1
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Lou H, Zhang Y, Kuczera K, Hageman MJ, Schöneich C. Molecular Dynamics Simulation of an Iron(III) Binding Site on the Fc Domain of IgG1 Relevant for Visible Light-Induced Protein Fragmentation. Mol Pharm 2024; 21:501-512. [PMID: 38128475 DOI: 10.1021/acs.molpharmaceut.3c00612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Molecular dynamics simulations were employed to investigate the interaction between Fe(III) and an iron-binding site composed of THR259, ASP252, and GLU261 on the Fc domain of an IgG1. The goal was to provide microscopic mechanistic information for the photochemical, iron-dependent site-specific oxidative fragmentation of IgG1 at THR259 reported in our previous paper. The distance between Fe(III) and residues of interest as well as the binding pocket size was examined for both protonated and deprotonated THR259. The Fe(III) binding free energy (ΔG) was estimated by using an umbrella sampling approach. The pKa shift of the THR259 hydroxyl group caused by the presence of nearby Fe(III) was estimated based on a thermodynamic cycle. The simulation results show that Fe(III) resides inside the proposed binding pocket and profoundly changes the pocket configuration. The ΔG values indicate that the pocket possesses a strong binding affinity for Fe(III). Furthermore, Fe(III) profoundly lowers the pKa value of the THR259 hydroxyl group by 5.4 pKa units.
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Affiliation(s)
- Hao Lou
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
- Biopharmaceutical Innovation and Optimization Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - Yilue Zhang
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Krzysztof Kuczera
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045, United States
| | - Michael J Hageman
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
- Biopharmaceutical Innovation and Optimization Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - Christian Schöneich
- Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
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2
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Zhang Y, Schöneich C. Visible Light Induces Site-Specific Oxidative Heavy Chain Fragmentation of a Monoclonal Antibody (IgG1) Mediated by an Iron(III)-Containing Histidine Buffer. Mol Pharm 2023; 20:650-662. [PMID: 36538763 DOI: 10.1021/acs.molpharmaceut.2c00840] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fragmentation of therapeutic monoclonal antibodies represents a critical quality attribute. Here, we report a novel visible light-induced heavy chain fragmentation of IgG1 mediated by an Fe(III)-containing histidine (His) buffer. Based on non-reducing sodium dodecylsulfate-polyacrylamide gel electrophoresis and mass spectrometry analysis, IgG1 fragments with apparent molecular weights of ∼130, ∼110, and ∼22 kDa were detected in photo-irradiated samples and were mechanistically rationalized with an oxidative cleavage at Thr259. Specifically, the reactions are proposed to involve the generation of an intermediary alkoxyl radical, which undergoes β-cleavage to yield a glycyl radical. The latter either converts into Gly or adds oxygen and follows a peroxyl radical chemistry. The cleavage process requires the presence of His, while only negligible yields of cleavage products are formed when His is replaced by acetate, succinate, or phosphate buffer. Importantly, the fragmentation can be prevented by ethylenediaminetetraacetic acid (EDTA) only when the EDTA concentrations are in significant excess over the concentrations of Fe(III) and proteins, suggesting a strong binding between Fe(III) and IgG1.
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Affiliation(s)
- Yilue Zhang
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Avenue, Lawrence, Kansas66047, United States
| | - Christian Schöneich
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Avenue, Lawrence, Kansas66047, United States
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3
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Moons J, Loosen A, Simms C, de Azambuja F, Parac-Vogt TN. Heterogeneous nanozymatic activity of Hf oxo-clusters embedded in a metal-organic framework towards peptide bond hydrolysis. NANOSCALE 2021; 13:12298-12305. [PMID: 34254101 DOI: 10.1039/d1nr01790j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Materials with enzyme-like activities and proteolytic potential are emerging as a robust and effective alternative to natural enzymes. Herein, a Hf6O8-based NU-1000 metal organic framework (Hf-MOF) is shown to act as a heterogeneous catalyst for the hydrolysis of peptide bonds under mild conditions. In the presence of Hf-MOF, a glycylglycine model dipeptide was hydrolysed with a rate constant of kobs = 8.33 × 10-7 s-1 (half-life (t1/2) of 231 h) at 60 °C and pD 7.4, which is significantly faster than the uncatalyzed reaction. Other Gly-X peptides (X = Ser, Asp, Ile, Ala, and His) were also smoothly hydrolysed under the same conditions with similar rates, except for the faster reactions observed for Gly-His and Gly-Ser. Moreover, the Hf6O8-based NU-1000 MOF also exhibits a high selectivity in the cleavage of a protein substrate, hen egg white lysozyme (HEWL). Our results suggest that embedding Hf6O8 oxo-clusters is an efficient strategy to conserve the hydrolytic activity while smoothing the strong substrate adsorption previously observed for a discrete Hf oxo-cluster that hindered further development of its proteolytic potential. Furthermore, comparison with isostructural Zr-NU-1000 shows that although the Hf variant afforded the same cleavage pattern towards HEWL but slightly slower reaction rates, it exhibited a larger stability window and a better recyclability profile. The results suggest that these differences originate from the intrinsic differences between HfIV and ZrIV centers, and from the lower surface area of Hf-NU-1000 in comparison to Zr-NU-1000.
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Affiliation(s)
- Jens Moons
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium.
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4
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SNAC-tag for sequence-specific chemical protein cleavage. Nat Methods 2019; 16:319-322. [PMID: 30923372 PMCID: PMC6443254 DOI: 10.1038/s41592-019-0357-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/06/2019] [Indexed: 11/25/2022]
Abstract
Biocompatible chemical protein cleavage methods have been long-sought to replace enzymatic cleavages, but have yet to be realized. Here, we report the development of the SNAC-tag (Sequence-specific Nickel Assisted Cleavage) to achieve sequence-specific chemical protein cleavage under biocompatible conditions with comparable efficiency to enzymes. We demonstrate that the SNAC-tag can be inserted before both water-soluble and membrane proteins to achieve fusion protein cleavage, even when enzymatic cleavages fail.
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5
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Ni J, Sohma Y, Kanai M. Scandium(iii) triflate-promoted serine/threonine-selective peptide bond cleavage. Chem Commun (Camb) 2018; 53:3311-3314. [PMID: 28144647 DOI: 10.1039/c6cc10300f] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The site-selective cleavage of peptide bonds is an important chemical modification that is useful not only for the structural determination of peptides, but also as an artificial modulator of peptide/protein function and properties. Here we report site-selective hydrolysis of peptide bonds at the Ser and Thr positions with a high conversion yield. This chemical cleavage relies on Sc(iii)-promoted N,O-acyl rearrangement and subsequent hydrolysis. The method is applicable to a broad scope of polypeptides with various functional groups, including a post-translationally modified peptide that is unsuitable for enzymatic hydrolysis. The system was further extended to site-selective cleavage of a native protein, Aβ1-42, which is closely related to the onset of Alzheimer's disease.
