Applications of rare event dynamics on the free energy calculations for membrane protein systems
Techniques of rare event dynamics were reviewed, including string methods, which will be implemented with the biochemical simulation packages. The existing methods were applied to study biological systems with relevance to drug design and drug metabolism. The rare event dynamics simulations were per...
Saved in:
| Published in | Canadian journal of chemistry Vol. 91; no. 9; pp. 769 - 774 |
|---|---|
| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Ottawa
NRC Research Press
01.09.2013
Canadian Science Publishing NRC Research Press |
| Subjects | |
| Online Access | Get full text |
| ISSN | 0008-4042 1480-3291 |
| DOI | 10.1139/cjc-2012-0391 |
Cover
| Abstract | Techniques of rare event dynamics were reviewed, including string methods, which will be implemented with the biochemical simulation packages. The existing methods were applied to study biological systems with relevance to drug design and drug metabolism. The rare event dynamics simulations were performed to understand the kinetic and thermodynamic free energy information on the drug binding sites in the M2 proton channel, the free energy of insertion and association of membrane proteins and membrane active peptides. Results give a theoretical framework to interpret and reconcile existing and often conflicting opinions. |
|---|---|
| AbstractList | Techniques of rare event dynamics were reviewed, including string methods, which will be implemented with the biochemical simulation packages. The existing methods were applied to study biological systems with relevance to drug design and drug metabolism. The rare event dynamics simulations were performed to understand the kinetic and thermodynamic free energy information on the drug binding sites in the M2 proton channel, the free energy of insertion and association of membrane proteins and membrane active peptides. Results give a theoretical framework to interpret and reconcile existing and often conflicting opinions. Techniques of rare event dynamics were reviewed, including string methods, which will be implemented with the biochemical simulation packages. The existing methods were applied to study biological systems with relevance to drug design and drug metabolism. The rare event dynamics simulations were performed to understand the kinetic and thermodynamic free energy information on the drug binding sites in the M2 proton channel, the free energy of insertion and association of membrane proteins and membrane active peptides. Results give a theoretical framework to interpret and reconcile existing and often conflicting opinions. [PUBLICATION ABSTRACT] Techniques of rare event dynamics were reviewed, including string methods, which will be implemented with the biochemical simulation packages. The existing methods were applied to study biological systems with relevance to drug design and drug metabolism. The rare event dynamics simulations were performed to understand the kinetic and thermodynamic free energy information on the drug binding sites in the M2 proton channel, the free energy of insertion and association of membrane proteins and membrane active peptides. Results give a theoretical framework to