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Tong M, Liu P, Li C, Zhang Z, Sun W, Dong P, Fan N, Wang X, Liu J, Lv C, Cao Z, Wang Y. Interaction of Asn297-Linked Glycan Ligands with the Fc Fragment of the Immunoglobulin Class G1: A Molecular Dynamics Simulation Study. J Chem Inf Model 2024; 64:785-798. [PMID: 38262973 DOI: 10.1021/acs.jcim.3c01584] [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: 01/25/2024]
Abstract
The allosteric modulation of the homodimeric H10-03-6 protein to glycan ligands L1 and L2, and the STAB19 protein to glycan ligands L3 and L4, respectively, has been studied by molecular dynamics simulations and free energy calculations. The results revealed that the STAB19 protein has a significantly higher affinity for L3 (-11.38 ± 2.32 kcal/mol) than that for L4 (-5.51 ± 1.92 kcal/mol). However, the combination of the H10-03-6 protein with glycan L2 (1.23 ± 6.19 kcal/mol) is energetically unfavorable compared with that of L1 (-13.96 ± 0.35 kcal/mol). Further, the binding of glycan ligands L3 and L4 to STAB19 would result in the significant closure of the two CH2 domains of the STAB19 conformation with the decrease of the centroid distances between the two CH2 domains compared with the H10-03-6/L1/L2 complex. The CH2 domain closure of STAB19 relates directly to the formation of new hydrogen bonds and hydrophobic interactions between the residues Ser239, Val240, Asp265, Glu293, Asn297, Thr299, Ser337, Asp376, Thr393, Pro395, and Pro396 in STAB19 and glycan ligands L3 and L4, which suggests that these key residues would contribute to the specific regulation of STAB19 to L3 and L4. In addition, the distance analysis revealed that the EF loop in the H10-03-6/L1/L2 model presents a high flexibility and partial disorder compared with the stabilized STAB19/L3/L4 complex. These results will be helpful in understanding the specific regulation through the asymmetric structural characteristics in the CH2 and CH3 domains of the H10-03-6 and STAB19 proteins.
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Affiliation(s)
- Mingqiong Tong
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Peng Liu
- Faculty of Electrical Engineering, Universiti Teknologi Malaysia, UTM, Johor Bahru, Johor Darul Takzim 81310, Malaysia
- The Office of Academic Affairs, Dezhou University, Dezhou 253023, China
| | - Chaoqun Li
- Hebei Key Laboratory of Heterocyclic Compounds, College of Chemistry, Chemical Engineering and Materials, Handan University, Handan, Hebei 056005, China
| | - Zhongyu Zhang
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Wan Sun
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Pingxuan Dong
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Na Fan
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Xiaoyue Wang
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Jing Liu
- Shandong Engineering Research Center of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou 253023, China
| | - Chao Lv
- College of Chemistry and Chemical Engineering, Dezhou University, Dezhou 253023, China
| | - Zanxia Cao
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, China
| | - Yan Wang
- College of Chemistry, Beijing Normal University, 19# Xinjiekouwai Street, Beijing 100875, China
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Negi I, Mahmi AS, Seelam Prabhakar P, Sharma P. Molecular Dynamics Simulations of the Aptamer Domain of Guanidinium Ion Binding Riboswitch ykkC-III: Structural Insights into the Discrimination of Cognate and Alternate Ligands. J Chem Inf Model 2021; 61:5243-5255. [PMID: 34609872 DOI: 10.1021/acs.jcim.1c01022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Guanidinium ion is a toxic cellular metabolite. The ykkC-III riboswitch, an mRNA stretch, regulates the gene expression by undergoing a conformational change in response to the binding of a free guanidinium ion and thereby plays a potentially important role in alleviating guanidinium toxicity in cells. An experimental crystal structure of the guanidinium-bound aptamer domain of the riboswitch from Thermobifida Fusca revealed the overall RNA architecture and mapped the specific noncovalent interactions that stabilize the ligand within the binding pocket aptamer. However, details of how the aptamer domain discriminates the cognate ligand from its closest structurally analogous physiological metabolites (arginine and urea), and how the binding of cognate ligand arrays information from the aptamer domain to the expression platform for regulating the gene expression, are not well understood. To fill this void, we perform a cumulative of 2 μs all-atom explicit-solvent molecular dynamics (MD) simulations on the full aptamer domain, augmented with quantum-chemical calculations on the ligand-binding pocket, to compare the structural and dynamical details of the guanidinium-bound state with the arginine or urea bound states, as well as the unbound (open) state. Analysis of the ligand-binding pocket reveals that due to unfavorable interactions with the binding-pocket residues, urea cannot bind the aptamer domain and thereby cannot alter the gene expression. Although interaction of the guanidyl moiety of arginine within the binding pocket is either comparable or stronger than the guanidinium ion, additional non-native hydrogen-bonding networks, as well as differences in the dynamical details of the arginine-bound state, explain why arginine cannot transmit the information from the aptamer domain to the expression platform. Based on our simulations, we propose a mechanism of how the aptamer domain communicates with the expression platform. Overall, our work provides interesting insights into the ligand recognition by a specific class of riboswitches and may hopefully inspire future studies to further understand the gene regulation by riboswitches.