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Affiliation(s)
- Jizhi Ni
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan. and Japan Science Technology Agency (JST), ERATO Kanai Life Science Catalysis Project, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan
| | - Youhei Sohma
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan. and Japan Science Technology Agency (JST), ERATO Kanai Life Science Catalysis Project, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan. and Japan Science Technology Agency (JST), ERATO Kanai Life Science Catalysis Project, 7-3-1 Bunkyo-ku, Tokyo 113-0033, Japan
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6
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McNiff ML, Chadwick JS. Metal-bound claMP Tag inhibits proteolytic cleavage. Protein Eng Des Sel 2017; 30:467-475. [PMID: 28541524 DOI: 10.1093/protein/gzx030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 05/05/2017] [Indexed: 11/13/2022] Open
Abstract
Biologics can be an improvement to small molecule drugs, providing high specificity for an identified target, lowering toxicity and limiting side effects. To achieve effective delivery, the biologic must have sufficient time to reach the target tissue. A prolonged half-life in the circulating environment is desired, but often serum stability is limited by proteases. Proteolysis in the serum causes degradation and inactivation as the biologic is fragmented and more rapidly cleared from the body. To improve the circulating half-life, large, hydrophilic polymers may be conjugated or stable fusion tags may be engineered to increase the effective size of the peptide and to hinder degradation by proteases. Improved resistance to proteases is essential for effective delivery. Here, a proof of concept study is presented using a metal-binding tripeptide tag known as the claMP Tag to create an inline conjugate and the ability of the tag to inhibit proteolysis was examined.
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Affiliation(s)
- Michaela L McNiff
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047
| | - Jennifer S Chadwick
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Ave, Lawrence, KS 66047.,BioAnalytix Inc., 790 Memorial Dr., Cambridge, MA 02139
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7
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Metal assisted peptide bond hydrolysis: Chemistry, biotechnology and toxicological implications. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2016.02.009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
Fragmentation in the hinge region of an IgG1 monoclonal antibody (mAb) can affect product stability, potentially causing changes in potency and efficacy. Metals ions, such as Cu(2+), can bind to the mAb and undergo hydrolysis or oxidation, which can lead to cleavage of the molecule. To better understand the mechanism of Cu(2+)-mediated mAb fragmentation, hinge region cleavage products and their rates of formation were studied as a function of pH with and without Cu(2+). More detailed analysis of the chemical changes was investigated using model linear and cyclic peptides (with the sequence of SCDKTHTC) derived from the upper hinge region of the mAb. Cu(2+) mediated fragmentation was determined to be predominantly via a hydrolytic pathway in solution. The sites and products of hydrolytic cleavage are pH and strain dependent. In more acidic environments, rates of Cu(2+) induced hinge fragmentation are significantly slower than at higher pH. Although the degradation reaction rates between the linear and cyclic peptides are not significantly different, the products of degradation vary. mAb fragmentation can be reduced by modifying His, which is a potential metal binding site and a known ligand in other metalloproteins. These results suggest that a charge may contribute to stabilization of a specific molecular structure involved in hydrolysis, leading to the possible formation of a copper binding pocket that causes increased susceptibility of the hinge region to degradation.
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Affiliation(s)
- Zephania Kwong Glover
- a Late Stage Pharmaceutical Development; Genentech, Inc. ; South San Francisco , CA USA
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9
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Trevisiol S, Ayoub D, Lesur A, Ancheva L, Gallien S, Domon B. The use of proteases complementary to trypsin to probe isoforms and modifications. Proteomics 2016; 16:715-28. [DOI: 10.1002/pmic.201500379] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/06/2015] [Accepted: 12/08/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Stéphane Trevisiol
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| | - Daniel Ayoub
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| | - Antoine Lesur
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| | - Lina Ancheva
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| | - Sébastien Gallien
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
| | - Bruno Domon
- Luxembourg Clinical Proteomics Center (LCP); Luxembourg Institute of Health; Strassen Luxembourg
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10
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Abstract
Site-selective peptide/protein degradation through chemical cleavage methods is an important modification of biologically relevant macromolecules which complements enzymatic hydrolysis. In this review, recent progress in chemical, site-selective peptide bond cleavage is overviewed, with an emphasis on postulated mechanisms and their implications on reactivity, selectivity, and substrate scope.
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11
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Atomic resolution structure of a protein prepared by non-enzymatic His-tag removal. Crystallographic and NMR study of GmSPI-2 inhibitor. PLoS One 2014; 9:e106936. [PMID: 25233114 PMCID: PMC4169406 DOI: 10.1371/journal.pone.0106936] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 08/09/2014] [Indexed: 12/03/2022] Open
Abstract
Purification of suitable quantity of homogenous protein is very often the bottleneck in protein structural studies. Overexpression of a desired gene and attachment of enzymatically cleavable affinity tags to the protein of interest made a breakthrough in this field. Here we describe the structure of Galleria mellonella silk proteinase inhibitor 2 (GmSPI-2) determined both by X-ray diffraction and NMR spectroscopy methods. GmSPI-2 was purified using a new method consisting in non-enzymatic His-tag removal based on a highly specific peptide bond cleavage reaction assisted by Ni(II) ions. The X-ray crystal structure of GmSPI-2 was refined against diffraction data extending to 0.98 Å resolution measured at 100 K using synchrotron radiation. Anisotropic refinement with the removal of stereochemical restraints for the well-ordered parts of the structure converged with R factor of 10.57% and Rfree of 12.91%. The 3D structure of GmSPI-2 protein in solution was solved on the basis of 503 distance constraints, 10 hydrogen bonds and 26 torsion angle restraints. It exhibits good geometry and side-chain packing parameters. The models of the protein structure obtained by X-ray diffraction and NMR spectroscopy are very similar to each other and reveal the same β2αβ fold characteristic for Kazal-family serine proteinase inhibitors.
