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Deng J, Yuan Y, Cui Q. Modulation of Allostery with Multiple Mechanisms by Hotspot Mutations in TetR. J Am Chem Soc 2024; 146:2757-2768. [PMID: 38231868 PMCID: PMC10843641 DOI: 10.1021/jacs.3c12494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Modulating allosteric coupling offers unique opportunities for biomedical applications. Such efforts can benefit from efficient prediction and evaluation of allostery hotspot residues that dictate the degree of cooperativity between distant sites. We demonstrate that effects of allostery hotspot mutations can be evaluated qualitatively and semiquantitatively by molecular dynamics simulations in a bacterial tetracycline repressor (TetR). The simulations recapitulate the effects of these mutations on abolishing the induction function of TetR and provide a rationale for the different rescuabilities observed to restore allosteric coupling of the hotspot mutations. We demonstrate that the same noninducible phenotype could be the result of perturbations in distinct structural and energetic properties of TetR. Our work underscores the value of explicitly computing the functional free energy landscapes to effectively evaluate and rank hotspot mutations despite the prevalence of compensatory interactions and therefore provides quantitative guidance to allostery modulation for therapeutic and engineering applications.
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Affiliation(s)
- Jiahua Deng
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Yuchen Yuan
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Qiang Cui
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
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2
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Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation. Nat Commun 2022; 13:7607. [PMID: 36494361 PMCID: PMC9734150 DOI: 10.1038/s41467-022-34960-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 11/11/2022] [Indexed: 12/13/2022] Open
Abstract
ATP phosphoribosyltransferase catalyses the first step of histidine biosynthesis and is controlled via a complex allosteric mechanism where the regulatory protein HisZ enhances catalysis by the catalytic protein HisGS while mediating allosteric inhibition by histidine. Activation by HisZ was proposed to position HisGS Arg56 to stabilise departure of the pyrophosphate leaving group. Here we report active-site mutants of HisGS with impaired reaction chemistry which can be allosterically restored by HisZ despite the HisZ:HisGS interface lying ~20 Å away from the active site. MD simulations indicate HisZ binding constrains the dynamics of HisGS to favour a preorganised active site where both Arg56 and Arg32 are poised to stabilise leaving-group departure in WT-HisGS. In the Arg56Ala-HisGS mutant, HisZ modulates Arg32 dynamics so that it can partially compensate for the absence of Arg56. These results illustrate how remote protein-protein interactions translate into catalytic resilience by restoring damaged electrostatic preorganisation at the active site.
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3
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Chen J, Liu J, Yuan Y, Chen X, Zhang F, Pu X. Molecular Mechanisms of Diverse Activation Stimulated by Different Biased Agonists for the β2-Adrenergic Receptor. J Chem Inf Model 2021; 62:5175-5192. [PMID: 34802238 DOI: 10.1021/acs.jcim.1c01016] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
β2AR is an important drug target protein involving many diseases. Biased drugs induce specific signaling and provide additional clinical utility to optimize β2AR-based therapies. However, the biased signaling mechanism has not been elucidated. Motivated by the issue, we chose four agonists with divergent bias (balanced agonist, G-protein-biased agonist, and β-arrestin-biased agonists) and utilized Gaussian accelerated molecular dynamics simulation coupled with a dynamic network to probe the molecular mechanisms of distinct biased activation induced by the structural differences between the four agonists. Our simulations reveal that the G-protein-biased agonist induces an open conformation with the outward shifts of TM6 and TM7 for the intracellular domain, which will be beneficial to couple G protein. In contrast, the β-arrestin-biased agonists regulate an occluded conformation with a slightly outward movement of TM6 and an inward shift of TM7, which should favor β-arrestin signaling. The balanced agonist does not induce an observable outward shift for TM6 but, along with a slight tilt for TM7, leads to an inactive-like conformation. In addition, our results reveal the first time that ICL3 presents specific conformations with different agonists. The G-protein-biased agonist drives ICL3 to open so that the G protein-binding pocket can be available, while the β-arrestin-biased agonists induce ICL3 to form a closed conformation with a stable local α-helix. MM/PBSA analysis further reveals that the hydroxyl groups in the resorcinol of the G-protein-biased agonist form strong interactions with Y5.38 and S5.42, thus preventing tilting of the TM5 extracellular end. The catechol of the balanced agonist and the β-arrestin-biased ones induces the rearrangement of two hydrophobic residues F6.52 and W6.48. However, different from the balanced agonist, the ethyl substituent of β-arrestin-biased agonists forms additional hydrophobic interactions with W6.48 and F6.51 after the rearrangement, which should contribute to the β-arrestin bias. The shortest pathway analysis further reveals that the three residues Y7.43, N7.45, and N7.49 are crucial for allosterically regulating G-protein-biased signaling, while the two residues W6.48 and F6.44 make an important contribution to regulate β-arrestin-biased signaling. For the balanced agonist NE, the allosteric regulation pathway simultaneously involves the residue associated with G-protein-biased signaling like S5.46 and the residues related to β-arrestin-biased signaling like W6.48 and F6.44, thus producing unbiased signaling. The observations could advance our understanding of the biased activation mechanism on class A GPCRs and provide a useful guideline for the design of biased drugs.
