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Heindel AJ, Brulet JW, Wang X, Founds MW, Libby AH, Bai DL, Lemke MC, Leace DM, Harris TE, Hafner M, Hsu KL. Chemoproteomic capture of RNA binding activity in living cells. Nat Commun 2023; 14:6282. [PMID: 37805600 PMCID: PMC10560261 DOI: 10.1038/s41467-023-41844-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 09/20/2023] [Indexed: 10/09/2023] Open
Abstract
Proteomic methods for RNA interactome capture (RIC) rely principally on crosslinking native or labeled cellular RNA to enrich and investigate RNA-binding protein (RBP) composition and function in cells. The ability to measure RBP activity at individual binding sites by RIC, however, has been more challenging due to the heterogenous nature of peptide adducts derived from the RNA-protein crosslinked site. Here, we present an orthogonal strategy that utilizes clickable electrophilic purines to directly quantify protein-RNA interactions on proteins through photoaffinity competition with 4-thiouridine (4SU)-labeled RNA in cells. Our photo-activatable-competition and chemoproteomic enrichment (PACCE) method facilitated detection of >5500 cysteine sites across ~3000 proteins displaying RNA-sensitive alterations in probe binding. Importantly, PACCE enabled functional profiling of canonical RNA-binding domains as well as discovery of moonlighting RNA binding activity in the human proteome. Collectively, we present a chemoproteomic platform for global quantification of protein-RNA binding activity in living cells.
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Affiliation(s)
- Andrew J Heindel
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Jeffrey W Brulet
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Xiantao Wang
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Michael W Founds
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Adam H Libby
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22903, USA
| | - Dina L Bai
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA
| | - Michael C Lemke
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - David M Leace
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Thurl E Harris
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA
| | - Markus Hafner
- RNA Molecular Biology Laboratory, National Institute of Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA
| | - Ku-Lung Hsu
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Virginia, Charlottesville, VA, 22904, USA.
- University of Virginia Cancer Center, University of Virginia, Charlottesville, VA, 22903, USA.
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, 22908, USA.
- Department of Chemistry, University of Texas at Austin, Austin, TX, 78712, USA.
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Hassan S, Ahmad B, Khan MW, Shah ZA, Ullah A, Ullah S, Khan D, Rizwan M, Ahmad A, Ali Q, Kaushik P, Yilmaz S. Cytotoxic Activity of Phytoconstituents Isolated from Monotheca buxifolia against Hepatocellular Carcinoma Cell Line HepG2: In Vitro and Molecular Docking Studies. ACS OMEGA 2023; 8:33572-33579. [PMID: 37744864 PMCID: PMC10515345 DOI: 10.1021/acsomega.3c03705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/23/2023] [Indexed: 09/26/2023]
Abstract
Natural products and conventional chemotherapeutic drugs are believed to enhance anticancer treatment efficacy while lowering toxicity. The current study investigates the cytotoxic and apoptogenic effects of Monotheca buxifolia bioactive compounds on HepG2 cell lines. MTT assay was used to assess the effect on the viability of HepG2 cells. Morphological changes were investigated. Annexin-V-FITC/PI was used to demonstrate apoptotic activity. A molecular dynamics simulation study was carried out to investigate the compound binding pattern in the active site of the PPRAδ protein. MTT and annexin V-FITC/PI assays revealed that the isolated compounds lauric acid, oleanolic acid, and bis(2-ethylhexyl) phthalate inhibited the growth of hepatocellular cancer cells. The IC50 value for lauric acid was 56.46 ± 1.20 μg/mL, 31.94 ± 1.03 μg/mL for oleanolic acid, and 83.80 ± 2.18 μg/mL for bis(2-ethylhexyl) phthalate. Apoptosis was observed in 29.5, 52.1 and 22.4% of HepG2 cells treated with lauric acid, oleanolic acid, and bis(2-ethylhexyl) phthalate, respectively, after 24 h of treatment. Morphological assays and Hoechst staining microscopy revealed that the treatment caused morphological changes in the cell membrane and nuclear condensation. The high fluctuation indicates that various interactions were highly potent and widely adopted, and vice versa. Oleanolic acid displayed high residue fluctuation, remaining stable in the active site of the PPRAδ protein and involved in various interactions while remaining locally fluctuating in the binding sites of the other two compounds. These findings concluded that lauric acid, oleanolic acid, and bis(2-ethylhexyl) phthalate have a significant apoptogenic effect against HepG2 cells in inducing apoptosis. Our findings suggest that these bioactive compounds could be used as adjuvant therapies.
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Affiliation(s)
- Said Hassan
- Institute
of Biotechnology and Microbiology, Bacha
Khan University Charsadda, Charsadda 24420, Pakistan
| | - Bashir Ahmad
- Center
of Biotechnology and Microbiology, University
of Peshawar, Peshawar 25120, Pakistan
| | - Muhammad Waseem Khan
- Institute
of Pharmaceutical Sciences, Khyber Medical
University, Peshawar 25001, Pakistan
| | - Zafar Abbass Shah
- Department
of Bioinformatics, Hazara University Mansehra, Mansehra 21300, Pakistan
| | - Amin Ullah
- Department
of Health & Biological Sciences, Abasyn
University, Peshawar 25120, Pakistan
| | - Sana Ullah
- Department
of Zoology, Division of Science and Technology, University of Education, Lahore 54000, Pakistan
| | - Dilfaraz Khan
- Institute
of Chemical Sciences, Gomal University Dera Ismail Khan 29050, Pakistan
| | - Muhammad Rizwan
- Center
for Biotechnology and Microbiology, Swat
University, Swat 19130, Pakistan
| | - Ajaz Ahmad
- Department
of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Qurban Ali
- Department
of Plant Breeding and Genetics, Faculty of Agricultural Sciences, University of the Punjab Lahore 54590, Pakistan
| | - Prashant Kaushik
- Instituto de Conservación y Mejora
de la Agrodiversidad Valenciana, Universitat
Politècnica de València, Valencia 46022, Spain
| | - Semih Yilmaz
- Department of Agriculture Biotechnology,
Division of Enzyme and Microbial
Biotechnology, Erciyes University, Talas 38280, Turkey
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3
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Sudhakar S, Barkau CL, Chilamkurthy R, Barber HM, Pater AA, Moran SD, Damha MJ, Pradeepkumar PI, Gagnon KT. Binding to the conserved and stably folded guide RNA pseudoknot induces Cas12a conformational changes during ribonucleoprotein assembly. J Biol Chem 2023; 299:104700. [PMID: 37059184 PMCID: PMC10200996 DOI: 10.1016/j.jbc.2023.104700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 04/16/2023] Open
Abstract
Ribonucleoproteins (RNPs) comprise one or more RNA and protein molecules that interact to form a stable complex, which commonly involves conformational changes in the more flexible RNA components. Here, we propose that Cas12a RNP assembly with its cognate CRISPR RNA (crRNA) guide instead proceeds primarily through Cas12a conformational changes during binding to more stable, prefolded crRNA 5' pseudoknot handles. Phylogenetic reconstructions and sequence and structure alignments revealed that the Cas12a proteins are divergent in sequence and structure while the crRNA 5' repeat region, which folds into a pseudoknot and anchors binding to Cas12a, is highly conserved. Molecular dynamics simulations of three Cas12a proteins and their cognate guides revealed substantial flexibility for unbound apo-Cas12a. In contrast, crRNA 5' pseudoknots were predicted to be stable and independently folded. Limited trypsin hydrolysis, differential scanning fluorimetry, thermal denaturation, and CD analyses supported conformational changes of Cas12a during RNP assembly and an independently folded crRNA 5' pseudoknot. This RNP assembly mechanism may be rationalized by evolutionary pressure to conserve CRISPR loci repeat sequence, and therefore guide RNA structure, to maintain function across all phases of the CRISPR defense mechanism.
