Journal articles: 'Terminal and internal amino and amidoalkynes'

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Sjöquist, J., and C. B. Laurell. "N-Terminal Amino Acids of Isolated M-components." Acta Medica Scandinavica 170, S367 (April 24, 2009): 65–68. http://dx.doi.org/10.1111/j.0954-6820.1961.tb12424.x.

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Nethery, Kimberly A., C. Kuyler Doyle, Xiaofeng Zhang, and Jere W. McBride. "Ehrlichia canis gp200 Contains Dominant Species-Specific Antibody Epitopes in Terminal Acidic Domains." Infection and Immunity 75, no. 10 (August 6, 2007): 4900–4908. http://dx.doi.org/10.1128/iai.00041-07.

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ABSTRACT Species-specific antibody epitopes within several major immunoreactive protein orthologs of Ehrlichia species have recently been identified and molecularly characterized. In this study, dominant B-cell epitopes within the acidic (pI 5.35) ankyrin repeat-containing 200-kDa major immunoreactive protein (gp200) of Ehrlichia canis were defined. The E. canis gp200 gene (4,263 bp; 1,421 amino acids) was cloned and expressed as four (N-terminal, 1,107 bp; N-internal, 910 bp; C-internal, 1,000 bp; and C-terminal, 1,280 bp) overlapping recombinant proteins. The N-terminal, C-internal, and C-terminal polypeptides (369, 332, and 426 amino acids, respectively) were strongly recognized by antibody, and the major epitope(s) in these polypeptides was mapped to four polypeptide regions (40 to 70 amino acids). Smaller overlapping recombinant polypeptides (14 to 15 amino acids) spanning these regions identified five strongly immunoreactive species-specific epitopes that exhibited conformational dependence. The majority of the epitopes (four) were located in two strongly acidic (pI 4 to 4.9) domains in the distal N- and C-terminal regions of the protein flanking the centralized ankyrin domain-containing region. The amino acid content of the epitope-containing domains included a high proportion of strongly acidic amino acids (glutamate and aspartate), and these domains appear to have important biophysical properties that influence the antibody response to gp200.

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Wright, Sue P., Tim C. R. Prickett, Robert N. Doughty, Chris Frampton, Greg D. Gamble, Tim G. Yandle, Norman Sharpe, and Mark Richards. "Amino-Terminal Pro–C-Type Natriuretic Peptide in Heart Failure." Hypertension 43, no. 1 (January 2004): 94–100. http://dx.doi.org/10.1161/01.hyp.0000105623.04382.c0.

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Hamilton, VaNae, Ujjal K. Singha, Joseph T. Smith, Ebony Weems, and Minu Chaudhuri. "Trypanosome Alternative Oxidase Possesses both an N-Terminal and Internal Mitochondrial Targeting Signal." Eukaryotic Cell 13, no. 4 (February 21, 2014): 539–47. http://dx.doi.org/10.1128/ec.00312-13.

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ABSTRACTRecognition of mitochondrial targeting signals (MTS) by receptor translocases of outer and inner membranes of mitochondria is one of the prerequisites for import of nucleus-encoded proteins into this organelle. The MTS for a majority of trypanosomatid mitochondrial proteins have not been well defined. Here we analyzed the targeting signal for trypanosome alternative oxidase (TAO), which functions as the sole terminal oxidase in the infective form ofTrypanosoma brucei. Deleting the first 10 of 24 amino acids predicted to be the classical N-terminal MTS of TAO did not affect its import into mitochondriain vitro. Furthermore, ectopically expressed TAO was targeted to mitochondria in both forms of the parasite even after deletion of first 40 amino acid residues. However, deletion of more than 20 amino acid residues from the N terminus reduced the efficiency of import. These data suggest that besides an N-terminal MTS, TAO possesses an internal mitochondrial targeting signal. In addition, both the N-terminal MTS and the mature TAO protein were able to target a cytosolic protein, dihydrofolate reductase (DHFR), to aT. bruceimitochondrion. Further analysis identified a cryptic internal MTS of TAO, located within amino acid residues 115 to 146, which was fully capable of targeting DHFR to mitochondria. The internal signal was more efficient than the N-terminal MTS for import of this heterologous protein. Together, these results show that TAO possesses a cleavable N-terminal MTS as well as an internal MTS and that these signals act together for efficient import of TAO into mitochondria.

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Campbell, Duncan J., Anthony J. Valentijn, and Rosemary Condron. "Purification and amino-terminal sequence of rat kidney renin." Journal of Hypertension 9, no. 1 (January 1991): 29–34. http://dx.doi.org/10.1097/00004872-199101000-00005.

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Campbell, Duncan J., Anthony J. Valentijn, and Rosemary Condron. "Purification and amino-terminal sequence of rat kidney renin." Journal of Hypertension 9, no. 1 (1991): 29???34. http://dx.doi.org/10.1097/00004872-199109010-00005.

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Buhi, W. C., I. M. Alvarez, V. M. Shille, M. J. Thatcher, J. P. Harney, and M. Cotton. "Purification and characterization of a uterine retinol-binding protein in the bitch." Biochemical Journal 311, no. 2 (October 15, 1995): 407–15. http://dx.doi.org/10.1042/bj3110407.

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A major canine endometrial secreted protein (cP6, 23,000-M(r)) was purified by ion-exchange and gel-filtration chromatography and characterized by two-dimensional gel electrophoresis. Anti-[human retinol-binding protein (hRBP)] serum identified cP6 on immunoblot analysis and immunoprecipitated cP6 from culture medium. This major protein was also shown to bind [3H]retinol. N-terminal and internal amino acid sequences were determined and compared with previously identified protein, RNA, or DNA sequences. N-terminal analysis revealed that cP6 had high identity and similarity to serum retinol-binding proteins (RBPs), while internal sequence analysis showed a strong similarity to rat androgen-dependent epididymal protein and beta-lactoglobulins. Amino acid analysis, however, showed significant differences between these proteins and cP6 in both total amino acid content and certain selected amino acids. Immunohistochemical analysis showed staining for RBP only in the uterine luminal epithelium. These studies suggest that bitch endometrium secretes a family of proteins (cP6), some of which bind [3H]retinol, are immunologically related to the RBP family, and have N-terminal and internal sequences with a high similarity to RBP, beta-lactoglobulins and other members of the lipocalin family. This family of proteins may be important in early development for supplying retinol or derivatives to the developing embryo.

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Sanchez, Aniel, Yassel Ramos, Yanni Solano, Luis Javier González, Lazaro Betancourt, Jeovanis Gil, Gabriel Padron, and Vladimir Besada. "Letter: Specific Isotope Labeling for the Identification of Free N-Terminal Peptides of Proteins Separated by Polyacrylamide Gel Electrophoresis." European Journal of Mass Spectrometry 13, no. 4 (August 2007): 307–9. http://dx.doi.org/10.1255/ejms.880.

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We report here a method for the identification of free N-terminal peptides of in gel digested isolated proteins. It is based on the difference between the isotopic ion distribution of the N-terminal peptide and internal peptides. After guanidination of lysine residues, the primary amino groups of the gel-entrapped protein are blocked with an equimolar mixture of normal and deuterated acetic anhydride. Upon MS analysis, internal peptides display a normal isotopic ion distribution while the N-terminal peptide shows a complex isotopic ion distribution.