interpret and reconcile existing and often conflicting opinions. Key words: rare event dynamics, umbrella sampling, membrane proteins, free energy calculations, molecular dynamics simulations. Les methodes basees sur la dynamique des evenements rares, y compris les methodes des chemins de transition dites stringmethods, destinees aetre mises enceuvre dans les progiciels de simulationbiochimique sont passees en revue. Les methodes existantes sont appliquees a l'etude de systemes biologiques importants sur le plan de la conception et du metabolisme des medicaments. Des simulations de la dynamique d'evenements rares sont effectuees pour interpreter l'information sur l'energie libre cinetique et thermodynamique aux sites de liaison des medicaments dans le canal protonique M2, ainsi que sur l'energie libre d'insertion et d'association des proteines membranaires et des peptides actifs membranaires. Les resultats fournissent un cadre theorique pour l'interpretation et le rapprochement des opinions existantes, souvent contradictoires. [Traduit par la Redaction] Mots-cles: dynamique des evenements rares, echantillonnage <>, proteines membranaires, calculs d'energie libre, simulations de la dynamique moleculaire. |
| Abstract_FL | Les méthodes basées sur la dynamique des événements rares, y compris les méthodes des chemins de transition dites string methods, destinées à être mises en œuvre dans les progiciels de simulation biochimique sont passées en revue. Les méthodes existantes sont appliquées à l’étude de systèmes biologiques importants sur le plan de la conception et du métabolisme des médicaments. Des simulations de la dynamique d’événements rares sont effectuées pour interpréter l’information sur l’énergie libre cinétique et thermodynamique aux sites de liaison des médicaments dans le canal protonique M2, ainsi que sur l’énergie libre d’insertion et d’association des protéines membranaires et des peptides actifs membranaires. Les résultats fournissent un cadre théorique pour l’interprétation et le rapprochement des opinions existantes, souvent contradictoires. [Traduit par la Rédaction] |
| Audience | Academic |
| Author | Wei, Dong-Qing Gu, Ruo-Xu Ulmschneider, Jakob Wang, Yun-Kun Fan, Huai-Meng |
| Author_xml | – sequence: 1 givenname: Yun-Kun surname: Wang fullname: Wang, Yun-Kun – sequence: 2 givenname: Dong-Qing surname: Wei fullname: Wei, Dong-Qing – sequence: 3 givenname: Ruo-Xu surname: Gu fullname: Gu, Ruo-Xu – sequence: 4 givenname: Huai-Meng surname: Fan fullname: Fan, Huai-Meng – sequence: 5 givenname: Jakob surname: Ulmschneider fullname: Ulmschneider, Jakob |
| BookMark | eNqVkstv1DAQxi1UJLaFI3cLThxS_EriHFcVj0oVSDzOxjsZb71KnNT2Iva_x0srQVEAIR8sj3_fjGbmOyUnYQpIyFPOzjmX3UvYQSUYFxWTHX9AVlxpVknR8ROyYozpSjElHpHTlHbl2TJRr8iX9TwPHmz2U0h0cjTaiBS_Ysi0PwQ7eijhQPM1UhexfAWM2wMFO8B-uJO5KdIRx020Aekcp4w-0HRIGcf0mDx0dkj45O4-I59fv_p08ba6ev_m8mJ9VUEtVa6QdbUG3bSubZjb9NpCo1xX96p2vGdCbOq-R80AWq56DW1BddfyrrW6UbCRZ-T5bd5S_2aPKZvdtI-hlDRCCal5wfjfKK6k4rUs2E9qawc0PrgpRwujT2DWsuYNF5rLQlUL1PY4IDuUzThfwvf4Zws8zP7G_AqdL0Dl9FhWsZj1xT1BYTJ-y1u7T8lcfvzwH-y7xe4gTilFdGaOfrTxYDgzR7uZYjdztJs52q3w8jcefP7hj9KAH_6oYreqECFiQhvh-h-FvgPFKeVP |
| CODEN | CJCHAG |
| CitedBy_id | crossref_primary_10_1007_s41745_018_0083_3 crossref_primary_10_1088_1674_1056_26_3_030501 crossref_primary_10_1002_chin_201352269 |
