H. Mechanical loading and the control of stem cell behavior. Arch Oral Biol 2021; 125:105092. [PMID: 33652301 DOI: 10.1016/j.archoralbio.2021.105092] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/08/2021] [Accepted: 02/21/2021] [Indexed: 12/14/2022]
Abstract
OBJECTIVE Mechanical stimulation regulates many cell responses. The present study describes the effects of different in vitro mechanical stimulation approaches on stem cell behavior. DESIGN The narrative review approach was performed. The articles published in English language that addressed the effects of mechanical force on stem cells were searched on Pubmed and Scopus database. The effects of extrinsic mechanical force on stem cell response was reviewed and discussed. RESULTS Cells sense mechanical stimuli by the function of mechanoreceptors and further transduce force stimulation into intracellular signaling. Cell responses to mechanical stimuli depend on several factors including type, magnitude, and duration. Further, similar mechanical stimuli exhibit distinct cell responses based on numerous factors including cell type and differentiation stage. Various mechanical applications modulate stemness maintenance and cell differentiation toward specific lineages. CONCLUSIONS Mechanical force application modulates stemness maintenance and differentiation. Modification of force regimens could be utilized to precisely control appropriate stem cell behavior toward specific applications.
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Affiliation(s)
- Jeeranan Manokawinchoke
- Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand; Dental Stem Cell Biology Research Unit, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand; Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, 980-8575, Japan.
| | - Prasit Pavasant
- Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Chalida Nakalekha Limjeerajarus
- Dental Stem Cell Biology Research Unit, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand; Department of Physiology, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Nuttapol Limjeerajarus
- Research Center for Advanced Energy Technology, Faculty of Engineering, Thai-Nichi Institute of Technology, Bangkok, 10250, Thailand.
| | - Thanaphum Osathanon
- Department of Anatomy, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand; Dental Stem Cell Biology Research Unit, Faculty of Dentistry, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Hiroshi Egusa
- Division of Molecular and Regenerative Prosthodontics, Tohoku University Graduate School of Dentistry, Sendai, 980-8575, Japan.
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Hunter GL, He L, Perrimon N, Charras G, Giniger E, Baum B. A role for actomyosin contractility in Notch signaling. BMC Biol 2019; 17:12. [PMID: 30744634 PMCID: PMC6369551 DOI: 10.1186/s12915-019-0625-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/04/2019] [Indexed: 12/24/2022] Open
Abstract
Background Notch-Delta signaling functions across a wide array of animal systems to break symmetry in a sheet of undifferentiated cells and generate cells with different fates, a process known as lateral inhibition. Unlike many other signaling systems, however, since both the ligand and receptor are transmembrane proteins, the activation of Notch by Delta depends strictly on cell-cell contact. Furthermore, the binding of the ligand to the receptor may not be sufficient to induce signaling, since recent work in cell culture suggests that ligand-induced Notch signaling also requires a mechanical pulling force. This tension exposes a cleavage site in Notch that, when cut, activates signaling. Although it is not known if mechanical tension contributes to signaling in vivo, others have suggested that this is how endocytosis of the receptor-ligand complex contributes to the cleavage and activation of Notch. In a similar way, since Notch-mediated lateral inhibition at a distance in the dorsal thorax of the pupal fly is mediated via actin-rich protrusions, it is possible that cytoskeletal forces generated by networks of filamentous actin and non-muscle myosin during cycles of protrusion extension and retraction also contribute to Notch signaling. Results To test this hypothesis, we carried out a detailed analysis of the role of myosin II-dependent tension in Notch signaling in the developing fly and in cell culture. Using dynamic fluorescence-based reporters of Notch, we found that myosin II is important for signaling in signal sending and receiving cells in both systems—as expected if myosin II-dependent tension across the Notch-Delta complex contributes to Notch activation. While myosin II was found to contribute most to signaling at a distance, it was also required for maximal signaling between adjacent cells that share lateral contacts and for signaling between cells in culture. Conclusions Together these results reveal a previously unappreciated role for non-muscle myosin II contractility in Notch signaling, providing further support for the idea that force contributes to the cleavage and activation of Notch in the context of ligand-dependent signaling, and a new paradigm for actomyosin-based mechanosensation. Electronic supplementary material The online version of this article (10.1186/s12915-019-0625-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ginger L Hunter
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, 20892, USA. .,MRC-LMCB, University College London, London, WC1E6BT, UK. .,Institute for the Physics of Living Systems, University College London, London, WC1E6BT, UK. .,Present Address: Department of Biology, Clarkson University, Potsdam, NY, 13699, USA.
| | - Li He
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Norbert Perrimon
- Department of Genetics, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Guillaume Charras
- London Centre for Nanotechnology, University College London, London, WC1E6BT, UK.,Department of Cell and Developmental Biology, University College London, London, WC1E6BT, UK
| | - Edward Giniger
- National Institute of Neurological Disorders and Stroke, NIH, Bethesda, MD, 20892, USA.
| | - Buzz Baum
- MRC-LMCB, University College London, London, WC1E6BT, UK.,Institute for the Physics of Living Systems, University College London, London, WC1E6BT, UK
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Significance of glycosylation in Notch signaling. Biochem Biophys Res Commun 2014; 453:235-42. [PMID: 24909690 DOI: 10.1016/j.bbrc.2014.05.115] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 05/27/2014] [Indexed: 12/15/2022]
Abstract
Notch signaling is essential for cell-fate specification in metazoans, and dysregulation of the pathway leads to a variety of human diseases including heart and vascular defects as well as cancer. Glycosylation of the Notch extracellular domain has emerged as an elegant means for regulating Notch activity, especially since the discovery that Fringe is a glycosyltransferase that modifies O-fucose in 2000. Since then, several other O-glycans on the extracellular domain have been demonstrated to modulate Notch activity. Here we will describe recent results on the molecular mechanisms by which Fringe modulates Notch activity, summarize recent work on how O-glucose, O-GlcNAc, and O-GalNAc glycans affect Notch, and discuss several human genetic disorders resulting from defects in Notch glycosylation.
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