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Affiliation(s)
- Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India
| | - Christopher L Barkau
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA
| | - Ramadevi Chilamkurthy
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA
| | - Halle M Barber
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - Adrian A Pater
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Sean D Moran
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Masad J Damha
- Department of Chemistry, McGill University, Montreal, Quebec, Canada
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, India.
| | - Keith T Gagnon
- Department of Biochemistry and Molecular Biology, School of Medicine, Southern Illinois University, Carbondale, Illinois, USA; Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA.
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4
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Ji X, Liu H, Zhang Y, Chen J, Chen HF. Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning. J Chem Inf Model 2023; 63:362-374. [PMID: 36533639 DOI: 10.1021/acs.jcim.2c01501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Intrinsically disordered proteins (IDPs) are proteins without a fixed three-dimensional (3D) structure under physiological conditions and are associated with Parkinson's disease, Alzheimer's disease, cancer, cardiovascular disease, amyloidosis, diabetes, and other diseases. Experimental methods can hardly capture the ensemble of diverse conformations for IDPs. Molecular dynamics (MD) simulations can sample continuous conformations that might provide a valuable complement to experimental data. However, the accuracy of MD simulations depends on the quality of force field. In particular, the evolutionary conservation and coevolution of IDPs introduce that current force fields could not precisely reproduce the conformation of IDPs. In order to improve the performance of force field, deep learning and reweighting methods were used to automatically generate personal force field parameters for intrinsically disordered and ordered proteins. At first, the deep learning method predicted more accuracy φ/ψ dihedral of residue than the previous method. Then, reweighting optimized the personal force field parameters for each residue. Finally, typical representative systems such as IDPs, structure protein, and fast-folding protein were used to evaluate this force field. The results indicate that two personal force field parameters (named PPFF1 and PPFF1_af2) could better reproduce the experimental observables than ff03CMAP force field. In summary, this strategy will provide feasibility for the development of precise personal force fields.
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Affiliation(s)
- Xiaoyue Ji
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Yangpeng Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Jun Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai200240, China.,Shanghai Center for Bioinformation Technology, Shanghai200235, China
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5
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Hong X, Li N, Lv J, Zhang Y, Li J, Zhang J, Chen HF. PTMint database of experimentally verified PTM regulation on protein-protein interaction. Bioinformatics 2022; 39:6957085. [PMID: 36548389 PMCID: PMC9848059 DOI: 10.1093/bioinformatics/btac823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 12/18/2022] [Accepted: 12/21/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Post-translational modification (PTM) is an important biochemical process. which includes six most well-studied types: phosphorylation, acetylation, methylation, sumoylation, ubiquitylation and glycosylation. PTM is involved in various cell signaling pathways and biological processes. Abnormal PTM status is closely associated with severe diseases (such as cancer and neurologic diseases) by regulating protein functions, such as protein-protein interactions (PPIs). A set of databases was constructed separately for PTM sites and PPI; however, the resource of regulation for PTM on PPI is still unsolved. RESULTS Here, we firstly constructed a public accessible database of PTMint (PTMs that are associated with PPIs) (https://ptmint.sjtu.edu.cn/) that contains manually curated complete experimental evidence of the PTM regulation on PPIs in multiple organisms, including Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Saccharomyces cerevisiae and Schizosaccharomyces pombe. Currently, the first version of PTMint encompassed 2477 non-redundant PTM sites in 1169 proteins affecting 2371 protein-protein pairs involving 357 diseases. Various annotations were systematically integrated, such as protein sequence, structure properties and protein complex analysis. PTMint database can help to insight into disease mechanism, disease diagnosis and drug discovery associated with PTM and PPI. AVAILABILITY AND IMPLEMENTATION PTMint is freely available at: https://ptmint.sjtu.edu.cn/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Xiaokun Hong
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ningshan Li
- Department of Bioinformatics and Biostatistics, SJTU-Yale Joint Center for Biostatistics and Data Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jiyang Lv
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yan Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jing Li
- To whom correspondence should be addressed. or or
| | - Jian Zhang
- To whom correspondence should be addressed. or or
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6
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Jing Z, Ren P. Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model. J Phys Chem B 2022; 126:7343-7353. [PMID: 36107618 PMCID: PMC9530969 DOI: 10.1021/acs.jpcb.2c05278] [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: 11/28/2022]
Abstract
Protein-RNA interactions are integral to the biological functions of RNA. It is well recognized that molecular dynamics (MD) simulations of protein-RNA complexes are more challenging than those of each component. The difficulty arises from the strong electrostatic interactions and the delicate balance between various types of physical forces at the interface. Previously, MD simulations of protein-RNA complexes have predominantly employed fixed-charge force fields. Although force field modifications have been developed to address problems identified in the simulations, some protein-RNA structures are still hard to reproduce by simulations. Here, we present MD simulations of two representative protein-RNA complexes using the AMOEBA polarizable force field. The van der Waals parameters were refined to reproduce accurate quantum-mechanical data of base-base and base-amino acid interactions. It was found that the refined parameters produced a more stable hydrogen-bond network in the interface. One of the complexes remained stable during the short simulations, whereas it could quickly break down in previous simulations using fixed-charge force fields. There was reversible breaking and formation of hydrogen bonds that are observed in the crystal structure, which may indicate the difference in solution and crystal structures. While further improvement and validation of the force fields are still needed, this work demonstrates that polarizable force fields are promising for the study of protein-RNA complexes.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
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Sharma M, Sharma S, Alawada A. Understanding the binding specificities of mRNA targets by the mammalian Quaking protein. Nucleic Acids Res 2020; 47:10564-10579. [PMID: 31602485 PMCID: PMC6847458 DOI: 10.1093/nar/gkz877] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/18/2019] [Accepted: 10/08/2019] [Indexed: 01/01/2023] Open
Abstract
Mammalian Quaking (QKI) protein, a member of STAR family of proteins is a mRNA-binding protein, which post-transcriptionally modulates the target RNA. QKI protein possesses a maxi-KH domain composed of single heterogeneous nuclear ribonucleoprotein K homology (KH) domain and C-terminal QUA2 domain, that binds a sequence-specific QKI RNA recognition element (QRE), CUAAC. To understand the binding specificities for different mRNA sequences of the KH-QUA2 domain of QKI protein, we introduced point mutations at different positions in the QRE resulting in twelve different mRNA sequences with single nucleotide change. We carried out long unbiased molecular dynamics simulations using two different sets of recently updated forcefield parameters: AMBERff14SB+RNAχOL3 and CHARMM36 (with CMAP correction). We analyzed the changes in intermolecular dynamics as a result of mutation. Our results show that AMBER forcefields performed better to model the interactions between mRNA and protein. We also calculated the binding affinities of different mRNA sequences and found that the relative order correlates to the reported experimental studies. Our study shows that the favorable binding with the formation of stable complex will occur when there is an increase of the total intermolecular contacts between mRNA and protein, but without the loss of native contacts within the KH-QUA domain.