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Affiliation(s)
- Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Jiangting Liu
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Yuan Yuan
- College of Management, Southwest University for Nationalities, Chengdu 610041, China
| | - Xin Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Fuhui Zhang
- College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu 610064, China
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4
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Tian X, Liu H, Chen HF. Catalytic mechanism of butane anaerobic oxidation for alkyl-coenzyme M reductase. Chem Biol Drug Des 2021; 98:701-712. [PMID: 34328701 DOI: 10.1111/cbdd.13931] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/02/2021] [Accepted: 07/24/2021] [Indexed: 12/18/2022]
Abstract
Methane is among the most potent of the greenhouse gases, which plays a key role in global climate change. As an excellent carbon and energy source, methane can be utilized by anaerobic methane oxidizing archaea and aerobic methane oxidizing bacteria. The previous work shows that an anaerobic thermophilic enrichment culture composed of dense consortia of archaea and bacteria apparently uses partly similar pathways to oxidize the C4 hydrocarbon butane. However, the catalytic mechanism of butane anaerobic oxidation for alkyl-coenzyme M reductase is still unknown. Therefore, molecular dynamics (MD) simulation was used to investigate the dynamics differences of catalytic mechanism between methane coenzyme M reductase (MCR) and alkyl-coenzyme M reductase (ACR). At first, the binding pocket of ACR is larger than that of MCR. Then, the complex of butane and ACR is more stable than that of methane and ACR. Protein conformation cloud suggests that the position of methane is dynamics and methane escapes from the binding pocket of ACR during most of the simulation time, while butane tightly binds in the pocket of ACR. The hydrophobic interactions between butane and ACR are more and stronger than those between methane and ACR. At the same time, the binding free energy between butane and ACR is significantly lower than that between methane and ACR. The dynamics correlation network indicates that the transformation of information flow for ACR-butane is smoother than that for ACR-methane. The shortest pathway for ACR-butane is from Gln144, Ala141, Hie135, Ile133, Ala160, Arg206, Asp97, Met94, Tyr347 to Phe345 with synergistic effect for two butane molecules. This study can insight into the catalytic mechanism for butane/ACR complex.
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Affiliation(s)
- Xiaopian Tian
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
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5
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Wang H, Song L, Zhou T, Zeng C, Jia Y, Zhao Y. A computational study of Tat-CDK9-Cyclin binding dynamics and its implication in transcription-dependent HIV latency. Phys Chem Chem Phys 2020; 22:25474-25482. [PMID: 33043947 DOI: 10.1039/d0cp03662e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
HIV is a virus that attacks the T cells. HIV may either actively replicate or become latent within host cells for years. Since HIV uses its own protein Tat to hijack the host CDK9-Cyclin complex for transcription, Tat is implicated in transcription-dependent HIV latency. To quantify the impact of Tat binding, we propose a computational framework to probe the dynamics of the CDK9-Cyclin interface and the ATP pocket reorganization upon binding by different Tat mutants. Specifically, we focus on mutations at three Tat residues P10, W11, and N12 that are known to interact directly with CDK9 based on the crystal structure of the Tat-CDK9-Cyclin complex. Our molecular dynamics simulations show that the CDK9-Cyclin interface becomes slightly weaker for P10S and W11R mutants but tighter for the K12N mutant. Furthermore, the side chain orientation of residue K48 in the ATP pocket of CDK9 is similar to the inactive state in P10S and W11R simulations, but similar to the active state in K12N simulations. These are consistent with some existing but puzzling observations of latency for these mutants. This framework may hence help gain a better understanding of the role of Tat in the transcription-dependent HIV latency establishment.
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Affiliation(s)
- Huiwen Wang
- Institute of Biophysics and Department of Physics, Central China Normal University, Wuhan 430079, China.
