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Tao P, Xiao Y. Role of cotranslational folding for β-sheet-enriched proteins: A perspective from molecular dynamics simulations. Phys Rev E 2022; 105:024402. [PMID: 35291071 DOI: 10.1103/physreve.105.024402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 01/14/2022] [Indexed: 06/14/2023]
Abstract
The formations of correct three-dimensional structures of proteins are essential to their functions. Cotranslational folding is vital for proteins to form correct structures in vivo. Although some experiments have shown that cotranslational folding can improve the efficiency of folding, its microscopic mechanism is not yet clear. Previously, we built a model of the ribosomal exit tunnel and investigated the cotranslational folding of a three-helix protein by using all-atom molecular dynamics simulations. Here we study the cotranslational folding of three β-sheet-enriched proteins using the same method. The results show that cotranslational folding can enhance the helical population in most cases and reduce non-native long-range contacts before emerging from the ribosomal exit tunnel. After exiting the tunnel, all proteins fall into local minimal states and the structural ensembles of cotranslational folding show more helical conformations than those of free folding. In particular, for one of the three proteins, the GTT WW domain, we find that one local minimum state of the cotranslational folding is the known folding intermediate, which is not found in free folding. This result suggests that the cotranslational folding may increase the folding efficiency by accelerating the sampling more than by avoiding the misfolded state, which is presently a mainstream viewpoint.
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Affiliation(s)
- Peng Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yi Xiao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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2
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Tao P, Wang E, Xiao Y. Pathway regulation mechanism revealed by cotranslational folding of villin headpiece subdomain HP35. Phys Rev E 2021; 101:052403. [PMID: 32575289 DOI: 10.1103/physreve.101.052403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 04/13/2020] [Indexed: 01/07/2023]
Abstract
Cotranslational folding is one of the most important features of protein folding in vivo. Although many studies have shown that the folding pathways of cotranslational folding are different from free folding in vitro, the detailed mechanism of folding dynamics is lacking. Here we combine all-atom molecular simulations with an ideal ribosome tunnel model to investigate the cotranslational folding of villin headpiece subdomain HP35. By comparing the folding dynamics between cotranslational folding and free folding, we found that cotranslational folding tends to fold along the pathway that is easier to fold into native state in the latter. In addition, the roles of the ribosome tunnel and sequential folding are analyzed separately. Our results show that the ribosome can prevent the untimely folding of the C segment of HP35 to reduce the non-native interactions, while the translation speed can regulate the amounts of native and non-native interactions and the balance between them. Overall, these results give insights into the general mechanisms of cotranslational protein folding.
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Affiliation(s)
- Peng Tao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Ercheng Wang
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China.,College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Yi Xiao
- School of Physics, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
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3
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Electrostatics of Prokaryotic Ribosome and Its Biological Implication. Biophys J 2020; 118:1205-1212. [PMID: 32023436 DOI: 10.1016/j.bpj.2020.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 12/26/2019] [Accepted: 01/09/2020] [Indexed: 12/19/2022] Open
Abstract
Ribosomes are essential machines for protein synthesis in cells. Their structures are very complex but conserved in different species. Because most parts of a ribosome are composed of negatively charged RNAs, its electrostatics should play a fundamental role in the realization of its functions. However, a complete picture of the electrostatics of ribosomes is still absent at present. Here, assisted by the latest version of DelPhi (version 8.4), we illustrate a picture of the electrostatics of a prokaryotic ribosome as well as its molecular chaperones. The revealed electrostatics features are consistent with available experimental data as well as the functions of the ribosome and its molecular chaperones and provides a basis for further studying the mechanism underlying these functions.
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Dao Duc K, Batra SS, Bhattacharya N, Cate JHD, Song YS. Differences in the path to exit the ribosome across the three domains of life. Nucleic Acids Res 2019; 47:4198-4210. [PMID: 30805621 PMCID: PMC6486554 DOI: 10.1093/nar/gkz106] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 02/22/2019] [Indexed: 01/07/2023] Open
Abstract
The ribosome exit tunnel is an important structure involved in the regulation of translation and other essential functions such as protein folding. By comparing 20 recently obtained cryo-EM and X-ray crystallography structures of the ribosome from all three domains of life, we here characterize the key similarities and differences of the tunnel across species. We first show that a hierarchical clustering of tunnel shapes closely reflects the species phylogeny. Then, by analyzing the ribosomal RNAs and proteins, we explain the observed geometric variations and show direct association between the conservations of the geometry, structure and sequence. We find that the tunnel is more conserved in the upper part close to the polypeptide transferase center, while in the lower part, it is substantially narrower in eukaryotes than in bacteria. Furthermore, we provide evidence for the existence of a second constriction site in eukaryotic exit tunnels. Overall, these results have several evolutionary and functional implications, which explain certain differences between eukaryotes and prokaryotes in their translation mechanisms. In particular, they suggest that major co-translational functions of bacterial tunnels were externalized in eukaryotes, while reducing the tunnel size provided some other advantages, such as facilitating the nascent chain elongation and enabling antibiotic resistance.