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Li, Wen-Yi, Fu-Chun Chiu, Yu-Fen Chien, Jou-Wei Lin, and Juey-Jen Hwang. "Association of Amino-terminal Pro-brain Natriuretic Peptide with Metabolic Syndrome." Internal Medicine 50, no. 11 (2011): 1143–47. http://dx.doi.org/10.2169/internalmedicine.50.4765.

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MOREIRA, C., F. SEREJO, P. ALCANTARA, M. GATOVARELA, C. SALDANHA, and J. BRAZNOGUEIRA. "Ambulatory blood pressure, procolagen amino-terminal polypeptide (P-III-P) and hemorreologyc parameters." American Journal of Hypertension 18, no. 5 (May 2005): A154—A155. http://dx.doi.org/10.1016/j.amjhyper.2005.03.429.

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11

Soppa, Jörg. "Protein Acetylation in Archaea, Bacteria, and Eukaryotes." Archaea 2010 (2010): 1–9. http://dx.doi.org/10.1155/2010/820681.

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Proteins can be acetylated at the alpha-amino group of the N-terminal amino acid (methionine or the penultimate amino acid after methionine removal) or at the epsilon-amino group of internal lysines. In eukaryotes the majority of proteins are N-terminally acetylated, while this is extremely rare in bacteria. A variety of studies about N-terminal acetylation in archaea have been reported recently, and it was revealed that a considerable fraction of proteins is N-terminally acetylated in haloarchaea andSulfolobus, while this does not seem to apply for methanogenic archaea. Many eukaryotic proteins are modified by differential internal acetylation, which is important for a variety of processes. Until very recently, only two bacterial proteins were known to be acetylation targets, but now 125 acetylation sites are known forE. coli. Knowledge about internal acetylation in archaea is extremely limited; only two target proteins are known, only one of which—Alba—was used to study differential acetylation. However, indications accumulate that the degree of internal acetylation of archaeal proteins might be underestimated, and differential acetylation has been shown to be essential for the viability of haloarchaea. Focused proteomic approaches are needed to get an overview of the extent of internal protein acetylation in archaea.

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Asleson, Erin N., Ron J. Okagaki, and Dennis M. Livingston. "A Core Activity Associated with the N Terminus of the Yeast RAD52 Protein Is Revealed by RAD51 Overexpression Suppression of C-Terminal rad52 Truncation Alleles." Genetics 153, no. 2 (October 1, 1999): 681–92. http://dx.doi.org/10.1093/genetics/153.2.681.

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Abstract C-terminal rad52 truncation and internal deletion mutants were characterized for their ability to repair MMS-induced double-strand breaks and to produce viable spores during meiosis. The rad52-Δ251 allele, encoding the N-terminal 251 amino acids of the predicted 504-amino-acid polypeptide, supports partial activity for both functions. Furthermore, RAD51 overexpression completely suppresses the MMS sensitivity of a rad52-Δ251 mutant. The absence of the C terminus in the truncated protein makes it likely that suppression occurs by bypassing the C-terminal functions of Rad52p. RAD51 overexpression does not suppress the low level of spore viability that the rad52-Δ251 allele causes and only partially suppresses the defect in rad52 alleles encoding the N-terminal 292 or 327 amino acids. The results of this study also show that intragenic complementation between rad52 alleles is governed by a complex relationship that depends heavily on the two alleles involved and their relative dosage. In heteroallelic rad52 diploids, the rad52-Δ251 allele does not complement rad52 missense mutations altering residues 61 or 64 in the N terminus. However, complementation is achieved with each of these missense alleles when the rad52-Δ251 allele is overexpressed. Complementation also occurs between rad52-Δ327 and an internal deletion allele missing residues 210 through 327. We suggest that the first 251 amino acids of Rad52p constitute a core domain that provides critical RAD52 activities.

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Lees-Miller, J. P., L. O. Goodwin, and D. M. Helfman. "Three novel brain tropomyosin isoforms are expressed from the rat alpha-tropomyosin gene through the use of alternative promoters and alternative RNA processing." Molecular and Cellular Biology 10, no. 4 (April 1990): 1729–42. http://dx.doi.org/10.1128/mcb.10.4.1729-1742.1990.

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cDNA clones encoding three novel tropomyosins, termed TMBr-1, TMBr-2, and TMBr-3, were isolated and characterized from a rat brain cDNA library. All are derived from a single gene, which was previously found to express striated muscle alpha-tropomyosin and a number of other tropomyosin isoforms via an alternative splicing mechanism (N. Ruiz-Opazo and B. Nadal-Ginard, J. Biol. Chem. 262:4755-4765, 1987; D. F. Wieczorek, C. W. J. Smith, and B. Nadal-Ginard, Mol. Cell. Biol. 8:679-694, 1988). The derived amino acid sequences revealed that TMBr-1 contains 281 amino acids, TMBr-2 contains 251 amino acids, and TMBr-3 contains 245 amino acids. All three proteins contain a region that is identical to amino acids 81 through 258 of skeletal muscle alpha-tropomyosin. TMBr-1 is identical to striated muscle alpha-tropomyosin from amino acids 1 through 258 but contains a novel COOH-terminal region from amino acids 259 through 281. TMBr-2 and TMBr-3 both contain identical NH2-terminal sequences from amino acids 1 through 44 which were found to be expressed from a novel promoter. TMBr-3 contains the same COOH-terminal region as TMBr-1, whereas TMBr-2 contains a second novel COOH-terminal region. The genomic organization of the exons encoding TMBr-1, TMBr-2, and TMBr-3 were determined. These studies revealed a previously uncharacterized promoter located in the internal region of the alpha-TM gene as well as two novel COOH-terminal coding exons. The alpha-TM gene is a complex transcription unit containing 15 exons including two alternative promoters, two internal mutually exclusive exon cassettes, and four alternatively spliced 3' exons that encode four different COOH-terminal coding regions. A total of nine distinct mRNAs are known to be expressed from the alpha-TM gene in a cell type-specific manner in tissues such as striated muscle, smooth muscle, kidney, liver, brain, and fibroblasts. The mRNAs encoding TMBr-1, TMBr-2, and TMBr-3 were found to be expressed only in brain tissue, with TMBr-3 being expressed at much greater levels than TMBr-1 and TMBr-2. The individual structural characteristics of each brain alpha-tropomyosin isoform and their possible functions are discussed.

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Lees-Miller, J. P., L. O. Goodwin, and D. M. Helfman. "Three novel brain tropomyosin isoforms are expressed from the rat alpha-tropomyosin gene through the use of alternative promoters and alternative RNA processing." Molecular and Cellular Biology 10, no. 4 (April 1990): 1729–42. http://dx.doi.org/10.1128/mcb.10.4.1729.