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6
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Torrens-Fontanals M, Stepniewski TM, Aranda-García D, Morales-Pastor A, Medel-Lacruz B, Selent J. How Do Molecular Dynamics Data Complement Static Structural Data of GPCRs. Int J Mol Sci 2020; 21:E5933. [PMID: 32824756 PMCID: PMC7460635 DOI: 10.3390/ijms21165933] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/11/2020] [Accepted: 08/15/2020] [Indexed: 01/08/2023] Open
Abstract
G protein-coupled receptors (GPCRs) are implicated in nearly every physiological process in the human body and therefore represent an important drug targeting class. Advances in X-ray crystallography and cryo-electron microscopy (cryo-EM) have provided multiple static structures of GPCRs in complex with various signaling partners. However, GPCR functionality is largely determined by their flexibility and ability to transition between distinct structural conformations. Due to this dynamic nature, a static snapshot does not fully explain the complexity of GPCR signal transduction. Molecular dynamics (MD) simulations offer the opportunity to simulate the structural motions of biological processes at atomic resolution. Thus, this technique can incorporate the missing information on protein flexibility into experimentally solved structures. Here, we review the contribution of MD simulations to complement static structural data and to improve our understanding of GPCR physiology and pharmacology, as well as the challenges that still need to be overcome to reach the full potential of this technique.
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Affiliation(s)
- Mariona Torrens-Fontanals
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Tomasz Maciej Stepniewski
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
- InterAx Biotech AG, PARK innovAARE, 5234 Villigen, Switzerland
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-093 Warsaw, Poland
| | - David Aranda-García
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Adrián Morales-Pastor
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Brian Medel-Lacruz
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
| | - Jana Selent
- Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM)—Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain; (M.T.-F.); (T.M.S.); (D.A.-G.); (A.M.-P.); (B.M.-L.)
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7
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Li Q, Luo R, Chen HF. Dynamical important residue network (DIRN): network inference via conformational change. Bioinformatics 2019; 35:4664-4670. [PMID: 31038692 PMCID: PMC6853687 DOI: 10.1093/bioinformatics/btz298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/19/2019] [Accepted: 04/18/2019] [Indexed: 01/18/2023] Open
Abstract
MOTIVATION Protein residue interaction network has emerged as a useful strategy to understand the complex relationship between protein structures and functions and how functions are regulated. In a residue interaction network, every residue is used to define a network node, adding noises in network post-analysis and increasing computational burden. In addition, dynamical information is often necessary in deciphering biological functions. RESULTS We developed a robust and efficient protein residue interaction network method, termed dynamical important residue network, by combining both structural and dynamical information. A major departure from previous approaches is our attempt to identify important residues most important for functional regulation before a network is constructed, leading to a much simpler network with the important residues as its nodes. The important residues are identified by monitoring structural data from ensemble molecular dynamics simulations of proteins in different functional states. Our tests show that the new method performs well with overall higher sensitivity than existing approaches in identifying important residues and interactions in tested proteins, so it can be used in studies of protein functions to provide useful hypotheses in identifying key residues and interactions. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Quan Li
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA 92697, USA
- Department of Chemical and Biomolecular Engineering, University of California, Irvine, CA 92697, USA
- Department of Materials Science and Engineering, University of California, Irvine, CA 92697, USA
- Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
- Department of Chemistry, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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8
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Zhang Y, Chen HF. Allosteric mechanism of an oximino-piperidino-piperidine antagonist for the CCR5 chemokine receptor. Chem Biol Drug Des 2019; 95:113-123. [PMID: 31571405 DOI: 10.1111/cbdd.13627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/29/2019] [Accepted: 09/04/2019] [Indexed: 11/30/2022]
Abstract
The first step for the HIV-1 virus infecting host cell is bound with the CCR5 chemokine receptor. A set of allosteric inhibitors of oximino-piperidino-piperidine antagonists for CCR5 chemokine receptor was discovered. However, the allosteric mechanism of these inhibitors is still unsolved. Therefore, residue-level dynamics correlation network combining with on molecular dynamics simulation was used to investigate the allosteric mechanism. The dynamics correlation network of bound CCR5 is significantly different from that of free CCR5. The community of the most active complex suggests that the allosteric information can freely transfer from the allosteric site to the effector site of the second extracellular loop, while the information transfers bottleneck for the less active one. Here, a hypothesis was proposed that "binding-induced allosteric mechanism" was used to reveal the allosteric regulation of antagonists and the network perturbation confirmed it. Finally, the shortest path algorithm was used to identify the possible allosteric pathway with Gly173-Lys171-Thr177-Tyr89-LIG which was evaluated by the network perturbation of key residue. Furthermore, the efficiency of allostery for the most active system is the highest among these antagonist complexes. The strategy targeting the allosteric pathway can be used to design novel inhibitors of HIV-1 virus.