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Affiliation(s)
- Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS Nagar, Punjab, India
| | - Shakshi Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS Nagar, Punjab, India
| | - Apoorv Alawada
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS Nagar, Punjab, India
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Interpreting the Dynamics of Binding Interactions of snRNA and U1A Using a Coarse-Grained Model. Biophys J 2019; 116:1625-1636. [PMID: 30975455 DOI: 10.1016/j.bpj.2019.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 03/04/2019] [Accepted: 03/12/2019] [Indexed: 12/14/2022] Open
Abstract
The binding interactions of small nuclear RNAs (snRNA) and the associated protein factors are critical to the function of spliceosomes in alternatively splicing primary RNA transcripts. Although molecular dynamics simulations are a powerful tool to interpret the mechanism of biological processes, the atomic-level simulations are, however, too expensive and with limited accuracy for the large-size systems, such as snRNA-protein complexes. We extend the coarse-grained Gaussian network model, which models the RNA-protein complexes as a harmonic chain of Cα, P, and O4' atoms, to investigating the impact of the snRNA-binding interaction on the dynamic stability of the human U1A protein, which is a major component of the spliceosomal U1 small nuclear ribonucleoprotein particle. The results reveal that the first and third loops and the C-terminal helix regions of the U1A domain undergo a significant loss of flexibility upon the RNA binding due to the forming of mostly electrostatic and hydrogen bond interactions with RNA 5' stem and loop. By examining the residues whose mutations significantly change the binding free energy between U1A and snRNA, the Gaussian network model-based calculations show that not only the residues at the binding sites that are traditionally considered to play a major role in U1A-RNA association but also those residues that are far away from the RNA-binding interface can participate in the long-range allosteric signal transmission; these calculations are quantitatively consistent with the data observed in the recent snRNA binding experiments. The study demonstrates a useful avenue to utilize the simplified elastic network model to investigate the dynamics characteristics of the biologically important macromolecular interactions.
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Rehman AU, Khan MT, Liu H, Wadood A, Malik SI, Chen HF. Exploring the Pyrazinamide Drug Resistance Mechanism of Clinical Mutants T370P and W403G in Ribosomal Protein S1 of Mycobacterium tuberculosis. J Chem Inf Model 2019; 59:1584-1597. [DOI: 10.1021/acs.jcim.8b00956] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ashfaq Ur Rehman
- 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
- Department of Biotechnology, Abdul Wali Khan University Marden, Mardan 23200, Pakistan
| | - Muhammad Tahir Khan
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 44000, Pakistan
| | - Hao Liu
- 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
| | - Abdul Wadood
- Department of Biotechnology, Abdul Wali Khan University Marden, Mardan 23200, Pakistan
| | - Shaukat Iqbal Malik
- Department of Bioinformatics and Biosciences, Capital University of Science and Technology, Islamabad 44000, Pakistan
| | - 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
- Shanghai Center for Bioinformation Technology, Shanghai, 200235, China
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10
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Inhibitory mechanism of 5-bromo-3-indoleacetic acid for non-structural-3 helicase hepatitis C virus with dynamics correlation network analysis. Comput Biol Chem 2018; 77:167-177. [DOI: 10.1016/j.compbiolchem.2018.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/03/2018] [Accepted: 10/06/2018] [Indexed: 01/20/2023]
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11
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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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12
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Kartje ZJ, Barkau CL, Rohilla KJ, Ageely EA, Gagnon KT. Chimeric Guides Probe and Enhance Cas9 Biochemical Activity. Biochemistry 2018; 57:3027-3031. [PMID: 29746102 DOI: 10.1021/acs.biochem.8b00107] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
DNA substitutions in RNA can probe the importance of A-form structure, 2'-hydroxyl contacts, and conformational constraints within RNA-guided enzymes. Using this approach, we found that Cas9 biochemical activity tolerated significant substitution with DNA nucleotides in the clustered regularly interspaced short palindromic repeat RNA (crRNA). Only minimal RNA content was needed in or near the seed region. Simultaneous substitution at all positions with predicted crRNA-Cas9 2'-hydroxyl contacts had no effect on enzyme activity. The trans-activating crRNA (tracrRNA) also tolerated >50% substitution with DNA. DNA substitutions in the tracrRNA-pairing region of crRNA consistently enhanced cleavage activity while maintaining or improving target specificity. Together, results point to a prominent role for guide:target A-form-like helical structure and a possible regulatory role for the crRNA-tracrRNA pairing motif. A model chimeric crRNA with high activity did not significantly alter RNP assembly or target binding but did reduce Cas9 ribonucleoprotein stability, suggesting effects through conformation or dynamics. Cas9 directed by chimeric RNA-DNA guides may represent a cost-effective synthetic or molecular biology tool for robust and specific DNA cleavage.
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Affiliation(s)
- Zachary J Kartje
- Department of Chemistry and Biochemistry , Southern Illinois University , Carbondale , Illinois 62901 , United States
| | - Christopher L Barkau
- Department of Biochemistry and Molecular Biology, School of Medicine , Southern Illinois University , Carbondale , Illinois 62901 , United States
| | - Kushal J Rohilla
- Department of Biochemistry and Molecular Biology, School of Medicine , Southern Illinois University , Carbondale , Illinois 62901 , United States
| | - Eman A Ageely
- Department of Chemistry and Biochemistry , Southern Illinois University , Carbondale , Illinois 62901 , United States
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry , Southern Illinois University , Carbondale , Illinois 62901 , United States
- Department of Biochemistry and Molecular Biology, School of Medicine , Southern Illinois University , Carbondale , Illinois 62901 , United States
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13
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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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14
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Flores JK, Ataide SF. Structural Changes of RNA in Complex with Proteins in the SRP. Front Mol Biosci 2018; 5:7. [PMID: 29459899 PMCID: PMC5807370 DOI: 10.3389/fmolb.2018.00007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 01/17/2018] [Indexed: 12/18/2022] Open
Abstract
The structural flexibility of RNA allows it to exist in several shapes and sizes. Thus, RNA is functionally diverse and is known to be involved in processes such as catalysis, ligand binding, and most importantly, protein recognition. RNA can adopt different structures, which can often dictate its functionality. When RNA binds onto protein to form a ribonucleoprotein complex (RNP), multiple interactions and conformational changes occur with the RNA and protein. However, there is the question of whether there is a specific pattern for these changes to occur upon recognition. In particular when RNP complexity increases with the addition of multiple proteins/RNA, it becomes difficult to structurally characterize the overall changes using the current structural determination techniques. Hence, there is a need to use a combination of biochemical, structural and computational modeling to achieve a better understanding of the processes that RNPs are involved. Nevertheless, there are well-characterized systems that are evolutionarily conserved [such as the signal recognition particle (SRP)] that give us important information on the structural changes of RNA and protein upon complex formation.
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Affiliation(s)
- Janine K Flores
- Ataide Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Sandro F Ataide
- Ataide Lab, School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
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15
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Nakatani K, Natsuhara N, Mori Y, Mukherjee S, Das B, Murata A. Synthesis of Naphthyridine Dimers with Conformational Restriction and Binding to DNA and RNA. Chem Asian J 2017; 12:3077-3087. [DOI: 10.1002/asia.201701293] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 09/30/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Nozomi Natsuhara
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Yuki Mori
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Sanjukta Mukherjee
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Bimolendu Das
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry; The Institute of Scientific and Industrial Research; Osaka University; 8-1 Mihogaoka Ibaraki 567-0047 Japan
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16
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Sharma M, Anirudh CR. Mechanism of mRNA-STAR domain interaction: Molecular dynamics simulations of Mammalian Quaking STAR protein. Sci Rep 2017; 7:12567. [PMID: 28974714 PMCID: PMC5626755 DOI: 10.1038/s41598-017-12930-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 09/20/2017] [Indexed: 01/08/2023] Open
Abstract
STAR proteins are evolutionary conserved mRNA-binding proteins that post-transcriptionally regulate gene expression at all stages of RNA metabolism. These proteins possess conserved STAR domain that recognizes identical RNA regulatory elements as YUAAY. Recently reported crystal structures show that STAR domain is composed of N-terminal QUA1, K-homology domain (KH) and C-terminal QUA2, and mRNA binding is mediated by KH-QUA2 domain. Here, we present simulation studies done to investigate binding of mRNA to STAR protein, mammalian Quaking protein (QKI). We carried out conventional MD simulations of STAR domain in presence and absence of mRNA, and studied the impact of mRNA on the stability, dynamics and underlying allosteric mechanism of STAR domain. Our unbiased simulations results show that presence of mRNA stabilizes the overall STAR domain by reducing the structural deviations, correlating the ‘within-domain’ motions, and maintaining the native contacts information. Absence of mRNA not only influenced the essential modes of motion of STAR domain, but also affected the connectivity of networks within STAR domain. We further explored the dissociation of mRNA from STAR domain using umbrella sampling simulations, and the results suggest that mRNA binding to STAR domain occurs in multi-step: first conformational selection of mRNA backbone conformations, followed by induced fit mechanism as nucleobases interact with STAR domain.