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cDNA clones encoding three novel tropomyosins, termed TMBr-1, TMBr-2, and TMBr-3, were isolated and characterized from a rat brain cDNA library. All are derived from a single gene, which was previously found to express striated muscle alpha-tropomyosin and a number of other tropomyosin isoforms via an alternative splicing mechanism (N. Ruiz-Opazo and B. Nadal-Ginard, J. Biol. Chem. 262:4755-4765, 1987; D. F. Wieczorek, C. W. J. Smith, and B. Nadal-Ginard, Mol. Cell. Biol. 8:679-694, 1988). The derived amino acid sequences revealed that TMBr-1 contains 281 amino acids, TMBr-2 contains 251 amino acids, and TMBr-3 contains 245 amino acids. All three proteins contain a region that is identical to amino acids 81 through 258 of skeletal muscle alpha-tropomyosin. TMBr-1 is identical to striated muscle alpha-tropomyosin from amino acids 1 through 258 but contains a novel COOH-terminal region from amino acids 259 through 281. TMBr-2 and TMBr-3 both contain identical NH2-terminal sequences from amino acids 1 through 44 which were found to be expressed from a novel promoter. TMBr-3 contains the same COOH-terminal region as TMBr-1, whereas TMBr-2 contains a second novel COOH-terminal region. The genomic organization of the exons encoding TMBr-1, TMBr-2, and TMBr-3 were determined. These studies revealed a previously uncharacterized promoter located in the internal region of the alpha-TM gene as well as two novel COOH-terminal coding exons. The alpha-TM gene is a complex transcription unit containing 15 exons including two alternative promoters, two internal mutually exclusive exon cassettes, and four alternatively spliced 3' exons that encode four different COOH-terminal coding regions. A total of nine distinct mRNAs are known to be expressed from the alpha-TM gene in a cell type-specific manner in tissues such as striated muscle, smooth muscle, kidney, liver, brain, and fibroblasts. The mRNAs encoding TMBr-1, TMBr-2, and TMBr-3 were found to be expressed only in brain tissue, with TMBr-3 being expressed at much greater levels than TMBr-1 and TMBr-2. The individual structural characteristics of each brain alpha-tropomyosin isoform and their possible functions are discussed.

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Miyazawa, S., T. Osumi, T. Hashimoto, K. Ohno, S. Miura, and Y. Fujiki. "Peroxisome targeting signal of rat liver acyl-coenzyme A oxidase resides at the carboxy terminus." Molecular and Cellular Biology 9, no. 1 (January 1989): 83–91. http://dx.doi.org/10.1128/mcb.9.1.83-91.1989.

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To identify the topogenic signal of peroxisomal acyl-coenzyme A oxidase (AOX) of rat liver, we carried out in vitro import experiments with mutant polypeptides of the enzyme. Full-length AOX and polypeptides that were truncated at the N-terminal region were efficiently imported into peroxisomes, as determined by resistance to externally added proteinase K. Polypeptides carrying internal deletions in the C-terminal region exhibited much lower import activities. Polypeptides that were truncated or mutated at the extreme C terminus were totally import negative. When the five amino acid residues at the extreme C terminus were attached to some of the import-negative polypeptides, the import activities were rescued. Moreover, the C-terminal 199 and 70 amino acid residues of AOX directed fusion proteins with two bacterial enzymes to peroxisomes. These results are interpreted to mean that the peroxisome targeting signal of AOX residues at the C terminus and the five or fewer residues at the extreme terminus have an obligatory function in targeting. The C-terminal internal region also has an important role for efficient import, possibly through a conformational effect.

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Miyazawa, S., T. Osumi, T. Hashimoto, K. Ohno, S. Miura, and Y. Fujiki. "Peroxisome targeting signal of rat liver acyl-coenzyme A oxidase resides at the carboxy terminus." Molecular and Cellular Biology 9, no. 1 (January 1989): 83–91. http://dx.doi.org/10.1128/mcb.9.1.83.

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To identify the topogenic signal of peroxisomal acyl-coenzyme A oxidase (AOX) of rat liver, we carried out in vitro import experiments with mutant polypeptides of the enzyme. Full-length AOX and polypeptides that were truncated at the N-terminal region were efficiently imported into peroxisomes, as determined by resistance to externally added proteinase K. Polypeptides carrying internal deletions in the C-terminal region exhibited much lower import activities. Polypeptides that were truncated or mutated at the extreme C terminus were totally import negative. When the five amino acid residues at the extreme C terminus were attached to some of the import-negative polypeptides, the import activities were rescued. Moreover, the C-terminal 199 and 70 amino acid residues of AOX directed fusion proteins with two bacterial enzymes to peroxisomes. These results are interpreted to mean that the peroxisome targeting signal of AOX residues at the C terminus and the five or fewer residues at the extreme terminus have an obligatory function in targeting. The C-terminal internal region also has an important role for efficient import, possibly through a conformational effect.

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Liu, Xiangli, Lidan Liu, Weizhen Bi, and Joseph L. Alcorn. "An internal amino-terminal FLAG-tag octapeptide alters oligomerization of expressed surfactant protein-A." Protein Expression and Purification 176 (December 2020): 105727. http://dx.doi.org/10.1016/j.pep.2020.105727.

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18

Seong, Won Joon, Seung Chan Kim, Dae Gy Hong, Tae Bon Koo, and Il Soo Park. "Amino-Terminal Pro-Brain Natriuretic Peptide Levels in Hypertensive Disorders Complicating Pregnancy." Hypertension in Pregnancy 30, no. 3 (August 11, 2010): 287–94. http://dx.doi.org/10.3109/10641950903115046.

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MONLEÓN, Daniel, Vicent ESTEVE, Helena KOVACS, Juan J. CALVETE, and Bernardo CELDA. "Conformation and concerted dynamics of the integrin-binding site and the C-terminal region of echistatin revealed by homonuclear NMR." Biochemical Journal 387, no. 1 (March 22, 2005): 57–66. http://dx.doi.org/10.1042/bj20041343.

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Echistatin is a potent antagonist of the integrins αvβ3, α5β1 and αIIbβ3. Its full inhibitory activity depends on an RGD (Arg-Gly-Asp) motif expressed at the tip of the integrin-binding loop and on its C-terminal tail. Previous NMR structures of echistatin showed a poorly defined integrin-recognition sequence and an incomplete C-terminal tail, which left the molecular basis of the functional synergy between the RGD loop and the C-terminal region unresolved. We report a high-resolution structure of echistatin and an analysis of its internal motions by off-resonance ROESY (rotating-frame Overhauser enhancement spectroscopy). The full-length C-terminal polypeptide is visible as a β-hairpin running parallel to the RGD loop and exposing at the tip residues Pro43, His44 and Lys45. The side chains of the amino acids of the RGD motif have well-defined conformations. The integrin-binding loop displays an overall movement with maximal amplitude of 30°. Internal angular motions in the 100–300 ps timescale indicate increased flexibility for the backbone atoms at the base of the integrin-recognition loop. In addition, backbone atoms of the amino acids Ala23 (flanking the R24GD26 tripeptide) and Asp26 of the integrin-binding motif showed increased angular mobility, suggesting the existence of major and minor hinge effects at the base and the tip, respectively, of the RGD loop. A strong network of NOEs (nuclear Overhauser effects) between residues of the RGD loop and the C-terminal tail indicate concerted motions between these two functional regions. A full-length echistatin–αvβ3 docking model suggests that echistatin's C-terminal amino acids may contact αv-subunit residues and provides new insights to delineate structure–function correlations.

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Silverman, L., and M. D. Resh. "Lysine residues form an integral component of a novel NH2-terminal membrane targeting motif for myristylated pp60v-src." Journal of Cell Biology 119, no. 2 (October 15, 1992): 415–25. http://dx.doi.org/10.1083/jcb.119.2.415.