| Cites_doi | 10.1103/PhysRevLett.100.018103 10.1529/biophysj.106.081224 10.1107/S0907444998009378 10.1016/0009-2614(87)80576-6 10.1021/jp0455430 10.1021/ja1114198 10.1021/cr00023a004 10.1063/1.477419 10.1038/72440 10.1103/PhysRevLett.108.108102 10.1007/978-3-540-38448-9 10.1063/1.2186639 10.1063/1.1738640 10.1021/ct3008556 10.1063/1.475562 10.1063/1.2212942 10.1063/1.2234477 10.1021/ja711239h 10.1002/0471231509.ch1 10.1126/science.3810157 10.1103/PhysRevLett.86.2050 10.1021/ja909347x 10.1063/1.431685 10.1021/ja050581y 10.1063/1.1562614 10.1103/PhysRevLett.94.018104 10.1016/j.cplett.2007.05.003 10.1016/S0009-2614(97)01074-9 10.1021/ja204042f 10.1002/jcc.20614 10.1016/S0009-2614(89)87314-2 10.1016/S0009-2614(99)01123-9 10.1146/annurev.physchem.040808.090412 10.1021/ct300128x |
| ContentType | Journal Article |
| Copyright | COPYRIGHT 2013 NRC Research Press Copyright Canadian Science Publishing NRC Research Press Sep 2013 2013 Published by NRC Research Press |
| Copyright_xml | – notice: COPYRIGHT 2013 NRC Research Press – notice: Copyright Canadian Science Publishing NRC Research Press Sep 2013 – notice: 2013 Published by NRC Research Press |
| DBID | AAYXX CITATION ISN ISR |
| DOI | 10.1139/cjc-2012-0391 |
| DatabaseName | CrossRef Gale In Context: Canada Gale In Context: Science |
| DatabaseTitle | CrossRef |
| DatabaseTitleList | CrossRef |
| DeliveryMethod | fulltext_linktorsrc |
| Discipline | Chemistry |
| EISSN | 1480-3291 |
| EndPage | 774 |
| ExternalDocumentID | 3077404551 A351612813 10_1139_cjc_2012_0391 cjc-2012-0391 |
| Genre | Feature |
| GeographicLocations | China |
| GeographicLocations_xml | – name: China |
| GroupedDBID | 02 0R 1AW 29B 3V. 4.4 4P2 53G 5GY 5RP 88I 8AF 8AO 8FE 8FG 8FH 8FQ 8G5 9M8 AAIKC ABDBF ABDEX ABEFU ABFLS ABJCF ABPPZ ABPTK ABUWG ACDCL ACGFS ACGOD ACIWK ACNCT ADACO ADKZR AENEX AETEA AFFNX AFKRA AFMIJ AGCDD ALMA_UNASSIGNED_HOLDINGS AZQEC BCR BENPR BES BGLVJ BHPHI BKSAR BLC BPHCQ CAG COF CS3 D0S D1I D8U DWQXO DZ EAD EAP EAS EBC EBD EBS ECC EDH EJD EMK EPL EST ESX F20 F5P G8K GNUQQ GUQSH HCIFZ HH5 HZ H~9 I-F IAO ICQ IEA IGS IOF ISE ISN ISR ITC KB. L7B LK5 M2O M2P M2Q M3C M3G M7R MBDVC MV1 MVM MYA NMEPN NRXXU NYCZX O9- OHM OHT OK1 OVD P2P PADUT PCBAR PDBOC PQEST PQQKQ PQUKI PRG PRINS PROAC QF4 QM9 QN7 QO4 QRP R.V RIG RNS RRCRK RRP S10 SJN TAE TN5 TUS TWZ U5U UHB VOH WH7 X XFK XHC XJT ZCG ZE2 ZKB ZY4 -DZ -~X 00T 0R~ 6J9 6P2 6TJ AAMNW AAYXX ABDPE ABJNI ACGFO ACUHS AEGXH AEUYN AIAGR CCPQU CITATION DATHI HZ~ IPNFZ ML- ONR PHGZM PHGZT PQGLB PV9 RZL TEORI XOL ~02 AAYOK |
| ID | FETCH-LOGICAL-c534t-e0958c867f760fbd8ac64f95d45f1d022b5dde80cc714d8c7867897197a864cb3 |
| ISSN | 0008-4042 |
| IngestDate | Sat Aug 16 15:22:21 EDT 2025 Fri Aug 15 23:11:35 EDT 2025 Tue Mar 18 23:56:37 EDT 2025 Fri Mar 14 03:14:43 EDT 2025 Wed Mar 12 02:17:45 EDT 2025 Sat Mar 08 18:29:53 EST 2025 Wed Mar 05 04:25:34 EST 2025 Wed Mar 05 05:20:21 EST 2025 Tue Aug 05 12:02:41 EDT 2025 Thu Apr 24 23:06:22 EDT 2025 Wed Nov 11 00:35:05 EST 2020 |
| IsPeerReviewed | true |
| IsScholarly | true |
| Issue | 9 |
| Language | English |
| License | http://www.nrcresearchpress.com/page/about/CorporateTextAndDataMining |
| LinkModel | OpenURL |