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Affiliation(s)
- Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS Nagar, Punjab, India.
| | - C R Anirudh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS Nagar, Punjab, India
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17
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Rahman MU, Liu H, Wadood A, Chen HF. Allosteric mechanism of cyclopropylindolobenzazepine inhibitors for HCV NS5B RdRp via dynamic correlation network analysis. MOLECULAR BIOSYSTEMS 2017; 12:3280-3293. [PMID: 27528077 DOI: 10.1039/c6mb00521g] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
HCV RNA dependent RNA polymerase (RdRp) nonstructural protein 5B (NS5B) is a major target against hepatitis C virus (HCV) for antiviral therapy. Recently discovered cyclopropylindolobenzazepine derivatives have been considered as the most potent for their ability to bind the thumb site 1 domain and allosterically inhibit HCV NS5B RdRp activity. However, the allosteric mechanism for these derivatives has not been clarified at the molecular level. In this study, fluctuation correlation networks were constructed based on all-atom molecular dynamics simulations to elucidate the allosteric mechanism. The fluctuation correlation networks between free and M2 bound NS5B are significantly different. Information can better transfer from the allosteric site to the catalytic site for bound NS5B than for free NS5B. Thus, the hypothesis of "binding induced allosteric regulation" is proposed to link the enzyme activation and inhibitor binding and then confirmed by the mutant network. Finally, one possible allosteric pathway was identified with the shortest path and evaluated by the perturbation of the network. These methods will be helpful to identify the allosteric pathway of other proteins and to design new drugs targeting the pathway.
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Affiliation(s)
- Mueed Ur Rahman
- 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.
| | - Hao Liu
- 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.
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan-23200, Pakistan.
| | - 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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18
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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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19
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Qian T, Wo J, Zhang Y, Song Q, Feng G, Luo R, Lin S, Wu G, Chen HF. Crystal Structure of StnA for the Biosynthesis of Antitumor Drug Streptonigrin Reveals a Unique Substrate Binding Mode. Sci Rep 2017; 7:40254. [PMID: 28074848 PMCID: PMC5225493 DOI: 10.1038/srep40254] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/02/2016] [Indexed: 01/16/2023] Open
Abstract
Streptonigrin methylesterase A (StnA) is one of the tailoring enzymes that modify the aminoquinone skeleton in the biosynthesis pathway of Streptomyces species. Although StnA has no significant sequence homology with the reported α/β-fold hydrolases, it shows typical hydrolytic activity in vivo and in vitro. In order to reveal its functional characteristics, the crystal structures of the selenomethionine substituted StnA (SeMet-StnA) and the complex (S185A mutant) with its substrate were resolved to the resolution of 2.71 Å and 2.90 Å, respectively. The overall structure of StnA can be described as an α-helix cap domain on top of a common α/β hydrolase domain. The substrate methyl ester of 10'-demethoxystreptonigrin binds in a hydrophobic pocket that mainly consists of cap domain residues and is close to the catalytic triad Ser185-His349-Asp308. The transition state is stabilized by an oxyanion hole formed by the backbone amides of Ala102 and Leu186. The substrate binding appears to be dominated by interactions with several specific hydrophobic contacts and hydrogen bonds in the cap domain. The molecular dynamics simulation and site-directed mutagenesis confirmed the important roles of the key interacting residues in the cap domain. Structural alignment and phylogenetic tree analysis indicate that StnA represents a new subfamily of lipolytic enzymes with the specific binding pocket located at the cap domain instead of the interface between the two domains.
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Affiliation(s)
- Tianle Qian
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jing Wo
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Yan Zhang
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Shanghai Institute of Immunology, Shanghai Jiao Tong University School of Medicine, 280 South Chongqing Road, Shanghai, 200025, China
| | - Quanwei Song
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
- Key laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, China
| | - Guoqiang Feng
- Key laboratory of Pesticide and Chemical Biology of Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan 430079, 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
| | - Shuangjin Lin
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Geng Wu
- State Key Laboratory of Microbial metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial metabolism, 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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20
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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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21
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Protein-RNA interactions: structural biology and computational modeling techniques. Biophys Rev 2016; 8:359-367. [PMID: 28510023 DOI: 10.1007/s12551-016-0223-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/20/2016] [Indexed: 12/30/2022] Open
Abstract
RNA-binding proteins are functionally diverse within cells, being involved in RNA-metabolism, translation, DNA damage repair, and gene regulation at both the transcriptional and post-transcriptional levels. Much has been learnt about their interactions with RNAs through structure determination techniques and computational modeling. This review gives an overview of the structural data currently available for protein-RNA complexes, and discusses the technical issues facing structural biologists working to solve their structures. The review focuses on three techniques used to solve the 3-dimensional structure of protein-RNA complexes at atomic resolution, namely X-ray crystallography, solution nuclear magnetic resonance (NMR) and cryo-electron microscopy (cryo-EM). The review then focuses on the main computational modeling techniques that use these atomic resolution data: discussing the prediction of RNA-binding sites on unbound proteins, docking proteins, and RNAs, and modeling the molecular dynamics of the systems. In conclusion, the review looks at the future directions this field of research might take.
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22
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Dynamics Correlation Network for Allosteric Switching of PreQ1 Riboswitch. Sci Rep 2016; 6:31005. [PMID: 27484311 PMCID: PMC4971525 DOI: 10.1038/srep31005] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 07/11/2016] [Indexed: 02/06/2023] Open
Abstract
Riboswitches are a class of metabolism control elements mostly found in bacteria. Due to their fundamental importance in bacteria gene regulation, riboswitches have been proposed as antibacterial drug targets. Prequeuosine (preQ1) is the last free precursor in the biosynthetic pathway of queuosine that is crucial for translation efficiency and fidelity. However, the regulation mechanism for the preQ1 riboswitch remains unclear. Here we constructed fluctuation correlation network based on all-atom molecular dynamics simulations to reveal the regulation mechanism. The results suggest that the correlation network in the bound riboswitch is distinctly different from that in the apo riboswitch. The community network indicates that the information freely transfers from the binding site of preQ1 to the expression platform of the P3 helix in the bound riboswitch and the P3 helix is a bottleneck in the apo riboswitch. Thus, a hypothesis of “preQ1-binding induced allosteric switching” is proposed to link riboswitch and translation regulation. The community networks of mutants support this hypothesis. Finally, a possible allosteric pathway of A50-A51-A52-U10-A11-G12-G56 was also identified based on the shortest path algorithm and confirmed by mutations and network perturbation. The novel fluctuation network analysis method can be used as a general strategy in studies of riboswitch structure-function relationship.