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Affiliation(s)
- Khanh Dao Duc
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | - Sanjit S Batra
- Computer Science Division, University of California, Berkeley, CA 94720, USA
| | | | - Jamie H D Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA.,Department of Chemistry, University of California, Berkeley, CA 94720, USA.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Yun S Song
- Computer Science Division, University of California, Berkeley, CA 94720, USA.,Department of Statistics, University of California, Berkeley, CA 94720, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
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5
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Wang E, Tao P, Wang J, Xiao Y. A novel folding pathway of the villin headpiece subdomain HP35. Phys Chem Chem Phys 2019; 21:18219-18226. [PMID: 31389931 DOI: 10.1039/c9cp01703h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The villin headpiece subdomain (HP35) is a fast-folding protein with 35 residues and its folding pathways have been extensively studied experimentally and theoretically but remain controversial. While experiments showed that HP35 might have multiple folding pathways, most theoretical studies only found one major pathway, although a few theoretical studies revealed two. Here we report our results of molecular dynamics simulations of HP35 folding by using the newest AMBER ff14SB force field and show that HP35 has a novel folding pathway in addition to the two pathways shown previously. We also study the mechanism of determining the folding pathways and found that the dynamics of Helix2 may play a special role in the folding of HP35. Our results may be helpful to understand the folding mechanism of HP35 further.
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Affiliation(s)
- Ercheng Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Wang E, Sun H, Wang J, Wang Z, Liu H, Zhang JZH, Hou T. End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design. Chem Rev 2019; 119:9478-9508. [DOI: 10.1021/acs.chemrev.9b00055] [Citation(s) in RCA: 578] [Impact Index Per Article: 115.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junmei Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - John Z. H. Zhang
- Shanghai Engineering Research Center of Molecular Therapeutics & New Drug Development, Shanghai Key Laboratory of Green Chemistry & Chemical Process, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China
- NYU−ECNU Center for Computational Chemistry, NYU Shanghai, Shanghai 200122, China
- Department of Chemistry, New York University, New York, New York 10003, United States
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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He E, Ren W, Wang J, Li W, Wang W. Effects of heme binding on myoglobin folding: Coarse grained molecular simulations. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1142/s0219633615500595] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Many proteins contain cofactors, such as heme, ATP and metal ions. Binding of cofactors is not only essential for their biological functions, but also can reshape the intrinsic energy landscape of protein molecules and modulate the folding and stability. However, the molecular mechanism of cofactor coupled protein folding is not well understood. In this work, we study the cofactor coupled folding of myoglobin, which is a typical cofactor (heme) containing protein, by performing molecular dynamics simulations with a structure-based protein model developed based on the energy landscape theory. We showed that the heme binding increases the stability of the myoglobin. More importantly, the heme binding tends to increase the protein folding cooperativity, and switch the folding process from a “three-state” mechanism to a “two-state” mechanism. We also showed that the folding pathways of the myoglobin can be modulated by the heme binding. By performing comparative simulations, we revealed that the above effects of heme binding are resulted from the heme induced folding of F-helix, which is otherwise unstructured at apo state, and the heme mediated contacting interactions around the heme binding site. The simulation results are consistent with available experimental data, and provide insights into the molecular mechanism of the effects of cofactor binding on the protein folding and stability.
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Affiliation(s)
- Erbin He
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Weitong Ren
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Jun Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Wenfei Li
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
| | - Wei Wang
- National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University Nanjing, 210093, P. R. China
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Wang E, Wang J, Chen C, Xiao Y. Computational evidence that fast translation speed can increase the probability of cotranslational protein folding. Sci Rep 2015; 5:15316. [PMID: 26486723 PMCID: PMC4614103 DOI: 10.1038/srep15316] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/17/2015] [Indexed: 11/09/2022] Open
Abstract
Translation speed can affect the cotranslational folding of nascent peptide. Experimental observations have indicated that slowing down translation rates of codons can increase the probability of protein cotranslational folding. Recently, a kinetic modeling indicates that fast translation can also increase the probability of cotranslational protein folding by avoiding misfolded intermediates. We show that the villin headpiece subdomain HP35 is an ideal model to demonstrate this phenomenon. We studied cotranslational folding of HP35 with different fast translation speeds by all-atom molecular dynamics simulations and found that HP35 can fold along a well-defined pathway that passes the on-pathway intermediate but avoids the misfolded off-pathway intermediate in certain case. This greatly increases the probability of HP35 cotranslational folding and the approximate mean first passage time of folding into native state is about 1.67μs. Since we also considered the space-confined effect of the ribosomal exit tunnel on the cotranslational folding, our simulation results suggested alternative mechanism for the increasing of cotranslational folding probability by fast translation speed.
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Affiliation(s)
- Ercheng Wang
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jun Wang
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Changjun Chen
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Yi Xiao
- Biomolecular Physics and Modeling Group, Department of Physics, Huazhong University of Science and Technology, Wuhan 430074, China
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