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Probing Transient Partial Unfolding in Proteins by Native-State Proteolysis
Chiwook Park 한국구조생물학회 2014 Biodesign Vol.2 No.4
Even under native conditions, proteins can have various non-native conformations, which are in equilibrium with the native functional conformations. Though the populations of the non-native conformation are usually small under native conditions, knowledge of the energy and the structure of the non-native forms is critical in understanding how proteins acquire and lose their structures. Native-state proteolysis is an experimental approach to selectively investigate a dominant partially unfolded form using proteolysis as a structural probe. From analyzing the kinetics of proteolysis of a protein under native conditions, we determine the energetics of unfolding to the partially unfolded form. The effect of urea on the energetics of partial unfolding reports the degree of unfolding in the partially unfolded form. Also, by assessing the effect of a point mutation on the energetics of partial unfolding, we elucidate the structure of the partially unfolded form. Partially unfolded forms probed by native-state proteolysis provide valuable information on the mechanisms of protein folding and protein degradation. In this review, we survey the principle and the applications of native-state proteolysis and also examine the pros and cons of the method in comparison with other experimental approaches.
Baek, Minkyung,Park, Taeyong,Heo, Lim,Park, Chiwook,Seok, Chaok Oxford University Press 2017 Nucleic acids research Vol.45 No.w1
<P><B>Abstract</B></P><P>Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions and their regulation. Currently available web servers predict protein homo-oligomer structures either by template-based modeling using homo-oligomer templates selected from the protein structure database or by <I>ab initio</I> docking of monomer structures resolved by experiment or predicted by computation. The GalaxyHomomer server, freely accessible at http://galaxy.seoklab.org/homomer, carries out template-based modeling, <I>ab initio</I> docking or both depending on the availability of proper oligomer templates. It also incorporates recently developed model refinement methods that can consistently improve model quality. Moreover, the server provides additional options that can be chosen by the user depending on the availability of information on the monomer structure, oligomeric state and locations of unreliable/flexible loops or termini. The performance of the server was better than or comparable to that of other available methods when tested on benchmark sets and in a recent CASP performed in a blind fashion.</P>