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Affiliation(s)
- Yangpeng Zhang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
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Seelam PP, Mitra A, Sharma P. Pairing interactions between nucleobases and ligands in aptamer:ligand complexes of riboswitches: crystal structure analysis, classification, optimal structures, and accurate interaction energies. RNA (NEW YORK, N.Y.) 2019; 25:1274-1290. [PMID: 31315914 PMCID: PMC6800475 DOI: 10.1261/rna.071530.119] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/12/2019] [Indexed: 06/10/2023]
Abstract
In the present work, 67 crystal structures of the aptamer domains of RNA riboswitches are chosen for analysis of the structure and strength of hydrogen bonding (pairing) interactions between nucleobases constituting the aptamer binding pockets and the bound ligands. A total of 80 unique base:ligand hydrogen-bonded pairs containing at least two hydrogen bonds were identified through visual inspection. Classification of these contacts in terms of the interacting edge of the aptamer nucleobase revealed that interactions involving the Watson-Crick edge are the most common, followed by the sugar edge of purines and the Hoogsteen edge of uracil. Alternatively, classification in terms of the chemical constitution of the ligand yields five unique classes of base:ligand pairs: base:base, base:amino acid, base:sugar, base:phosphate, and base:other. Further, quantum mechanical (QM) geometry optimizations revealed that 67 out of 80 pairs exhibit stable geometries and optimal deviations from their macromolecular crystal occurrences. This indicates that these contacts are well-defined RNA aptamer:ligand interaction motifs. QM calculated interaction energies of base:ligand pairs reveal a rich hydrogen bonding landscape, ranging from weak interactions (base:other, -3 kcal/mol) to strong (base:phosphate, -48 kcal/mol) contacts. The analysis was further extended to study the biological importance of base:ligand interactions in the binding pocket of the tetrahydrofolate riboswitch and thiamine pyrophosphate riboswitch. Overall, our study helps in understanding the structural and energetic features of base:ligand pairs in riboswitches, which could aid in developing meaningful hypotheses in the context of RNA:ligand recognition. This can, in turn, contribute toward current efforts to develop antimicrobials that target RNAs.
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Affiliation(s)
- Preethi P Seelam
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology (IIIT-H), Gachibowli, Hyderabad, Telangana 500032, India
| | - Abhijit Mitra
- 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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Unraveling RNA dynamical behavior of TPP riboswitches: a comparison between Escherichia coli and Arabidopsis thaliana. Sci Rep 2019; 9:4197. [PMID: 30862893 PMCID: PMC6414600 DOI: 10.1038/s41598-019-40875-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 02/19/2019] [Indexed: 01/03/2023] Open
Abstract
Riboswitches are RNA sensors that affect post-transcriptional processes through their ability to bind to small molecules. Thiamine pyrophosphate (TPP) riboswitch class is the most widespread riboswitch occurring in all three domains of life. Even though it controls different genes involved in the synthesis or transport of thiamine and its phosphorylated derivatives in bacteria, archaea, fungi, and plants, the TPP aptamer has a conserved structure. In this study, we aimed at understanding differences in the structural dynamics of TPP riboswitches from Escherichia coli and Arabidopsis thaliana, based on their crystallographic structures (TPPswec and TPPswat, respectively) and dynamics in aqueous solution, both in apo and holo states. A combination of Molecular Dynamics Simulations and Network Analysis empowered to find out slight differences in the dynamical behavior of TPP riboswitches, although relevant for their dynamics in bacteria and plants species. Our results suggest that distinct interactions in the microenvironment surrounding nucleotide U36 of TPPswec (and U35 in TPPswat) are related to different responses to TPP. The network analysis showed that minor structural differences in the aptamer enable enhanced intramolecular communication in the presence of TPP in TPPswec, but not in TPPswat. TPP riboswitches of plants present subtler and slower regulation mechanisms than bacteria do.
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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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Ho KC, Hamelberg D. Combinatorial Coarse-Graining of Molecular Dynamics Simulations for Detecting Relationships between Local Configurations and Overall Conformations. J Chem Theory Comput 2018; 14:6026-6034. [DOI: 10.1021/acs.jctc.8b00333] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ka Chun Ho
- Department of Chemistry and the Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
| | - Donald Hamelberg
- Department of Chemistry and the Center for Diagnostics & Therapeutics, Georgia State University, Atlanta, Georgia 30302-3965, United States
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13
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Dan A, Chen HF. Secondary structures transition of tau protein with intrinsically disordered proteins specific force field. Chem Biol Drug Des 2018; 93:242-253. [PMID: 30259679 DOI: 10.1111/cbdd.13407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/13/2018] [Accepted: 09/15/2018] [Indexed: 02/06/2023]
Abstract
Microtubule-associated Tau protein plays a key role in assembling microtubule and modulating the functional organization of the neuron and developing axonal morphology, growth, and polarity. The pathological Tau can aggregate into cross-beta amyloid as one of the hallmarks for Alzheimer's disease (AD). Therefore, one of the top priorities in AD research is to figure out the structural model of Tau aggregation and to screen the inhibitors. The latest generation intrinsically disordered protein specific force field ff14IDPSFF significantly improved the distributions of heterogeneous conformations for intrinsically disordered proteins (IDPs). Here, the molecular dynamics (MD) simulations with three force fields of ff14SB, ff14IDPs, and ff14IDPSFF were employed to investigate the secondary structures transition of Tau (267-312) fragment. The results indicate that ff14IDPSFF can generate more heterogeneous conformers, and the predicted secondary structural distribution is closer to that of the experimental observation. In addition, predicted secondary chemical shifts from ff14IDPSFF are the most approach to those of experiment. Secondary structures transition kinetics for Tau(267-312) with ff14IDPSFF shows that the secondary structures were gradually transformed from α-helix to β-strand and the β-strand located at the regions of the residues 274-280 and residues 305-311. Besides, the driving force for the secondary structures transition of Tau(267-312) is mainly hydrophobic interactions which located at hexa-peptides 275 VQIINK280 and 306 VQIVYK311 . Secondary structure transition of Tau protein can give insight into the aggregation mechanism for AD.
