Investigation of Indazole Unbinding Pathways in CYP2E1 by Molecular Dynamics Simulations
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{"title"=>"Investigation of indazole unbinding pathways in CYP2E1 by molecular dynamics simulations", "type"=>"journal", "authors"=>[{"first_name"=>"Zhonghua", "last_name"=>"Shen", "scopus_author_id"=>"55109152300"}, {"first_name"=>"Feixiong", "last_name"=>"Cheng", "scopus_author_id"=>"36514277000"}, {"first_name"=>"You", "last_name"=>"Xu", "scopus_author_id"=>"36547205600"}, {"first_name"=>"Jing", "last_name"=>"Fu", "scopus_author_id"=>"57199932774"}, {"first_name"=>"Wen", "last_name"=>"Xiao", "scopus_author_id"=>"55703622100"}, {"first_name"=>"Jie", "last_name"=>"Shen", "scopus_author_id"=>"57199270521"}, {"first_name"=>"Guixia", "last_name"=>"Liu", "scopus_author_id"=>"55706595300"}, {"first_name"=>"Weihua", "last_name"=>"Li", "scopus_author_id"=>"7501794094"}, {"first_name"=>"Yun", "last_name"=>"Tang", "scopus_author_id"=>"35312761700"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"sgr"=>"84863348961", "doi"=>"10.1371/journal.pone.0033500", "pui"=>"364464860", "scopus"=>"2-s2.0-84863348961", "issn"=>"19326203", "pmid"=>"22442693"}, "id"=>"c94eb63b-075a-33dd-a618-77626587df97", "abstract"=>"Human microsomal cytochrome P450 2E1 (CYP2E1) can oxidize not only low molecular weight xenobiotic compounds such as ethanol, but also many endogenous fatty acids. The crystal structure of CYP2E1 in complex with indazole reveals that the active site is deeply buried into the protein center. Thus, the unbinding pathways and associated unbinding mechanisms remain elusive. In this study, random acceleration molecular dynamics simulations combined with steered molecular dynamics and potential of mean force calculations were performed to identify the possible unbinding pathways in CYP2E1. The results show that channel 2c and 2a are most likely the unbinding channels of CYP2E1. The former channel is located between helices G and I and the B-C loop, and the latter resides between the region formed by the F-G loop, the B-C loop and the β1 sheet. Phe298 and Phe478 act as the gate keeper during indazole unbinding along channel 2c and 2a, respectively. Previous site-directed mutagenesis experiments also supported these findings.", "link"=>"http://www.mendeley.com/research/investigation-indazole-unbinding-pathways-cyp2e1-molecular-dynamics-simulations", "reader_count"=>21, "reader_count_by_academic_status"=>{"Professor > Associate Professor"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>9, "Student > Master"=>5, "Student > Bachelor"=>3, "Professor"=>2}, "reader_count_by_user_role"=>{"Professor > Associate Professor"=>1, "Researcher"=>1, "Student > Ph. D. Student"=>9, "Student > Master"=>5, "Student > Bachelor"=>3, "Professor"=>2}, "reader_count_by_subject_area"=>{"Engineering"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>7, "Medicine and Dentistry"=>1, "Arts and Humanities"=>1, "Physics and Astronomy"=>1, "Chemistry"=>8, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>1}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Chemistry"=>{"Chemistry"=>8}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>7}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Arts and Humanities"=>{"Arts and Humanities"=>1}}, "reader_count_by_country"=>{"Czech Republic"=>1, "Germany"=>2}, "group_count"=>1}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/342207", "https://ndownloader.figshare.com/files/342256", "https://ndownloader.figshare.com/files/342296", "https://ndownloader.figshare.com/files/342350"], "description"=>"<div><p>Human microsomal cytochrome P450 2E1 (CYP2E1) can oxidize not only low molecular weight xenobiotic compounds such as ethanol, but also many endogenous fatty acids. The crystal structure of CYP2E1 in complex with indazole reveals that the active site is deeply buried into the protein center. Thus, the unbinding pathways and associated unbinding mechanisms remain elusive. In this study, random acceleration molecular dynamics simulations combined with steered molecular dynamics and potential of mean force calculations were performed to identify the possible unbinding pathways in CYP2E1. The results show that channel 2c and 2a are most likely the unbinding channels of CYP2E1. The former channel is located between helices G and I and the B-C loop, and the latter resides between the region formed by the F-G loop, the B-C loop and the β1 sheet. Phe298 and Phe478 act as the gate keeper during indazole unbinding along channel 2c and 2a, respectively. Previous site-directed mutagenesis experiments also supported these findings.</p> </div>", "links"=>[], "tags"=>["indazole", "unbinding", "pathways", "cyp2e1", "molecular", "simulations"], "article_id"=>127648, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Pharmacology"], "users"=>["Zhonghua Shen", "Feixiong Cheng", "You Xu", "Jing Fu", "Wen Xiao", "Jie Shen", "Guixia Liu", "Weihua Li", "Yun Tang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033500.s001", "https://dx.doi.org/10.1371/journal.pone.0033500.s002", "https://dx.doi.org/10.1371/journal.pone.0033500.s003", "https://dx.doi.org/10.1371/journal.pone.0033500.s004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Investigation_of_Indazole_Unbinding_Pathways_in_CYP2E1_by_Molecular_Dynamics_Simulations/127648", "title"=>"Investigation of Indazole Unbinding Pathways in CYP2E1 by Molecular Dynamics Simulations", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-03-19 02:07:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/665250"], "description"=>"<p>The major helices are labeled. Heme is shown as black spheres; indazole is shown as magenta sticks. All figures were generated with Pymol.</p>", "links"=>[], "tags"=>["cyp2e1", "complexed"], "article_id"=>335730, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Pharmacology"], "users"=>["Zhonghua Shen", "Feixiong Cheng", "You Xu", "Jing Fu", "Wen Xiao", "Jie Shen", "Guixia Liu", "Weihua Li", "Yun Tang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033500.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_crystal_structure_of_CYP2E1_complexed_with_indazole_/335730", "title"=>"The crystal structure of CYP2E1 complexed with indazole.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-19 01:35:30"}
  • {"files"=>["https://ndownloader.figshare.com/files/665375"], "description"=>"<p>Channel 2c is shown in cyan and channel 2a is shown in magenta. The major secondary elements of CYP2E1 are labeled.</p>", "links"=>[], "tags"=>["unbinding", "routes", "cyp2e1", "illustrated", "mole"], "article_id"=>335857, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Pharmacology"], "users"=>["Zhonghua Shen", "Feixiong Cheng", "You Xu", "Jing Fu", "Wen Xiao", "Jie Shen", "Guixia Liu", "Weihua Li", "Yun Tang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033500.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Indazole_unbinding_routes_from_CYP2E1_illustrated_by_using_the_MOLE_program_/335857", "title"=>"Indazole unbinding routes from CYP2E1 illustrated by using the MOLE program.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-19 01:37:37"}
  • {"files"=>["https://ndownloader.figshare.com/files/665509"], "description"=>"<p>Three different lines represent data from three representative SMD simulations.</p>", "links"=>[], "tags"=>["profiles", "2c", "2a"], "article_id"=>335989, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Pharmacology"], "users"=>["Zhonghua Shen", "Feixiong Cheng", "You Xu", "Jing Fu", "Wen Xiao", "Jie Shen", "Guixia Liu", "Weihua Li", "Yun Tang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033500.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Force_profiles_along_channel_2c_A_and_2a_B_/335989", "title"=>"Force profiles along channel 2c (A) and 2a (B).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-19 01:39:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/665700"], "description"=>"<p>Indazole is shown as green sticks. Heme is shown as a red stick. Phe106, Phe116 and Phe207 are shown as blue sticks.</p>", "links"=>[], "tags"=>["positions", "indazole", "smd", "simulation", "2c", "200", "500", "800"], "article_id"=>336164, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Pharmacology"], "users"=>["Zhonghua Shen", "Feixiong Cheng", "You Xu", "Jing Fu", "Wen Xiao", "Jie Shen", "Guixia Liu", "Weihua Li", "Yun Tang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033500.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Snapshots_of_the_relative_positions_of_indazole_and_the_protein_throughout_the_SMD_simulation_along_channel_2c_A_200_ps_B_500_ps_and_C_800_ps_/336164", "title"=>"Snapshots of the relative positions of indazole and the protein throughout the SMD simulation along channel 2c (A, 200 ps; B, 500 ps; and C, 800 ps).", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-19 01:42:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/665805"], "description"=>"<p>Three different lines represent data from three representative SMD simulations.</p>", "links"=>[], "tags"=>["benzene", "f298", "shown", "smd"], "article_id"=>336282, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Pharmacology"], "users"=>["Zhonghua Shen", "Feixiong Cheng", "You Xu", "Jing Fu", "Wen Xiao", "Jie Shen", "Guixia Liu", "Weihua Li", "Yun Tang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033500.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Variation_of_the_benzene_ring_of_F298_is_shown_as_a_function_of_time_during_SMD_simulation_/336282", "title"=>"Variation of the benzene ring of F298 is shown as a function of time during SMD simulation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-03-19 01:44:42"}
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  • {"files"=>["https://ndownloader.figshare.com/files/666247"], "description"=>"<p>Statistical summary of RAMD simulations of CYP2E1.</p>", "links"=>[], "tags"=>["ramd", "simulations"], "article_id"=>336731, "categories"=>["Biological Sciences", "Biochemistry", "Chemistry", "Pharmacology"], "users"=>["Zhonghua Shen", "Feixiong Cheng", "You Xu", "Jing Fu", "Wen Xiao", "Jie Shen", "Guixia Liu", "Weihua Li", "Yun Tang"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0033500.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Statistical_summary_of_RAMD_simulations_of_CYP2E1_/336731", "title"=>"Statistical summary of RAMD simulations of CYP2E1.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-03-19 01:52:11"}

