Anisotropy
and Polarization 
Index 
References Anisotropy
and Polarization Index References
Dynamics of Protein Folding
The use of fluorescent spectroscopy to study protein folding kinetics has a long history, and is a fairly broad subject. This page briefly describes a single example only, a relatively new fast measurement technique, picosecond/nanosecond time resolved decay data acquisition, which can be used to provide detailed physical information on the early stages of protein folding.
In this technique, the laser-induced fluorescence can be monitored for up to 60,000 pulses, which corresponds to one millisecond. By studying how the fluorescence decays over time, one can tell how the amino acids are coming together during folding and how different parts of the protein are moving around. Fast measurement techniques can identify events occurring within nanoseconds.
To study how proteins fold, first they need to be unfoldeded. This is done by supercooling the proteins in an aqueous solution. Then, to initiate the folding, the solution is heated rapidly by a single pulse from an infrared laser. As the proteins begin folding into their native structure, a series of pulses from an ultraviolet laser causes the aromatic amino acids to fluoresce. This can reveal a time-sequence of folding events.
Folding of Apomyoglobin
In experiments conducted on the small, oxygen-carrying protein apomyoglobin (shown below), it has been found that the initial steps of helix formation can occur within several hundred nanoseconds. The entire collapse to a compact structure appears nearly complete after just a few microseconds.
Two distinct phases in the folding process have been identified from time resolved decay acquisitions:
In the first phase, which lasts several
hundred nanoseconds, the amino acids quickly fold into
helixes. In the second phase, which takes three to
four microseconds, the helixes search and fit into their
appropriate locations in the protein chain. At that point,
the collapse phase of the folding process is complete.From these experiments it appears that protein folding is not a slow and inefficient process. At the observed time range of microseconds, protein folding appears to be highly efficient.
With this fast picosecond/nanosecond detection and measurement scheme, time-resolved information about the the exact nature of the folding sequencre can be obtained, which can help to answer such questions as whether the folding begins with an initial random collapse of the protein structure or with the formation of helices.
Follow the appropriate PDB link in the PDBsum
database, and download the coordinate file of apomyoglobin (1bvc).
You can examine in
Rasmol, which residues may have contributed to the fluorescence
of this protein in the fast folding experiments described above.
Consider all possible intrinsic fluorophores.
