Brownian dynamics study of the interaction between plastocyanin and cytochrome f.
Identifieur interne : 004958 ( Main/Exploration ); précédent : 004957; suivant : 004959Brownian dynamics study of the interaction between plastocyanin and cytochrome f.
Auteurs : D C Pearson [États-Unis] ; E L GrossSource :
- Biophysical journal [ 0006-3495 ] ; 1998.
Descripteurs français
- KwdFr :
- Algorithmes (MeSH), Arbres (MeSH), Biophysique (MeSH), Concentration osmolaire (MeSH), Conformation des protéines (MeSH), Cytochromes (composition chimique), Cytochromes f (MeSH), Logiciel (MeSH), Légumes (MeSH), Modèles moléculaires (MeSH), Phénomènes biophysiques (MeSH), Plastocyanine (composition chimique), Structures macromoléculaires (MeSH), Thermodynamique (MeSH), Transport d'électrons (MeSH), Électricité statique (MeSH).
- MESH :
- composition chimique : Cytochromes, Plastocyanine.
- Algorithmes, Arbres, Biophysique, Concentration osmolaire, Conformation des protéines, Cytochromes f, Logiciel, Légumes, Modèles moléculaires, Phénomènes biophysiques, Structures macromoléculaires, Thermodynamique, Transport d'électrons, Électricité statique.
English descriptors
- KwdEn :
- Algorithms (MeSH), Biophysical Phenomena (MeSH), Biophysics (MeSH), Cytochromes (chemistry), Cytochromes f (MeSH), Electron Transport (MeSH), Macromolecular Substances (MeSH), Models, Molecular (MeSH), Osmolar Concentration (MeSH), Plastocyanin (chemistry), Protein Conformation (MeSH), Software (MeSH), Static Electricity (MeSH), Thermodynamics (MeSH), Trees (MeSH), Vegetables (MeSH).
- MESH :
Abstract
The electrostatic interaction between plastocyanin (PC) and cytochrome f (cyt f), electron transfer partners in photosynthesis was studied using Brownian dynamics (BD) simulations. By using the software package MacroDox, which implements the BD algorithm of Northrup et al. (Northrup, S. H., J. O. Boles, and J. C. L. Reynolds. 1987. J. Phys. Chem. 91:5991-5998), we have modeled the interaction of the two proteins based on crystal structures of poplar PC and turnip cyt f at pH 7 and a variety of ionic strengths. We find that the electrostatic attraction between positively charged residues (K58, K65, K187, and R209, among others) on cyt f and negatively charged residues (E43, D44, E59, and E60, among others) on PC steers PC into a single dominant orientation with respect to cyt f, and furthermore, that the single dominant orientation that we observe is one that we had predicted in our previous work (Pearson, D. C., E. L. Gross, and E. S. David. 1996. Biophys. J. 71:64-76). This dominant orientation permits the formation of hydrophobic interactions, which are not implemented in the MacroDox algorithm. This proposed complex between PC and cyt f implicates H87, a copper ligand on PC, as the residue that accepts electrons from the heme on cyt f (and possibly through Y1 as we proposed previously). We argue for the existence of this single dominant complex on the basis of observations that the most favorable orientations of the interaction between PC and cyt f, as determined by grouping successful BD trajectories on the basis of closest contacts of charged residues, tend to overlap one another and have very close distances between the metal centers on the two proteins (copper on PC, iron on cyt f). We use this knowledge to develop a model for PC/cyt f interaction that places a reaction between the two proteins occurring when the copper-to-iron distance is between 16 and 17 A. This reaction distance gives a good estimate of the experimentally observed rate constant for PC-cyt f interaction. Analysis of BD results as a function of ionic strength predicts an interaction that happens less frequently and becomes less specific as ionic strength increases.