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23
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Yang J, Liu H, Liu X, Gu C, Luo R, Chen HF. Synergistic Allosteric Mechanism of Fructose-1,6-bisphosphate and Serine for Pyruvate Kinase M2 via Dynamics Fluctuation Network Analysis. J Chem Inf Model 2016; 56:1184-1192. [PMID: 27227511 DOI: 10.1021/acs.jcim.6b00115] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Pyruvate kinase M2 (PKM2) plays a key role in tumor metabolism and regulates the rate-limiting final step of glycolysis. In tumor cells, there are two allosteric effectors for PKM2: fructose-1,6-bisphosphate (FBP) and serine. However, the relationship between FBP and serine for allosteric regulation of PKM2 is unknown. Here we constructed residue/residue fluctuation correlation network based on all-atom molecular dynamics simulations to reveal the regulation mechanism. The results suggest that the correlation network in bound PKM2 is distinctly different from that in the free state, FBP/PKM2, or Ser/PKM2. The community network analysis indicates that the information can freely transfer from the allosteric sites of FBP and serine to the substrate site in bound PKM2, while there exists a bottleneck for information transfer in the network of the free state. Furthermore, the binding free energy between the substrate and PKM2 for bound PKM2 is significantly lower than either of FBP/PKM2 or Ser/PKM2. Thus, a hypothesis of "synergistic allosteric mechanism" is proposed for the allosteric regulation of FBP and serine. This hypothesis was further confirmed by the perturbational and mutational analyses of community networks and binding free energies. Finally, two possible synergistic allosteric pathways of FBP-K433-T459-R461-A109-V71-R73-MG2-OXL and Ser-I47-C49-R73-MG2-OXL were identified based on the shortest path algorithm and were confirmed by the network perturbation analysis. Interestingly, no similar pathways could be found in the free state. The process targeting on the allosteric pathways can better regulate the glycolysis of PKM2 and significantly inhibit the progression of tumor.
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Affiliation(s)
- Jingxu Yang
- 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
| | - Hao Liu
- 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
| | - Xiaorui Liu
- International Peace Maternity and Child Health Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200030, China.,Institute of Embryo-Fetal Original Adult Disease Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200030, China
| | - Chengbo Gu
- 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, 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, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, 200240, China.,Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
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24
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Xu L, Ye W, Jiang C, Yang J, Zhang J, Feng Y, Luo R, Chen HF. Recognition Mechanism between Lac Repressor and DNA with Correlation Network Analysis. J Phys Chem B 2015; 119:2844-56. [DOI: 10.1021/jp510940w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lishi Xu
- 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
| | - 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
| | - Jingxu Yang
- 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
| | - Jinmai 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
| | - Yan Feng
- State
Key Laboratory of Microbial Metabolism, Department of Biotechnology,
College of Life Sciences and Biotechnology, Shanghai Jiaotong 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, Irvine, California 92697-3900, United States
| | - 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
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
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25
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Wu K, Pang J, Song D, Zhu Y, Wu C, Shao T, Chen H. Selectivity Mechanism of ATP-Competitive Inhibitors for PKB and PKA. Chem Biol Drug Des 2014; 86:9-18. [PMID: 25376656 DOI: 10.1111/cbdd.12472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/16/2014] [Accepted: 10/29/2014] [Indexed: 11/29/2022]
Abstract
Protein kinase B (PKB) acts as a central node on the PI3K kinase pathway. Constitutive activation and overexpression of PKB have been identified to involve in various cancers. However, protein kinase A (PKA) sharing high homology with PKB is essential for metabolic regulation. Therefore, specific targeting on PKB is crucial strategy in drug design and development for antitumor. Here, we had revealed the selectivity mechanism for PKB inhibitors with molecular dynamics simulation and 3D-QSAR methods. Selective inhibitors of PKB could form more hydrogen bonds and hydrophobic contacts with PKB than those with PKA. This could explain that selective inhibitor M128 is more potent to PKB than to PKA. Then, 3D-QSAR models were constructed for these selective inhibitors and evaluated by test set compounds. 3D-QSAR model comparison of PKB inhibitors and PKA inhibitors reveals possible methods to improve the selectivity of inhibitors. These models can be used to design new chemical entities and make quantitative prediction of the specific selective inhibitors before resorting to in vitro and in vivo experiment.
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Affiliation(s)
- Ke Wu
- 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
| | - Jingzhi Pang
- 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
| | - Dong Song
- 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
| | - Ying Zhu
- 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
| | - Congwen Wu
- 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
| | - Tianqu Shao
- 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
| | - Haifeng 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.,Shanghai Center for Bioinformation Technology, 1275 Keyuan Road, Shanghai, 200235, China
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Yu Q, Ye W, Jiang C, Luo R, Chen HF. Specific Recognition Mechanism between RNA and the KH3 Domain of Nova-2 Protein. J Phys Chem B 2014; 118:12426-34. [DOI: 10.1021/jp5079289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Qingfen Yu
- 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
| | - 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
| | - Ray Luo
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California 92697-3900, United States
| | - 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
- Shanghai Center for Bioinformation Technology, 1278 Keyuan Road, Shanghai, 200235, China
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Kurisaki I, Takayanagi M, Nagaoka M. Combined mechanism of conformational selection and induced fit in U1A-RNA molecular recognition. Biochemistry 2014; 53:3646-57. [PMID: 24828852 DOI: 10.1021/bi401708q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
In this study, we demonstrate that U1A-RNA molecular recognition is mediated by a combined mechanism of conformational selection and induced fit. The binding of U1A to RNA has been discussed in the context of induced fit that involves the reorientation of the α-helix in the C-terminal region (Helix-C) of U1A to permit RNA access only when U1A correctly recognizes RNA. However, according to our molecular dynamics simulations, even in the absence of RNA, Helix-C spontaneously reoriented to permit RNA access. Nonetheless, such a conformational change was still incomplete. Helix-C was often partially or even fully unfolded and in an infrequent RNA-accessible conformation, which can be detected using state-of-the-art nuclear magnetic resonance methodology. These results suggest that the formation of an energetically stabilized complex is promoted by specific interactions between U1A and RNA. In conclusion, in the recognition of RNA by U1A protein, we propose a combined mechanism that requires the reorientation of Helix-C and the subsequent contact with RNA through conformational selection, although the stabilization of the U1A-RNA complex is caused by induced fit. We further propose a modification to the conventional assumption regarding the mechanism of U1A-RNA molecular recognition.
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Affiliation(s)
- Ikuo Kurisaki
- Graduate School of Information Science, Nagoya University , Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
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28
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Ye W, Yang J, Yu Q, Wang W, Hancy J, Luo R, Chen HF. Kink turn sRNA folding upon L7Ae binding using molecular dynamics simulations. Phys Chem Chem Phys 2014; 15:18510-22. [PMID: 24072031 DOI: 10.1039/c3cp53145g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The kink-turn sRNA motif in archaea, whose combination with protein L7Ae initializes the assembly of small ribonucleoprotein particles (sRNPs), plays a key role in ribosome maturation and the translation process. Although many studies have been reported on this motif, the mechanism of sRNA folding coupled with protein binding is still poorly understood. Here, room and high temperature molecular dynamics (MD) simulations were performed on the complex of 25-nt kink-turn sRNA and L7Ae. The average RMSD values between the bound and corresponding apo structures and Kolmogorov-Smirnov P test analysis indicate that sRNA may follow an induced fit mechanism upon binding with L7Ae, both locally and globally. These conclusions are further supported by high-temperature unfolding kinetic analysis. Principal component analysis (PCA) found both closing and opening motions of the kink-turn sRNA. This might play a key role in the sRNP assembly and methylation catalysis. These combined computational methods can be used to study the specific recognition of other sRNAs and proteins.