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12
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Lv XL, Wei Y, Luo SZ. A "turn-on" fluorescent chemosensor based on peptidase for detecting copper(II). ANAL SCI 2014; 28:749-52. [PMID: 22878628 DOI: 10.2116/analsci.28.749] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
A new fluorescent chemosensor for Cu(II) ions was designed and synthesized on the basis of the sequence-specific cleavage of the peptide bond by the peptidase (metal or metal complexes). In the chemosensor system, the substrate was labeled with a FAM fluorophore (6-carboxyfluorescein) at the N-terminal and with a Dabcyl quencher 4-(4'-dimethylaminophenylazo)benzoic acid at the ε-N of C-terminal Lys. In the presence of Cu(II), the substrate strand is cleaved, and the release of the cleaved fragment results in a significant fluorescence increase. The design was aided by the FRET study that showed a "turn-on" response for Cu(II) in an aqueous medium. Under optimum conditions, the novel chemosensor described here had a linear response range for Cu(II) from 1.0 × 10(-8) to 1.0 × 10(-6) mol dm(-3) with a detection limit of 1.0 × 10(-8) mol dm(-3).
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Affiliation(s)
- Xiao-Li Lv
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, PR China
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13
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Belczyk-Ciesielska A, Zawisza IA, Mital M, Bonna A, Bal W. Sequence-specific Cu(II)-dependent peptide bond hydrolysis: similarities and differences with the Ni(II)-dependent reaction. Inorg Chem 2014; 53:4639-46. [PMID: 24735221 DOI: 10.1021/ic5003176] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Potentiometry and UV-vis and circular dichroism spectroscopies were applied to characterize Cu(II) coordination to the Ac-GASRHWKFL-NH2 peptide. Using HPLC and ESI-MS, we demonstrated that Cu(II) ions cause selective hydrolysis of the Ala-Ser peptide bond in this peptide and characterized the pH and temperature dependence of the reaction. We found that Cu(II)-dependent hydrolysis occurs solely in 4N complexes, in which the equatorial coordination positions of the Cu(II) ion are saturated by peptide donor atoms, namely, the pyridine-like nitrogen of the His imidazole ring and three preceding peptide bond nitrogens. Analysis of the reaction products led to the conclusion that Cu(II)-dependent hydrolysis proceeds according to the mechanism demonstrated previously for Ni(II) ions (Kopera, E.; Krężel, A.; Protas, A. M.; Belczyk, A.; Bonna, A.; Wysłouch-Cieszyńska, A.; Poznański, J.; Bal, W. Inorg. Chem. 2010, 49, 6636-6645). However, the pseudo-first-order reaction rate found for Cu(II) is, on average, 100 times lower than that for Ni(II) ions. The greater ability of Cu(II) ions to form 4N complexes at lower pH partially compensates for this difference in rates, resulting in similar hydrolytic activities for the two ions around pH 7.
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14
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Kasten BB, Ma X, Liu H, Hayes TR, Barnes CL, Qi S, Cheng K, Bottorff SC, Slocumb WS, Wang J, Cheng Z, Benny PD. Clickable, hydrophilic ligand for fac-[M(I)(CO)3](+) (M = Re/(99m)Tc) applied in an S-functionalized α-MSH peptide. Bioconjug Chem 2014; 25:579-92. [PMID: 24568284 PMCID: PMC3983144 DOI: 10.1021/bc5000115] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The copper(I)-catalyzed azide–alkyne
cycloaddition (CuAAC)
click reaction was used to incorporate alkyne-functionalized dipicolylamine
(DPA) ligands (1 and 3) for fac-[MI(CO)3]+ (M = Re/99mTc) complexation into an α-melanocyte stimulating hormone (α-MSH)
peptide analogue. A novel DPA ligand with carboxylate substitutions
on the pyridyl rings (3) was designed to increase the
hydrophilicity and to decrease in vivo hepatobiliary retention of fac-[99mTcI(CO)3]+ complexes used in single photon emission computed tomography (SPECT)
imaging studies with targeting biomolecules. The fac-[ReI(CO)3(3)] complex (4) was used for chemical characterization and X-ray crystal
analysis prior to radiolabeling studies between 3 and fac-[99mTcI(OH2)3(CO)3]+. The corresponding 99mTc
complex (4a) was obtained in high radiochemical yields,
was stable in vitro for 24 h during amino acid challenge and serum
stability assays, and showed increased hydrophilicity by log P analysis compared to an analogous complex with nonfunctionalized
pyridine rings (2a). An α-MSH peptide functionalized
with an azide was labeled with fac-[MI(CO)3]+ using both click, then chelate (CuAAC reaction with 1 or 3 followed by
metal complexation) and chelate, then click (metal
complexation of 1 and 3 followed by CuAAC
with the peptide) strategies to assess the effects of CuAAC conditions
on fac-[MI(CO)3]+ complexation within a peptide framework. The peptides from the click, then chelate strategy had different HPLC tR’s and in vitro stabilities compared
to those from the chelate, then click strategy, suggesting
nonspecific coordination of fac-[MI(CO)3]+ using this synthetic route. The fac-[MI(CO)3]+-complexed peptides from
the chelate, then click strategy showed >90% stability
during in vitro challenge conditions for 6 h, demonstrated high affinity
and specificity for the melanocortin 1 receptor (MC1R) in IC50 analyses, and led to moderately high uptake in B16F10 melanoma cells.
Log P analysis of the 99mTc-labeled peptides
confirmed the enhanced hydrophilicity of the peptide bearing the novel,
carboxylate-functionalized DPA chelate (10a′)
compared to the peptide with the unmodified DPA chelate (9a′). In vivo biodistribution analysis of 9a′ and 10a′ showed moderate tumor uptake in a B16F10 melanoma
xenograft mouse model with enhanced renal uptake and surprising intestinal
uptake for 10a′ compared to predominantly hepatic
accumulation for 9a′. These results, coupled with
the versatility of CuAAC, suggests this novel, hydrophilic chelate
can be incorporated into numerous biomolecules containing azides for
generating targeted fac-[MI(CO)3]+ complexes in future studies.
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Affiliation(s)
- Benjamin B Kasten
- Department of Chemistry, Washington State University , Pullman, Washington 99164, United States
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15
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Tanabe K, Taniguchi A, Matsumoto T, Oisaki K, Sohma Y, Kanai M. Asparagine-selective cleavage of peptide bonds through hypervalent iodine-mediated Hofmann rearrangement in neutral aqueous solution. Chem Sci 2014. [DOI: 10.1039/c3sc53037j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Ly HGT, Absillis G, Bajpe SR, Martens JA, Parac-Vogt TN. Hydrolysis of Dipeptides Catalyzed by a Zirconium(IV)-Substituted Lindqvist Type Polyoxometalate. Eur J Inorg Chem 2013. [DOI: 10.1002/ejic.201300270] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Kopera E, Belczyk-Ciesielska A, Bal W. Application of Ni(II)-assisted peptide bond hydrolysis to non-enzymatic affinity tag removal. PLoS One 2012; 7:e36350. [PMID: 22574150 PMCID: PMC3344860 DOI: 10.1371/journal.pone.0036350] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 04/02/2012] [Indexed: 11/18/2022] Open
Abstract
In this study, we demonstrate a non-enzymatic method for hydrolytic peptide bond cleavage, applied to the removal of an affinity tag from a recombinant fusion protein, SPI2-SRHWAP-His(6). This method is based on a highly specific Ni(II) reaction with (S/T)XHZ peptide sequences. It can be applied for the protein attached to an affinity column or to the unbound protein in solution. We studied the effect of pH, temperature and Ni(II) concentration on the efficacy of cleavage and developed an analytical protocol, which provides active protein with a 90% yield and ∼100% purity. The method works well in the presence of non-ionic detergents, DTT and GuHCl, therefore providing a viable alternative for currently used techniques.
