1
|
Lu J, Wang M, Meng Y, An W, Wang X, Sun G, Wang H, Liu W. Current advances in biomaterials for inner ear cell regeneration. Front Neurosci 2024; 17:1334162. [PMID: 38282621 PMCID: PMC10811200 DOI: 10.3389/fnins.2023.1334162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/28/2023] [Indexed: 01/30/2024] Open
Abstract
Inner ear cell regeneration from stem/progenitor cells provides potential therapeutic strategies for the restoration of sensorineural hearing loss (SNHL), however, the efficiency of regeneration is low and the functions of differentiated cells are not yet mature. Biomaterials have been used in inner ear cell regeneration to construct a more physiologically relevant 3D culture system which mimics the stem cell microenvironment and facilitates cellular interactions. Currently, these biomaterials include hydrogel, conductive materials, magneto-responsive materials, photo-responsive materials, etc. We analyzed the characteristics and described the advantages and limitations of these materials. Furthermore, we reviewed the mechanisms by which biomaterials with different physicochemical properties act on the inner ear cell regeneration and depicted the current status of the material selection based on their characteristics to achieve the reconstruction of the auditory circuits. The application of biomaterials in inner ear cell regeneration offers promising opportunities for the reconstruction of the auditory circuits and the restoration of hearing, yet biomaterials should be strategically explored and combined according to the obstacles to be solved in the inner ear cell regeneration research.
Collapse
Affiliation(s)
- Junze Lu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
- Shandong Institute of Otorhinolaryngology, Jinan, China
| | - Man Wang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
- Shandong Institute of Otorhinolaryngology, Jinan, China
| | - Yu Meng
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
- Shandong Institute of Otorhinolaryngology, Jinan, China
| | - Weibin An
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
- Shandong Institute of Otorhinolaryngology, Jinan, China
| | - Xue Wang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
- Shandong Institute of Otorhinolaryngology, Jinan, China
| | - Gaoying Sun
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
- Shandong Institute of Otorhinolaryngology, Jinan, China
| | - Haibo Wang
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
- Shandong Institute of Otorhinolaryngology, Jinan, China
| | - Wenwen Liu
- Department of Otolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, China
- Shandong Institute of Otorhinolaryngology, Jinan, China
| |
Collapse
|
2
|
Sora V, Tiberti M, Beltrame L, Dogan D, Robbani SM, Rubin J, Papaleo E. PyInteraph2 and PyInKnife2 to Analyze Networks in Protein Structural Ensembles. J Chem Inf Model 2023; 63:4237-4245. [PMID: 37437128 DOI: 10.1021/acs.jcim.3c00574] [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: 07/14/2023]
Abstract
Due to the complex nature of noncovalent interactions and their long-range effects, analyzing protein conformations using network theory can be enlightening. Protein Structure Networks (PSNs) provide a convenient formalism to study protein structures in relation to essential properties such as key residues for structural stability, allosteric communication, and the effects of modifications of the protein. PSNs can be defined according to very different principles, and the available tools have limitations in input formats, supported models, and version control. Other outstanding problems are related to the definition of network cutoffs and the assessment of the stability of the network properties. The protein science community could benefit from a common framework to carry out these analyses and make them easier to reproduce, reuse, and evaluate. We here provide two open-source software packages, PyInteraph2 and PyInKnife2, to implement and analyze PSNs in a reproducible and documented manner. PyInteraph2 interfaces with multiple formats for protein ensembles and incorporates different network models with the possibility of integrating them into a macronetwork and performing various downstream analyses, including hubs, connected components, and several other centrality measures, and visualizes the networks or further analyzes them thanks to compatibility with Cytoscape.PyInKnife2 that supports the network models implemented in PyInteraph2. It employs a jackknife resampling approach to estimate the convergence of network properties and streamline the selection of distance cutoffs. We foresee that the modular structure of the code and the supported version control system will promote the transition to a community-driven effort, boost reproducibility, and establish common protocols in the PSN field. As developers, we will guarantee the introduction of new functionalities and maintenance, assistance, and training of new contributors.
