A new strategy to prevent degradation of recombinant proteins caused by non-specific cleavage by thrombin is described. We demonstrate that degradation due to non-specific cleavage of recombinant protein mediated by thrombin can be completely prevented by separation of thrombin from the recombinant protein on spin columns packed with heparin-sepharose. This method is generally applicable to all recombinant proteins that require the thrombin for the cleavage of affinity tags for purification. To our knowledge, this is the first report of an efficient and reliable method for the separation of residual thrombin from purified recombinant proteins.Keywords recombinant protein; thrombin; heparin; degradation; structure; non-specific Large scale production and purification of pure recombinant proteins is the first important step towards understanding their structure-function relationship [1,2]. In general, recombinant proteins are bioengineered with affinity tag either at their N-or C-terminus [2]. These affinity tags not only facilitate easy purification of recombinant proteins, but are also known to aid in overexpression of proteins in soluble forms [3]. To eliminate downstream interference, many fusion vectors are designed such that the fusion partner (affinity tag) can be easily eliminated from the protein of interest after cell lysis. This is most often accomplished by the insertion of a protease-specific cleavage site between the affinity tag and the recombinant protein of interest [3]. Thrombin is one of the common and popular restriction proteases used for removal of affinity tags from recombinant fusion proteins [4,5]. It is preferred to other restriction proteases due to its relatively low cost and optimum cleavage activity in the pH range of 6-8. Thrombin, an endoprotease, is known to preferentially recognize the -Leu-Val-Pro-Arg-Gly-Sersequence and cleave at the Arg-Gly bond [6]. Despite its extensive use, thrombin has been reported to non-specifically cleave at secondary sites located in some overexpressed recombinant proteins [6]. Non-specific cleavage mediated by thrombin is quite common. However, to date there is no efficient experimental procedure to prevent the undesired nonspecific cleavage of recombinant proteins caused by thrombin. Heterogeneous protein samples generated by non-specific thrombin catalyzed cleavage would pose a major hurdle for structural studies such as X-ray crystallography and NMR spectroscopy. In this study, we report a novel *To whom all correspondence should be addressed. Dr. Thallapuranam Krishnaswamy Suresh Kumar (Department of Chemistry & Biochemistry, University of Arkansas, Fayetteville, AR 72701). E-mail:sthalla@uark.edu, Fax: 479-575-5646, Phone: 479-575-4049. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in...