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Affiliation(s)
- Edyta Kopera
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | | | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- * E-mail:
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18
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Rustandi RR, Wang Y. Use of CE-SDS gel for characterization of monoclonal antibody hinge region clipping due to copper and high pH stress. Electrophoresis 2011; 32:3078-84. [DOI: 10.1002/elps.201100186] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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19
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Abstract
Fragmentation is a degradation pathway ubiquitously observed in proteins despite the remarkable stability of peptide bond; proteins differ only by how much and where cleavage occurs. The goal of this review is to summarize reports regarding the non-enzymatic fragmentation of the peptide backbone of monoclonal antibodies (mAbs). The sites in the polypeptide chain susceptible to fragmentation are determined by a multitude of factors. Insights are provided on the intimate chemical mechanisms that can make some bonds prone to cleavage due to the presence of specific side-chains. In addition to primary structure, the secondary, tertiary and quaternary structures have a significant impact in modulating the distribution of cleavage sites by altering local flexibility, accessibility to solvent or bringing in close proximity side chains that are remote in sequence. This review focuses on cleavage sites observed in the constant regions of mAbs, with special emphasis on hinge fragmentation. The mechanisms responsible for backbone cleavage are strongly dependent on pH and can be catalyzed by metals or radicals. The distribution of cleavage sites are different under acidic compared to basic conditions, with fragmentation rates exhibiting a minimum in the pH range 5 to 6; therefore, the overall fragmentation pattern observed for a mAb is a complex result of structural and solvent conditions. A critical review of the techniques used to monitor fragmentation is also presented; usually a compromise has to be made between a highly sensitive method with good fragment separation and the capability to identify the cleavage site. The effect of fragmentation on the function of a mAb must be evaluated on a case-by-case basis depending on whether cleavage sites are observed in the variable or constant regions, and on the mechanism of action of the molecule.
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Affiliation(s)
- Josef Vlasak
- BioProcess Analytical and Formulation Sciences Department; Merck Research Laboratories; Merck Sharp and Dohme Corp., West Point, PA, USA
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20
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Miskevich F, Davis A, Leeprapaiwong P, Giganti V, Kostić NM, Angel LA. Metal complexes as artificial proteases in proteomics: A palladium(II) complex cleaves various proteins in solutions containing detergents. J Inorg Biochem 2011; 105:675-83. [DOI: 10.1016/j.jinorgbio.2011.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2010] [Revised: 01/14/2011] [Accepted: 01/18/2011] [Indexed: 11/15/2022]
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21
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Luo XM, He WJ, Zhang Y, Guo ZJ, Zhu LG. Metal compound-mediated hydrolytic cleavage of oxidized insulin B chain: Regioselectivity and influence of peptide secondary structure. CHINESE J CHEM 2010. [DOI: 10.1002/cjoc.20000180611] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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22
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Kopera E, Krȩżel A, Protas AM, Belczyk A, Bonna A, Wysłouch-Cieszyńska A, Poznański J, Bal W. Sequence-Specific Ni(II)-Dependent Peptide Bond Hydrolysis for Protein Engineering: Reaction Conditions and Molecular Mechanism. Inorg Chem 2010; 49:6636-45. [DOI: 10.1021/ic1005709] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Edyta Kopera
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Artur Krȩżel
- Laboratory of Protein Engineering, Faculty of Biotechnology, University of Wrocław, Tamka 2, 50-137 Wrocław, Poland
| | - Anna Maria Protas
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Agnieszka Belczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Arkadiusz Bonna
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | | | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Wojciech Bal
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland
- Central Institute for Labour Protection—National Research Institute, Czerniakowska 16, 00-701 Warsaw, Poland
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23
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Schreiner B, Beck W. Coordination of the Ester Group - Hydrido-Rhodium(III) and Iridium(III) Complexes of Orthometallated Diphenylmethylene Glycine Esters [1]. Z Anorg Allg Chem 2010. [DOI: 10.1002/zaac.200900474] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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24
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Krȩżel A, Kopera E, Protas AM, Poznański J, Wysłouch-Cieszyńska A, Bal W. Sequence-Specific Ni(II)-Dependent Peptide Bond Hydrolysis for Protein Engineering. Combinatorial Library Determination of Optimal Sequences. J Am Chem Soc 2010; 132:3355-66. [DOI: 10.1021/ja907567r] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Artur Krȩżel
- Laboratory of Protein Engineering, Faculty of Biotechnology, University of Wrocław, Tamka 2, 50-137 Wrocław, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Central Institute for Labour Protection—National Research Institute, Czerniakowska 16, 00-701 Warsaw, Poland
| | - Edyta Kopera
- Laboratory of Protein Engineering, Faculty of Biotechnology, University of Wrocław, Tamka 2, 50-137 Wrocław, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Central Institute for Labour Protection—National Research Institute, Czerniakowska 16, 00-701 Warsaw, Poland
| | - Anna Maria Protas
- Laboratory of Protein Engineering, Faculty of Biotechnology, University of Wrocław, Tamka 2, 50-137 Wrocław, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Central Institute for Labour Protection—National Research Institute, Czerniakowska 16, 00-701 Warsaw, Poland
| | - Jarosław Poznański
- Laboratory of Protein Engineering, Faculty of Biotechnology, University of Wrocław, Tamka 2, 50-137 Wrocław, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Central Institute for Labour Protection—National Research Institute, Czerniakowska 16, 00-701 Warsaw, Poland
| | - Aleksandra Wysłouch-Cieszyńska
- Laboratory of Protein Engineering, Faculty of Biotechnology, University of Wrocław, Tamka 2, 50-137 Wrocław, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Central Institute for Labour Protection—National Research Institute, Czerniakowska 16, 00-701 Warsaw, Poland
| | - Wojciech Bal
- Laboratory of Protein Engineering, Faculty of Biotechnology, University of Wrocław, Tamka 2, 50-137 Wrocław, Poland, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland, Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland, and Central Institute for Labour Protection—National Research Institute, Czerniakowska 16, 00-701 Warsaw, Poland
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25
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Mhidia R, Melnyk O. Selective cleavage of an azaGly peptide bond by copper(II). Long-range effect of histidine residue. J Pept Sci 2010; 16:141-7. [DOI: 10.1002/psc.1211] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Bröhmer MC, Bannwarth W. Forced Complexation of Nitrogen Leading to a Weakening of Amide Bonds: Application to a New Linker for Solid-Phase Chemistry. European J Org Chem 2008. [DOI: 10.1002/ejoc.200800642] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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27
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Abstract
Heterogeneity of monoclonal antibodies is common due to the various modifications introduced over the lifespan of the molecules from the point of synthesis to the point of complete clearance from the subjects. The vast number of modifications presents great challenge to the thorough characterization of the molecules. This article reviews the current knowledge of enzymatic and nonenzymatic modifications of monoclonal antibodies including the common ones such as incomplete disulfide bond formation, glycosylation, N-terminal pyroglutamine cyclization, C-terminal lysine processing, deamidation, isomerization, and oxidation, and less common ones such as modification of the N-terminal amino acids by maleuric acid and amidation of the C-terminal amino acid. In addition, noncovalent associations with other molecules, conformational diversity and aggregation of monoclonal antibodies are also discussed. Through a complete understanding of the heterogeneity of monoclonal antibodies, strategies can be employed to better identify the potential modifications and thoroughly characterize the molecules.
