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Conformational change
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<h2 id="laboratory-analysis">Laboratory analysis</h2> <p>Many biophysical techniques such as <a href="/facts/Crystallography/9B5toeqG">crystallography</a>, <a href="/facts/NMR/pGYAn9Bz">NMR</a>, <a href="/facts/Electron_paramagnetic_resonance/TDHV8c9e">electron paramagnetic resonance</a> (EPR) using <a href="/facts/Spin_label/2KCmqQYG">spin label</a> techniques, <a href="/facts/Circular_dichroism/sMKgzpF2">circular dichroism (CD)</a>, <a href="/facts/Hydrogen-deuterium_exchange/fkp4fcQs">hydrogen exchange</a>, and <a href="/facts/F%25C3%25B6rster_resonance_energy_transfer/6dJTdAC6">FRET</a> can be used to study macromolecular conformational change. <a href="/facts/Dual-polarization_interferometry/opICunH9">Dual-polarization interferometry</a> is a benchtop technique capable of providing information about conformational changes in biomolecules.<a class="footnote-ref" id="fnref:3" href="#fn:3"><sup>3</sup></a> </p><p>A specific nonlinear optical technique called second-harmonic generation (SHG) has been recently applied to the study of conformational change in proteins.<a class="footnote-ref" id="fnref:4" href="#fn:4"><sup>4</sup></a> In this method, a second-harmonic-active probe is placed at a site that undergoes motion in the protein by mutagenesis or non-site-specific attachment, and the protein is adsorbed or specifically immobilized to a surface. A change in protein conformation produces a change in the net orientation of the dye relative to the surface plane and therefore the intensity of the second harmonic beam. In a protein sample with a well-defined orientation, the tilt angle of the probe can be quantitatively determined, in real space and real time. Second-harmonic-active unnatural amino acids can also be used as probes. </p><p>Another method applies <a href="/facts/Electro-switchable_biosurface/LsmMbfCH">electro-switchable biosurfaces</a> where proteins are placed on top of short DNA molecules which are then dragged through a buffer solution by application of alternating electrical potentials. By measuring their speed which ultimately depends on their hydrodynamic friction, conformational changes can be visualized. </p><p><a href="/facts/Biosensor/MaUAS0gD">"Nanoantennas" made out of DNA</a> – a novel type of nano-scale optical antenna – can be attached to proteins and produce a signal via <a href="/facts/Fluorescence/qsJVT2qP">fluorescence</a> for their distinct conformational changes.<a class="footnote-ref" id="fnref:5" href="#fn:5"><sup>5</sup></a><a class="footnote-ref" id="fnref:6" href="#fn:6"><sup>6</sup></a> </p> <h2 id="computational-analysis">Computational analysis</h2> <p><a href="/facts/X-ray_crystallography/WtI0F5DN">X-ray crystallography</a> can provide information about changes in conformation at the atomic level, but the expense and difficulty of such experiments make computational methods an attractive alternative.<a class="footnote-ref" id="fnref:7" href="#fn:7"><sup>7</sup></a> Normal <a href="/facts/Modal_analysis/BLxYhRcE">mode analysis</a> with elastic network models, such as the <a href="/facts/Gaussian_network_model/Kg220Imr">Gaussian network model</a>, can be used to probe <a href="/facts/Molecular_dynamics/yR3DNt6U">molecular dynamics</a> trajectories as well as known structures.<a class="footnote-ref" id="fnref:8" href="#fn:8"><sup>8</sup></a><a class="footnote-ref" id="fnref:9" href="#fn:9"><sup>9</sup></a> ProDy is a popular tool for such analysis.<a class="footnote-ref" id="fnref:10" href="#fn:10"><sup>10</sup></a> </p> <h2 id="examples">Examples</h2> <p>Conformational changes are important for: </p> <ul><li><a href="/facts/ABC_transporter/aXPf4sA9">ABC transporters</a> <a class="footnote-ref" id="fnref:11" href="#fn:11"><sup>11</sup></a></li> <li>catalysis<a class="footnote-ref" id="fnref:12" href="#fn:12"><sup>12</sup></a></li> <li>cellular locomotion and <a href="/facts/Motor_proteins/g5PE2m9F">motor proteins</a><a class="footnote-ref" id="fnref:13" href="#fn:13"><sup>13</sup></a></li> <li>formation of <a href="/facts/Protein_complexes/GW11Ee34">protein complexes</a><a class="footnote-ref" id="fnref:14" href="#fn:14"><sup>14</sup></a></li> <li><a href="/facts/Ion_channel/A46LARFH">ion channels</a><a class="footnote-ref" id="fnref:15" href="#fn:15"><sup>15</sup></a></li> <li><a href="/facts/Mechanoreceptor/rj6j4Nt3">mechanoreceptors</a> and <a href="/facts/Mechanotransduction/thwtBaQs">mechanotransduction</a><a class="footnote-ref" id="fnref:16" href="#fn:16"><sup>16</sup></a></li> <li>regulatory activity <a class="footnote-ref" id="fnref:17" href="#fn:17"><sup>17</sup></a></li> <li>transport of metabolites across <a href="/facts/Cell_membrane/vAXSD0DT">cell membranes</a> <a class="footnote-ref" id="fnref:18" href="#fn:18"><sup>18</sup></a><a class="footnote-ref" id="fnref:19" href="#fn:19"><sup>19</sup></a></li></ul> <h2 id="see-also">See also</h2> <ul><li><a href="/facts/Database_of_protein_conformational_diversity/xg8ctYCV">Database of protein conformational diversity</a></li> <li><a href="/facts/Protein_dynamics/YGd6hP9U">Protein dynamics</a></li> <li><a href="/facts/Molmovdb/k0HswqsF">The Database of Macromolecular Motions (molmovdb)</a></li></ul> <h2 id="external-links">External links</h2> <ul><li><a href="http://www.nature.com/nature/journal/v338/n6217/abs/338623a0.html">Frauenfelder, H. New looks at protein motions Nature 338, 623 - 624 (20 April 1989)</a>.</li> <li><a href="https://link.springer.com/article/10.1007%2Fs12566-012-0030-0">Sensing with electro-switchable biosurfaces</a></li></ul> <h2 id="references">References</h2> <ol> <li id="fn:1"><p>Bu Z, Callaway DJ (2011). "Proteins move! Protein dynamics and long-range allostery in cell signaling". Protein Structure and Diseases. Vol. 83. pp. 163–221. doi:10.1016/B978-0-12-381262-9.00005-7. ISBN 9780123812629. PMID 21570668. {{cite book}}: |journal= ignored (help) <a href="9780123812629" target="_blank">9780123812629</a> <a href="#fnref:1" class="footnote-back-ref">↩</a></p></li> <li id="fn:2"><p>Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T (December 2009). "Hidden alternative structures of proline isomerase essential for catalysis". Nature. 462 (7273): 669–73. Bibcode:2009Natur.462..669F. doi:10.1038/nature08615. PMC 2805857. PMID 19956261. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805857" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805857</a> <a href="#fnref:2" class="footnote-back-ref">↩</a></p></li> <li id="fn:3"><p>Freeman NJ, Peel LL, Swann MJ, Cross GH, Reeves A, Brand S, Lu JR (2004-06-19). "Real time, high resolution studies of protein adsorption and structure at the solid–liquid interface using dual polarization interferometry". Journal of Physics: Condensed Matter. 16 (26): S2493 – S2496. Bibcode:2004JPCM...16S2493F. doi:10.1088/0953-8984/16/26/023. ISSN 0953-8984. S2CID 250737643. <a href="https://iopscience.iop.org/article/10.1088/0953-8984/16/26/023" target="_blank">https://iopscience.iop.org/article/10.1088/0953-8984/16/26/023</a> <a href="#fnref:3" class="footnote-back-ref">↩</a></p></li> <li id="fn:4"><p>Salafsky JS, Cohen B (November 2008). "A second-harmonic-active unnatural amino acid as a structural probe of biomolecules on surfaces". The Journal of Physical Chemistry B. 112 (47): 15103–7. doi:10.1021/jp803703m. PMID 18928314. <a href="/wiki/Doi_(identifier)" target="_blank">/wiki/Doi_(identifier)</a> <a href="#fnref:4" class="footnote-back-ref">↩</a></p></li> <li id="fn:5"><p>"Chemists use DNA to build the world's tiniest antenna". University of Montreal. Retrieved 19 January 2022. <a href="https://phys.org/news/2022-01-chemists-dna-world-tiniest-antenna.html" target="_blank">https://phys.org/news/2022-01-chemists-dna-world-tiniest-antenna.html</a> <a href="#fnref:5" class="footnote-back-ref">↩</a></p></li> <li id="fn:6"><p>Harroun, Scott G.; Lauzon, Dominic; Ebert, Maximilian C. C. J. C.; Desrosiers, Arnaud; Wang, Xiaomeng; Vallée-Bélisle, Alexis (January 2022). "Monitoring protein conformational changes using fluorescent nanoantennas". Nature Methods. 19 (1): 71–80. doi:10.1038/s41592-021-01355-5. ISSN 1548-7105. PMID 34969985. S2CID 245593311. <a href="https://doi.org/10.1038%2Fs41592-021-01355-5" target="_blank">https://doi.org/10.1038%2Fs41592-021-01355-5</a> <a href="#fnref:6" class="footnote-back-ref">↩</a></p></li> <li id="fn:7"><p>Kim Y, Bigelow L, Borovilos M, Dementieva I, Duggan E, Eschenfeldt W, et al. (2008-01-01). "Chapter 3. High-throughput protein purification for x-ray crystallography and NMR". Advances in Protein Chemistry and Structural Biology. 75: 85–105. doi:10.1016/S0065-3233(07)75003-9. PMC 3366499. PMID 20731990. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366499" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3366499</a> <a href="#fnref:7" class="footnote-back-ref">↩</a></p></li> <li id="fn:8"><p>Tang QY, Kaneko K (February 2020). "Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis". PLOS Computational Biology. 16 (2): e1007670. Bibcode:2020PLSCB..16E7670T. doi:10.1371/journal.pcbi.1007670. PMC 7043781. PMID 32053592. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7043781" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7043781</a> <a href="#fnref:8" class="footnote-back-ref">↩</a></p></li> <li id="fn:9"><p>Zheng W, Doniach S (November 2003). "A comparative study of motor-protein motions by using a simple elastic-network model". Proceedings of the National Academy of Sciences of the United States of America. 100 (23): 13253–8. Bibcode:2003PNAS..10013253Z. doi:10.1073/pnas.2235686100. PMC 263771. PMID 14585932. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC263771" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC263771</a> <a href="#fnref:9" class="footnote-back-ref">↩</a></p></li> <li id="fn:10"><p>Bakan A, Meireles LM, Bahar I (June 2011). "ProDy: protein dynamics inferred from theory and experiments". Bioinformatics. 27 (11): 1575–7. doi:10.1093/bioinformatics/btr168. PMC 3102222. PMID 21471012. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102222" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3102222</a> <a href="#fnref:10" class="footnote-back-ref">↩</a></p></li> <li id="fn:11"><p>Ponte-Sucre A, ed. (2009). ABC Transporters in Microorganisms. Caister Academic. ISBN 978-1-904455-49-3. <a href="978-1-904455-49-3" target="_blank">978-1-904455-49-3</a> <a href="#fnref:11" class="footnote-back-ref">↩</a></p></li> <li id="fn:12"><p>Kamerlin SC, Warshel A (May 2010). "At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?". Proteins. 78 (6): 1339–75. doi:10.1002/prot.22654. PMC 2841229. PMID 20099310. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841229" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2841229</a> <a href="#fnref:12" class="footnote-back-ref">↩</a></p></li> <li id="fn:13"><p>Howard J (2001). Mechanics of motor proteins and the cytoskeleton (1st ed.). Sunderland,MA: Sinauer Associates. ISBN 9780878933334. <a href="9780878933334" target="_blank">9780878933334</a> <a href="#fnref:13" class="footnote-back-ref">↩</a></p></li> <li id="fn:14"><p>Callaway DJ, Matsui T, Weiss T, Stingaciu LR, Stanley CB, Heller WT, Bu Z (April 2017). "Controllable Activation of Nanoscale Dynamics in a Disordered Protein Alters Binding Kinetics". Journal of Molecular Biology. 429 (7): 987–998. doi:10.1016/j.jmb.2017.03.003. PMC 5399307. PMID 28285124. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5399307" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5399307</a> <a href="#fnref:14" class="footnote-back-ref">↩</a></p></li> <li id="fn:15"><p>Hille B (2001) [1984]. Ion Channels of Excitable Membranes (3rd ed.). Sunderland, Mass: Sinauer Associates, Inc. p. 5. ISBN 978-0-87893-321-1. <a href="978-0-87893-321-1" target="_blank">978-0-87893-321-1</a> <a href="#fnref:15" class="footnote-back-ref">↩</a></p></li> <li id="fn:16"><p>Nicholl ID, Matsui T, Weiss TM, Stanley CB, Heller WT, Martel A, et al. (August 2018). "α-Catenin Structure and Nanoscale Dynamics in Solution and in Complex with F-Actin". Biophysical Journal. 115 (4): 642–654. Bibcode:2018BpJ...115..642N. doi:10.1016/j.bpj.2018.07.005. hdl:2436/621755. PMC 6104293. PMID 30037495. <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104293" target="_blank">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6104293</a> <a href="#fnref:16" class="footnote-back-ref">↩</a></p></li> <li id="fn:17"><p>Donald V (2011). Biochemistry. Voet, Judith G. (4th ed.). Hoboken, NJ: John Wiley & Sons. ISBN 9780470570951. OCLC 690489261. <a href="9780470570951" target="_blank">9780470570951</a> <a href="#fnref:17" class="footnote-back-ref">↩</a></p></li> <li id="fn:18"><p>Kimball's Biology pages Archived 2009-01-25 at the Wayback Machine, Cell Membranes <a href="http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellMembranes.html" target="_blank">http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/CellMembranes.html</a> <a href="#fnref:18" class="footnote-back-ref">↩</a></p></li> <li id="fn:19"><p>Singleton P (1999). Bacteria in Biology, Biotechnology and Medicine (5th ed.). New York: Wiley. ISBN 978-0-471-98880-9. <a href="978-0-471-98880-9" target="_blank">978-0-471-98880-9</a> <a href="#fnref:19" class="footnote-back-ref">↩</a></p></li> </ol>