Reconciling the lock‐and‐key and dynamic views of canonical serine protease inhibitor action

The efficiency of canonical serine protease inhibitors is conventionally attributed to the rigidity of their protease binding loop with no conformational change upon enzyme binding, yielding an example of the lock‐and‐key model for biomolecular interactions. However, solution‐state structural studies revealed considerable flexibility in their protease binding loop. We resolve this apparent contradiction by showing that enzyme binding of small, 35‐residue inhibitors is actually a dynamic conformer selection process on the nanosecond‐timescale. Thus, fast timescale dynamics enables the association rate to be solely diffusion‐controlled just like in the rigid‐body model.

[1]  M. Mathieu,et al.  Complexation of Two Proteic Insect Inhibitors to the Active Site of Chymotrypsin Suggests Decoupled Roles for Binding and Selectivity* , 2001, The Journal of Biological Chemistry.

[2]  R. Huber,et al.  Natural protein proteinase inhibitors and their interaction with proteinases. , 1992, European journal of biochemistry.

[3]  G. Katona,et al.  Extended intermolecular interactions in a serine protease-canonical inhibitor complex account for strong and highly specific inhibition. , 2005, Journal of molecular biology.

[4]  Ivet Bahar,et al.  Principal component analysis of native ensembles of biomolecular structures (PCA_NEST): insights into functional dynamics , 2009, Bioinform..

[5]  L. Kay,et al.  Intrinsic dynamics of an enzyme underlies catalysis , 2005, Nature.

[6]  J. Otlewski,et al.  The many faces of protease–protein inhibitor interaction , 2005, The EMBO journal.

[7]  Michael Nilges,et al.  Flexibility and conformational entropy in protein-protein binding. , 2006, Structure.

[8]  B. Sarg,et al.  Functional aspects of the solution structure and dynamics of PAF – a highly‐stable antifungal protein from Penicillium chrysogenum , 2009, The FEBS journal.

[9]  X. Salvatella,et al.  The MUMO (minimal under-restraining minimal over-restraining) method for the determination of native state ensembles of proteins , 2007, Journal of biomolecular NMR.

[10]  Oliver F. Lange,et al.  Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution , 2008, Science.

[11]  W L Jorgensen,et al.  Rusting of the lock and key model for protein-ligand binding. , 1991, Science.

[12]  L. Gráf,et al.  When the surface tells what lies beneath: combinatorial phage-display mutagenesis reveals complex networks of surface-core interactions in the pacifastin protease inhibitor family. , 2007, Journal of molecular biology.

[13]  W. M. Westler,et al.  Local binding with globally distributed changes in a small protease inhibitor upon enzyme binding , 2006, The FEBS journal.

[14]  M. Gerstein,et al.  Conformational changes associated with protein-protein interactions. , 2004, Current opinion in structural biology.

[15]  Andrew L. Lee,et al.  Long-range dynamic effects of point mutations propagate through side chains in the serine protease inhibitor eglin c. , 2004, Biochemistry.

[16]  M. Cai,et al.  Solution structure and backbone dynamics of recombinant Cucurbita maxima trypsin inhibitor-V determined by NMR spectroscopy. , 1996, Biochemistry.

[17]  M. Qasim,et al.  What can the structures of enzyme-inhibitor complexes tell us about the structures of enzyme substrate complexes? , 2000, Biochimica et biophysica acta.

[18]  A. Fersht,et al.  Backbone dynamics of chymotrypsin inhibitor 2: effect of breaking the active site bond and its implications for the mechanism of inhibition of serine proteases. , 1995, Biochemistry.

[19]  C. Boudier,et al.  Stopped Flow Fluorescence Energy Transfer Measurement of the Rate Constants Describing the Reversible Formation and the Irreversible Rearrangement of the Elastase-α1-Proteinase Inhibitor Complex* , 1998, The Journal of Biological Chemistry.

[20]  J. Markley,et al.  Protein inhibitors of serine proteinases: role of backbone structure and dynamics in controlling the hydrolysis constant. , 2003, Biochemistry.

[21]  András Perczel,et al.  A simple fold with variations: the pacifastin inhibitor family , 2004, Bioinform..

[22]  E. Fischer.  Einfluss der Configuration auf die Wirkung der Enzyme , 1894 .

[23]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[24]  O. Prakash,et al.  NMR studies of internal dynamics of serine proteinase protein inhibitors: Binding region mobilities of intact and reactive‐site hydrolyzed Cucurbita maxima trypsin inhibitor (CMTI)‐III of the squash family and comparison with those of counterparts of CMTI‐V of the potato I family , 1998, Protein science : a publication of the Protein Society.

[25]  L. Gráf,et al.  Remarkable phylum selectivity of a Schistocerca gregaria trypsin inhibitor: the possible role of enzyme-inhibitor flexibility. , 2002, Archives of biochemistry and biophysics.

[26]  L. Gráf,et al.  Comparative structure analysis of proteinase inhibitors from the desert locust, Schistocerca gregaria. , 2002, European journal of biochemistry.

[27]  M. Karplus,et al.  A hierarchy of timescales in protein dynamics is linked to enzyme catalysis , 2007, Nature.

[28]  J. Hus,et al.  Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data , 2000, Journal of biomolecular NMR.

[29]  A. Nagy,et al.  Same fold with different mobility: backbone dynamics of small protease inhibitors from the desert locust, Schistocerca gregaria. , 2004, Biochemistry.