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Affiliation(s)
- Hongcheng Liu
- Process Sciences Department, Abbott Bioresearch Center, 100 Research Drive, Worcester, Massachusetts 01605, USA.
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28
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29
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Cepeda SS, Grant KB. Hydrolysis of insulin chain B using zirconium(iv) at neutral pH. NEW J CHEM 2008. [DOI: 10.1039/b715589a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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30
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Andberg M, Jäntti J, Heilimo S, Pihkala P, Paananen A, Koskinen AMP, Söderlund H, Linder MB. Cleavage of recombinant proteins at poly-His sequences by Co(II) and Cu(II). Protein Sci 2007; 16:1751-61. [PMID: 17600148 PMCID: PMC2203371 DOI: 10.1110/ps.072846407] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Improved ways to cleave peptide chains at engineered sites easily and specifically would form useful tools for biochemical research. Uses of such methods include the activation or inactivation of enzymes or the removal of tags for enhancement of recombinant protein expression or tags used for purification of recombinant proteins. In this work we show by gel electrophoresis and mass spectroscopy that salts of Co(II) and Cu(II) can be used to cleave fusion proteins specifically at sites where sequences of His residues have been introduced by protein engineering. The His residues could be either consecutive or spaced with other amino acids in between. The cleavage reaction required the presence of low concentrations of ascorbate and in the case of Cu(II) also hydrogen peroxide. The amount of metal ions required for cleavage was very low; in the case of Cu(II) only one to two molar equivalents of Cu(II) to protein was required. In the case of Co(II), 10 molar equivalents gave optimal cleavage. The reaction occurred within minutes, at a wide pH range, and efficiently at temperatures ranging from 0 degrees C to 70 degrees C. The work described here can also have implications for understanding protein stability in vitro and in vivo.
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Affiliation(s)
- Martina Andberg
- VTT Technical Research Centre of Finland, Espoo FIN-02044 VTT, Finland
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31
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Stoffregen SA, Griffin AKK, Kostić NM. Thioether Complexes of Palladium(II) and Platinum(II) as Artificial Peptidases. Residue-Selective Peptide Cleavage by a Palladium(II) Complex. Inorg Chem 2005; 44:8899-907. [PMID: 16296845 DOI: 10.1021/ic0506613] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the synthesis and characterization of perchlorate salts containing the following three novel complex cations each with a bidentate thioether ligand: binuclear cis-[Pt(CH3SCH2CH2CH2SCH3)(mu-OH)]22+, mononuclear cis-[Pt(CH3SCH2CH2CH2SCH3)(H2O)2]2+, and mononuclear cis-[Pd(CH3SCH2CH2CH2SCH3)(H2O)2]2+. Despite their analogous compositions, the mononuclear Pt(II) and Pd(II) complexes differ in the selectivity with which they promote the hydrolysis of polypeptides. The complex cis-[Pt(CH3SCH2CH2CH2SCH3)(H2O)2]2+ promotes slow but selective cleavage of Met-Pro peptide bonds at pH 2.0. The selectivity of the complex cis-[Pd(CH3SCH2CH2CH2SCH3)(H2O)2]2+ is pH-dependent. At pH 2.0, this Pd(II) complex promotes residue-selective hydrolysis of the X-Y bond in X-Y-Met and X-Y-His sequences; the rate is enhanced when residue Y is proline. At pH 7.0, this kinetic preference becomes sequence-selective in that the Pd(II) complex exclusively cleaves the X-Pro bond in X-Pro-Met and X-Pro-His sequences. The enhanced reactivity of the X-Pro amide group is attributed to the high basicity of its carbonyl oxygen atom. Binding of the metal(II) atom enhances the electrophilicity of the carbonyl carbon atom and promotes nucleophilic attack by a solvent water molecule. The bidentate thioether ligand disfavors the formation of hydrolytically unreactive complexes, allowing the Pd(II) complex to promote the cleavage reaction.
