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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.
159:
A specific nonlinear optical technique called second-harmonic generation (SHG) has been recently applied to the study of conformational change in proteins. 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
20:
167:
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.
71:
A macromolecule is usually flexible and dynamic. Its shape can change in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a
193:
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. Normal
108:. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as
1079:
175:
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Harroun, Scott G.; Lauzon, Dominic; Ebert, Maximilian C. C. J. C.; Desrosiers, Arnaud; Wang, Xiaomeng; Vallée-Bélisle, Alexis (January 2022).
417:"Real time, high resolution studies of protein adsorption and structure at the solid–liquid interface using dual polarization interferometry"
267:
145:
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Salafsky JS, Cohen B (November 2008). "A second-harmonic-active unnatural amino acid as a structural probe of biomolecules on surfaces".
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Bu Z, Callaway DJ (2011). "Proteins move! Protein dynamics and long-range allostery in cell signaling".
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is a benchtop technique capable of providing information about conformational changes in biomolecules.
638:"Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis"
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830:"At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?"
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Kim Y, Bigelow L, Borovilos M, Dementieva I, Duggan E, Eschenfeldt W, et al. (2008-01-01).
904:"Controllable Activation of Nanoscale Dynamics in a Disordered Protein Alters Binding Kinetics"
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Nicholl ID, Matsui T, Weiss TM, Stanley CB, Heller WT, Martel A, et al. (August 2018).
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Callaway DJ, Matsui T, Weiss T, Stingaciu LR, Stanley CB, Heller WT, Bu Z (April 2017).
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trajectories as well as known structures. ProDy is a popular tool for such analysis.
981:"α-Catenin Structure and Nanoscale Dynamics in Solution and in Complex with F-Actin"
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Frauenfelder, H. New looks at protein motions Nature 338, 623 - 624 (20 April 1989)
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Freeman NJ, Peel LL, Swann MJ, Cross GH, Reeves A, Brand S, Lu JR (2004-06-19).
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Proceedings of the
National Academy of Sciences of the United States of America
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Change in the shape of a macromolecule, often induced by environmental factors
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Fraser JS, Clarkson MW, Degnan SC, Erion R, Kern D, Alber T (December 2009).
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360:"Hidden alternative structures of proline isomerase essential for catalysis"
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532:"Monitoring protein conformational changes using fluorescent nanoantennas"
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1048:. Voet, Judith G. (4th ed.). Hoboken, NJ: John Wiley & Sons.
958:(3rd ed.). Sunderland, Mass: Sinauer Associates, Inc. p. 5.
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756:"ProDy: protein dynamics inferred from theory and experiments"
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76:. Factors that may induce such changes include temperature,
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can be used to study macromolecular conformational change.
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506:"Chemists use DNA to build the world's tiniest antenna"
178:– can be attached to proteins and produce a signal via
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Advances in
Protein Chemistry and Structural Biology
881:(1st ed.). Sunderland,MA: Sinauer Associates.
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23:Conformational changes can elicit the motion of a
278:The Database of Macromolecular Motions (molmovdb)
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879:Mechanics of motor proteins and the cytoskeleton
1098:Bacteria in Biology, Biotechnology and Medicine
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268:Database of protein conformational diversity
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754:Bakan A, Meireles LM, Bahar I (June 2011).
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182:for their distinct conformational changes.
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421:Journal of Physics: Condensed Matter
124:Many biophysical techniques such as
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828:Kamerlin SC, Warshel A (May 2010).
636:Tang QY, Kaneko K (February 2020).
472:The Journal of Physical Chemistry B
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805:ABC Transporters in Microorganisms
307:10.1016/B978-0-12-381262-9.00005-7
301:. Vol. 83. pp. 163–221.
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1100:(5th ed.). New York: Wiley.
254:transport of metabolites across
154:Dual-polarization interferometry
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172:"Nanoantennas" made out of DNA
165:electro-switchable biosurfaces
64:is a change in the shape of a
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772:10.1093/bioinformatics/btr168
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174:– a novel type of nano-scale
908:Journal of Molecular Biology
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803:Ponte-Sucre A, ed. (2009).
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1005:10.1016/j.bpj.2018.07.005
920:10.1016/j.jmb.2017.03.003
225:cellular locomotion and
1146:Microbiology techniques
1077:Kimball's Biology pages
722:10.1073/pnas.2235686100
201:, can be used to probe
163:Another method applies
142:circular dichroism (CD)
41:protein domain dynamics
510:University of Montreal
199:Gaussian network model
186:Computational analysis
104:, or the binding of a
62:conformational change
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191:X-ray crystallography
74:conformational change
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1096:Singleton P (1999).
807:. Caister Academic.
251:regulatory activity
110:allosteric signaling
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985:Biophysical Journal
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433:2004JPCM...16S2493F
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384:10.1038/nature08615
376:2009Natur.462..669F
247:mechanotransduction
120:Laboratory analysis
1082:2009-01-25 at the
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203:molecular dynamics
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37:biological machine
1107:978-0-471-98880-9
1044:Donald V (2011).
965:978-0-87893-321-1
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599:: 85–105.
515:19 January
284:References
138:spin label
45:nanoscales
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343:ignored (
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262:See also
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517:2022
488:PMID
445:ISSN
398:PMID
345:help
321:PMID
311:ISBN
245:and
150:FRET
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1017:PMC
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