Sequence-specific Ni(II)-dependent peptide bond hydrolysis for protein engineering. Combinatorial library determination of optimal sequences.

Previously we demonstrated for several examples that peptides having a general internal sequence R(N)-Yaa-Ser/Thr-Xaa-His-Zaa-R(C) (Yaa = Glu or Ala, Xaa = Ala or His, Zaa = Lys, R(N) and R(C) = any N- and C-terminal amino acid sequence) were hydrolyzed specifically at the Yaa-Ser/Thr peptide bond in the presence of Ni(II) ions at alkaline pH (Krezel, A., Mylonas, M., Kopera, E. and Bal, E. Acta Biochim. Polon. 2006, 53, 721-727 and references therein). Hereby we report the synthesis of a combinatorial library of CH(3)CO-Gly-Ala-(Ser/Thr)-Xaa-His-Zaa-Lys-Phe-Leu-NH(2) peptides, where Xaa residues included 17 common alpha-amino acids (except Asp, Glu, and Cys) and Zaa residues included 19 common alpha-amino acids (except Cys). The Ni(II)-dependent hydrolysis at 37 and 45 degrees C of batches of combinatorial peptide mixtures randomized at Zaa was monitored by MALDI-TOF mass spectrometry. The correctness of library-based predictions was confirmed by accurate measurements of hydrolysis rates of seven selected peptides using HPLC. The hydrolysis was strictly limited to the Ala-Ser/Thr bond in all library and individual peptide experiments. The effects of individual residues on hydrolysis rates were quantified and correlated with physical properties of their side chains according to a model of independent contributions of Xaa and Zaa residues. The principal component analysis calculations demonstrated partial molar side chain volume and the free energy of amino acid vaporization for both Xaa and Zaa residues and the amine pK(a) for Zaa residues to be the most significant empirical parameters influencing the hydrolysis rate. Therefore, efficient hydrolysis required bulky and hydrophobic residues at both variable positions Xaa and Zaa, which contributed independently to the hydrolysis rate. This relationship between the peptide sequence and the hydrolysis rate provides a basis for further research, aimed at the elucidation of the reaction mechanism and biotechnological applications of Ni(II)-dependent peptide bond hydrolysis.

[1]  E. Gross [27] The cyanogen bromide reaction , 1967 .

[2]  J. A. Hartigan,et al.  A k-means clustering algorithm , 1979 .

[3]  D. W. Margerum,et al.  Effect of noncoordinative axial blocking on the stability and kinetic behavior of ternary 2,6-lutidine-nickel(II)-oligopeptide complexes , 1980 .

[4]  A. Gronenborn,et al.  Determination of three‐dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms Circumventing problems associated with folding , 1988, FEBS letters.

[5]  T. Rana,et al.  Specific cleavage of a protein by an attached iron chelate , 1990 .

[6]  H. Kozłowski,et al.  Transition metal complexes of L-cysteine containing di- and tripeptides. , 1990, Journal of inorganic biochemistry.

[7]  T. Rana,et al.  Iron chelate mediated proteolysis: Protein structure dependence , 1991 .

[8]  P. Sadler,et al.  Dioxygen-induced decarboxylation and hydroxylation of [Ni II (glycyl-glycyl-L-histidine)] occurs via Ni III : X-ray crystal structure of [Ni II (glycyl-glycyl-?-hydroxy-D,L-histamine)]3H2O , 1994 .

[9]  R A Houghten,et al.  Peptide libraries: Determination of relative reaction rates of protected amino acids in competitive couplings , 1994, Biopolymers.

[10]  H. Kozłowski,et al.  Competition between the terminal amino and imidazole nitrogen donors for coordination to Ni(II) ions in oligopeptides , 1995 .

[11]  H. Kozłowski,et al.  The influence of aspartic or glutamic acid residues in tetrapeptides on the formation of complexes with nickel(II) and zinc(II) , 1995 .

[12]  E. Hegg,et al.  Hydrolysis of unactivated peptide bonds by a macrocyclic copper(II) complex: Cu([9]aneN3)Cl2 hydrolyzes both dipeptides and proteins , 1995 .

[13]  P. Sadler,et al.  Axial Hydrophobic Fence in Highly-Stable Ni(II) Complex of Des-Angiotensinogen N-Terminal Peptide , 1996 .

[14]  G. Allen,et al.  Specific cleavage of histidine-containing peptides by copper(II). , 2009, International journal of peptide and protein research.

[15]  M A Smith,et al.  Specific cleavage of immunoglobulin G by copper ions. , 2009, International journal of peptide and protein research.

[16]  Richard Wolfenden,et al.  Rates of Uncatalyzed Peptide Bond Hydrolysis in Neutral Solution and the Transition State Affinities of Proteases , 1996 .

[17]  M. Billeter,et al.  MOLMOL: a program for display and analysis of macromolecular structures. , 1996, Journal of molecular graphics.

[18]  M. Komiyama,et al.  Sequence-specific hydrolysis of peptides by metal assisted autocatalysis of an internal hydroxy group , 1997 .

[19]  G. Fields,et al.  Trifluoroacetic acid cleavage and deprotection of resin-bound peptides following synthesis by Fmoc chemistry. , 1997, Methods in enzymology.

[20]  P. Sadler,et al.  Multi-metal binding site of serum albumin. , 1998, Journal of inorganic biochemistry.