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Affiliation(s)
- Stacey A Stoffregen
- Department of Chemistry, Gilman Hall, Iowa State University, Ames, Iowa 50011-3111, USA
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32
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Yang G, Miao R, Li Y, Hong J, Zhao C, Guo Z, Zhu L. Synergic effect of two metal centers in catalytic hydrolysis of methionine-containing peptides promoted by dinuclear palladium(ii) hexaazacyclooctadecane complex. Dalton Trans 2005:1613-9. [PMID: 15852110 DOI: 10.1039/b500210a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The species obtained by the reaction of [Pd2([18]aneN6)Cl2](ClO4)2(where [18]aneN6 is 1,4,7,10,13,16-hexaazacyclooctadecane) with AgBF4 have been determined by electrospray ionization mass spectrometry (ESI-MS) to be an equilibrium mixture of three major types of dinuclear Pd(II) complex cations, [Pd2(mu-O)([18]aneN6)]2+, [Pd2(mu-OH)([18]aneN6)]3+ and [Pd2(H2O)(OH)([18]aneN6)](3+), in aqueous solution. The hydroxo-group-bridged one, [Pd2(mu-OH)([18]aneN6)]3+, is a dominant species, whose crystal structure has been obtained. The crystal structure of [Pd2(mu-OH)([18]aneN6)](ClO4)3 shows that each Pd(II) ion in the dinuclear complex is tetra-coordinated by three nitrogen atoms and one hydroxo group bridge in a distorted square configuration. The two Pd(II) ions are 3.09 A apart from each other. The dinuclear Pd(II) complex cations [Pd2(mu-OH)([18]aneN6)]3+ and [Pd2(H2O)(OH)([18]aneN6)]3+ can efficiently catalyze hydrolysis of the amide bond involving the carbonyl group of methionine in methionine-containing peptides with turnover number of larger than 20. In these hydrolytic reactions, the two Pd(II) ions are synergic; one Pd(II) ion anchors to the side chain of methionine and the other one delivers hydroxo group or aqua ligand to carbonyl carbon of methionine, or acts as a Lewis acid to activate the carbonyl group of methionine, resulting in cleavage of Met-X bond. The binding constant of dinuclear Pd(II) complex cations with AcMet-Gly and AcMet were determined by 1H NMR titration to be 282 +/- 2 M(-1) and 366 +/- 4 M(-1), respectively. The relatively low binding constants enable the catalytic cycle and the possible catalytic mechanism is proposed. This is the first artificial mimic of metallopeptidases with two metal active centers.
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Affiliation(s)
- Gaosheng Yang
- State Key Laboratory of Coordination Chemistry, Coordination Chemistry Institute, Nanjing University, Nanjing 210093, P. R. China
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33
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Manka S, Becker F, Hohage O, Sheldrick WS. Cisplatin-mediated selective hydrolytic cleavage of methionine-containing peptides with neighboring serine or histidine residues. J Inorg Biochem 2004; 98:1947-56. [PMID: 15522420 DOI: 10.1016/j.jinorgbio.2004.08.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2004] [Revised: 08/18/2004] [Accepted: 08/24/2004] [Indexed: 10/26/2022]
Abstract
The pH- and time-dependent reactions of the anticancer drug cisplatin, cis-[PtCl(2)(NH(3))(2)], with the peptides Ac-Gly-Met-Gly-OH, Ac-Ser-Met-OH and Ac-Met-His-OH (Gly=glycyl, Met=methionyl, Ser=seryl, His=histidyl) at 313 K have been investigated by high-performance liquid chromatography, nuclear magnetic resonance and mass spectrometry. In the major equimolar reaction pathway for Ac-Gly-Met-Gly-OH, rapid anchoring at the methionine sulphur (kappaS) is followed by successive metalations of the methionine N(M) and glycyl N(G1) amide nitrogens in N-terminal direction to afford bidentate kappa(2)S,N(M) and tridentate kappa(3)S, N(M),N(G1) complexes. Cleavage of acetic acid at the second upstream amide bond is observed after 10 h leading to slow formation of [Pt(H-Gly-MetH(-1)-Gly-OH-kappa(3)S,N(M),N(G1))(NH(3))](+) at pH<6. [Pt(H-Ser-MetH(-1)-OH-kappa(3)S,N(M),N(S))(NH(3))](+) results from an analogous cisplatin-mediated regioselective hydrolytic cleavage reaction for Ac-Ser-Met-OH in moderately acid solution (pH<4). After passing through a minimum at pH 4.4, the concentration of the cleavage product in the reaction mixture after 500 h increases steadily on raising the pH and release of acetic acid is effectively quantitative for 7pH9.5. A competing mechanism involving nucleophilic attack of the serine side chain on the acetyl function can be inferred for pH>6 by the HPLC detection of a second intermediate kappa(3)S,N(M),N(S) species. In striking contrast, the reaction of cisplatin with Ac-Met-His-OH leads to release of acetylmethionine and formation of a final histidine product cis-[PtCl(H-His-OH-kappa(2)N3,N(H)) (NH(3))](+) at pH<6 by a kappaS-->kappa(2)S, N3-->kappa(3)S, N(H),N3-->kappa(2)N3,N(H)(H-His-OH) pathway.
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Affiliation(s)
- Sven Manka
- Lehrstuhl für Analytische Chemie, Ruhr-Universität Bochum, Universitätsstrasse 150, D-44780 Bochum, Germany
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34
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Kassai M, Ravi RG, Shealy SJ, Grant KB. Unprecedented Acceleration of Zirconium(IV)-Assisted Peptide Hydrolysis at Neutral pH. Inorg Chem 2004; 43:6130-2. [PMID: 15446852 DOI: 10.1021/ic049433j] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
4,13-Diaza-18-crown-6 substantially increases the rate of zirconium(IV) hydrolysis of unactivated peptide amide bonds under near-physiological conditions of temperature and pH. In the presence of this azacrown ether, ZrCl(4) efficiently hydrolyses both neutral and negatively charged peptides (pH 7.0-7.3, 37-60 degrees C).
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Affiliation(s)
- Miki Kassai
- Department of Chemistry, Center for Biotechnology and Drug Design, Georgia State University, P.O. Box 4098, Atlanta, Georgia 30302-4098, USA
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35
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Sun X, Jin C, Mei Y, Yang G, Guo Z, Zhu L. Interaction of Palladium(II) and Platinum(II) Complexes with Microperoxidase-11 Studied by Electrospray Mass Spectrometry and MS/MS Analysis. Inorg Chem 2003; 43:290-6. [PMID: 14704079 DOI: 10.1021/ic034491a] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Interactions of cis-[Pd(en)(H(2)O)(2)](2+) (en, ethylenediamine) and cis-[Pt(NH(3))(2)(H(2)O)(2)](2+) with microperoxidase-11 (MP-11) in a molar ratio of 1:1 or 2:1 at pH 1.4 were investigated via electrospray mass spectrometry and MS/MS analysis at room temperature and at 40 degrees C with an incubation time of 2 or 3 days. The composition of the Pd(II)- and Pt(II)-anchored MP-11 was confirmed on the basis of the precise molecular mass and the simulated isotope distribution pattern. MS/MS analysis revealed that the Pd(II) center anchored to the side chain of Cys7 as Pd(II) and MP-11 were mixed in an equimolar ratio and to side chains of Cys7 and Cys4 as Pd(II) and MP-11 mixed in a 2:1 molar ratio. When Pt(II) and MP-11 were mixed in a 2:1 molar ratio, Pt(II) first anchored to the side chain of Cys7, and then to the side chain of Cys4 with time. The initial coordination of Pd(II) and Pt(II) to the side chain of Cys7 is the essential step for the Pd(II)- and Pt(II)-promoted cleavage of the His8-Thr9 bond in MP-11. These results support the hypothesis that the Pd(II)-mediated cleavage of the His18-Thr19 bond in cytochorome c is due to the identical binding mode.