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Association of pp60v-src with the plasma membrane is fundamental to generation of the transformed phenotype. Although myristylation of pp60v-src is required for interaction with a membrane-bound receptor, the importance of NH2-terminal amino acids in receptor binding has not yet been uncoupled from their role in signaling myristylation. Using chimeric src proteins, peptides identical or related to the NH2 terminus of src, and site-directed mutagenesis, we demonstrate that NH2-terminal lysines in conjunction with myristate are essential for membrane localization. Subsequent to NH2-terminal interaction with the "src receptor," internal regions of the src protein also participate in membrane binding. This novel NH2-terminal motif and internal contact mechanism may direct other members of the src family of tyrosine kinases to their membrane receptors.

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Morishita, Masayo, and JoAnne Engebrecht. "Sorting Signals within the Saccharomyces cerevisiae Sporulation-Specific Dityrosine Transporter, Dtr1p, C Terminus Promote Golgi-to-Prospore Membrane Transport." Eukaryotic Cell 7, no. 10 (August 1, 2008): 1674–84. http://dx.doi.org/10.1128/ec.00151-08.

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ABSTRACT During sporulation in Saccharomyces cerevisiae, the dityrosine transporter Dtr1p, which is required for formation of the outermost layer of the spore wall, is specifically expressed and transported to the prospore membrane, a novel double-lipid-bilayer membrane. Dtr1p consists of 572 amino acids with predicted N- and C-terminal cytoplasmic extensions and 12 transmembrane domains. Dtr1p missing the largest internal cytoplasmic loop was trapped in the endoplasmic reticulum in both mitotically dividing cells and cells induced to sporulate. Deletion of the carboxyl 15 amino acids, but not the N-terminal extension of Dtr1p, resulted in a protein that failed to localize to the prospore membrane and was instead observed in cytoplasmic puncta. The puncta colocalized with a cis-Golgi marker, suggesting that Dtr1p missing the last 15 amino acids was trapped in an early Golgi compartment. Deletion of the C-terminal 10 amino acids resulted in a protein that localized to the prospore membrane with a delay and accumulated in cytoplasmic puncta that partially colocalized with a trans-Golgi marker. Both full-length Dtr1p and Dtr1p missing the last 10 amino acids expressed in vegetative cells localized to the plasma membrane and vacuoles, while Dtr1p deleted for the carboxyl-terminal 15 amino acids was observed only at vacuoles, suggesting that transport to the prospore membrane is mediated by distinct signals from those that specify plasma membrane localization. Transfer-of-function experiments revealed that both the carboxyl transmembrane domain and the C-terminal tail are important for Golgi complex-to-prospore membrane transport.

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Vanfleteren, J. R., E. A. I. M. Evers, G. Van de Werken, and J. J. Van Beeumen. "The primary structure of cytochrome c from the nematode Caenorhabditis elegans." Biochemical Journal 271, no. 3 (November 1, 1990): 613–20. http://dx.doi.org/10.1042/bj2710613.

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The complete amino acid sequence of cytochrome c from the nematode Caenorhabditis elegans was determined. The native protein displays the same spectral properties in the oxidized and reduced states as horse heart cytochrome c. The apoprotein consists of 110 amino acid residues and differs from human cytochrome c by 44 substitutions, one internal deletion, five N-terminal additions and two C-terminal additions. One of the substitutions is the replacement of an ‘invariant’ phenylalanine residue at position 15 by tyrosine. The N-terminal sequence extension contains a short peptide motif, which is highly homologous with a peptide fragment present at the N-terminus of annelid and insect cytochrome c sequences. From the number of amino acid changes and the evolutionary rate of cytochrome c it would appear that nematodes diverged from a line leading to man about 1.4 billion years ago. When similar data based on the amino acid sequences of the histones H1, H2A, H2B and H3 are taken into account, the average estimate is 1.1 +/- 0.1 billion years.

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Wu, H., and J. T. Parsons. "Cortactin, an 80/85-kilodalton pp60src substrate, is a filamentous actin-binding protein enriched in the cell cortex." Journal of Cell Biology 120, no. 6 (March 15, 1993): 1417–26. http://dx.doi.org/10.1083/jcb.120.6.1417.

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Two related cellular proteins, p80 and p85 (cortactin), become phosphorylated on tyrosine in pp60src-transformed cells and in cells stimulated with certain growth factors. The amino-terminal half of cortactin is comprised of multiple copies of an internal, tandem 37-amino acid repeat. The carboxyl-terminal half contains a distal SH3 domain. We report that cortactin is an F-actin-binding protein. The binding to F-actin is specific and saturable. The amino-terminal repeat region appears to be both necessary and sufficient to mediate actin binding, whereas the SH3 domain had no apparent effect on the actin-binding activity. Cortactin, present in several different cell types, is enriched in cortical structures such as membrane ruffles and lamellipodia. The properties of cortactin indicate that it may be important for microfilament-membrane interactions as well as transducing signals from the cell surface to the cytoskeleton. We suggest the name cortactin, reflecting the cortical subcellular localization and its actin-binding activity.

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Brand, S. R., R. M. Bernstein, and M. B. Mathews. "Autoreactive epitope profiles of the proliferating cell nuclear antigen define two classes of autoantibodies." Journal of Immunology 152, no. 8 (April 15, 1994): 4120–28. http://dx.doi.org/10.4049/jimmunol.152.8.4120.

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Abstract The proliferating cell nuclear antigen (PCNA) is a conserved protein required for cellular DNA replication. PCNA was first recognized using serum from the autoimmune disease SLE. To analyze the regions on PCNA that confer autoantibody binding, we modified the cDNA encoding full-length PCNA to generate a series of amino terminal, carboxyl terminal and internally deleted constructs, which were transcribed and then translated in vitro using the wheat germ cell-free translation system. An immunoprecipitation assay was used to study the ability of these mutated forms of PCNA to bind anti-PCNA Abs from patients with SLE. Eight of the ten sera studied required a protein of nearly full length for binding: antigenicity was abrogated by removal of 39 amino acids from the amino terminus, by various internal deletions, or by the removal of 15 (but not 11) amino acids from the carboxyl terminus. The remaining two sera exhibited an Ab-binding specificity to the carboxyl-terminally truncated proteins similar to that of the majority of anti-PCNA sera, but their specificity was different in the amino terminus: these sera were able to recognize PCNA lacking over 40% of sequence in the amino terminus, but they did not bind proteins with short internal deletions in that region. Thus, these epitopes appear to be conformational and distinguish two classes of autoimmune sera.

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OH, Young L., Bumsuk HAHM, Yoon K. KIM, Hae K. LEE, Joo W. LEE, Ok K. SONG, Kyoko TSUKIYAMA-KOHARA, Michinori KOHARA, Akio NOMOTO, and Sung K. JANG. "Determination of functional domains in polypyrimidine-tract-binding protein." Biochemical Journal 331, no. 1 (April 1, 1998): 169–75. http://dx.doi.org/10.1042/bj3310169.

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Polypyrimidine-tract-binding protein (PTB) is involved in pre-mRNA splicing and internal-ribosomal-entry-site-dependent translation. The biochemical properties of various segments of PTB were analysed in order to understand the molecular basis of the PTB functions. The protein exists in oligomeric as well as monomeric form. The central part of PTB (amino acids 169–293) plays a major role in the oligomerization. PTB contains several RNA-binding motifs. Among them, the C-terminal part of PTB (amino acids 329–530) exhibited the strongest RNA-binding activity. The N-terminal part of PTB is responsible for the enhancement of RNA binding by HeLa cell cytoplasmic factor(s).

