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Yuan L, Sun H, Ma X, Wang Y, Guo Z, Qi X, Le S, Chen H. Ligand-dependent folding and unfolding dynamics and free energy landscapes of acylphosphatase. SOFT MATTER 2024; 20:3780-3786. [PMID: 38639061 DOI: 10.1039/d4sm00131a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Acylphosphatase (AcP) is an enzyme which catalyses the hydrolysis of acylphosphate. The binding with the phosphate ion (Pi) assumes significance in preserving both the stability and enzymatic activity of AcP. While previous studies using single molecule force spectroscopy explored the mechanical properties of AcP, the influence of Pi on its folding and unfolding dynamic behaviors remains unexplored. In this work, using stable magnetic tweezers, we measured and compared the force-dependent folding and unfolding rates of AcP in the Tris buffer and phosphate buffer within a force range from 2 pN to 40 pN. We found that Pi exerts no discernible effect on the folding dynamics but consistently decreases the force-dependent unfolding rate of AcP by a constant ratio across the entire force spectrum. The free energy landscapes of AcP in the absence and presence of Pi are constructed. Our results reveal that Pi selectively binds to the native state of AcP, stabilizing it and suggesting the general properties of specific ligand-receptor interactions.
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Affiliation(s)
- Li Yuan
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
| | - Hao Sun
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Xuening Ma
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
| | - Yang Wang
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Zilong Guo
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Xingyu Qi
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Shimin Le
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
| | - Hu Chen
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China.
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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Sun H, Le S, Guo Z, Chen H. Exploring the free energy landscape of proteins using magnetic tweezers. Methods Enzymol 2024; 694:237-261. [PMID: 38492953 DOI: 10.1016/bs.mie.2023.12.008] [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] [Indexed: 03/18/2024]
Abstract
Proteins fold to their native states by searching through the free energy landscapes. As single-domain proteins are the basic building block of multiple-domain proteins or protein complexes composed of subunits, the free energy landscapes of single-domain proteins are of critical importance to understand the folding and unfolding processes of proteins. To explore the free energy landscapes of proteins over large conformational space, the stability of native structure is perturbed by biochemical or mechanical means, and the conformational transition process is measured. In single molecular manipulation experiments, stretching force is applied to proteins, and the folding and unfolding transitions are recorded by the extension time course. Due to the broad force range and long-time stability of magnetic tweezers, the free energy landscape over large conformational space can be obtained. In this article, we describe the magnetic tweezers instrument design, protein construct design and preparation, fluid chamber preparation, common-used measuring protocols including force-ramp and force-jump measurements, and data analysis methods to construct the free energy landscape. Single-domain cold shock protein is introduced as an example to build its free energy landscape by magnetic tweezers measurements.
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Affiliation(s)
- Hao Sun
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China
| | - Shimin Le
- Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, P.R. China
| | - Zilong Guo
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China.
| | - Hu Chen
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, P.R. China; Department of Physics, Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Xiamen University, Xiamen, P.R. China.
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Sun H, Guo Z, Hong H, Zhang Z, Zhang Y, Wang Y, Le S, Chen H. Free Energy Landscape of Type III Fibronectin Domain with Identified Intermediate State and Hierarchical Symmetry. PHYSICAL REVIEW LETTERS 2023; 131:218402. [PMID: 38072617 DOI: 10.1103/physrevlett.131.218402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 10/23/2023] [Indexed: 12/18/2023]
Abstract
The tenth domain of type III fibronectin (FNIII_{10}) mediates cell adhesion to the extracellular matrix. Despite its structural similarity to immunoglobulin domains, FNIII_{10} exhibits unique unfolding behaviors. We employed magnetic tweezers to investigate the unfolding and folding dynamics of FNIII_{10} under physiological forces (4-50 pN). Our results showed that FNIII_{10} follows a consistent transition pathway with an intermediate state characterized by detached A and G β strands. We determined the folding free energies and all force-dependent transition rates of FNIII_{10} and found that both unfolding rates from the native state to the intermediate state and from the intermediate state to the unfolded state deviate from Bell's model. We constructed a quantitative free energy landscape with well-defined traps and barriers that exhibits a hierarchical symmetrical pattern. Our findings provide a comprehensive understanding of FNIII_{10} conformational dynamics and demonstrate how free energy landscape of multistate biomolecules can be precisely mapped, illuminating the relationship between thermal stability, intermediate states, and folding rates in protein folding.
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Affiliation(s)
- Hao Sun
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Zilong Guo
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Haiyan Hong
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Zhuwei Zhang
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Yuhang Zhang
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Yang Wang
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
| | - Shimin Le
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
| | - Hu Chen
- Research Institute for Biomimetics and Soft Matter, Fujian Provincial Key Lab for Soft Functional Materials Research, Department of Physics, Xiamen University, Xiamen 361005, China
- Center of Biomedical Physics, Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
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