2004, 5: R21-10.1186/gb-2004-5-3-r21.Boutin JA, Marande W, Petit L, Loynel A, Desmet C, Canet E, Fauchere JL: Investigation of S-farnesyl transferase substrate specificity with combinatorial tetrapeptide libraries. Int J Pept Protein Res. However, enzymatic activity for isoprenoid kinases capable converting isoprenoid alcohols to isoprenoid pyrophosphates have been shown.In addition, FTIs have shown some promise in treating a mouse model of A 2012 study found that statin treatment increases lifespan and improves cardiac health in Drosophila by decreasing specific protein prenylation. 2004, 117: 749-760. Proteins. The frequency of occurrence The primary role of the physical property term is to exclude query sequences that do not fit into the determined physical property profile of the motif (see Figure The natural logarithms (to be comparable to the profile score) of these single terms enter We have performed three jackknife tests to validate the robustness of our predictors. 10.1002/prot.340190207.Krigbaum WR, Komoriya A: Local interactions as a structure determinant for protein molecules: II. Naturwiss.

First, cross-validation over the whole scoring function (To address the role of homologous sequences remaining in the learning set for jackknife tests, we have extended the cross-validation to the more stringent case where not only the sequence to be predicted is excluded from the learning procedure but also its close homologs (estimated by a threshold of 40% sequence identity over the 30 carboxy-terminal residues). Accession numbers are as follows (GenBank unless indicated otherwise): Hs (Construction and calculation of the scoring function essentially follows the methodologies [The composite score function consists of a profile and physical property term.The profile matrix is calculated using the PSIC algorithm to account for redundancy in the learning set.

1994, 269: 19271-19278.Pereira-Leal JB, Seabra MC: Evolution of the Rab family of small GTP-binding proteins. 1A) (1). Hence, the CRPQ sequences remain below the prediction threshold in the jackknife test if no example of this motif is present in the learning set. "A 2012 clinical trial explored the approach of inhibiting protein prenylation with some degree of success in the treatment of Farnesyltransferase and geranylgeranyltransferase IFarnesyltransferase and geranylgeranyltransferase I Nucleic Acids Res. Polynoms with degrees higher than six would not result in an increase of the relative improvement of the residual. The CAAX-box proteins undergo three sequential, enzymatic, post-translational modifications essential to their targeting: First, the proteins are prenylated by one of two prenyltransferases called farnesyltransferase and geranylgeranyltransferase-I. 1994, 91: 1275-1279.Prendergast GC: Actin' up: RhoB in cancer and apoptosis. Edited by: Andrade MM. 2002, 317: 541-557. © 2020 BioMed Central Ltd unless otherwise stated. 10.1074/jbc.271.10.5289.Maurer-Stroh S, Washietl S, Eisenhaber F: Protein prenyltransferases. Cell. Hence, the self-consistencies or upper bounds of sensitivities of the FT and GGT1 predictors are 100%. 2003, 31: 3631-3634. 10.1093/nar/gkg095.Maurer-Stroh S, Eisenhaber B, Eisenhaber F: N-terminal N-myristoylation of proteins: refinement of the sequence motif and its taxon-specific differences. Biochem Biophys Res Commun. 1994, 1205: 39-48.Wilson AL, Erdman RA, Castellano F, Maltese WA: Prenylation of Rab8 GTPase by type I and type II geranylgeranyl transferases. 10.1002/elps.1150181505.Eisenhaber F, Eisenhaber B, Kubina W, Maurer-Stroh S, Neuberger G, Schneider G, Wildpaner M: Prediction of lipid posttranslational modifications and localization signals from protein sequences: big-Pi, NMT and PTS1. Most of CAAX box proteins do not have a transmembrane domain, thus, the prenylation process is crucial for the function of many signal transduction proteins. The lipid modification increases the hydrophobicity of proteins and enhances their affinity for cellular membranes (1). Oncogene. 2000, 301: 1077-1087.

2001, 58: 1636-1649.Sebti SM, Der CJ: Opinion: Searching for the elusive targets of farnesyltransferase inhibitors. Few questions regarding the CaaX motif and Prenylation. 1997, 18: 2714-2723. Can FTase prenylate CaaL and vice versa with GGTase Thanks! 2003, 303: 1-7. 10.1093/nar/30.7.1575.Tomii K, Kanehisa M: Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Proc Int Conf Intell Syst Mol Biol. Genome Res. 1996, 9: 27-36.Eisenhaber B, Bork P, Eisenhaber F: Sequence properties of GPI-anchored proteins near the omega-site: constraints for the polypeptide binding site of the putative transamidase. J Biol Chem. 1988, 32: 269-278.Finkelstein AV, Badretdinov AY, Ptitsyn OB: Physical reasons for secondary structure stability: alpha-helices in short peptides. Electrophoresis. Typically, a good starting point is the Swiss-Prot database [Unfortunately, such justified concerns dramatically lower the amount of data in the learning set. 10.1093/nar/30.1.235.Horton P, Nakai K: Better prediction of protein cellular localization sites with the k nearest neighbors classifier. Proc Natl Acad Sci USA. Biochim Biophys Acta. J Mol Biol. Electrophoresis. Protein Eng. 1979, 282: 109-111.Vihinen M, Torkkila E, Riikonen P: Accuracy of protein flexibility predictions. 1993, 330: 323-328. 10.1016/0022-2836(76)90191-1.Zvelebil MJ, Barton GJ, Taylor WR, Sternberg MJ: Prediction of protein secondary structure and active sites using the alignment of homologous sequences. 10.1016/0014-5793(93)80897-4.Sunyaev SR, Eisenhaber F, Rodchenkov IV, Eisenhaber B, Tumanyan VG, Kuznetsov EN: PSIC: profile extraction from sequence alignments with position-specific counts of independent observations. 10.1016/S1097-2765(03)00044-3.We thank Boehringer Ingelheim for continuous support. 10.1093/nar/25.24.4876.Pei J, Grishin NV: AL2CO: calculation of positional conservation in a protein sequence alignment. 2003, Wymondham, UK: Horizon Scientific Press, 81-105.Eisenhaber B, Bork P, Eisenhaber F: Prediction of potential GPI-modification sites in proprotein sequences. Given that appearance of a cysteine at this position is rare in databases (1.7%), the independent general probabilities of false-positive prediction by FT and GGT1 for all protein sequences are as low as 0.11% and 0.02%, respectively.

2004, 343: 417-433.

Membrane targeting of Rab GTPases is influenced by the prenylation motif.