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Voorberg, J., R. Fontijn, J. Calafat, H. Janssen, J. A. van Mourik, and H. Pannekoek. "Assembly and routing of von Willebrand factor variants: the requirements for disulfide-linked dimerization reside within the carboxy-terminal 151 amino acids." Journal of Cell Biology 113, no. 1 (April 1, 1991): 195–205. http://dx.doi.org/10.1083/jcb.113.1.195.

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The precursor protein of von Willebrand factor (pro-vWF) consists of four different repeated domains, denoted D1-D2-D'-D3-A1-A2-A3-D4-B1-B2-B3-C1-C2, followed by a carboxy-terminal region of 151 amino acids without obvious internal homology. Previously, we have shown the requirement of the domains D1, D2, D', and D3 of pro-vWF in the assembly of pro-vWF dimers into multimers. Here, we define the domains of vWF involved in dimerization, using deletion mutants of full-length vWF cDNA transiently expressed in monkey kidney COS-1 cells. It is shown that only the carboxy-terminal 151 amino acid residues of vWF are required for dimerization. In addition, by analyzing a construct, encoding only the carboxy-terminal 151 amino acids of vWF, we find that the formation of dimers is an event independent of other domains present on pro-vWF, such as the domains C1 and C2 previously suggested to be involved in dimerization. Furthermore, it is shown that a deletion mutant of vWF, lacking the carboxy-terminal 151 amino acid residues and thus unable to dimerize, is proteolytically degraded in the ER. In contrast, a mutant protein, composed only of the carboxy-terminal 151 amino acids of vWF, and able to dimerize, is transported from the ER in a similar fashion as wild-type vWF. The role of the ER in the assembly of vWF is discussed with regard to the data presented in this paper on the intracellular fate of several vWF mutant proteins.

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Engle, Sarah M., Justin J. Crowder, Sheldon G. Watts, Christopher J. Indovina, Samuel Z. Coffey, and Eric M. Rubenstein. "Acetylation of N-terminus and two internal amino acids is dispensable for degradation of a protein that aberrantly engages the endoplasmic reticulum translocon." PeerJ 5 (August 22, 2017): e3728. http://dx.doi.org/10.7717/peerj.3728.

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Conserved homologues of the Hrd1 ubiquitin ligase target for degradation proteins that persistently or aberrantly engage the endoplasmic reticulum translocon, including mammalian apolipoprotein B (apoB; the major protein component of low-density lipoproteins) and the artificial yeast protein Deg1-Sec62. A complete understanding of the molecular mechanism by which translocon-associated proteins are recognized and degraded may inform the development of therapeutic strategies for cholesterol-related pathologies. Both apoB and Deg1-Sec62 are extensively post-translationally modified. Mass spectrometry of a variant of Deg1-Sec62 revealed that the protein is acetylated at the N-terminal methionine and two internal lysine residues. N-terminal and internal acetylation regulates the degradation of a variety of unstable proteins. However, preventing N-terminal and internal acetylation had no detectable consequence for Hrd1-mediated proteolysis of Deg1-Sec62. Our data highlight the importance of empirically validating the role of post-translational modifications and sequence motifs on protein degradation, even when such elements have previously been demonstrated sufficient to destine other proteins for destruction.

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Motté, P., G. Alberici, M. Ait-Abdellah, and D. Bellet. "Monoclonal antibodies distinguish synthetic peptides that differ in one chemical group." Journal of Immunology 138, no. 10 (May 15, 1987): 3332–38. http://dx.doi.org/10.4049/jimmunol.138.10.3332.

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Abstract By using human calcitonin (hCT), human calcitonin-gene-related peptide (hCGRP), and a synthetic peptide with a sequence analogous to the 34 C-terminal amino acids of human preprocalcitonin (designated as PQN-34) as haptens in the generation of monoclonal antibodies, we assessed the role of amido and amino groups in paratope-epitope binding. By using peptide inhibition experiments and solid-phase immunoassays, monoclonal anti-hCT antibody CT07 and monoclonal anti-hCGRP antibody CGR01 were found to bind to an antigenic determinant located in the C-terminal segment of the hormones. These epitopes comprise the seven C-terminal amino acids of the hormones, and the presence of the hormone-ending carboxamide group was found to be essential for antibody binding. The corresponding heptapeptides, either bearing a carboxyl group or else linked to a glycine residue at their C-terminal part, failed to react with the antibodies. Moreover, these monoclonal antibodies did not bind to synthetic peptides analogous to the C-terminal region of the hormone precursor molecules that comprised the epitope site flanked by a peptide sequence. In an attempt to assess whether amido groups when present on the side-chain of amino acids may also modulate antibody binding, a monoclonal antibody referred to as QPO1 was produced and was found to recognize an antigenic determinant localized in the N-terminal region of the PQN-34 peptide bearing a glutamine residue as the N-terminal amino acid. The epitope was found to correspond to a topographic assembled site, and binding of QPO1 was found to be substantially dependent on the presence of the free amino and the side-chain amido groups borne by the N-terminal glutamine residue of this peptide PQN-34. In contrast to these findings, an antigenic determinant located in the internal sequence of calcitonin and recognized by monoclonal anti-hCT antibody CT08 was found to be expressed on the mature form of the hormone, as well as on synthetic peptides with sequence mimicking that of preprocalcitonin. These data should guide the choice of synthetic peptide haptens for the production of anti-protein antibodies.

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Lillquist, J. S., P. L. Simon, M. Summers, Z. Jonak, and P. R. Young. "Structure-activity studies of human IL-1 beta with mature and truncated proteins expressed in Escherichia coli." Journal of Immunology 141, no. 6 (September 15, 1988): 1975–81. http://dx.doi.org/10.4049/jimmunol.141.6.1975.

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Abstract IL-1 beta is synthesized as an inactive 31-kDa intracellular protein, which is then processed upon secretion to an active 17-kDa carboxyl-terminal fragment. To identify the minimal portion of IL-1 beta required for activity, we constructed several deletion mutants of mature IL-1 beta. These included three amino-terminal deletions of 10, 16, and 81 amino acids, two carboxyl-terminal deletions of 17 and 72 amino acids, and one internal fragment between amino acids 17 and 81. Expression of the mutants was monitored by Western blots and immunoprecipitation. With one exception, all of these mutants and the full length 17-kDa IL-1 beta were expressed as soluble protein in Escherichia coli and could be assayed for activity and receptor binding in lysates without further purification. Whereas the intact 17-kDa IL-1 beta retained full biologic activity (greater than 10(7) U/ml of lysate) and competed for binding with 125I-labeled IL-1 beta, none of the lysates containing IL-1 beta deletion mutant proteins had activity or competed for binding to receptor at significantly higher concentrations. The loss of function in the smallest C-terminal deletion mutant does not appear to be due to the direct involvement of these C-terminal residues in receptor binding because both monoclonal and polyclonal antisera directed to this region bind to IL-1 beta but do not neutralize its activity. Therefore, this region is probably indirectly involved in sustaining the structure of the receptor-binding site.

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30

Navarro, Salvador, Rodrigo Valderrama, José M. Lopez, America Giménez, Juan Caballería, Albert Parés, and Laureano Fernandez-Cruz. "Serum Amino-Terminal Propeptide of Type III Procollagen Levels in Chronic Pancreatitis." Pancreas 12, no. 2 (March 1996): 153–58. http://dx.doi.org/10.1097/00006676-199603000-00008.

