Simulation of fluorescence resonance energy transfer experiments: effect of the dyes on protein folding
Fluorescence resonance energy transfer is a powerful technique which is often used to probe the properties of proteins and complex macromolecules. The technique relies on relatively large fluorescent dyes which are engineered into the molecule of interest. In the case of small proteins, these dyes m...
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| Veröffentlicht in: | Journal of physics. Condensed matter 2010-06, Vol.22 (23), p.235103-235103 |
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| container_title | Journal of physics. Condensed matter |
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| creator | Allen, Lucy R Paci, Emanuele |
| description | Fluorescence resonance energy transfer is a powerful technique which is often used to probe the properties of proteins and complex macromolecules. The technique relies on relatively large fluorescent dyes which are engineered into the molecule of interest. In the case of small proteins, these dyes may affect the stability of the protein, and modify the folding kinetics and the folding mechanisms which are being probed. Here we use atomistic simulation to investigate the effect that commonly used fluorescent dyes have on the folding of a four-helix bundle protein. We show that, depending on where the dyes are attached, their effect on the kinetic and thermodynamic properties of the protein may be significant. We find that, while the overall folding mechanism is not affected by the dyes, they can destabilize, or even stabilize, intermediate states. |
| doi_str_mv | 10.1088/0953-8984/22/23/235103 |
| format | Article |
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The technique relies on relatively large fluorescent dyes which are engineered into the molecule of interest. In the case of small proteins, these dyes may affect the stability of the protein, and modify the folding kinetics and the folding mechanisms which are being probed. Here we use atomistic simulation to investigate the effect that commonly used fluorescent dyes have on the folding of a four-helix bundle protein. We show that, depending on where the dyes are attached, their effect on the kinetic and thermodynamic properties of the protein may be significant. We find that, while the overall folding mechanism is not affected by the dyes, they can destabilize, or even stabilize, intermediate states.</description><identifier>ISSN: 0953-8984</identifier><identifier>EISSN: 1361-648X</identifier><identifier>DOI: 10.1088/0953-8984/22/23/235103</identifier><identifier>PMID: 21393762</identifier><identifier>CODEN: JCOMEL</identifier><language>eng</language><publisher>Bristol: IOP Publishing</publisher><subject>Analytical, structural and metabolic biochemistry ; Biological and medical sciences ; Biophysics - methods ; Computer Simulation ; Fluorescence Resonance Energy Transfer - methods ; Fluorescent Dyes - chemistry ; Fluorescent Dyes - pharmacology ; Fundamental and applied biological sciences. 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We find that, while the overall folding mechanism is not affected by the dyes, they can destabilize, or even stabilize, intermediate states.</description><subject>Analytical, structural and metabolic biochemistry</subject><subject>Biological and medical sciences</subject><subject>Biophysics - methods</subject><subject>Computer Simulation</subject><subject>Fluorescence Resonance Energy Transfer - methods</subject><subject>Fluorescent Dyes - chemistry</subject><subject>Fluorescent Dyes - pharmacology</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>General aspects, investigation methods</subject><subject>Kinetics</subject><subject>Models, Molecular</subject><subject>Models, Theoretical</subject><subject>Molecular Conformation</subject><subject>Peptides - chemistry</subject><subject>Protein Folding</subject><subject>Proteins</subject><subject>Proteins - chemistry</subject><subject>Thermodynamics</subject><issn>0953-8984</issn><issn>1361-648X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2010</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqNkEuLFDEURoMoTjv6F4ZsxFXZeVRe7mTwBQMuVHAXUlX3tiXVSZlUgf3vTdHtuNCFEMhdnO9-3EPIDWcvObN2z5ySjXW23QuxF7I-xZl8QHZcat7o1n59SHb30BV5Usp3xlhrZfuYXAkunTRa7Mjh03hcp7CMKdKEFKc1ZSg9xB5oHVIM2wQR8uFElxxiQcgUfs6QxyPEpbyigAj9sqWXb0CHExRal805LTBGimkaxnh4Sh5hmAo8u_zX5MvbN59v3zd3H999uH191_StYEsjFDLsMWjeoWKohFFswMEoEUKHTBtnBoNCOhscKCdZcNwJFKFzTIeOyWvy4ry39v9YoSz-ONZzpilESGvxVmljONOqkvpM9jmVkgH9XE8K-eQ585tjv-nzmz4vhBfSnx3X4M2lYu2OMNzHfkutwPMLEEofJqzW-rH84YR1zLS6cvzMjWn-__Lm78y_WT8PKH8B0SKiKA</recordid><startdate>20100616</startdate><enddate>20100616</enddate><creator>Allen, Lucy R</creator><creator>Paci, Emanuele</creator><general>IOP Publishing</general><general>Institute of Physics</general><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope></search><sort><creationdate>20100616</creationdate><title>Simulation of fluorescence resonance energy transfer experiments: effect of the dyes on protein folding</title><author>Allen, Lucy R ; Paci, Emanuele</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c420t-25f0fcfa61bf50f52750dfd752aabf06797d7f2398a9e5930a9192f2ab906ab03</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2010</creationdate><topic>Analytical, structural and metabolic biochemistry</topic><topic>Biological and medical sciences</topic><topic>Biophysics - methods</topic><topic>Computer Simulation</topic><topic>Fluorescence Resonance Energy Transfer - methods</topic><topic>Fluorescent Dyes - chemistry</topic><topic>Fluorescent Dyes - pharmacology</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>General aspects, investigation methods</topic><topic>Kinetics</topic><topic>Models, Molecular</topic><topic>Models, Theoretical</topic><topic>Molecular Conformation</topic><topic>Peptides - chemistry</topic><topic>Protein Folding</topic><topic>Proteins</topic><topic>Proteins - chemistry</topic><topic>Thermodynamics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Allen, Lucy R</creatorcontrib><creatorcontrib>Paci, Emanuele</creatorcontrib><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><jtitle>Journal of physics. 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| ispartof | Journal of physics. Condensed matter, 2010-06, Vol.22 (23), p.235103-235103 |
| issn | 0953-8984 1361-648X |
| language | eng |
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| source | MEDLINE; Institute of Physics Journals |
| subjects | Analytical, structural and metabolic biochemistry Biological and medical sciences Biophysics - methods Computer Simulation Fluorescence Resonance Energy Transfer - methods Fluorescent Dyes - chemistry Fluorescent Dyes - pharmacology Fundamental and applied biological sciences. Psychology General aspects, investigation methods Kinetics Models, Molecular Models, Theoretical Molecular Conformation Peptides - chemistry Protein Folding Proteins Proteins - chemistry Thermodynamics |
| title | Simulation of fluorescence resonance energy transfer experiments: effect of the dyes on protein folding |
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