Abgent

Abgent is a San Diego biotechnology company that develops tools to profile post-translational modifications related to cellular function and disease. Abgent's antibodies cover targeting protein kinases (kinome), phosphatases, methyl and acetyl transferases, ubiquitin and SUMO, glycosylases and other protein modification enzymes.

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Peer review

Abgent's was listed as a selected supplier in Nature Magazine^[1], Antibody Technology, Drug Discovery Features and The Scientist's cell signaling feature Full list of citations^[2].

Core business

Abgent specilizes in FMOC solid-phase synthesis of peptides using pseudoproline to improve the quality of synthetic peptides^[3]. Pseudoproline dipeptides have been shown to increase the success rate for synthesizing both long and difficult peptides.^{[citation needed]} Pseudoproline dipeptides can be introduced in the same manner as other amino acid derivatives. The routine use of pseudoproline (oxazolidine) dipeptides in the FMOC solid phase pepdide sysnthesis (SPPS) of serine- and threonine-containing peptides has been shown to improve the quality and yield of crude products and helps avoid unnecessary repeat synthesis of failed sequences^[4]. Pseudoproline dipeptides have also been shown to be effective in the synthesis of intractable peptides, long peptides/small proteins, and cyclic peptides, enabling in many cases the production of peptides that are otherwise difficult to produce. The dipeptides are used by substituting a serine or threonine residue together with the preceding amino acid residue in the peptide sequence with the appropriate pseudoproline dipeptide. The native sequence is regenerated on cleavage and deprotection^[5][6][7].

SUMOplot

Most SUMO-modified proteins contain the tetrapeptide motif B-K-x-D/E where B is a hydrophobic residue, K is the lysine conjugated to SUMO, x is any amino acid (aa), D or E is an acidic residue. Substrate specificity appears to be derived directly from Ubc9 and the respective substrate motif. SUMOplot predicts the probability for the SUMO consensus sequence (SUMO-CS) to be engaged in SUMO attachment. The SUMOplot score system is based on two criteria: 1) direct amino acid match to the SUMO-CS observed and shown to bind Ubc9, and 2) substitution of the consensus amino acid residues with amino acid residues exhibiting similar hydrophobicity. SUMOplot has been used in the past to predict Ubc9 dependent sites^{[8][9][10][11][12][13][14][15][16]}.

References

1. ^ Technology Feature - Table of Suppliers. (2004) Nature 428(6979) p232
2. ^ Abgent's Full list of articles produced
3. ^ P. White, et al. (2004) J. Pept. Sci. 10, 18
4. ^ Balbach J, Schmid FX. (2000). Proline isomerization and its catalysis in protein folding. In Mechanisms of Protein Folding 2nd ed. Editor RH Pain. Oxford University Press.
5. ^ T. Haack & M. Mutter (1992) Tetrahedron Lett. 33, 1589
6. ^ W.R.Sampson, et al. (1999) J. Pept. Sci. 5, 403
7. ^ P. White, et al. (2003) Biopolymers, 71, 338.P156
8. ^ Gramatikoff K. et al. In Frontiers of Biotechnology and Pharmaceuticals, Science Press USA Inc 2004; 4: 181 - 210
9. ^ Vyacheslav Yurchenko, Zhu Xue, and Moshe J. Sadofsky. SUMO Modification of Human XRCC4 Regulates Its Localization and Function in DNA Double-Strand Break Repair Mol. Cell. Biol., Mar 2006; 26: 1786 - 1794
10. ^ Meiluen Yang, Chia-Tse Hsu, Chun-Yuan Ting, Leroy F. Liu, and Jaulang Hwang. Assembly of a Polymeric Chain of SUMO1 on Human Topoisomerase I in Vitro J. Biol. Chem., Mar 2006; 281: 8264 - 8274
11. ^ Yutaka Morita, Chie Kanei-Ishii, Teruaki Nomura, and Shunsuke Ishii. TRAF7 Sequesters c-Myb to the Cytoplasm by Stimulating Its Sumoylation. Mol. Biol. Cell, Nov 2005; 16: 5433 - 5444
12. ^ Zhongshu Tang, Oussama El Far, Heinrich Betz, and Astrid Scheschonka. Pias1 Interaction and Sumoylation of Metabotropic Glutamate Receptor 8. J. Biol. Chem., Nov 2005; 280: 38153 - 38159
13. ^ Brigit E. Riley, Huda Y. Zoghbi, and Harry T. Orr. SUMOylation of the Polyglutamine Repeat Protein, Ataxin-1, Is Dependent on a Functional Nuclear Localization Signal. J. Biol. Chem., Jun 2005; 280: 21942 - 21948
14. ^ Timothy A. Hinsley, Pamela Cunliffe, Hannah J. Tipney, Andrew Brass, and May Tassabehji. Comparison of TFII-I gene family members deleted in Williams-Beuren syndrome. Protein Sci., Oct 2004; 13: 2588 - 2599
15. ^ Frederik Van Dyck, Els L. D. Delvaux, Wim J. M. Van de Ven, and Marcela V. Chavez. Repression of the Transactivating Capacity of the Oncoprotein PLAG1 by SUMOylation. J. Biol. Chem., Aug 2004; 279: 36121 - 36131.
16. ^ Tianwei Li, Evgenij Evdokimov, Rong-Fong Shen, Chien-Chung Chao, Ephrem Tekle, Tao Wang, Earl R. Stadtman, David C. H. Yang, and P. Boon Chock. Sumoylation of heterogeneous nuclear ribonucleoproteins, zinc finger proteins, and nuclear pore complex proteins: A proteomic analysis. PNAS, Jun 2004; 101: 8551 - 8556

See also

• SUMO protein
• SUMO pathway
• SUMO network
• Autophagy network
• Ubiquitin
• Pseudoproline
• Aurora inhibitors
• Kinome
• Diet and cancer
• PRMT4 pathway