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31

Naik, U. P., Y. H. Ehrlich, and E. Kornecki. "Mechanisms of platelet activation by a stimulatory antibody: cross-linking of a novel platelet receptor for monoclonal antibody F11 with the FcγRII receptor." Biochemical Journal 310, no. 1 (August 15, 1995): 155–62. http://dx.doi.org/10.1042/bj3100155.

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The mechanisms by which a stimulatory monoclonal antibody (mAb), called mAb F11, induces granular secretion and aggregation in human platelets have been characterized. Fab fragments of mAb F11, as well as an mAb directed against the platelet Fc gamma RII receptor (mAb IV.3) were found to inhibit mAb F11-induced platelet secretion and aggregation, indicating that the mAb F11 IgG molecule interacts with the Fc gamma RII receptor through its Fc domain and with its own antigen through its Fab domain. The mAb F11 recognized two platelet proteins of 32 and 35 kDa on the platelet membrane surface, as identified by Western blot analysis. We purified both proteins from human platelet membranes using DEAE-Sepharose chromatography followed by mAb F11 affinity chromatography. When added to platelet-rich plasma, the purified proteins dose-dependently inhibited mAb F11-induced platelet aggregation. The purified protein preparation also competitively inhibited the binding of 125I-labelled mAb F11 to intact platelets. The N-terminal 26 amino acid sequences of both the 32 and 35 kDa proteins were identical and contained a single unblocked serine in the N-terminal position. When digested with N-glycanase, the 32 and 35 kDa proteins were converted into a single approximately 29 kDa protein, indicating that these two proteins are derived from the same core protein but differ in their degree of glycosylation. Internal amino acid sequence analysis of the F11 antigen provided information concerning 68 amino acids and suggested two consensus phosphorylation sites for protein kinase C (PKC). The phosphorylation by PKC of the isolated F11 antigen was observed following stimulation by phorbol 12-myristate 13-acetate. Databank analysis of the N-terminal and internal amino acid sequences of the F11 antigen indicated that the N-terminal sequence exhibited the highest degree of similarity to the variable region of the alpha-chain of human T-cell receptors (TCR). In contrast, the F11 internal sequences did not exhibit any similarity to the TCR. Our results demonstrate that the F11 antigen is a novel platelet membrane surface glycoprotein which becomes cross-linked with the Fc gamma RII receptor when platelets are activated by the stimulatory mAb F11. These mechanisms may be relevant to the production of immune thrombocytopenia by platelet-activating antibodies.

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Chung, L. P., D. R. Bentley, and K. B. Reid. "Molecular cloning and characterization of the cDNA coding for C4b-binding protein, a regulatory protein of the classical pathway of the human complement system." Biochemical Journal 230, no. 1 (August 15, 1985): 133–41. http://dx.doi.org/10.1042/bj2300133.

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By using synthetic oligonucleotides as probes, plasmid clones containing portions of cDNA coding for human C4b-binding protein were isolated from a liver cDNA library. The entire amino acid sequence of the C4b-binding protein can be predicted from this study of the cloned cDNA when allied to a previous sequence study at the protein level [Chung, Gagnon & Reid (1985) Mol. Immunol. 22, 427-435], in which over 55% of the amino acid sequence, including the N-terminal 62 residues, was obtained. The plasmid clones isolated allowed the unambiguous determination of 1717 nucleotides of cDNA sequence between the codon for the 32nd amino acid in the sequence of C4b-binding protein and the 164th nucleotide in the 3′ non-translated region. The sequence studies show that the secreted form of C4b-binding protein, found in plasma, is composed of chains of apparent Mr 70 000 that contains 549 amino acid residues. Examination of the protein and cDNA sequence results show that there are at least two polymorphic sites in the molecule. One is at position 44, which can be glutamine or threonine, and the other is at position 309, which can be tyrosine or histidine. Northern-blot analysis indicated that the mRNA for C4b-binding protein is approx. 2.5 kilobases long. The N-terminal 491 amino acids of C4b-binding protein can be divided into eight internal homologous regions, each approx. 60 amino acids long, which can be aligned by the presence in each region of four half-cystine, one tryptophan and several other conserved residues. These regions in C4b-binding protein are homologous with the three internal-homology regions that have been reported to be present within the Ba region of the complement enzyme factor B and also to the internal-homology regions found in the non-complement beta 2-glycoprotein I.

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Purdue, P. E., and P. B. Lazarow. "Targeting of human catalase to peroxisomes is dependent upon a novel COOH-terminal peroxisomal targeting sequence." Journal of Cell Biology 134, no. 4 (August 15, 1996): 849–62. http://dx.doi.org/10.1083/jcb.134.4.849.

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We have identified a novel peroxisomal targeting sequence (PTS) at the extreme COOH terminus of human catalase. The last four amino acids of this protein (-KANL) are necessary and sufficient to effect targeting to peroxisomes in both human fibroblasts and Saccharomyces cerevisiae, when appended to the COOH terminus of the reporter protein, chloramphenicol acetyl transferase. However, this PTS differs from the extensive family of COOH-terminal PTS tripeptides collectively termed PTS1 in two major aspects. First, the presence of the uncharged amino acid, asparagine, at the penultimate residue of the human catalase PTS is highly unusual, in that a basic residue at this position has been previously found to be a common and critical feature of PTS1 signals. Nonetheless, this asparagine residue appears to constitute an important component of the catalase PTS, in that replacement with aspartate abolished peroxisomal targeting (as did deletion of the COOH-terminal four residues). Second, the human catalase PTS comprises more than the COOH-terminal three amino acids, in that COOH-terminal-ANL cannot functionally replace the PTS1 signal-SKL in targeting a chloramphenicol acetyl transferase fusion protein to peroxisomes. The critical nature of the fourth residue from the COOH terminus of the catalase PTS (lysine) is emphasized by the fact that substitution of this residue with a variety of other amino acids abolished or reduced peroxisomal targeting. Targeting was not reduced when this lysine was replaced with arginine, suggesting that a basic amino acid at this position is required for maximal functional activity of this PTS. In spite of these unusual features, human catalase is sorted by the PTS1 pathway, both in yeast and human cells. Disruption of the PAS10 gene encoding the S. cerevisiae PTS1 receptor resulted in a cytosolic location of chloramphenicol acetyl transferase appended with the human catalase PTS, as did expression of this protein in cells from a neonatal adrenoleukodystrophy patient specifically defective in PTS1 import. Furthermore, through the use of the two-hybrid system, it was demonstrated that both the PAS10 gene product (Pas10p) and the human PTS1 receptor can interact with the COOH-terminal region of human catalase, but that this interaction is abolished by substitutions at the penultimate residue (asparagine-to- aspartate) and at the fourth residue from the COOH terminus (lysine-to-glycine) which abolish PTS functionality. We have found no evidence of additional targeting information elsewhere in the human catalase protein. An internal tripeptide (-SHL-, which conforms to the mammalian PTS1 consensus) located nine to eleven residues from the COOH terminus has been excluded as a functional PTS. Additionally, in contrast to the situation for S. cerevisiae catalase A, which contains an internal PTS in addition to a COOH-terminal PTS1, human catalase lacks such a redundant PTS, as evidenced by the exclusive cytosolic location of human catalase mutated in the COOH-terminal PTS. Consistent with this species difference, fusions between catalase A and human catalase which include the catalase A internal PTS are targeted, at least in part, to peroxisomes regardless of whether the COOH-terminal human catalase PTS is intact.