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Affiliation(s)
- 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
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Baker CM, Best RB. Insights into the Binding of Intrinsically Disordered Proteins from Molecular Dynamics Simulation. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013; 4:182-198. [PMID: 34354764 DOI: 10.1002/wcms.1167] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Intrinsically disordered proteins (IDPs) are a class of protein that, in the native state, possess no well-defined secondary or tertiary structure, existing instead as dynamic ensembles of conformations. They are biologically important, with approximately 20% of all eukaryotic proteins disordered, and found at the heart of many biochemical networks. To fulfil their biological roles, many IDPs need to bind to proteins and/or nucleic acids. And while unstructured in solution, IDPs typically fold into a well-defined three-dimensional structure upon interaction with a binding partner. The flexibility and structural diversity inherent to IDPs makes this coupled folding and binding difficult to study at atomic resolution by experiment alone, and computer simulation currently offers perhaps the best opportunity to understand this process. But simulation of coupled folding and binding is itself extremely challenging; these molecules are large and highly flexible, and their binding partners, such as DNA or cyclins, are also often large. Therefore, their study requires either or both simplified representations and advanced enhanced sampling schemes. It is not always clear that existing simulation techniques, optimized for studying folded proteins, are well-suited to IDPs. In this article, we examine the progress that has been made in the study of coupled folding and binding using molecular dynamics simulation. We summarise what has been learnt, and examine the state of the art in terms of both methodologies and models. We also consider the lessons to be learnt from advances in other areas of simulation and highlight the issues that remain of be addressed.
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Affiliation(s)
- Christopher M Baker
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, USA
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30
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Wang W, Ye W, Yu Q, Jiang C, Zhang J, Luo R, Chen HF. Conformational Selection and Induced Fit in Specific Antibody and Antigen Recognition: SPE7 as a Case Study. J Phys Chem B 2013; 117:4912-23. [DOI: 10.1021/jp4010967] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Wang
- 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
| | - Qingfen Yu
- 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
| | - Jian Zhang
- Department of Pathophysiology,
Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry
of Education, School of Medicine, Shanghai Jiaotong University, 280 Chongqing Road, Shanghai, 200025, China
| | - Ray Luo
- Departments of Molecular Biology
and Biochemistry and Biomedical Engineering, University of California, Irvine, California 92697-3900, United
States
| | - 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
- Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai,
200235, China
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31
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Global conformational selection and local induced fit for the recognition between intrinsic disordered p53 and CBP. PLoS One 2013; 8:e59627. [PMID: 23555731 PMCID: PMC3608666 DOI: 10.1371/journal.pone.0059627] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 02/15/2013] [Indexed: 11/26/2022] Open
Abstract
The transactivation domain (TAD) of tumor suppressor p53 can bind with the nuclear coactivator binding domain (NCBD) of cyclic-AMP response element binding protein (CBP) and activate transcription. NMR experiments demonstrate that both apo-NCBD and TAD are intrinsic disordered and bound NCBD/TAD undergoes a transition to well folded. The recognition mechanism between intrinsic disordered proteins is still hotly debated. Molecular dynamics (MD) simulations in explicit solvent are used to study the recognition mechanism between intrinsic disordered TAD and NCBD. The average RMSD values between bound and corresponding apo states and Kolmogorov-Smirnov P test analysis indicate that TAD and NCBD may follow an induced fit mechanism. Quantitative analysis indicates there is also a global conformational selection. In summary, the recognition of TAD and NCBD might obey a local induced fit and global conformational selection. These conclusions are further supported by high-temperature unbinding kinetics and room temperature landscape analysis. These methods can be used to study the recognition mechanism of other intrinsic disordered proteins.
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Wang J, Fessl T, Schroeder KT, Ouellet J, Liu Y, Freeman ADJ, Lilley DMJ. Single-molecule observation of the induction of k-turn RNA structure on binding L7Ae protein. Biophys J 2012; 103:2541-8. [PMID: 23260056 DOI: 10.1016/j.bpj.2012.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 11/02/2012] [Accepted: 11/06/2012] [Indexed: 10/27/2022] Open
Abstract
The k-turn is a commonly occurring structural motif that introduces a tight kink into duplex RNA. In free solution, it can exist in an extended form, or by folding into the kinked structure. Binding of proteins including the L7Ae family can induce the formation of the kinked geometry, raising the question of whether this occurs by passive selection of the kinked structure, or a more active process in which the protein manipulates the RNA structure. We have devised a single-molecule experiment whereby immobilized L7Ae protein binds Cy3-Cy5-labeled RNA from free solution. We find that all bound RNA is in the kinked geometry, with no evidence for transitions to an extended form at the millisecond timescale of the camera. Furthermore, real-time binding experiments provide no evidence for a more extended intermediate even at the earliest times, at a time resolution of 16 ms. The data support a passive conformational selection model by which the protein selects a fraction of RNA that is already in the kinked conformation, thereby drawing the equilibrium into this form.
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Affiliation(s)
- Jia Wang
- Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee, Dundee, United Kingdom
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33
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Rau M, Stump WT, Hall KB. Intrinsic flexibility of snRNA hairpin loops facilitates protein binding. RNA (NEW YORK, N.Y.) 2012; 18:1984-1995. [PMID: 23012481 PMCID: PMC3479389 DOI: 10.1261/rna.035006.112] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 08/02/2012] [Indexed: 06/01/2023]
Abstract
Stem-loop II of U1 snRNA and Stem-loop IV of U2 snRNA typically have 10 or 11 nucleotides in their loops. The fluorescent nucleobase 2-aminopurine was used as a substitute for the adenines in each loop to probe the local and global structures and dynamics of these unusually long loops. Using steady-state and time-resolved fluorescence, we find that, while the bases in the loops are stacked, they are able to undergo significant local motion on the picosecond/nanosecond timescale. In addition, the loops have a global conformational change at low temperatures that occurs on the microsecond timescale, as determined using laser T-jump experiments. Nucleobase and loop motions are present at temperatures far below the melting temperature of the hairpin stem, which may facilitate the conformational change required for specific protein binding to these RNA loops.
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Affiliation(s)
- Michael Rau
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri 63110, USA
| | - W. Tom Stump
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri 63110, USA
| | - Kathleen B. Hall
- Department of Biochemistry and Molecular Biophysics, Washington University Medical School, St. Louis, Missouri 63110, USA
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34
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Atomistic mechanism of microRNA translation upregulation via molecular dynamics simulations. PLoS One 2012; 7:e43788. [PMID: 22952765 PMCID: PMC3428290 DOI: 10.1371/journal.pone.0043788] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2012] [Accepted: 07/24/2012] [Indexed: 01/16/2023] Open
Abstract
MicroRNAs are endogenous 23–25 nt RNAs that play important gene-regulatory roles in animals and plants. Recently, miR369-3 was found to upregulate translation of TNFα mRNA in quiescent (G0) mammalian cell lines. Knock down and immunofluorescence experiments suggest that microRNA-protein complexes (with FXR1 and AGO2) are necessary for the translation upregulation. However the molecular mechanism of microRNA translation activation is poorly understood. In this study we constructed the microRNA-mRNA-AGO2-FXR1 quadruple complex by bioinformatics and molecular modeling, followed with all atom molecular dynamics simulations in explicit solvent to investigate the interaction mechanisms for the complex. A combined analysis of experimental and computational data suggests that AGO2-FXR1 complex relocalize microRNA:mRNA duplex to polysomes in G0. The two strands of dsRNA are then separated upon binding of AGO2 and FXR1. Finally, polysomes may improve the translation efficiency of mRNA. The mutation research confirms the stability of microRNA-mRNA-FXR1 and illustrates importance of key residue of Ile304. This possible mechanism can shed more light on the microRNA-dependent upregulation of translation.