| MergedId | FETCHMERGED-LOGICAL-c534t-e0958c867f760fbd8ac64f95d45f1d022b5dde80cc714d8c7867897197a864cb3 |
| Notes | SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-1 ObjectType-Feature-2 |
| PQID | 1434153864 |
| PQPubID | 47615 |
| PageCount | 6 |
| ParticipantIDs | gale_infotraccpiq_351612813 gale_infotracgeneralonefile_A351612813 crossref_citationtrail_10_1139_cjc_2012_0391 crossref_primary_10_1139_cjc_2012_0391 gale_incontextgauss_ISR_A351612813 gale_incontextgauss_ISN_A351612813 gale_infotracacademiconefile_A351612813 nrcresearch_primary_10_1139_cjc_2012_0391 proquest_journals_1434153864 proquest_journals_2423818641 gale_infotracmisc_A351612813 |
| PublicationCentury | 2000 |
| PublicationDate | 2013-09-01 |
| PublicationDateYYYYMMDD | 2013-09-01 |
| PublicationDate_xml | – month: 09 year: 2013 text: 2013-09-01 day: 01 |
| PublicationDecade | 2010 |
| PublicationPlace | Ottawa |
| PublicationPlace_xml | – name: Ottawa |
| PublicationTitle | Canadian journal of chemistry |
| PublicationYear | 2013 |
| Publisher | NRC Research Press Canadian Science Publishing NRC Research Press |
| Publisher_xml | – name: NRC Research Press – name: Canadian Science Publishing NRC Research Press |
| References | refg18/ref18 refg20/ref20 refg22/ref22 refg31/ref31 refg9/ref9 refg11/ref11 refg25/ref25 refg6/ref6 refg15/ref15 refg29/ref29 refg34/ref34 refg26/ref26 refg14/ref14 refg8/ref8 refg5/ref5 refg2/ref2 refg23/ref23 refg17/ref17 refg19/ref19 refg30/ref30 refg21/ref21 refg7/ref7 refg4/ref4 refg12/ref12 refg1/ref1 refg28/ref28 refg32/ref32 refg3/ref3 refg24/ref24 refg16/ref16 E W. (refg10/ref10) 2005; 109 refg33/ref33 refg13/ref13 refg27/ref27 |
| References_xml | – ident: refg25/ref25 doi: 10.1103/PhysRevLett.100.018103 – ident: refg30/ref30 doi: 10.1529/biophysj.106.081224 – ident: refg1/ref1 doi: 10.1107/S0907444998009378 – ident: refg9/ref9 doi: 10.1016/0009-2614(87)80576-6 – volume: 109 start-page: 6688 year: 2005 ident: refg10/ref10 publication-title: J. Phys. Chem. B doi: 10.1021/jp0455430 – ident: refg22/ref22 doi: 10.1021/ja1114198 – ident: refg2/ref2 doi: 10.1021/cr00023a004 – ident: refg7/ref7 doi: 10.1063/1.477419 – ident: refg28/ref28 doi: 10.1038/72440 – ident: refg33/ref33 doi: 10.1103/PhysRevLett.108.108102 – ident: refg3/ref3 doi: 10.1007/978-3-540-38448-9 – ident: refg21/ref21 doi: 10.1063/1.2186639 – ident: refg16/ref16 doi: 10.1063/1.1738640 – ident: refg34/ref34 doi: 10.1021/ct3008556 – ident: refg12/ref12 doi: 10.1063/1.475562 – ident: refg11/ref11 doi: 10.1063/1.2212942 – ident: refg14/ref14 doi: 10.1063/1.2234477 – ident: refg32/ref32 doi: 10.1021/ja711239h – ident: refg13/ref13 doi: 10.1002/0471231509.ch1 – ident: refg8/ref8 doi: 10.1126/science.3810157 – ident: refg20/ref20 doi: 10.1103/PhysRevLett.86.2050 – ident: refg24/ref24 doi: 10.1021/ja909347x – ident: refg5/ref5 doi: 10.1063/1.431685 – ident: refg29/ref29 doi: 10.1021/ja050581y – ident: refg15/ref15 doi: 10.1063/1.1562614 – ident: refg17/ref17 doi: 10.1103/PhysRevLett.94.018104 – ident: refg26/ref26 doi: 10.1016/j.cplett.2007.05.003 – ident: refg19/ref19 doi: 10.1016/S0009-2614(97)01074-9 – ident: refg23/ref23 doi: 10.1021/ja204042f – ident: refg31/ref31 doi: 10.1002/jcc.20614 – ident: refg4/ref4 doi: 10.1016/S0009-2614(89)87314-2 – ident: refg18/ref18 doi: 10.1016/S0009-2614(99)01123-9 – ident: refg6/ref6 doi: 10.1146/annurev.physchem.040808.090412 – ident: refg27/ref27 doi: 10.1021/ct300128x |