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Pike, Sandra E., Lei Yao, Joyce Setsuda, Karen D. Jones, Barry Cherney, Ettore Appella, Kazuyasu Sakaguchi, et al. "Calreticulin and Calreticulin Fragments Are Endothelial Cell Inhibitors That Suppress Tumor Growth." Blood 94, no. 7 (October 1, 1999): 2461–68. http://dx.doi.org/10.1182/blood.v94.7.2461.419a26_2461_2468.

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Several angiogenesis inhibitors are fragments of larger proteins that are themselves not active as angiogenesis inhibitors. Vasostatin, the N-terminal domain of calreticulin inclusive of amino acids 1-180, is an angiogenesis inhibitor that exerts antitumor effects in vivo. In the present study, we examined whether the full-length calreticulin molecule shares the antiangiogenic and antitumor activities of vasostatin. Similar to vasostatin, calreticulin selectively inhibited endothelial cell proliferation in vitro, but not cells of other lineages, and suppressed angiogenesis in vivo. When inoculated into athymic mice, calreticulin inhibited Burkitt tumor growth comparably with vasostatin. Calreticulin lacking the N-terminal 1-120 amino acids inhibited endothelial cell proliferation in vitro and Burkitt tumor growth in vivo comparably with vasostatin. An internal calreticulin fragment encompassing amino acids 120-180 also inhibited endothelial cell proliferation in vitro and angiogenesis in vivo comparably with calreticulin and vasostatin. These results suggest that the antiangiogenic activities of vasostatin reside in a domain that is accessible from the full-length calreticulin molecule and localize to calreticulin N-terminal amino acids 120-180. Thus, calreticulin and calreticulin fragments are inhibitors of angiogenesis that directly target endothelial cells, inhibit angiogenesis, and suppress tumor growth. This information may be critical in designing targeted inhibitors of pathological angiogenesis that underlies cancer and other diseases.

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35

HOPPER, David J., and Mustak A. KADERBHAI. "2,4′-Dihydroxyacetophenone dioxygenase (EC 1.13.11.41) from Alcaligenes sp. 4HAP: a novel enzyme with an atypical dioxygenase sequence." Biochemical Journal 344, no. 2 (November 24, 1999): 397–402. http://dx.doi.org/10.1042/bj3440397.

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2,4′-Dihydroxyacetophenone dioxygenase (EC 1.13.11.41) was purified to homogeneity from Alcaligenes sp. 4HAP grown on 4-hydroxyacetophenone. Measurements of the Mr of the native enzyme ranged from 81600 to 87000, whereas values of 21000 and 20379 were given by SDS/PAGE and electrospray MS respectively. The enzyme is a homotetramer and contains one atom of iron per molecule of enzyme. From C- and N-terminal analyses, primers for PCR were designed and the dad gene cloned and sequenced. The predicted amino acid sequence of dad, deduced from the nucleotide sequence, confirms the N-terminal amino acid sequencing data and contains the sequence of an internal tryptic peptide. It gave a calculated Mr of 20364. The gene was expressed in Escherichia coli and yielded active enzyme. The derived amino acid sequence does not show significant similarity to other dioxygenases or any strong similarity to protein sequences presently available in the databases.

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Campbell, Duncan J., Michele McGrady, David L. Prior, Jennifer M. Coller, Umberto Boffa, Louise Shiel, Danny Liew, et al. "Amino-terminal-pro-B-type natriuretic peptide levels and low diastolic blood pressure." Journal of Hypertension 32, no. 11 (November 2014): 2158–65. http://dx.doi.org/10.1097/hjh.0000000000000320.

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37

Laviades, C., G. Mayor, and Javier D??ez. "113 Increased serum concentrations of procollagen III amino-terminal propeptide in essential hypertension." Journal of Hypertension 11, no. 5 (December 1993): S446. http://dx.doi.org/10.1097/00004872-199312050-00281.

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38

Selden, Lynn A., Henry J. Kinosian, Jay Newman, Bryan Lincoln, Charles Hurwitz, Lewis C. Gershman, and James E. Estes. "Severing of F-Actin by the Amino-Terminal Half of Gelsolin Suggests Internal Cooperativity in Gelsolin." Biophysical Journal 75, no. 6 (December 1998): 3092–100. http://dx.doi.org/10.1016/s0006-3495(98)77750-1.

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39

Sáenz de Miera, L. E., J. Ramos, and M. Pérez de la Vega. "A comparative study of convicilin storage protein gene sequences in species of the tribe Vicieae." Genome 51, no. 7 (July 2008): 511–23. http://dx.doi.org/10.1139/g08-036.

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Convicilins, a set of seed storage proteins, differ from vicilins, a related group of seed storage proteins, mainly because of the presence of the N-terminal extension, an additional sequence of amino acids in the sequence corresponding to the first exon. Convicilins have been described only in species of the legume tribe Vicieae. One or two genes for convicilins have been identified in most species of this tribe. The genus Pisum is the main exception, since two genes have been identified in most of its species. Thirty-four new convicilin gene sequences from 29 different species ( Lathyrus , Lens , Pisum, and Vicia spp.) have been analyzed here. Convicilin gene sequences are generally organized in 6 exons, but in some instances one of the internal introns (2nd or 4th) is lost. In these 29 species, the N-terminal extension is formed by a stretch of 99 to 196 amino acids particularly rich in polar and charged amino acids (on average, it contains 29.43% glutamic acid and 15.38% arginine residues). This N-terminal extension has the characteristics of an intrinsically unstructured region (IUR), one of the categories of protein “degenerate sequences”. A comparative analysis indicates that the N-terminal extension sequence has evolved faster than the surrounding sequence, which is common to all vicilins, and it evolved mainly through a series of duplications of short internal sequences and triplet expansions, the predominant one being GAA. This agrees with the evolution of IURs, which is faster than the evolution of surrounding sequences and is mainly due to replication slippage and unequal crossover recombination. Alternative maximum-likelihood trees of phylogenetic relationships among the 29 Vicieae species based on the convicilin exon sequences are presented and discussed.

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40

Sáenz de Miera, L. E., and M. Pérez de la Vega. "Evidence that the N-terminal extension of the Vicieae convicilin genes evolved by intragenic duplications and trinucleotide expansions." Genome 44, no. 6 (December 1, 2001): 1022–30. http://dx.doi.org/10.1139/g01-107.

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This study was aimed to identify lentil (Lens culinaris subsp. culinaris) convicilin genes and to carry out a comparative analysis of these genes in the tribe Vicieae. Convicilins differ from vicilins, a related group of plant seed storage proteins, mainly by the presence of an additional sequence of amino acids in the sequence corresponding to the first exon, referred as the N-terminal extension. A single gene for convicilin, a component of legume seed storage proteins, was identified in the cultivated lentil. In this species, the N-terminal extension is formed by a stretch of 126 amino acids of which 59.2% are charged amino acids: 29.6% glutamic acid, 3.2% aspartic acid, 14.4% arginine, 8.8% lysine, and 3.2% histidine. This lentil convicilin sequence is similar to the sequence of convicilins in other species of the tribe Vicieae. However, the size of the N-terminal extension clearly differs among convicilins. Sequence comparison and phylogenetic analyses including convicilin and vicilin of Vicieae species indicated that the differentiation between vicilins and convicilins predated the differentiation of the two vicilin gene families (47- and 50-kDa vicilins), and that the N-terminal extension evolved mainly by a series of duplications of short internal sequences and triplet expansions, the predominant one being GAA.Key words: convicilin, evolution by duplications, Lens culinaris Medik., lentil, legumes, trinucleotide expansion.