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Affiliation(s)
- Indu Negi
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Amanpreet Singh Mahmi
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Preethi Seelam Prabhakar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - Purshotam Sharma
- Computational Biochemistry Laboratory, Department of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
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Tong M, Liu P, Sun W, Liu J, Fan N, Wang X, Zhang Z, Song X, Lv C, Wang Y. Molecular dynamics simulation studies on the specific regulation of PTPN18 to the HER2 phospho-peptides. J Mol Recognit 2021; 34:e2890. [PMID: 33620127 DOI: 10.1002/jmr.2890] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/15/2021] [Accepted: 01/26/2021] [Indexed: 11/09/2022]
Abstract
The specific regulation of PTPN18 protein to three HER2 phospho-peptides has been studied by molecular dynamics simulations and free energy calculations. The results revealed that the three HER2 phospho-peptides binding to the PTPN18 catalytic domain is energetically favorable due to substrate specificity of PTPN18, and moreover, the PTPN18 protein have significantly higher affinity to pY1248 peptide (-45.22 kcal/mol) than that of pY1112 (-25.3 kcal/mol) and pY1196 (-31.86 kcal/mol) peptides. Further, the binding of HER2 phospho-peptides to PTPN18 have also caused the closure of WPD-loop with the decrease of the centroid distances between the P-loop and the WPD loop. The WPD-loop closure of PTPN18 relates directly to the new hydrogen bond and hydrophobic interaction formations between the residues Tyr62, Asp64, Val65, Ala231, Arg235, and Ala273 in PTPN18 and Tyr(PO3) in the HER2 phospho-peptides, which suggests that these key residues would contribute to the specific regulation of PTPN18 to the substrates. The correlation analysis revealed the allosteric communication networks from the pY binding loop to the WPD loop through the structural change and the residue interactions in PTPN18. These results will be helpful to understand the specific regulation through the allosteric communication network in the PTPN18 catalytic domain.
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Affiliation(s)
- Mingqiong Tong
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Peng Liu
- The Office of Academic Affairs, Dezhou University, Dezhou, China
| | - Wan Sun
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Jing Liu
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Na Fan
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Xiaoyue Wang
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Zhongyu Zhang
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Xinfeng Song
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Chao Lv
- Shandong Provincial Engineering Laboratory of Novel Pharmaceutical Excipients, Sustained and Controlled Release Preparations, College of Medicine and Nursing, Dezhou University, Dezhou, China
| | - Yan Wang
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing, China
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Li C, Zhao X, Liu W, Yin F, Hu J, Zhang G, Chen G. DNA Structural Distortions Induced by a Monofunctional Trinuclear Platinum Complex with Various Cross-Links Using Molecular Dynamics Simulation. J Chem Inf Model 2020; 60:1700-1708. [PMID: 32096984 DOI: 10.1021/acs.jcim.0c00002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The monofunctional trinuclear platinum complex (MTPC), as a promising antitumor agent, can form MTPC-DNA adducts via bifunctional and trifunctional cross-links. Molecular dynamics simulations were used to investigate DNA structural distortions of the MTPC-DNA adducts. MTPC coordinating to DNA results in the decrease of base-pair thermal stability and DNA structural distortions. It is found that there are more significant DNA structural distortions in the trifunctional cross-link than in the bifunctional cross-link, in the 1,4-GG than in the 1,3-GG cross-link, and in the intrastrand than in the interstrand cross-link with the same spans. The results provide a better understanding of DNA structural distortions induced by MTPC with various cross-links at the nucleotide level and are helpful for exploring novel Pt-based anticancer drugs.