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Affiliation(s)
- Aohuan Dan
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
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Kesherwani M, N H V K, Velmurugan D. Conformational Dynamics of thiM Riboswitch To Understand the Gene Regulation Mechanism Using Markov State Modeling and the Residual Fluctuation Network Approach. J Chem Inf Model 2018; 58:1638-1651. [PMID: 29939019 DOI: 10.1021/acs.jcim.8b00155] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Thiamine pyrophosphate (TPP) riboswitch is a cis-regulatory element in the noncoding region of mRNA. The aptamer domain of TPP riboswitch detects the high abundance of coenzyme thiamine pyrophosphate (TPP) and modulates the gene expression for thiamine synthetic gene. The mechanistic understanding in recognition of TPP in aptamer domain and ligand-induced compactness for folding of expression platform are most important to designing novel modulators. To understand the dynamic behavior of TPP riboswitch upon TPP binding, molecular dynamics simulations were performed for 400 ns in both apo and TPP bound forms of thiM riboswitch from E. coli and analyzed in terms of eRMSD-based Markov state modeling and residual fluctuation network. Markov state models show good correlations in transition probability among metastable states from simulated trajectory and generated models. Structural compactness in TPP bound form is observed which is correlated with SAXS experiment. The importance of junction of P4 and P5 is evident during dynamics, which correlates with FRET analysis. The dynamic nature of two sensor forearms is due to the flexible P1 helix, which is its intrinsic property. The transient state in TPP-bound form was observed in the Markov state model, along with stable states. We believe that this transient state is responsible to assist the influx and outflux of ligand molecule by creating a solvent channel around the junction region of P4 and P5 and such a structure was anticipated in FRET analysis. The dynamic nature of riboswitch is dependent on the interaction between residues on distal loops L3 and L5/P3 and junction P4 and P5, J3/2 which stabilize the J2/4. It helps in the transfer of allosteric information between J2/4 and P3/L5 tertiary docking region through the active site residues. Understanding such information flow will benefit in highlighting crucial residues in highly dynamic and kinetic systems. Here, we report the residues and segments in riboswitch that play vital roles in providing stability and this can be exploited in designing inhibitors to regulate the functioning of riboswitches.
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Affiliation(s)
- Manish Kesherwani
- Centre for Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai - 600025 India
| | - Kutumbarao N H V
- Centre for Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai - 600025 India
| | - Devadasan Velmurugan
- Centre for Advanced Study in Crystallography and Biophysics , University of Madras, Guindy Campus , Chennai - 600025 India
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15
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Li C, Zhao X, Xie P, Hu J, Bi H. Molecular dynamics simulation on the allosteric analysis of the c-di-GMP class I riboswitch induced by ligand binding. J Mol Recognit 2018; 32:e2756. [PMID: 30033590 DOI: 10.1002/jmr.2756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 06/20/2018] [Accepted: 06/21/2018] [Indexed: 02/02/2023]
Abstract
Riboswitches are RNA molecules that regulate gene expression using conformation change, affected by binding of small molecule ligands. Although a number of ligand-bound aptamer complex structures have been solved, it is important to know ligand-free conformations of the aptamers in order to understand the mechanism of specific binding by ligands. In this paper, we use dynamics simulations on a series of models to characterize the ligand-free and ligand-bound aptamer domain of the c-di-GMP class I (GEMM-I) riboswitch. The results revealed that the ligand-free aptamer has a stable state with a folded P2 and P3 helix, an unfolded P1 helix and open binding pocket. The first Mg ions binding to the aptamer is structurally favorable for the successive c-di-GMP binding. The P1 helix forms when c-di-GMP is successive bound. Three key junctions J1/2, J2/3 and J1/3 in the GEMM-I riboswitch contributing to the formation of P1 helix have been found. The binding of the c-di-GMP ligand to the GEMM-I riboswitch induces the riboswitch's regulation through the direct allosteric communication network in GEMM-I riboswitch from the c-di-GMP binding sites in the J1/2 and J1/3 junctions to the P1 helix, the indirect ones from those in the J2/3 and P2 communicating to P1 helix via the J1/2 and J1/3 media.
