Conformational change
Encyclopedia
A macromolecule is usually flexible and dynamic. It can change its shape 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 conformational change. A macromolecular conformational change may be induced by many factors such as a change in temperature, pH, voltage, ion concentration, phosphorylation, or the binding of a ligand
.
Many biophysical techniques such as crystallography
, NMR
, electron paramagnetic resonance
(EPR) using Spin label
techniques, Circular Dichroism (CD), Hydrogen Exchange, and FRET can be used to study macromolecular conformational change. Dual Polarisation Interferometry
is a benchtop technique capable of measuring conformational changes in biomolecules in real time at very high resolution.
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 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.
Ligand
In coordination chemistry, a ligand is an ion or molecule that binds to a central metal atom to form a coordination complex. The bonding between metal and ligand generally involves formal donation of one or more of the ligand's electron pairs. The nature of metal-ligand bonding can range from...
.
Many biophysical techniques such as crystallography
Crystallography
Crystallography is the experimental science of the arrangement of atoms in solids. The word "crystallography" derives from the Greek words crystallon = cold drop / frozen drop, with its meaning extending to all solids with some degree of transparency, and grapho = write.Before the development of...
, NMR
NMR
NMR may refer to:Applications of Nuclear Magnetic Resonance:* Nuclear magnetic resonance* NMR spectroscopy* Solid-state nuclear magnetic resonance* Protein nuclear magnetic resonance spectroscopy* Proton NMR* Carbon-13 NMR...
, electron paramagnetic resonance
Electron paramagnetic resonance
Electron paramagnetic resonance or electron spin resonance spectroscopyis a technique for studying chemical species that have one or more unpaired electrons, such as organic and inorganic free radicals or inorganic complexes possessing a transition metal ion...
(EPR) using Spin label
Spin label
A spin label is an organic molecule which possesses an unpaired electron, usually on a nitrogen atom, and the ability to bind to another molecule. Spin labels are normally used as tools for probing proteins or biological membrane-local dynamics using EPR spectroscopy. The site-directed spin...
techniques, Circular Dichroism (CD), Hydrogen Exchange, and FRET can be used to study macromolecular conformational change. Dual Polarisation Interferometry
Dual Polarisation Interferometry
Dual polarization interferometry is an analytical technique that can probe molecular scale layers adsorbed to the surface of a waveguide by using the evanescent wave of a laser beam confined to the waveguide...
is a benchtop technique capable of measuring conformational changes in biomolecules in real time at very high resolution.
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 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.
External links
- Book Chapter on Protein Motions from website of RH Austin http://www.physics.princeton.edu/~austin/ at Princeton UniversityPrinceton UniversityPrinceton University is a private research university located in Princeton, New Jersey, United States. The school is one of the eight universities of the Ivy League, and is one of the nine Colonial Colleges founded before the American Revolution....
- Frauenfelder, H. New looks at protein motions Nature 338, 623 - 624 (20 April 1989).
- http://scitation.aip.org/vsearch/servlet/VerityServlet?KEY=VIRT02&smode=strresults&CURRENT=&ONLINE=YES&SMODE=&ver=&sti=&possible1=&possible1zone=article&bool1=and&possible2=&possible2zone=multi&bool4=and&possible4=salafsky&possible4zone=author&sort=chron&maxdisp=25&threshold=0&%5Bsearch%5D.x=0&%5Bsearch%5D.y=0&frommonth=&fromday=&fromyear=&tomonth=&today=&toyear=&fromvolume=&fromissue=&tovolume=&toissue=&page=1&origquery=&vdk_query=&chapter=0&docdisp=0Detection of Protein Conformational Change by Optical Second-Harmonic Generation]
- Biodesy
See also
- The Database of Macromolecular Motions (molmovdb)
- Protein dynamics
- Database of protein conformational diversityDatabase of protein conformational diversityThe Database of protein conformational diversity is a database of diversity of protein tertiary structures within protein domains as determined by X-ray crystallography. Proteins are inherently flexible and this database collects information on this subject for use in molecular research...