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Chu WT, Yan Z, Chu X, Zheng X, Liu Z, Xu L, Zhang K, Wang J. Physics of biomolecular recognition and conformational dynamics. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2021; 84:126601. [PMID: 34753115 DOI: 10.1088/1361-6633/ac3800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 11/09/2021] [Indexed: 06/13/2023]
Abstract
Biomolecular recognition usually leads to the formation of binding complexes, often accompanied by large-scale conformational changes. This process is fundamental to biological functions at the molecular and cellular levels. Uncovering the physical mechanisms of biomolecular recognition and quantifying the key biomolecular interactions are vital to understand these functions. The recently developed energy landscape theory has been successful in quantifying recognition processes and revealing the underlying mechanisms. Recent studies have shown that in addition to affinity, specificity is also crucial for biomolecular recognition. The proposed physical concept of intrinsic specificity based on the underlying energy landscape theory provides a practical way to quantify the specificity. Optimization of affinity and specificity can be adopted as a principle to guide the evolution and design of molecular recognition. This approach can also be used in practice for drug discovery using multidimensional screening to identify lead compounds. The energy landscape topography of molecular recognition is important for revealing the underlying flexible binding or binding-folding mechanisms. In this review, we first introduce the energy landscape theory for molecular recognition and then address four critical issues related to biomolecular recognition and conformational dynamics: (1) specificity quantification of molecular recognition; (2) evolution and design in molecular recognition; (3) flexible molecular recognition; (4) chromosome structural dynamics. The results described here and the discussions of the insights gained from the energy landscape topography can provide valuable guidance for further computational and experimental investigations of biomolecular recognition and conformational dynamics.
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Affiliation(s)
- Wen-Ting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zhiqiang Yan
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Xiakun Chu
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
| | - Xiliang Zheng
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Zuojia Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Li Xu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Kun Zhang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, People's Republic of China
| | - Jin Wang
- Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY 11794, United States of America
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Gao M, Han Y, Zeng Y, Su Z, Huang Y. Introducing intrinsic disorder reduces electrostatic steering in protein-protein interactions. Biophys J 2021; 120:2998-3007. [PMID: 34214536 DOI: 10.1016/j.bpj.2021.06.021] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 04/03/2021] [Accepted: 06/17/2021] [Indexed: 02/05/2023] Open
Abstract
Protein-protein interactions underlie many critical biology functions, such as cellular signaling and gene expression, in which electrostatic interactions can play a critical role in mediating the specificity and stability of protein complexes. A substantial portion of proteins are intrinsically disordered, and the influences of structural disorder on binding kinetics and thermodynamics have been widely investigated. However, whether the effect of electrostatic steering depends on structural disorder remains unexplored. In this work, we addressed the consequence of introducing intrinsic disorder in the electrostatic steering of the E3/Im3 complex using molecular dynamics simulation. Our results recapitulated the experimental observations that the responses of stability and kinetics to salt concentration for the ordered E3/Im3 complex were larger than those for the disordered E3/Im3 complex. Mechanistic analysis revealed that the native contact interactions involved in the encounter state and the transition state were essentially identical for both ordered and disordered E3. Therefore, the observed difference in electrostatic steering between ordered E3 and disordered E3 may result from their difference in conformation rather than their difference in binding mechanism. Because charged residues are frequently involved in protein-protein interactions, our results suggest that increasing structural disorder is expected to generally modulate the effect of electrostatic steering.
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Affiliation(s)
- Meng Gao
- Key Laboratory of Industrial Fermentation, Ministry of Education, Wuhan, China; Hubei Key Laboratory of Industrial Microbiology, Department of Biological Engineering, Wuhan, China; National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China
| | - Yue Han
- Key Laboratory of Industrial Fermentation, Ministry of Education, Wuhan, China; Hubei Key Laboratory of Industrial Microbiology, Department of Biological Engineering, Wuhan, China; National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China
| | - Yifan Zeng
- Key Laboratory of Industrial Fermentation, Ministry of Education, Wuhan, China; Hubei Key Laboratory of Industrial Microbiology, Department of Biological Engineering, Wuhan, China; National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation, Ministry of Education, Wuhan, China; Hubei Key Laboratory of Industrial Microbiology, Department of Biological Engineering, Wuhan, China; National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation, Ministry of Education, Wuhan, China; Hubei Key Laboratory of Industrial Microbiology, Department of Biological Engineering, Wuhan, China; National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.
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Yang J, Zeng Y, Liu Y, Gao M, Liu S, Su Z, Huang Y. Electrostatic interactions in molecular recognition of intrinsically disordered proteins. J Biomol Struct Dyn 2019; 38:4883-4894. [DOI: 10.1080/07391102.2019.1692073] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Jing Yang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Yifan Zeng
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Yunfei Liu
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Meng Gao
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Sen Liu
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Zhengding Su
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
| | - Yongqi Huang
- Key Laboratory of Industrial Fermentation (Ministry of Education), Hubei University of Technology, Wuhan, China
- Hubei Key Laboratory of Industrial Microbiology, Hubei University of Technology, Wuhan, China
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Shang X, Chu W, Chu X, Xu L, Longhi S, Wang J. Exploration of nucleoprotein α-MoRE and XD interactions of Nipah and Hendra viruses. J Mol Model 2018; 24:113. [PMID: 29691656 DOI: 10.1007/s00894-018-3643-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 03/28/2018] [Indexed: 11/28/2022]
Abstract
Henipavirus, including Hendra virus (HeV) and Nipah virus (NiV), is a newly discovered human pathogen genus. The nucleoprotein of Henipavirus contains an α-helical molecular recognition element (α-MoRE) that folds upon binding to the X domain (XD) of the phosphoprotein (P). In order to explore the conformational dynamics of free α-MoREs and the underlying binding-folding mechanism with XD, atomic force field-based and hybrid structure-based MD simulations were carried out. In our empirical force field-based simulations, characteristic structures and helicities of α-MoREs reveal the co-existence of partially structured and disordered conformations, as in the case of the well characterized cognate measles virus (MeV) α-MoRE. In spite of their overall similarity, the two α-MoREs display subtle helicity differences in their C-terminal region, but much different from that of MeV. For the α-MoRE/XD complexes, the results of our hybrid structure-based simulations provide the coupled binding-folding landscapes, and unveil a wide conformational selection mechanism at early binding stages, followed by a final induce-fit mechanism selection process. However, the HeV and NiV complexes have a lower binding barrier compared to that of MeV. Moreover, the HeV α-MoRE/XD complex shows much less coupling effects between binding and folding compared to that from both NiV and MeV. Our analysis revealed that contrary to NiV and MeV, the N- and C-terminal regions of the HeV α-MoRE maintains a low helicity also in the bound form.
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Affiliation(s)
- Xu Shang
- College of Physics, Jilin University, Changchun, 130012, China.,State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Wenting Chu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China
| | - Xiakun Chu
- IMDEA-Nanociencia, Campus Cantoblanco, Madrid, 28049, Spain
| | - Liufang Xu
- College of Physics, Jilin University, Changchun, 130012, China
| | - Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, CNRS and Aix-Marseille University, Marseille, France
| | - Jin Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin, 130022, China. .,Department of Chemistry & Physics, State University of New York at Stony Brook, Stony Brook, NY, 11794, USA.
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