| SSID | ssj0007025 |
| Score | 1.9949297 |
| SecondaryResourceType | review_article |
| Snippet | Techniques of rare event dynamics were reviewed, including string methods, which will be implemented with the biochemical simulation packages. The existing... |
| SourceID | proquest gale crossref nrcresearch |
| SourceType | Aggregation Database Enrichment Source Index Database Publisher |
| StartPage | 769 |
| SubjectTerms | Binding sites calculs d’énergie libre dynamique des événements rares Free energy free energy calculations Gibbs' free energy Insertion Membrane proteins Membranes Metabolism Molecular dynamics molecular dynamics simulations Peptides Properties Proteins protéines membranaires rare event dynamics Simulation simulations de la dynamique moléculaire Strings Thermodynamics umbrella sampling échantillonnage « parapluie |
| Title | Applications of rare event dynamics on the free energy calculations for membrane protein systems |
| URI | http://www.nrcresearchpress.com/doi/abs/10.1139/cjc-2012-0391 https://www.proquest.com/docview/1434153864 https://www.proquest.com/docview/2423818641 |
| Volume | 91 |
| hasFullText | 1 |
| inHoldings | 1 |
| isFullTextHit | |
| isPrint | |
| link | http://utb.summon.serialssolutions.com/2.0.0/link/0/eLvHCXMwnV3db9MwELfQ9gA8ID7FWEEWQkNomDWJkziPXWEqIFVibKI8hcSxyxBLRtu88NdzFztprHV8vURVfLJc3y_2nX33O0Kehb7yuSo0E1xrxmWiGBj1AdORp_M8ypDDDqMtptHklL-bhbN1QGaTXbLKX8mfG_NK_ker8A70ilmy_6DZrlN4Ab9Bv_AEDcPzr3Q86t0-o9W3wDCuhpJpvzCV5tvLgH29UNBkEv1ALbJuY-AwzPBcnYPTXGLOVIXVLy2_87JvuXY0Bj2uCdlWi1sfy5ul43Ndsvd1h7tPyqSzV-WcfWj3Sgz6qRsN1xWb1R2QzInspM7OGIbc9o8lsERE0j-WmB6Pu9hBJ5rErMIC_FburMKmZpdFW9JbUmNTyuXyUh8gU6r8JgESGF4S2B5c9uxREIJN6wssbLztxzFe5W-PDl8fHnX7dTz0TZ0LO6qWiTVIDpzeHcvF7t83y4W0rExfL-3mjYlycpvcsr4FHRmg3CHXVHmXXB-3SrpHvvQBQytNETC0AQxtAUOrkgJgKAKGGsDQPmAoAIa2gKEWMNQC5j45PXpzMp4wW2KDyTDgK6bAwhZSRLGOo6HOC5HJiOskLHiovQLsuzyE_U8MpYw9XggZg6hIYi-JMxFxmQcPyFZZleohoVzLHHzhYRD4knNfJ5InQSKUBJc5ivNoh7xspy-Vln8ey6B8Txs_NEhSmO0UZzvF2d4he534hSFeuUrwKeoiRTKTEqOl5lm9XKZvP07TtfKvFDp2hJ5bIV3ByGRmM1Tg_yFJmiO560jKi7Mfaa91z2mdGwL5Td0MHEFAg3SaX_Tg9adZGLTgS-06sAS3HmxUsGgivrEZXSkktOTeo98PZJfcWH_iA7K1WtTqMdjiq_yJ_Zh-AX-q3nQ |
| linkProvider | EBSCOhost |
| openUrl | ctx_ver=Z39.88-2004&ctx_enc=info%3Aofi%2Fenc%3AUTF-8&rfr_id=info%3Asid%2Fsummon.serialssolutions.com&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.genre=article&rft.atitle=Applications+of+rare+event+dynamics+on+the+free+energy+calculations+for+membrane+protein+systems&rft.jtitle=Canadian+journal+of+chemistry&rft.au=Wang%2C+Yun-Kun&rft.au=Wei%2C+Dong-Qing&rft.au=Gu%2C+Ruo-Xu&rft.au=Fan%2C+Huai-Meng&rft.date=2013-09-01&rft.pub=NRC+Research+Press&rft.issn=0008-4042&rft.volume=91&rft.issue=9&rft.spage=769&rft_id=info:doi/10.1139%2Fcjc-2012-0391&rft.externalDocID=A351612813 |
| thumbnail_l | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/lc.gif&issn=0008-4042&client=summon |
| thumbnail_m | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/mc.gif&issn=0008-4042&client=summon |
| thumbnail_s | http://covers-cdn.summon.serialssolutions.com/index.aspx?isbn=/sc.gif&issn=0008-4042&client=summon |