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Affiliation(s)
- Xiaojuan Sun
- State Key Laboratory of Coordination Chemistry, Coordination Chemistry Institute, Nanjing University, Nanjing 210093, China
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36
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Milović NM, Dutca LM, Kostić NM. Combined use of platinum(II) complexes and palladium(II) complexes for selective cleavage of peptides and proteins. Inorg Chem 2003; 42:4036-45. [PMID: 12817959 DOI: 10.1021/ic026280w] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study shows, for the first time, the advantages of combining two transition-metal complexes as selective proteolytic reagents. In this procedure, cis-[Pt(en)(H(2)O)(2)](2+) is followed by [Pd(H(2)O)(4)](2+). In the peptide AcAla-Lys-Tyr-Gly-Gly-Met-Ala-Ala-Arg-Ala, the Pt(II) reagent cleaves the Met6-Ala7 peptide bond, whereas the Pd(II) reagent cleaves the Gly4-Gly5 bond. In the peptide AcVal-Lys-Gly-Gly-His-Ala-Lys-Tyr-Gly-Gly-Met-Ala-Ala-Arg-Ala, the Pt(II) reagent cleaves the Met11-Ala12 peptide bond, whereas the Pd(II) reagent cleaves the Gly3-Gly4 bond. All cleavage reactions are regioselective and complete at pH 2.0 and 60 degrees C. Each metal ion binds to an anchoring side chain and then, as a Lewis acid, activates a proximal peptide bond toward hydrolysis by the solvent water. The selectivity in cleavage is a consequence of the selectivity in this initial anchoring. Both Pt(II) and Pd(II) reagents bind to the methionine side chain, whereas only the Pd(II) reagent binds to the histidine side chain under the reaction conditions. Consequently, only methionine residues direct the cleavage by the Pt(II) reagent, whereas both methionine and histidine residues direct the cleavage by the Pd(II) reagent. The Pt(II) reagent cleaves the first bond downstream from the anchor, i.e., the Met-Z bond. The Pd(II) reagent cleaves the second bond upstream from the anchor, i.e., the X-Y bond in the X-Y-Met-Z and in the X-Y-His-Z segments. The diethylenetriamine complex [Pt(dien)(H(2)O)](2+) cannot promote cleavage. Its prior binding to the Met11 residue in the second peptide prevents the Pd(II) reagents from binding to Met11 and cleaving the Gly9-Gly10 bond and directs the cleavage by the Pd(II) reagent exclusively at the Gly3-Gly4 bond. Our new method was tested on equine myoglobin, which contains 2 methionine residues and 11 histidine residues. The complete methionine-directed cleavage of the Met55-Lys56 and Met131-Thr132 bonds by the Pt(II) reagent produced three fragments, suitable for various biochemical applications because they are relatively long and contain amino and carboxylic terminal groups. The deliberately incomplete histidine-directed cleavage of the long fragments 1.55 and 56.131 at many sites by the Pd(II) reagent produced numerous short fragments, suitable for protein identification by mass spectrometry. The ability of combined Pt(II) and Pd(II) complexes to cleave proteins with explicable and adjustable selectivity and with good yields bodes well for their greater use in biochemical and bioanalytical practice.
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Affiliation(s)
- Nebojsa M Milović
- Department of Chemistry, Gilman Hall, Iowa State University, Ames, Iowa 50011-3111, USA
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37
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Zhang L, Mei Y, Zhang Y, Li S, Sun X, Zhu L. Regioselective cleavage of myoglobin with copper(II) compounds at neutral pH. Inorg Chem 2003; 42:492-8. [PMID: 12693231 DOI: 10.1021/ic025619b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Selective hydrolytic cleavage of myoglobin was studied with CuCl2, Cu(ClO4)2, Cu(AC)2, and binuclear Cu(II) complexes of 3,6,9,16,19,22-hexaaza-6,19-bis (2-hydroxyethyl)-tricyclo- [22,2,2,2(11,14)]-triaconta-1,11,13,24,27,29-hexaene (1) and 3,6,9,16,19,22-hexaaza-tricyclo-[22,2,2,2(11,14)]-triaconta- 1,11,13,24,27,29-hexaene (2). The sites of cleavage were precisely determined by LC-ESIMS and further confirmed by an MS/MS method through fragmentation from both the N-terminal and C-terminal. The peptide bonds of Gln91-Ser92 and Ala94-Thr95 were remarkably cleaved by Cu(II) anchored to the side chain of the His93 residue. The data presented in this study show that Cu(II)-mediated cleavage of myoglobin is able to proceed at neutral pH, more selectively than Pd(II)-mediated cleavage, and buffer solution of phosphate and NH4HCO3 accelerates the cleavage reaction.
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Affiliation(s)
- Lin Zhang
- State Key Laboratory of Coordination Chemistry, Coordination Chemistry Institute, Nanjing University, Nanjing, 210093, China
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38
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Milović NM, Kostić NM. Interplay of terminal amino group and coordinating side chains in directing regioselective cleavage of natural peptides and proteins with palladium(II) complexes. Inorg Chem 2002; 41:7053-63. [PMID: 12495344 DOI: 10.1021/ic025640c] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Palladium(II) ions anchored to side chains of histidine and methionine residues in peptides and proteins in weakly acidic aqueous solutions promote hydrolytic cleavage of proximate amide bonds in the backbone. In this study, we determine how attachment of Pd(II) ions to histidine and methionine anchors and also to the terminal amino group in six natural peptides (chains A and B of insulin, segment 11-14 of angiotensinogen, pentagastrin, angiotensin II, and segment 3-8 of angiotensin II) and two proteins (ubiquitin and cytochrome c) affects regioselectivity and rate of backbone cleavage. These Pd(II)-promoted reactions follow a clear pattern of regioselectivity, directed by the anchoring side chains. When the Pd(II) reagent is nonspecifically anchored to the terminal amino group, the ligating site that is present in almost all proteins, the cleavage is fortunately absent. When the reagent is anchored to a residue in positions 1, 2, or 3, cleavage is absent, because the terminal amino group and deprotonated amide nitrogen atom(s) interposed between it and the anchor "lock" the Pd(II) ion in hydrolytically inactive chelate complexes. When the reagent is anchored to residues in positions beyond 3, the second amide bond upstream from the anchor is regioselectively cleaved in all cases when the anchor was "isolated," that is, flanked by noncoordinating side chains. Segment 3-8 of angiotensin II undergoes additional cleavage, which we explain by determining the rate constants for the cleavage, identifying the rate-limiting displacement of ethylenediamine ligand from the Pd(II) ion, and detecting several intermediates. Experiments with cytochrome c demonstrate that the number of cleavage sites can be controlled by adjusting the mole ratio of the Pd(II) reagent to the substrate. Our inorganic peptidases are useful for biochemical applications because their regioselectivity and reactivity set them apart from proteolytic enzymes and organic chemical reagents.
