A postreductionist framework for protein biochemistry

TY - JOUR

T1 - A postreductionist framework for protein biochemistry

AU - Laue, Tom

AU - Demeler, Borries

N1 - Funding Information: One key tool will be fluorescence-detected sedimentation (FDS) using an analytical ultracentrifuge14. This instrument allows the chemical potential of one component to be monitored in a complex, concentrated fluid. Both thermodynamic15 and hydrodynamic16 information may be obtained by FDS with a small volume (100 μl) of sample and a minimum of sample manipulation. For biological fluids (for example, plasma), there is little disruption of the native environment, and the interactions of a labeled molecule with other, unlabeled plasma components may be detected16. Cohort interactions also may be detected14. For cellular samples, cell disruption is required, thus changing the native protein’s native environment. With this caveat, FDS is useful for characterizing complexes and cohort interactions in cell extracts14. However, the development of FDS is a good example of the challenges facing the new instrumentation needed for postreductionist biochemistry. The difficulty FDS faced is that it requires an analytical ultracentrifuge, an instrument that is viewed widely in biochemistry as archaic technology. Furthermore, the currently available instrument is not a suitable platform for the development of new optics, which leads to design compromises and the need for expensive, custom-made parts. Partly for these reasons, the instrument’s manufacturer announced in 2000 that it would no longer develop new optics for the analytical ultracentrifuge. Consequently, the prototype FDS instrument, which was developed in the late 1990s in an academic laboratory with US National Science Foundation and National Institutes of Health backing, required nearly eight years to commercialize. Without the possibility of ready commercialization and with analytical ultracentrifugation viewed as ‘old technology,’ National Science Foundation and National Institutes of Health funding for further developments ended. Meanwhile, there has been a thriving community of scientists advancing the analysis of sedimentation data. This community has developed time-derivative methods17, whole-boundary fitting methods based on efficient finite element solutions18, such as c(s)19, two-dimensional spectrum analysis20, genetic algorithms21 and high-performance computing22 for the analysis of sedimentation velocity data. Primarily, these analysis programs were developed for the analysis of simple, dilute solutions. The programs generally outstrip the capabilities of the older optical systems. Furthermore, the high cost of the FDS optical system limits the number of laboratories that have access to them. This is a shame because FDS could be a staple method for molecular and cell biologists. The relatively few published applications of FDS to complex, concentrated solutions have had to make use of the existing analysis programs and can only draw qualitative conclusions. To date, there has been limited program development to handle the FDS data from complex, concentrated solutions. It is likely that as the capabilities of FDS technology are recognized, this situation will change.

PY - 2011/6

Y1 - 2011/6

UR - http://www.scopus.com/inward/record.url?scp=79956144642&partnerID=8YFLogxK

U2 - 10.1038/nchembio.575

DO - 10.1038/nchembio.575

M3 - Comment/debate

AN - SCOPUS:79956144642

SN - 1552-4450

VL - 7

SP - 331

EP - 334

JO - Nature Chemical Biology

JF - Nature Chemical Biology

IS - 6

ER -