[21]  W. Bal,et al.  Interactions of Nickel(II) with histones: interactions of Nickel(II) with CH3CO-Thr-Glu-Ser-His-His-Lys-NH2, a peptide modeling the potential metal binding site in the "C-Tail" region of histone H2A. , 1998, Chemical research in toxicology.

[22]  Natalia V. Kaminskaia,et al.  Regioselective Hydrolysis of Tryptophan-Containing Peptides Promoted by Palladium(II) Complexes , 1999 .

[23]  H. Kozłowski,et al.  Specific structure–stability relations in metallopeptides , 1999 .

[24]  P. Stephens,et al.  Efficient site specific removal of a C-terminal FLAG fusion from a Fab' using copper(II) ion catalysed protein cleavage. , 1999, Protein engineering.

[25]  M. Dizdaroglu,et al.  Ni(II) specifically cleaves the C-terminal tail of the major variant of histone H2A and forms an oxidative damage-mediating complex with the cleaved-off octapeptide. , 2000, Chemical research in toxicology.

[26]  M. Maciejczyk,et al.  Induction of a secondary structure in the N-terminal pentadecapeptide of human protamine HP2 through Ni(II) coordination. An NMR study. , 2000, Chemical research in toxicology.

[27]  P. Stephens,et al.  Improved efficiency of site-specific copper(II) ion-catalysed protein cleavage effected by mutagenesis of cleavage site. , 2000, Protein engineering.

[28]  N. Kostić,et al.  New selectivity in peptide hydrolysis by metal complexes. Platinum(II) complexes promote cleavage of peptides next to the tryptophan residue. , 2001, Inorganic chemistry.

[29]  Y. Nakano,et al.  Copper(II)-cis,cis-1,3,5-triaminocyclohexane complex-promoted hydrolysis of dipeptides: kinetic, speciation and structural studies , 2002, JBIC Journal of Biological Inorganic Chemistry.

[30]  A. Krężel,et al.  Short peptides are not reliable models of thermodynamic and kinetic properties of the N-terminal metal binding site in serum albumin. , 2002, European journal of biochemistry.

[31]  A. Krężel,et al.  The binding of Ni(II) ions to terminally blocked hexapeptides derived from the metal binding -ESHH- motif of histone H2A , 2002 .

[32]  Long-gen Zhu,et al.  Sequence-dependent cleavage of albumins with palladium(II) complexes: role of serine residue in controlling the high regioselectivity of protein cleavage , 2002 .

[33]  N. Kostić,et al.  Palladium(II) complexes, as synthetic peptidases, regioselectively cleave the second peptide bond "upstream" from methionine and histidine side chains. , 2002, Journal of the American Chemical Society.

[34]  N. Kostić,et al.  Combined use of platinum(II) complexes and palladium(II) complexes for selective cleavage of peptides and proteins. , 2003, Inorganic chemistry.

[35]  T. Muir Semisynthesis of proteins by expressed protein ligation. , 2003, Annual review of biochemistry.

[36]  M. Komiyama,et al.  Metal-ion-assisted hydrolysis of dipeptides involving a serine residue in a neutral aqueous solution. , 2003, Organic & biomolecular chemistry.

[37]  N. Kostić,et al.  Transition-metal complexes as enzyme-like reagents for protein cleavage: complex cis-[Pt(en)(H2O)2]2+ as a new methionine-specific protease. , 2003, Chemistry.

[38]  Oliviero Carugo,et al.  Prediction of polypeptide fragments exposed to the solvent. , 2003, In silico biology.

[39]  D. Goldenberg,et al.  The Cys-Xaa-His metal-binding motif: {N} versus {S} coordination and nickel-mediated formation of cysteinyl sulfinic acid , 2003, JBIC Journal of Biological Inorganic Chemistry.

[40]  A. Krężel,et al.  Correlations between complexation modes and redox activities of Ni(II)-GSH complexes. , 2003, Chemical research in toxicology.

[41]  Long-gen Zhu,et al.  Regioselective cleavage of myoglobin with copper(II) compounds at neutral pH. , 2003, Inorganic chemistry.

[42]  N. Kostić,et al.  Palladium(II) complex as a sequence-specific peptidase: hydrolytic cleavage under mild conditions of X-Pro peptide bonds in X-Pro-Met and X-Pro-His segments. , 2003, Journal of the American Chemical Society.

[43]  William S Sheldrick,et al.  Cisplatin-mediated selective hydrolytic cleavage of methionine-containing peptides with neighboring serine or histidine residues. , 2004, Journal of inorganic biochemistry.

[44]  Miki Kassai,et al.  Unprecedented acceleration of zirconium(IV)-assisted peptide hydrolysis at neutral pH. , 2004, Inorganic chemistry.

[45]  E. D. de Souza,et al.  Hydrolytic protein cleavage mediated by unusual mononuclear copper(II) complexes: X-ray structures and solution studies. , 2005, Inorganic chemistry.

[46]  G. Petersen,et al.  Current strategies for the use of affinity tags and tag removal for the purification of recombinant proteins. , 2006, Protein expression and purification.

[47]  A. Krężel,et al.  Sequence-specific Ni(II)-dependent peptide bond hydrolysis in a peptide containing threonine and histidine residues. , 2006, Acta biochimica Polonica.

[48]  Kathryn B. Grant and Miki Kassai Major Advances in the Hydrolysis of Peptides and Proteins by Metal Ions and Complexes , 2006 .

[49]  J. Jäntti,et al.  Cleavage of recombinant proteins at poly‐His sequences by Co(II) and Cu(II) , 2007, Protein science : a publication of the Protein Society.