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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, Hebei province, China
| | - Xiaojia Zhao
- College of Chemistry, Chemical Engineering and Materials, Handan University, No.530 North Xueyuan Road, Hanshan District, Han Dan, Hebei province, China
| | - Pengtao Xie
- College of Chemistry, Chemical Engineering and Materials, Handan University, No.530 North Xueyuan Road, Hanshan District, Han Dan, Hebei province, China
| | - Junping Hu
- College of Chemistry, Chemical Engineering and Materials, Handan University, No.530 North Xueyuan Road, Hanshan District, Han Dan, Hebei province, China
| | - Huimin Bi
- College of Chemistry, Chemical Engineering and Materials, Handan University, No.530 North Xueyuan Road, Hanshan District, Han Dan, Hebei province, China
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16
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Liu H, Guo X, Han J, Luo R, Chen HF. Order-disorder transition of intrinsically disordered kinase inducible transactivation domain of CREB. J Chem Phys 2018; 148:225101. [PMID: 29907037 DOI: 10.1063/1.5027869] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Transcription factor cyclic Adenosine monophosphate response-element binding protein plays a critical role in the cyclic AMP response pathway via its intrinsically disordered kinase inducible transactivation domain (KID). KID is one of the most studied intrinsically disordered proteins (IDPs), although most previous studies focus on characterizing its disordered state structures. An interesting question that remains to be answered is how the order-disorder transition occurs at experimental conditions. Thanks to the newly developed IDP-specific force field ff14IDPSFF, the quality of conformer sampling for IDPs has been dramatically improved. In this study, molecular dynamics (MD) simulations were used to study the order-to-disorder transition kinetics of KID based on the good agreement with the experiment on its disordered-state properties. Specifically, we tested four force fields, ff99SBildn, ff99IDPs, ff14IDPSFF, and ff14IDPs in the simulations of KID and found that ff14IDPSFF can generate more diversified disordered conformers and also reproduce more accurate experimental secondary chemical shifts. Kinetics analysis of MD simulations demonstrates that the order-disorder transition of KID obeys the first-order kinetics, and the transition nucleus is I127/L128/L141. The possible transition pathways from the nucleus to the last folded residues were identified as I127-R125-L138-L141-S143-A145 and L128-R125-L138-L141-S143-A145 based on a residue-level dynamical network analysis. These computational studies not only provide testable prediction/hypothesis on the order-disorder transition of KID but also confirm that the ff14IDPSFF force field can be used to explore the correlation between the structure and function of IDPs.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Xiang Guo
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Jingcheng Han
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, Biomedical Engineering, University of California, Irvine, California 92697-3900, USA
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
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17
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Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem Rev 2018; 118:4177-4338. [PMID: 29297679 PMCID: PMC5920944 DOI: 10.1021/acs.chemrev.7b00427] [Citation(s) in RCA: 327] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Indexed: 12/14/2022]
Abstract
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most pluripotent chemical species in molecular biology, and its functions are intimately linked to its structure and dynamics. Computer simulations, and in particular atomistic molecular dynamics (MD), allow structural dynamics of biomolecular systems to be investigated with unprecedented temporal and spatial resolution. We here provide a comprehensive overview of the fast-developing field of MD simulations of RNA molecules. We begin with an in-depth, evaluatory coverage of the most fundamental methodological challenges that set the basis for the future development of the field, in particular, the current developments and inherent physical limitations of the atomistic force fields and the recent advances in a broad spectrum of enhanced sampling methods. We also survey the closely related field of coarse-grained modeling of RNA systems. After dealing with the methodological aspects, we provide an exhaustive overview of the available RNA simulation literature, ranging from studies of the smallest RNA oligonucleotides to investigations of the entire ribosome. Our review encompasses tetranucleotides, tetraloops, a number of small RNA motifs, A-helix RNA, kissing-loop complexes, the TAR RNA element, the decoding center and other important regions of the ribosome, as well as assorted others systems. Extended sections are devoted to RNA-ion interactions, ribozymes, riboswitches, and protein/RNA complexes. Our overview is written for as broad of an audience as possible, aiming to provide a much-needed interdisciplinary bridge between computation and experiment, together with a perspective on the future of the field.