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Enhancing the promiscuous phosphotriesterase activity of a thermostable lactonase (GkaP) for the efficient degradation of organophosphate pesticides. Appl Environ Microbiol 2012; 78:6647-55. [PMID: 22798358 DOI: 10.1128/aem.01122-12] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The phosphotriesterase-like lactonase (PLL) enzymes in the amidohydrolase superfamily hydrolyze various lactones and exhibit latent phosphotriesterase activities. These enzymes serve as attractive templates for in vitro evolution of neurotoxic organophosphates (OPs) with hydrolytic capabilities that can be used as bioremediation tools. Here, a thermostable PLL from Geobacillus kaustophilus HTA426 (GkaP) was targeted for joint laboratory evolution with the aim of enhancing its catalytic efficiency against OP pesticides. By a combination of site saturation mutagenesis and whole-gene error-prone PCR approaches, several improved variants were isolated. The most active variant, 26A8C, accumulated eight amino acid substitutions and demonstrated a 232-fold improvement over the wild-type enzyme in reactivity (k(cat)/K(m)) for the OP pesticide ethyl-paraoxon. Concomitantly, this variant showed a 767-fold decrease in lactonase activity with δ-decanolactone, imparting a specificity switch of 1.8 × 10(5)-fold. 26A8C also exhibited high hydrolytic activities (19- to 497-fold) for several OP pesticides, including parathion, diazinon, and chlorpyrifos. Analysis of the mutagenesis sites on the GkaP structure revealed that most mutations are located in loop 8, which determines substrate specificity in the amidohydrolase superfamily. Molecular dynamics simulation shed light on why 26A8C lost its native lactonase activity and improved the promiscuous phosphotriesterase activity. These results permit us to obtain further insights into the divergent evolution of promiscuous enzymes and suggest that laboratory evolution of GkaP may lead to potential biological solutions for the efficient decontamination of neurotoxic OP compounds.
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36
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Ye W, Chen Y, Wang W, Yu Q, Li Y, Zhang J, Chen HF. Insight into the stability of cross-β amyloid fibril from VEALYL short peptide with molecular dynamics simulation. PLoS One 2012; 7:e36382. [PMID: 22590535 PMCID: PMC3349666 DOI: 10.1371/journal.pone.0036382] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 03/30/2012] [Indexed: 12/13/2022] Open
Abstract
Amyloid fibrils are found in many fatal neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, type II diabetes, and prion disease. The VEALYL short peptide from insulin has been confirmed to aggregate amyloid-like fibrils. However, the aggregation mechanism of amyloid fibril is poorly understood. Here, we utilized molecular dynamics simulation to analyse the stability of VEALYL hexamer. The statistical results indicate that hydrophobic residues play key roles in stabilizing VEALYL hexamer. Single point and two linkage mutants confirmed that Val1, Leu4, and Tyr5 of VEALYL are key residues. The consistency of the results for the VEALYL oligomer suggests that the intermediate states might be trimer (3-0) and pentamer(3-2). These results can help us to obtain an insight into the aggregation mechanism of amyloid fibril. These methods can be used to study the stability of amyloid fibril from other short peptides.
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Affiliation(s)
- Wei Ye
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Yue Chen
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Wei Wang
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Qingfen Yu
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, College of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai, China
| | - Yixue Li
- Shanghai Center for Bioinformation Technology, Shanghai, China
- * E-mail: (HC); (YL); (JZ)
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, School of Medicine, Shanghai Jiaotong University, Shanghai, China
- * E-mail: (HC); (YL); (JZ)
| | - 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
- * E-mail: (HC); (YL); (JZ)
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37
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Yan GW, Chen Y, Li Y, Chen HF. Revealing interaction mode between HIV-1 protease and mannitol analog inhibitor. Chem Biol Drug Des 2012; 79:916-25. [PMID: 22296911 DOI: 10.1111/j.1747-0285.2012.01348.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
HIV protease is a key enzyme to play a key role in the HIV-1 replication cycle and control the maturation from HIV viruses to an infectious virion. HIV-1 protease has become an important target for anti-HIV-1 drug development. Here, we used molecular dynamics simulation to study the binding mode between mannitol derivatives and HIV-1 protease. The results suggest that the most active compound (M35) has more stable hydrogen bonds and stable native contacts than the less active one (M17). These mannitol derivatives might have similar interaction mode with HIV-1 protease. Then, 3D-QSAR was used to construct quantitative structure-activity models. The cross-validated q(2) values are found as 0.728 and 0.611 for CoMFA and CoMSIA, respectively. And the non-cross-validated r(2) values are 0.973 and 0.950. Nine test set compounds validate the model. The results show that this model possesses better prediction ability than the previous work. This model can be used to design new chemical entities and make quantitative prediction of the bioactivities for HIV-1 protease inhibitors before resorting to in vitro and in vivo experiment.
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Affiliation(s)
- Guan-Wen Yan
- 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
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38
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Qin F, Ye W, Chen Y, Chen X, Li Y, Zhang J, Chen HF. Specific recognition between intrinsically disordered LEF and DNA. Phys Chem Chem Phys 2012; 14:538-45. [DOI: 10.1039/c1cp22610j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Abstract
Many RNAs do not directly code proteins but are nonetheless indispensable to cellular function. These strands fold into intricate three-dimensional shapes that are essential structures in protein synthesis, splicing, and many other processes of gene regulation and expression. A variety of biophysical and biochemical methods are now showing, in real time, how ribosomal subunits and other ribonucleoprotein complexes assemble from their molecular components. Footprinting methods are particularly useful for studying the folding of long RNAs: they provide quantitative information about the conformational state of each residue and require little material. Data from footprinting complement the global information available from small-angle X-ray scattering or cryo-electron microscopy, as well as the dynamic information derived from single-molecule Förster resonance energy transfer (FRET) and NMR methods. In this Account, I discuss how we have used hydroxyl radical footprinting and other experimental methods to study pathways of RNA folding and 30S ribosome assembly. Hydroxyl radical footprinting probes the solvent accessibility of the RNA backbone at each residue in as little as 10 ms, providing detailed views of RNA folding pathways in real time. In conjunction with other methods such as solution scattering and single-molecule FRET, time-resolved footprinting of ribozymes showed that stable domains of RNA tertiary structure fold in less than 1 s. However, the free energy landscapes for RNA folding are rugged, and individual molecules kinetically partition into folding pathways that lead through metastable intermediates, stalling the folding or assembly process. Time-resolved footprinting was used to follow the formation of tertiary structure and protein interactions in the 16S ribosomal RNA (rRNA) during the assembly of 30S ribosomes. As previously observed in much simpler ribozymes, assembly occurs in stages, with individual molecules taking different routes to the final complex. Interactions occur concurrently in all domains of the 16S rRNA, and multistage protection of binding sites of individual proteins suggests that initial encounter complexes between the rRNA and ribosomal proteins are remodeled during assembly. Equilibrium footprinting experiments showed that one primary binding protein was sufficient to stabilize the tertiary structure of the entire 16S 5'-domain. The rich detail available from the footprinting data showed that the secondary assembly protein S16 suppresses non-native structures in the 16S 5'-domain. In doing so, S16 enables a conformational switch distant from its own binding site, which may play a role in establishing interactions with other domains of the 30S subunit. Together, the footprinting results show how protein-induced changes in RNA structure are communicated over long distances, ensuring cooperative assembly of even very large RNA-protein complexes such as the ribosome.