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Affiliation(s)
- Nebojsa M Milović
- Department of Chemistry, Gilman Hall, Iowa State University, Ames 50011-3111, USA
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39
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Mylonas M, Plakatouras JC, Hadjiliadis N, Krężel A, Bal W. Potentiometric and spectroscopic studies of the interaction of Cu(II) ions with the hexapeptides AcThrAlaSerHisHisLysNH2, AcThrGluAlaHisHisLysNH2, AcThrGluSerAlaHisLysNH2 and AcThrGluSerHisAlaLysNH2, models of C-terminal tail of histone H2A. Inorganica Chim Acta 2002. [DOI: 10.1016/s0020-1693(02)00925-8] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Sequence-dependent cleavage of albumins with palladium(II) complexes: role of serine residue in controlling the high regioselectivity of protein cleavage. Inorganica Chim Acta 2002. [DOI: 10.1016/s0020-1693(02)00928-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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41
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Mylonas M, Krężel A, Plakatouras JC, Hadjiliadis N, Bal W. The binding of Ni(ii) ions to terminally blocked hexapeptides derived from the metal binding -ESHH- motif of histone H2A. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b206585a] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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42
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Quagraine EK, Kraatz HB, Reid RS. Peptides mimicking the N-terminal Cu(II)-binding site of bovine serum albumin: synthesis, characterization and coordination with Cu(II) ions. J Inorg Biochem 2001; 85:23-32. [PMID: 11377692 DOI: 10.1016/s0162-0134(00)00227-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The N-terminal region of bovine serum albumin (Asp-Thr-His-Lys) is known to provide a specific binding site for Cu(II) ions, with the histidine residue thought to be mainly responsible for the specificity. Thiomolybdates have been found to increase the binding affinity of Cu(II) to some serum albumins. As part of a series of studies to study the interactions between Cu(II), thiomolybdates and bovine serum albumin, we have performed the syntheses and characterization of small model peptides such as His-Lys, Thr(Ac)-His-Lys and Thr-His-Lys. Proton NMR spectra have been monitored in H(2)O solution as a function of pH and added Cu(II) concentration. Reliable K(a) values for His-Lys and Thr(Ac)-His-Lys have been established. Probable binding sites of Cu(II) and the relative strengths of binding to these peptides are also discussed.
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Affiliation(s)
- E K Quagraine
- Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan, Canada S7N 5C9
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Grant KB, Pattabhi S. Use of a fluorescence microplate reader for the detection and characterization of metal-assisted peptide hydrolysis. Anal Biochem 2001; 289:196-201. [PMID: 11161313 DOI: 10.1006/abio.2000.4963] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Metal ions and complexes that hydrolyze peptides under nondenaturing conditions of temperature and pH hold great promise for use in protein structural studies. However, the extreme stability of the peptide amide bond has placed limits on the number of reagents available. In addition, the development of new cleavage strategies has been hindered by the fact that no facile procedure exists for the detection and characterization of metal-assisted peptide hydrolysis. Here we describe a rapid assay in which a microplate reader is used to detect fluorescence produced by the reaction of fluorescamine with hydrolyzed peptides. We have employed this assay to detect Zn(II) and Pd(II)-assisted peptide hydrolysis in multiple samples and in each case have extended our approach to a successful analysis of reaction kinetics. Aliquots from multiple time points are treated with fluorescamine in a single 96-well plate. Because the plate is scanned in a microplate reader in only 58 s, the assay is very convenient compared to conventional approaches which rely on NMR and HPLC to monitor individual reactions. Using our assay, rate constants and half-lives are easily derived from the kinetic data by means of linear regression curve fits of triplicate runs.
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Affiliation(s)
- K B Grant
- Department of Chemistry, Center for Biotechnology and Drug Design, Georgia State University, University Plaza, Atlanta, GA 30303-3083, USA.
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Luo X, He W, Zhang Y, Guo Z, Zhu L. Pd(II) Complexes Mediated Hydrolytic Cleavage of Insulin B Chain: Regioselectivity and Influence of Peptide Secondary Structure. CHEM LETT 2000. [DOI: 10.1246/cl.2000.1030] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
Nickel compounds are known human carcinogens, but the exact molecular mechanisms of nickel carcinogenesis are not known. Due to their abundance, histones are likely targets for Ni(II) ions among nuclear macromolecules. This paper reviews our recent studies of peptide and protein models of Ni(II) binding to histones. The results allowed us to propose several mechanisms of Ni(II)-inflicted damage, including nucleobase oxidation and sequence-specific histone hydrolysis. Quantitative estimations of Ni(II) speciation, based on these studies, support the likelihood of Ni(II) binding to histones in vivo, and the protective role of high levels of glutathione. These calculations indicate the importance of histidine in the intracellular Ni(II) speciation.
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Affiliation(s)
- W Bal
- Faculty of Chemistry, University of Wrocław, Poland.
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Humphreys DP, King LM, West SM, Chapman AP, Sehdev M, Redden MW, Glover DJ, Smith BJ, Stephens PE. Improved efficiency of site-specific copper(II) ion-catalysed protein cleavage effected by mutagenesis of cleavage site. PROTEIN ENGINEERING 2000; 13:201-6. [PMID: 10775662 DOI: 10.1093/protein/13.3.201] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The peptide sequence (N)DKTH(C) was previously investigated as a site for efficient, specific cleavage of a fusion protein by cupric ions using a humanized gamma1 Fab' as a model protein. Here we show that conservative mutations to three of the residues in the introduced cleavage site resulted in cleavage sites that were significantly improved. They were cleaved more efficiently by Cu(2+), such that cleavage reactions could be shorter, of lower pH or at a lower temperature. Some were even found to be measurably cleaved by Ni(2+). Use of these new cleavage sequences along with cupric ions may provide a more rapid and less harsh method for cost-effective, large-scale proteolytic cleavage of fusion proteins and peptides.
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Affiliation(s)
- D P Humphreys
- Celltech Therapeutics, 216 Bath Road, Slough, Berkshire SL1 4EN, UK.
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Site-specific hydrolysis of horse heart cytochrome c and apocytochrome c promoted by palladium(II) complex. Polyhedron 1999. [DOI: 10.1016/s0277-5387(99)00037-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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