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Affiliation(s)
- Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
| | - Giovanni Bussi
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences , Kralovopolska 135 , Brno 612 65 , Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Sandro Bottaro
- Structural Biology and NMR Laboratory, Department of Biology , University of Copenhagen , Copenhagen 2200 , Denmark
| | - Richard A Cunha
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Alejandro Gil-Ley
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Giovanni Pinamonti
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Simón Poblete
- Scuola Internazionale Superiore di Studi Avanzati , Via Bonomea 265 , Trieste 34136 , Italy
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science , Palacky University Olomouc , 17. listopadu 12 , Olomouc 771 46 , Czech Republic
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18
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Li Q, Chen HF. Synergistic regulation mechanism of iperoxo and LY2119620 for muscarinic acetylcholine M2 receptor. RSC Adv 2018; 8:13067-13074. [PMID: 35542505 PMCID: PMC9079678 DOI: 10.1039/c8ra01545g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/30/2018] [Indexed: 11/21/2022] Open
Abstract
Muscarinic acetylcholine receptors are GPCRs that regulate the activity of a diverse array of central and peripheral functions in the human body, including the parasympathetic actions of acetylcholine. The M2 muscarinic receptor subtype plays a key role in modulating cardiac function and many important central processes. The orthosteric agonist and allosteric modulator can bind the pocket of M2. However, the detailed relationship between orthosteric agonist and allosteric modulator of M2 is still unclear. In this study, we intend to elucidate the residue-level regulation mechanism and pathway via a combined approach of dynamical correlation network and molecular dynamics simulation. Specifically computational residue-level fluctuation correlation data was analyzed to reveal detailed dynamics signatures in the regulation process. A hypothesis of "synergistic regulation" is proposed to reveal the cooperation affection between the orthosteric agonist and allosteric modulator, which is subsequently validated by perturbation and mutation analyses. Two possible synergistic regulation pathways of 2CU-I178-Y403-W400-F396-L114-Y440-Nb9 and IXO-V111-F396-L114-Y440-Nb9 were identified by the shortest path algorithm and were confirmed by the mutation of junction node. Furthermore, the efficiency of information transfer of bound M2 is significant higher than any single binding system. Our study shows that targeting the synergistic regulation pathways may better regulate the calcium channel of M2. The knowledge gained in this study may help develop drugs for diseases of the central nervous system and metabolic disorders.
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Affiliation(s)
- Quan Li
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiaotong University Shanghai 200240 China +86-21-34204348 +86-21-34204348
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiaotong University Shanghai 200240 China +86-21-34204348 +86-21-34204348
- Shanghai Center for Bioinformation Technology Shanghai 200235 China
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19
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Cai Y, Liu H, Chen H. Allosteric mechanism of quinoline inhibitors for HIV RT-associated RNase with MD simulation and dynamics fluctuation network. Chem Biol Drug Des 2017; 91:805-816. [DOI: 10.1111/cbdd.13146] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 10/23/2017] [Accepted: 11/01/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Yi Cai
- Shanghai High School; Shanghai China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; College of Life Sciences and Biotechnology; Shanghai Jiaotong University; Shanghai China
| | - Haifeng Chen
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; National Experimental Teaching Center for Life Sciences and Biotechnology; College of Life Sciences and Biotechnology; Shanghai Jiaotong University; Shanghai China
- Shanghai Center for Bioinformation Technology; Shanghai China
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20
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Kots ED, Lushchekina SV, Varfolomeev SD, Nemukhin AV. Role of Protein Dimeric Interface in Allosteric Inhibition of N-Acetyl-Aspartate Hydrolysis by Human Aspartoacylase. J Chem Inf Model 2017; 57:1999-2008. [PMID: 28737906 DOI: 10.1021/acs.jcim.7b00133] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The results of molecular modeling suggest a mechanism of allosteric inhibition upon hydrolysis of N-acetyl-aspartate (NAA), one of the most abundant amino acid derivatives in brain, by human aspartoacylase (hAsp). Details of this reaction are important to suggest the practical ways to control the enzyme activity. Search for allosteric sites using the Allosite web server and SiteMap analysis allowed us to identify substrate binding pockets located at the interface between the subunits of the hAsp dimer molecule. Molecular docking of NAA to the pointed areas at the dimer interface predicted a specific site, in which the substrate molecule interacts with the Gly237, Arg233, Glu290, and Lys292 residues. Analysis of multiple long-scaled molecular dynamics trajectories (the total simulation time exceeded 1.5 μs) showed that binding of NAA to the identified allosteric site induced significant rigidity to the protein loops with the amino acid side chains forming gates to the enzyme active site. Application of the protein dynamical network algorithms showed that substantial reorganization of the signal propagation pathways of intersubunit communication in the dimer occurred upon allosteric NAA binding to the remote site. The modeling approaches provide an explanation to the observed decrease of the reaction rate of NAA hydrolysis by hAsp at high substrate concentrations.