DOI: 10.1016/S0006-3495(98)77714-8
PubMed: 9826593
PubMed Central: PMC1299944
Affiliations:
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of Biochemistry and Biophysics Program, The Ohio State University, Columbus</wicri:cityArea></affiliation></author><author><name sortKey="Gross, E L" sort="Gross, E L" uniqKey="Gross E" first="E L" last="Gross">E L Gross</name></author></analytic><series><title level="j">Biophysical journal</title><idno type="ISSN">0006-3495</idno><imprint><date when="1998" type="published">1998</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms (MeSH)</term><term>Biophysical Phenomena (MeSH)</term><term>Biophysics (MeSH)</term><term>Cytochromes (chemistry)</term><term>Cytochromes f (MeSH)</term><term>Electron Transport (MeSH)</term><term>Macromolecular Substances (MeSH)</term><term>Models, Molecular (MeSH)</term><term>Osmolar Concentration (MeSH)</term><term>Plastocyanin (chemistry)</term><term>Protein Conformation (MeSH)</term><term>Software (MeSH)</term><term>Static Electricity 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statique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The electrostatic interaction between plastocyanin (PC) and cytochrome f (cyt f), electron transfer partners in photosynthesis was studied using Brownian dynamics (BD) simulations. By using the software package MacroDox, which implements the BD algorithm of Northrup et al. (Northrup, S. H., J. O. Boles, and J. C. L. Reynolds. 1987. J. Phys. Chem. 91:5991-5998), we have modeled the interaction of the two proteins based on crystal structures of poplar PC and turnip cyt f at pH 7 and a variety of ionic strengths. We find that the electrostatic attraction between positively charged residues (K58, K65, K187, and R209, among others) on cyt f and negatively charged residues (E43, D44, E59, and E60, among others) on PC steers PC into a single dominant orientation with respect to cyt f, and furthermore, that the single dominant orientation that we observe is one that we had predicted in our previous work (Pearson, D. C., E. L. Gross, and E. S. David. 1996. Biophys. J. 71:64-76). This dominant orientation permits the formation of hydrophobic interactions, which are not implemented in the MacroDox algorithm. This proposed complex between PC and cyt f implicates H87, a copper ligand on PC, as the residue that accepts electrons from the heme on cyt f (and possibly through Y1 as we proposed previously). We argue for the existence of this single dominant complex on the basis of observations that the most favorable orientations of the interaction between PC and cyt f, as determined by grouping successful BD trajectories on the basis of closest contacts of charged residues, tend to overlap one another and have very close distances between the metal centers on the two proteins (copper on PC, iron on cyt f). We use this knowledge to develop a model for PC/cyt f interaction that places a reaction between the two proteins occurring when the copper-to-iron distance is between 16 and 17 A. This reaction distance gives a good estimate of the experimentally observed rate constant for PC-cyt f interaction. Analysis of BD results as a function of ionic strength predicts an interaction that happens less frequently and becomes less specific as ionic strength increases.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">9826593</PMID><DateCompleted><Year>1999</Year><Month>01</Month><Day>25</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Print">0006-3495</ISSN><JournalIssue CitedMedium="Print"><Volume>75</Volume><Issue>6</Issue><PubDate><Year>1998</Year><Month>Dec</Month></PubDate></JournalIssue><Title>Biophysical journal</Title><ISOAbbreviation>Biophys J</ISOAbbreviation></Journal><ArticleTitle>Brownian dynamics study of the interaction between plastocyanin and cytochrome f.</ArticleTitle><Pagination><MedlinePgn>2698-711</MedlinePgn></Pagination><Abstract><AbstractText>The electrostatic interaction between plastocyanin (PC) and cytochrome f (cyt f), electron transfer partners in photosynthesis was studied using Brownian dynamics (BD) simulations. By using the software package MacroDox, which implements the BD algorithm of Northrup et al. (Northrup, S. H., J. O. Boles, and J. C. L. Reynolds. 1987. J. Phys. Chem. 91:5991-5998), we have modeled the interaction of the two proteins based on crystal structures of poplar PC and turnip cyt f at pH 7 and a variety of ionic strengths. We find that the electrostatic attraction between positively charged residues (K58, K65, K187, and R209, among others) on cyt f and negatively charged residues (E43, D44, E59, and E60, among others) on PC steers PC into a single dominant orientation with respect to cyt f, and furthermore, that the single dominant orientation that we observe is one that we had predicted in our previous work (Pearson, D. C., E. L. Gross, and E. S. David. 1996. Biophys. J. 71:64-76). This dominant orientation permits the formation of hydrophobic interactions, which are not implemented in the MacroDox algorithm. This proposed complex between PC and cyt f implicates H87, a copper ligand on PC, as the residue that accepts electrons from the heme on cyt f (and possibly through Y1 as we proposed previously). We argue for the existence of this single dominant complex on the basis of observations that the most favorable orientations of the interaction between PC and cyt f, as determined by grouping successful BD trajectories on the basis of closest contacts of charged residues, tend to overlap one another and have very close distances between the metal centers on the two proteins (copper on PC, iron on cyt f). We use this knowledge to develop a model for PC/cyt f interaction that places a reaction between the two proteins occurring when the copper-to-iron distance is between 16 and 17 A. This reaction distance gives a good estimate of the experimentally observed rate constant for PC-cyt f interaction. Analysis of BD results as a function of ionic strength predicts an interaction that happens less frequently and becomes less specific as ionic strength increases.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Pearson</LastName><ForeName>D C</ForeName><Initials>DC</Initials><Suffix>Jr</Suffix><AffiliationInfo><Affiliation>Department of Biochemistry and Biophysics Program, The Ohio State University, Columbus, Ohio 43210 USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Gross</LastName><ForeName>E L</ForeName><Initials>EL</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Biophys 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