Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
Identifieur interne : 000681 ( Ncbi/Checkpoint ); précédent : 000680; suivant : 000682Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning
Auteurs : Lane W. Votapka ; Rommie E. AmaroSource :
- PLoS Computational Biology [ 1553-734X ] ; 2015.
Abstract
The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations. The rate constants found using this method agreed well with experimentally and theoretically obtained values. We predicted the association rate of a small charged molecule toward both a charged and an uncharged spherical receptor and verified the estimated value with Smoluchowski theory. We also calculated the kon rate constant for superoxide dismutase with its natural substrate, O2−, in a validation of a previous experiment using similar methods but with a number of important improvements. We also calculated the kon for a new system: the N-terminal domain of Troponin C with its natural substrate Ca2+. The kon calculated for the latter two systems closely resemble experimentally obtained values. This novel multiscale approach is computationally cheaper and more parallelizable when compared to other methods of similar accuracy. We anticipate that this methodology will be useful for predicting kinetic rate constants and for understanding the process of binding between a small molecule and a protein receptor.
Url:
DOI: 10.1371/journal.pcbi.1004381
PubMed: 26505480
PubMed Central: 4624728
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning</title><author><name sortKey="Votapka, Lane W" sort="Votapka, Lane W" uniqKey="Votapka L" first="Lane W." last="Votapka">Lane W. Votapka</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E." last="Amaro">Rommie E. Amaro</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26505480</idno><idno type="pmc">4624728</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4624728</idno><idno type="RBID">PMC:4624728</idno><idno type="doi">10.1371/journal.pcbi.1004381</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000118</idno><idno type="wicri:Area/Pmc/Curation">000118</idno><idno type="wicri:Area/Pmc/Checkpoint">000082</idno><idno type="wicri:Area/Ncbi/Merge">000681</idno><idno type="wicri:Area/Ncbi/Curation">000681</idno><idno type="wicri:Area/Ncbi/Checkpoint">000681</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning</title><author><name sortKey="Votapka, Lane W" sort="Votapka, Lane W" uniqKey="Votapka L" first="Lane W." last="Votapka">Lane W. Votapka</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Amaro, Rommie E" sort="Amaro, Rommie E" uniqKey="Amaro R" first="Rommie E." last="Amaro">Rommie E. Amaro</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS Computational Biology</title><idno type="ISSN">1553-734X</idno><idno type="eISSN">1553-7358</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The kinetic rate constants of binding were estimated for four biochemically relevant molecular systems by a method that uses milestoning theory to combine Brownian dynamics simulations with more detailed molecular dynamics simulations. The rate constants found using this method agreed well with experimentally and theoretically obtained values. We predicted the association rate of a small charged molecule toward both a charged and an uncharged spherical receptor and verified the estimated value with Smoluchowski theory. We also calculated the k<sub>on</sub> rate constant for superoxide dismutase with its natural substrate, O<sub>2</sub><sup>−</sup>, in a validation of a previous experiment using similar methods but with a number of important improvements. We also calculated the k<sub>on</sub> for a new system: the N-terminal domain of Troponin C with its natural substrate Ca<sup>2+</sup>. The k<sub>on</sub> calculated for the latter two systems closely resemble experimentally obtained values. This novel multiscale approach is computationally cheaper and more parallelizable when compared to other methods of similar accuracy. We anticipate that this methodology will be useful for predicting kinetic rate constants and for understanding the process of binding between a small molecule and a protein receptor.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Bar Even, A" uniqKey="Bar Even A">A Bar-Even</name></author><author><name sortKey="Noor, E" uniqKey="Noor E">E Noor</name></author><author><name sortKey="Savir, Y" uniqKey="Savir Y">Y Savir</name></author><author><name sortKey="Liebermeister, W" uniqKey="Liebermeister W">W Liebermeister</name></author><author><name sortKey="Davidi, D" uniqKey="Davidi D">D Davidi</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Copeland, Ra" uniqKey="Copeland R">RA Copeland</name></author><author><name sortKey="Pompliano, Dl" uniqKey="Pompliano D">DL Pompliano</name></author><author><name sortKey="Meek, Td" uniqKey="Meek T">TD 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Amaro</name><name sortKey="Votapka, Lane W" sort="Votapka, Lane W" uniqKey="Votapka L" first="Lane W." last="Votapka">Lane W. Votapka</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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