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Zhao Y, Zhang X, Liu L, Hu F, Chang F, Han Z, Li C. Insights into Activation Dynamics and Functional Sites of Inwardly Rectifying Potassium Channel Kir3.2 by an Elastic Network Model Combined with Perturbation Methods. J Phys Chem B 2024; 128:1360-1370. [PMID: 38308647 DOI: 10.1021/acs.jpcb.3c06739] [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: 02/05/2024]
Abstract
The inwardly rectifying potassium channel Kir3.2, a member of the inward rectifier potassium (Kir) channel family, exerts important biological functions through transporting potassium ions outside of the cell, during which a large-scale synergistic movement occurs among its different domains. Currently, it is not fully understood how the binding of the ligand to the Kir3.2 channel leads to the structural changes and which key residues are responsible for the channel gating and allosteric dynamics. Here, we construct the Gaussian network model (GNM) of the Kir3.2 channel with the secondary structure and covalent interaction information considered (sscGNM), which shows a better performance in reproducing the channel's flexibility compared with the traditional GNM. In addition, the sscANM-based perturbation method is used to simulate the channel's conformational transition caused by the activator PIP2's binding. By applying certain forces to the PIP2 binding pocket, the coarse-grained calculations generate the similar conformational changes to the experimental observation, suggesting that the topology structure as well as PIP2 binding are crucial to the allosteric activation of the Kir3.2 channel. We also utilize the sscGNM-based thermodynamic cycle method developed by us to identify the key residues whose mutations significantly alter the channel's binding free energy with PIP2. We identify not only the residues important for the specific binding but also the ones critical for the allosteric transition coupled with PIP2 binding. This study is helpful for understanding the working mechanism of Kir3.2 channels and can provide important information for related drug design.
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Affiliation(s)
- Yingchun Zhao
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Xinyu Zhang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Lamei Liu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Fangrui Hu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Fubin Chang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
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Soto P, Gloeb GM, Tsuchida KA, Charles AA, Greenwood NM, Hendrickson H. Insight into the conserved structural dynamics of the C-terminus of mammal PrPC identifies structural core and possible structural role of pharmacological chaperones. Prion 2023; 17:55-66. [PMID: 36892160 PMCID: PMC10012922 DOI: 10.1080/19336896.2023.2186674] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/10/2023] Open
Abstract
Misfolding of the prion protein is central to prion disease aetiology. Although understanding the dynamics of the native fold helps to decipher the conformational conversion mechanism, a complete depiction of distal but coupled prion protein sites common across species is lacking. To fill this gap, we used normal mode analysis and network analysis to examine a collection of prion protein structures deposited on the protein data bank. Our study identified a core of conserved residues that sustains the connectivity across the C-terminus of the prion protein. We propose how a well-characterized pharmacological chaperone may stabilize the fold. Also, we provide insight into the effect on the native fold of initial misfolding pathways identified by others using kinetics studies.
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Affiliation(s)
- Patricia Soto
- Physics department, Creighton University, Omaha, NE, USA
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Liu X, Zhang H, Zhou Z, Prabhakaran P, Vongsangnak W, Hu G, Xiao F. Functional insight into Cordyceps militaris sugar transporters by structure modeling, network analysis and allosteric regulation. Phys Chem Chem Phys 2023; 25:14311-14323. [PMID: 37183444 DOI: 10.1039/d2cp05611a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Insights into the structures, functions and dynamics of Cordyceps militaris (C. militaris) sugar transporters are necessary for understanding their versatile metabolic capability for fungal growth. The sequence-function relationship study of 85 C. militaris sugar transporters showed that there is a gap between phylogenetic-based subfamily classification and their functions. Beyond protein sequences, structural modeling and principal component analysis of the structural ensemble revealed the different folds of the Car and Org subfamilies. Performing channel detection and network analysis found that the Alp and Hex subfamilies can be specifically distinguished from others by the betweenness of channel residues. Signature dynamics analysis further suggested that the Hex subfamily demonstrates different dynamics, with high flexibility at the H1 region in TM11. Furthermore, the H1 region as an allosteric site was examined by network parameter calculations that guided allosteric pathways between this region and the channel cavity. Together with gene expression data of C. militaris, e.g., Hex06741 in the Hex subfamily, it was promisingly expressed when sugar utilization was altered. This work demonstrates an in silico framework for investigating C. militaris sugar transporters as an example case study of the allosteric activity of the Hex subfamily and can facilitate sugar transporter engineering design that can further optimize the preferable sugar utilization and fermentation process of C. militaris.
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Affiliation(s)
- Xin Liu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.
- Institute of Blood and Marrow Transplantation, Medical College of Soochow University, Jiangsu Institute of Hematology, The first Affiliated Hospital of Soochow University, Collaborative Innovation Center of Hematology, National Clinical Research Center for Hematologic Diseases, Soochow University, Suzhou 215123, China
| | - Hanyang Zhang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.
| | - Ziyun Zhou
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, 215123, China
| | - Pranesha Prabhakaran
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Wanwipa Vongsangnak
- Omics Center for Agriculture, Bioresources, Food, and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand.
| | - Guang Hu
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.
- Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Soochow University, Suzhou, 215123, China
| | - Fei Xiao
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Suzhou Medical College of Soochow University, Suzhou 215123, China.
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Chen L, Gong W, Han Z, Zhou W, Yang S, Li C. Key Residues in δ Opioid Receptor Allostery Explored by the Elastic Network Model and the Complex Network Model Combined with the Perturbation Method. J Chem Inf Model 2022; 62:6727-6738. [PMID: 36073904 DOI: 10.1021/acs.jcim.2c00513] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Opioid receptors, a kind of G protein-coupled receptors (GPCRs), mainly mediate an analgesic response via allosterically transducing the signal of endogenous ligand binding in the extracellular domain to couple to effector proteins in the intracellular domain. The δ opioid receptor (DOP) is associated with emotional control besides pain control, which makes it an attractive therapeutic target. However, its allosteric mechanism and key residues responsible for the structural stability and signal communication are not completely clear. Here we utilize the Gaussian network model (GNM) and amino acid network (AAN) combined with perturbation methods to explore the issues. The constructed fcfGNMMD, where the force constants are optimized with the inverse covariance estimation based on the correlated fluctuations from the available DOP molecular dynamics (MD) ensemble, shows a better performance than traditional GNM in reproducing residue fluctuations and cross-correlations and in capturing functionally low-frequency modes. Additionally, fcfGNMMD can consider implicitly the environmental effects to some extent. The lowest mode can well divide DOP segments and identify the two sodium ion (important allosteric regulator) binding coordination shells, and from the fastest modes, the key residues important for structure stabilization are identified. Using fcfGNMMD combined with a dynamic perturbation-response method, we explore the key residues related to the sodium ion binding. Interestingly, we identify not only the key residues in sodium ion binding shells but also the ones far away from the perturbation sites, which are involved in binding with DOP ligands, suggesting the possible long-range allosteric modulation of sodium binding for the ligand binding to DOP. Furthermore, utilizing the weighted AAN combined with attack perturbations, we identify the key residues for allosteric communication. This work helps strengthen the understanding of the allosteric communication mechanism in δ opioid receptor and can provide valuable information for drug design.
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Affiliation(s)
- Lei Chen
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Weikang Gong
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Wenxue Zhou
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Shuang Yang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing 100124, China
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