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Affiliation(s)
- Chaoqun Li
- Hebei Key Laboratory of Heterocyclic Compounds, College of Chemistry, Chemical Engineering and Materials, Handan University, Handan, 056005 Hebei province, China
| | - Xiaojia Zhao
- Hebei Key Laboratory of Heterocyclic Compounds, College of Chemistry, Chemical Engineering and Materials, Handan University, Handan, 056005 Hebei province, China
| | - Wei Liu
- College of Chemistry, Beijing Normal University, 19# Xinjiekouwai Street, Beijing 100875, China
| | - Fangqian Yin
- Hebei Key Laboratory of Heterocyclic Compounds, College of Chemistry, Chemical Engineering and Materials, Handan University, Handan, 056005 Hebei province, China
| | - Junping Hu
- Hebei Key Laboratory of Heterocyclic Compounds, College of Chemistry, Chemical Engineering and Materials, Handan University, Handan, 056005 Hebei province, China
| | - Guangjie Zhang
- Hebei Key Laboratory of Heterocyclic Compounds, College of Chemistry, Chemical Engineering and Materials, Handan University, Handan, 056005 Hebei province, China
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, 19# Xinjiekouwai Street, Beijing 100875, China
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Li C, Zhao X, Zhu X, Xie P, Chen G. Structural Studies of the 3',3'-cGAMP Riboswitch Induced by Cognate and Noncognate Ligands Using Molecular Dynamics Simulation. Int J Mol Sci 2018; 19:ijms19113527. [PMID: 30423927 PMCID: PMC6274999 DOI: 10.3390/ijms19113527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/03/2018] [Accepted: 11/04/2018] [Indexed: 01/09/2023] Open
Abstract
Riboswtich RNAs can control gene expression through the structural change induced by the corresponding small-molecule ligands. Molecular dynamics simulations and free energy calculations on the aptamer domain of the 3′,3′-cGAMP riboswitch in the ligand-free, cognate-bound and noncognate-bound states were performed to investigate the structural features of the 3′,3′-cGAMP riboswitch induced by the 3′,3′-cGAMP ligand and the specificity of ligand recognition. The results revealed that the aptamer of the 3′,3′-cGAMP riboswitch in the ligand-free state has a smaller binding pocket and a relatively compact structure versus that in the 3′,3′-cGAMP-bound state. The binding of the 3′,3′-cGAMP molecule to the 3′,3′-cGAMP riboswitch induces the rotation of P1 helix through the allosteric communication from the binding sites pocket containing the J1/2, J1/3 and J2/3 junction to the P1 helix. Simultaneously, these simulations also revealed that the preferential binding of the 3′,3′-cGAMP riboswitch to its cognate ligand, 3′,3′-cGAMP, over its noncognate ligand, c-di-GMP and c-di-AMP. The J1/2 junction in the 3′,3′-cGAMP riboswitch contributing to the specificity of ligand recognition have also been found.
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Affiliation(s)
- Chaoqun Li
- College of Chemistry, Chemical Engineering and Materials, Handan University, No. 530 North Xueyuan Road, Hanshan District, Han Dan 056005, Hebei, China.
| | - Xiaojia Zhao
- College of Chemistry, Chemical Engineering and Materials, Handan University, No. 530 North Xueyuan Road, Hanshan District, Han Dan 056005, Hebei, China.
| | - Xiaomin Zhu
- College of Chemistry, Chemical Engineering and Materials, Handan University, No. 530 North Xueyuan Road, Hanshan District, Han Dan 056005, Hebei, China.
| | - Pengtao Xie
- College of Chemistry, Chemical Engineering and Materials, Handan University, No. 530 North Xueyuan Road, Hanshan District, Han Dan 056005, Hebei, China.
| | - Guangju Chen
- College of Chemistry, Beijing Normal University, 19# Xinjiekouwai Street, Beijing 100875, China.
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