Collapse
Affiliation(s)
- Valentina Sora
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Cancer Systems Biology, Section of Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Matteo Tiberti
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Ludovica Beltrame
- Cancer Systems Biology, Section of Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Deniz Dogan
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Shahriyar Mahdi Robbani
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Joshua Rubin
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
| | - Elena Papaleo
- Cancer Structural Biology, Danish Cancer Institute, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Cancer Systems Biology, Section of Bioinformatics, Department of Health and Technology, Technical University of Denmark, 2800 Lyngby, Denmark
| |
Collapse
|
3
|
Ooka K, Liu R, Arai M. The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics. Molecules 2022; 27:molecules27144460. [PMID: 35889332 PMCID: PMC9319528 DOI: 10.3390/molecules27144460] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/07/2022] [Accepted: 07/08/2022] [Indexed: 11/16/2022] Open
Abstract
Despite the recent advances in the prediction of protein structures by deep neutral networks, the elucidation of protein-folding mechanisms remains challenging. A promising theory for describing protein folding is a coarse-grained statistical mechanical model called the Wako-Saitô-Muñoz-Eaton (WSME) model. The model can calculate the free-energy landscapes of proteins based on a three-dimensional structure with low computational complexity, thereby providing a comprehensive understanding of the folding pathways and the structure and stability of the intermediates and transition states involved in the folding reaction. In this review, we summarize previous and recent studies on protein folding and dynamics performed using the WSME model and discuss future challenges and prospects. The WSME model successfully predicted the folding mechanisms of small single-domain proteins and the effects of amino-acid substitutions on protein stability and folding in a manner that was consistent with experimental results. Furthermore, extended versions of the WSME model were applied to predict the folding mechanisms of multi-domain proteins and the conformational changes associated with protein function. Thus, the WSME model may contribute significantly to solving the protein-folding problem and is expected to be useful for predicting protein folding, stability, and dynamics in basic research and in industrial and medical applications.
Collapse
Affiliation(s)
- Koji Ooka
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan;
- Komaba Organization for Educational Excellence, College of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Runjing Liu
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan;
| | - Munehito Arai
- Department of Physics, Graduate School of Science, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan;
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan;
- Correspondence:
| |
Collapse
|
4
|
Arora N, Hazra JP, Rakshit S. Anisotropy in mechanical unfolding of protein upon partner-assisted pulling and handle-assisted pulling. Commun Biol 2021; 4:925. [PMID: 34326473 PMCID: PMC8322310 DOI: 10.1038/s42003-021-02445-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
Proteins as force-sensors respond to mechanical cues and regulate signaling in physiology. Proteins commonly connect the source and response points of mechanical cues in two conformations, independent proteins in end-to-end geometry and protein complexes in handshake geometry. The force-responsive property of independent proteins in end-to-end geometry is studied extensively using single-molecule force spectroscopy (SMFS). The physiological significance of the complex conformations in force-sensing is often disregarded as mere surge protectors. However, with the potential of force-steering, protein complexes possess a distinct mechano-responsive property over individual force-sensors. To decipher, we choose a force-sensing protein, cadherin-23, from tip-link complex and perform SMFS using end-to-end geometry and handshake complex geometry. We measure higher force-resilience of cadherin-23 with preferential shorter extensions in handshake mode of pulling over the direct mode. The handshake geometry drives the force-response of cadherin-23 through different potential-energy landscapes than direct pulling. Analysis of the dynamic network structure of cadherin-23 under tension indicates narrow force-distributions among residues in cadherin-23 in direct pulling, resulting in low force-dissipation paths and low resilience to force. Overall, the distinct and superior mechanical responses of cadherin-23 in handshake geometry than single protein geometry highlight a probable evolutionary drive of protein-protein complexes as force-conveyors over independent ones.
Collapse
Affiliation(s)
- Nisha Arora
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India
| | - Jagadish Prasad Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
| | - Sabyasachi Rakshit
- Department of Chemical Sciences, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
- Centre for Protein Science Design and Engineering, Indian Institute of Science Education and Research Mohali, Mohali, Punjab, India.
| |
Collapse
|