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Affiliation(s)
- Ekaterina D Kots
- Department of Chemistry, Lomonosov Moscow State University , Moscow 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow 119334, Russia
| | - Sofya V Lushchekina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow 119334, Russia
| | - Sergey D Varfolomeev
- Department of Chemistry, Lomonosov Moscow State University , Moscow 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow 119334, Russia
| | - Alexander V Nemukhin
- Department of Chemistry, Lomonosov Moscow State University , Moscow 119991, Russia.,Emanuel Institute of Biochemical Physics, Russian Academy of Sciences , Moscow 119334, Russia
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21
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Zhang JM, Jiang C, Ye W, Luo R, Chen HF. Allosteric pathways in tetrahydrofolate sensing riboswitch with dynamics correlation network. MOLECULAR BIOSYSTEMS 2017; 13:156-164. [PMID: 27841427 DOI: 10.1039/c6mb00630b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Riboswitches are cis-acting genetic control elements. Due to their fundamental importance in bacteria gene regulation, they have been proposed as antibacterial drug targets. Tetrahydrofolate (THF) is an essential cofactor of one-carbon transfer reactions and downregulates the expression of downstream genes. However, information on how to transfer from the binding site of THF to the expression platform is still unavailable. Herein, a nucleotide/nucleotide dynamics correlation network based on an all-atom molecular dynamic simulation was used to reveal the regulation mechanism of a THF-sensing riboswitch. Shortest pathway analysis based on the network illustrates that there is an allosteric pathway through the P2 helix to the pseudoknot, then to the P1 helix in the THF-riboswitch. Thus the hypothesis of "THF-binding induced allosteric switching" was proposed and evaluated using THF and pseudoknot weakened experiments. Furthermore, a possible allosteric pathway of C30-C31-G33-A34-G35-G36-G37-A38-G48-G47-U46-A90-U91-C92-G93-C94-G95-C96 was identified and confirmed through the perturbation of the network. The proposed allosteric mechanism and the underlying allosteric pathway provide fundamental insights for the regulation of THF sensing riboswitches.
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Affiliation(s)
- Jin-Mai Zhang
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Cheng Jiang
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Wei Ye
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry and Biomedical Engineering, University of California, Irvine, CA 92697-3900, USA.
| | - Hai-Feng Chen
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China. and Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
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22
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Guo X, Han J, Luo R, Chen HF. Conformation Dynamics of the Intrinsically Disordered Protein c-Myb with the ff99IDPs Force Field. RSC Adv 2017; 7:29713-29721. [PMID: 29104751 DOI: 10.1039/c7ra04133k] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The intrinsically disordered protein c-Myb plays a critical role in cellular proliferation and differentiation. Loss of c-myb function results in embryonic lethality due to failure of fetal hepatic hematopoiesis. The conformation dynamics of the intrinsically disordered c-Myb are still unknown. Here, molecular dynamics (MD) simulations with the intrinsically disordered protein force field ff99IDPs were used to study the conformation dynamics. In comparison with ff99SBildn, ff99IDPs can reproduce more diverse disordered conformers of c-Myb. The predicted secondary chemical shift under ff99IDPs is more close to that of experiment data than that under ff99SBildn. Therefore, ff99IDPs can sample native molten globule, native pre-molten globule and native coil conformers for c-Myb. These results are consistent with those of other intrinsically disordered proteins. Kinetic analysis of MD simulations shows that c-Myb folds via a two-state process and indicates that c-Myb folds in the order of tertiary folding and helical folding. The folding nucleus of KEL plays an essential role in stabilizing the folding state with dynamic correlation networks. The influences of solvent models for TIP3P, TIP4P-EW and TIP5P were also investigated and it was found that TIP3P and ff99IDPs are the best combination to research the conformer sampling of c-Myb. These results reveal the conformation dynamics of c-Myb and confirm that the ff99IDPs force field can be used to research the relationship between structure and function of other intrinsically disordered proteins.
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Affiliation(s)
- Xiang Guo
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jincheng Han
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Ray Luo
- Departments of Molecular Biology and Biochemistry, Chemical Engineering and Materials Science, and Biomedical Engineering, University of California, Irvine, California 92697-3900, USA
| | - Hai-Feng Chen
- State Key Laboratory of Microbial metabolism, Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China.,Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
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23
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Liu H, Ye W, Chen HF. Positive cooperative regulation of double binding sites for human acetylcholinesterase. Chem Biol Drug Des 2016; 89:694-704. [DOI: 10.1111/cbdd.12891] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 09/06/2016] [Accepted: 09/26/2016] [Indexed: 12/17/2022]
Affiliation(s)
- Hao Liu
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; College of Life Sciences and Biotechnology; Shanghai Jiaotong University; Shanghai China
| | - Wei Ye
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; College of Life Sciences and Biotechnology; Shanghai Jiaotong University; Shanghai China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism; Department of Bioinformatics and Biostatistics; College of Life Sciences and Biotechnology; Shanghai Jiaotong University; Shanghai China
- Shanghai Center for Bioinformation Technology; Shanghai China
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