Article

Open source platform for the execution and analysis of mechanical refolding experiments.

Department of Biochemistry G.Moruzzi, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy.
Bioinformatics (impact factor: 5.47). 02/2011; 27(3):423-5. DOI:10.1093/bioinformatics/btq663 pp.423-5
Source: PubMed

ABSTRACT Single-molecule force spectroscopy has facilitated the experimental investigation of biomolecular force-coupled kinetics, from which the kinetics at zero force can be extrapolated via explicit theoretical models. The atomic force microscope (AFM) in particular is routinely used to study protein unfolding kinetics, but only rarely protein folding kinetics. The discrepancy arises because mechanical protein refolding studies are more technically challenging.
We developed software that can drive and analyse mechanical refolding experiments when used with the commercial AFM setup 'Picoforce AFM', Bruker (previously Digital Instruments). We expect the software to be easily adaptable to other AFM setups. We also developed an improved method for the statistical characterization of protein folding kinetics, and implemented it into an AFM-independent software module.
Software and documentation are available at http://code.google.com/p/refolding under Apache License 2.0.

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Data provided are for informational purposes only. Although carefully collected, accuracy cannot be guaranteed. The impact factor represents a rough estimation of the journal's impact factor and does not reflect the actual current impact factor. Publisher conditions are provided by RoMEO. Differing provisions from the publisher's actual policy or licence agreement may be applicable.

Keywords

adaptable
 
AFM
 
AFM setups
 
AFM-independent software module
 
analyse mechanical refolding experiments
 
Apache License 2.0
 
atomic force microscope
 
biomolecular force-coupled kinetics
 
commercial AFM setup 'Picoforce AFM'
 
Digital Instruments
 
discrepancy
 
experimental investigation
 
explicit theoretical models
 
improved method
 
mechanical protein refolding studies
 
protein folding kinetics
 
Single-molecule force spectroscopy