PMC Usage Stats | Further Information

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Relative Metric

{"start_date"=>"2012-01-01T00:00:00Z", "end_date"=>"2012-12-31T00:00:00Z", "subject_areas"=>[{"subject_area"=>"/Biology and life sciences", "average_usage"=>[322, 550, 671, 773, 864, 955, 1048, 1135, 1223, 1308, 1387, 1465, 1534, 1602, 1673, 1744, 1813, 1885, 1955, 2026, 2093, 2160, 2228, 2290, 2349]}, {"subject_area"=>"/Physical sciences", "average_usage"=>[304, 506, 616, 712, 799, 879, 968, 1052, 1134, 1212, 1284, 1357, 1427, 1494, 1557, 1621, 1689, 1756, 1823, 1883, 1944, 1997, 2056, 2118, 2171]}, {"subject_area"=>"/Physical sciences/Chemistry", "average_usage"=>[302, 508, 622, 720, 804, 888, 973, 1054, 1141, 1219, 1299, 1370, 1442, 1511, 1574, 1644, 1711, 1782, 1846, 1911, 1971, 2030, 2097, 2155, 2217]}, {"subject_area"=>"/Physical sciences/Physics", "average_usage"=>[298, 476, 578, 665, 743, 821, 891, 962, 1036, 1108, 1174, 1240, 1312, 1371, 1430, 1494, 1551, 1609, 1673, 1736, 1795, 1857, 1913, 1976, 2035]}]}
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