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Affiliation(s)
- Sarah A. Woodson
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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40
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Zhang H, Qin F, Ye W, Li Z, Ma S, Xia Y, Jiang Y, Zhu J, Li Y, Zhang J, Chen HF. Revealing the Drug-Resistant Mechanism for Diarylpyrimidine Analogue Inhibitors of HIV-1 Reverse Transcriptase. Chem Biol Drug Des 2011; 78:427-37. [DOI: 10.1111/j.1747-0285.2011.01163.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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41
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Vértessy BG, Orosz F. From "fluctuation fit" to "conformational selection": evolution, rediscovery, and integration of a concept. Bioessays 2011; 33:30-4. [PMID: 21053308 DOI: 10.1002/bies.201000068] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Beáta G Vértessy
- Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary.
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42
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Male germ cell apoptosis and epigenetic histone modification induced by Tripterygium wilfordii Hook F. PLoS One 2011; 6:e20751. [PMID: 21698297 PMCID: PMC3115959 DOI: 10.1371/journal.pone.0020751] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Accepted: 05/12/2011] [Indexed: 01/21/2023] Open
Abstract
Multiglycosides of Tripterygium wilfordii Hook f (GTW), a Chinese herb-derived medicine used as a remedy for rheumatoid arthritis, are considered to be a reversible anti-fertility drug affecting the mammalian spermatids. However, the mechanism behind this effect is still unknown. To study the possible mechanism behind the impact of GTW on spermatogenesis, we administered 4 groups of 4-week-old male mice with different doses of GTW. We found a dose-dependent decrease in the number of germ cells after 40 days of GTW treatment, and an increase in apoptotic cells from the low-dose to the high-dose group. During this same period the dimethylated level of histone H3 lysine 9 (H3K9me2) in GTW-treated testes germ cells declined. Additionally, spermatogonial stem cells (SSCs) from 6-day-old mice were isolated to evaluate the possible effect of GTW or triptolide on development of SSCs. We found a significantly higher incidence of apoptosis and lower dimethylation level of H3K9me2 in the SSCs of GTW or triptolide treatment than in controls. Thus, these data suggest that the GTW-induced apoptosis might be responsible for the fertility impairment in mice. This damage could be traced back to the early stages of spermatogenesis. GTW also affected the epigenetic modification of H3K9 in spermatogenesis. Molecular dynamics simulation suggested that triptolide and dimethylated or trimethylated H3K9 might have similar interaction mechanisms with EED (embryonic ectoderm development). These candidate activation mechanisms provide the first glimpse into the pathway of GTW-induced gonad toxicity, which is crucial for further research and clinical application.
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43
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In silico elucidation of the recognition dynamics of ubiquitin. PLoS Comput Biol 2011; 7:e1002035. [PMID: 21533067 PMCID: PMC3080845 DOI: 10.1371/journal.pcbi.1002035] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 03/04/2011] [Indexed: 01/07/2023] Open
Abstract
Elucidation of the mechanism of biomacromolecular recognition events has been a topic of intense interest over the past century. The inherent dynamic nature of both protein and ligand molecules along with the continuous reshaping of the energy landscape during the binding process renders it difficult to characterize this process at atomic detail. Here, we investigate the recognition dynamics of ubiquitin via microsecond all-atom molecular dynamics simulation providing both thermodynamic and kinetic information. The high-level of consistency found with respect to experimental NMR data lends support to the accuracy of the in silico representation of the conformational substates and their interconversions of free ubiquitin. Using an energy-based reweighting approach, the statistical distribution of conformational states of ubiquitin is monitored as a function of the distance between ubiquitin and its binding partner Hrs-UIM. It is found that extensive and dense sampling of conformational space afforded by the µs MD trajectory is essential for the elucidation of the binding mechanism as is Boltzmann sampling, overcoming inherent limitations of sparsely sampled empirical ensembles. The results reveal a population redistribution mechanism that takes effect when the ligand is at intermediate range of 1–2 nm from ubiquitin. This mechanism, which may be depicted as a superposition of the conformational selection and induced fit mechanisms, also applies to other binding partners of ubiquitin, such as the GGA3 GAT domain. Molecular recognition plays a central role in many biological processes, ensuring specific and efficient interaction between binding partners. Various models for describing the mechanisms of molecular recognition have been proposed, but the validation of these models has been traditionally difficult due to the transient and complex nature of the dynamic recognition process. In the present study, we aim at visually characterizing the mutual interplay between human ubiquitin and its ligands via microsecond time scale molecular dynamics simulation, which is validated rigorously against experimental NMR data. Taking advantage of Boltzmann sampling of molecular dynamics snapshots, we statistically reweight the populations of ubiquitin in the presence of its ligand molecule at intermediate distance range (1–2 nm) to examine the population redistribution mechanisms. These results offer new atomistic insights into this vital protein-protein recognition event.
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Multistep kinetics of the U1A-SL2 RNA complex dissociation. J Mol Biol 2011; 408:896-908. [PMID: 21419778 DOI: 10.1016/j.jmb.2011.02.054] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Revised: 02/20/2011] [Accepted: 02/22/2011] [Indexed: 11/23/2022]
Abstract
The U1A-SL2 RNA complex is a model system for studying interactions between RNA and the RNA recognition motif (RRM), which is one of the most common RNA binding domains. We report here kinetic studies of dissociation of the U1A-SL2 RNA complex, using laser temperature jump and stopped-flow fluorescence methods with U1A proteins labeled with the intrinsic chromophore tryptophan. An analysis of the kinetic data suggests three phases of dissociation with time scales of ∼100 μs, ∼50 ms, and ∼2 s. We propose that the first step of dissociation is a fast rearrangement of the complex to form a loosely bound complex. The intermediate step is assigned to be the dissociation of the U1A-SL2 RNA complex, and the final step is assigned to a reorganization of the U1A protein structure into the conformation of the free protein. These assignments are consistent with previous proposals based on thermodynamic, NMR, and surface plasmon resonance experiments and molecular dynamics simulations. Together, these results begin to build a comprehensive model of the complex dynamic processes involved in the formation and dissociation of an RRM-RNA complex.
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Qin F, Jiang Y, Chen Y, Wu M, Yan G, Ye W, Li Y, Zhang J, Chen HF. Conformational selection or induced fit for Brinker and DNA recognition. Phys Chem Chem Phys 2011; 13:1407-12. [DOI: 10.1039/c0cp00701c] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Li Z, Zhang H, Li Y, Zhang J, Chen HF. Drug resistant mechanism of diaryltriazine analog inhibitors of HIV-1 reverse transcriptase using molecular dynamics simulation and 3D-QSAR. Chem Biol Drug Des 2010; 77:63-74. [PMID: 21134218 DOI: 10.1111/j.1747-0285.2010.01049.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Diaryltriazine inhibitors have highly potent and effective bioactivities for the wild type of HIV-1 reverse transcription. To design new drug of antimutant HIV-1 reverse transcriptase, the mechanism of drug resistance for four types of mutants was revealed. Molecular dynamics simulations suggest that Lys101, Leu100, Lys103, Tyr181, and Tyr188 are key residues. Different mutants of key residues may have different interaction modes and lead to different drug resistances. Then, CoMFA and CoMSIA methods were employed to construct 3D quantitative structure-activity relationship models. These models were evaluated by test set compounds. These models can be used to make quantitative prediction of their bioactivities for lead compounds before resorting to in vitro and in vivo experimentation.
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Affiliation(s)
- Zeng Li
- College of Life Sciences and Biotechnology, Shanghai Jiaotong University, 800 Dongchuan Road, Shanghai, China
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