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Struck, Joachim, Martina Strebelow, Sonja Tietz, Christine Alonso, Nils G. Morgenthaler, Johannes G. van der Hoeven, Peter Pickkers, and Andreas Bergmann. "Method for the Selective Measurement of Amino-Terminal Variants of Procalcitonin." Clinical Chemistry 55, no. 9 (September 1, 2009): 1672–79. http://dx.doi.org/10.1373/clinchem.2008.123018.

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Abstract Background: Procalcitonin (PCT) is an established marker for diagnosing and monitoring bacterial infections. Full-length PCT [116 amino acids that make up procalcitonin (PCT1–116)] can be truncated, leading to des-Ala-Pro-PCT (des-Alanin-Prolin-Procalcitonin; PCT3–116). Current immunoassays for PCT (“total PCT”) use antibodies directed against internal epitopes and are unable to distinguish amino-terminal PCT variants. Here we describe the development of monoclonal antibodies recognizing the amino-termini of PCT1–116 and PCT3–116 and their use in the selective measurement of these PCT species. Methods: With newly developed monoclonal antibodies against the amino-termini of PCT1–116 and PCT3–116, and an antibody against the katacalcin moiety of PCT, we developed and characterized immunoluminometric assays for the 2 PCT peptides. We comparatively assessed the kinetics of PCT variants in a human endotoxemia model. Results: Monoclonal antibodies against the amino-termini of PCT1–116 and PCT3–116 showed <1% cross-reactivity with other PCT-related peptides. The sandwich assays for PCT1–116 and PCT3–116 had functional assay sensitivities of 5 and 1.2 pmol/L, respectively, and exhibited recoveries within 20% of expected values. Plasma PCT1–116 was stable for 6 h at 22 °C and 24 h at 4 °C, and PCT3–116 was stable for at least 24 h at both temperatures. During experimental endotoxemia in healthy people, both PCT1–116 and PCT3–116 increased early in parallel with total PCT, but further increases in PCT1–116 were significantly slower than for PCT3–116 (P = 0.0049) and total PCT (P = 0.0024). Conclusions: The new assays selectively measure PCT1–116 and PCT3–116. Both PCT species increase early during endotoxemia but differ in their kinetics thereafter. The selective measurement of PCT species with different in vivo kinetics may be useful in improving PCT-guided therapies.

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Eksi, Saliha, and Kim C. Williamson. "Protein Targeting to the Parasitophorous Vacuole Membrane of Plasmodium falciparum." Eukaryotic Cell 10, no. 6 (April 15, 2011): 744–52. http://dx.doi.org/10.1128/ec.00008-11.

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ABSTRACTRed blood cell (RBC) invasion and parasitophorous vacuole (PV) formation byPlasmodium falciparumare critical for the development and pathogenesis of malaria, a continuing global health problem. Expansion of the PV membrane (PVM) during growth is orchestrated by the parasite. This is particularly important in mature RBCs, which lack internal organelles and no longer actively synthesize membranes. Pfs16, a 16-kDa integral PVM protein expressed by gametocytes, was chosen as a model for studying the trafficking of material from the parasite across the PV space to the PVM. The locations of Pfs16-green fluorescent protein (GFP) reporter proteins containing distinct regions of Pfs16 were tracked from RBC invasion to emergence. Inclusion of the 53 C-terminal amino acids (aa) of Pfs16 to a GFP reporter construct already containing the N-terminal secretory signal sequence was sufficient for targeting to and retention on the PVM. An amino acid motif identified in this region was also found in seven other known PVM proteins. Removal of the 11 C-terminal aa did not affect PVM targeting, but membrane retention was decreased. Additionally, during emergence from the PVM and RBC, native Pfs16 and the full-length Pfs16-GFP reporter protein were found to concentrate on the ends of the gametocyte. Capping was not observed in constructs lacking the amino acids between the N-terminal secretory signal sequence and the transmembrane domain, suggesting that this region, which is not required for PVM targeting, is involved in capping. This is the first report to define the amino acid domains required for targeting to theP. falciparumPVM.

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43

Chang, Perng-Kuang, Jiujiang Yu, Deepak Bhatnagar, and Thomas E. Cleveland. "The Carboxy-Terminal Portion of the Aflatoxin Pathway Regulatory Protein AFLR of Aspergillus parasiticus ActivatesGAL1::lacZ Gene Expression inSaccharomyces cerevisiae." Applied and Environmental Microbiology 65, no. 6 (June 1, 1999): 2508–12. http://dx.doi.org/10.1128/aem.65.6.2508-2512.1999.

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ABSTRACT AFLR, a DNA-binding protein of 444 amino acids, transactivates the expression of aflatoxin biosynthesis genes in Aspergillus parasiticus and Aspergillus flavus, as well as the sterigmatocystin synthesis genes in Aspergillus nidulans. We show here by fusion of various aflR coding regions to the GAL4 DNA-binding coding region that the AFLR carboxyl terminus contained a region that activatedGAL1::lacZ gene expression inSaccharomyces cerevisiae and that the AFLR internal region was required for the activation activity. Compared to the AFLR carboxy-terminal fusion protein (AFLRC), a mutant AFLRC retained approximately 75% of the activation activity after deletion of three acidic amino acids, Asp365, Glu366, and Glu367, in a previously identified acidic stretch. Removal of the carboxy-terminal amino acid, Glu444, did not affect the activation activity. Substitutions of acidic Glu423, Asp439, or Asp436/Asp439 with basic amino acids, Lys and His, resulted in 10- to 15-fold-lower activation activities. Strikingly, the Asp436His mutation abolished the activation activity. Substitutions of basic His428 and His442 with acidic Asp resulted in 20 and 40% decreases in the activation activities, respectively. Simultaneous substitutions of Arg427, Arg429, and Arg431 with Leu also significantly decreased the activation activity; the decrease was approximately 50-fold. Results suggest that the AFLR carboxy-terminal region is involved in transcription activation and that total acidity in this region is not a major determinant of AFLR’s activation ability inS. cerevisiae.

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44

Kilponen, J. M., H. M. Häyrinen, M. Rehn, and J. K. Hiltunen. "cDNA cloning and amino acid sequence of human mitochondrial Δ3Δ2-enoyl-CoA isomerase: comparison of the human enzyme with its rat counterpart, mitochondrial short-chain isomerase." Biochemical Journal 300, no. 1 (May 15, 1994): 1–5. http://dx.doi.org/10.1042/bj3000001.

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We report the isolation of a cDNA encoding a mature human monofunctional delta 3 delta 2-enoyl-CoA isomerase and the determination of its nucleotide sequence. The purified uncleaved protein, as well as several internal tryptic and CNBr fragments, were subjected to N-terminal peptide sequencing. The deduced amino acid sequence of the mature protein consists of 260 amino acids with a predicted M(r) of 28735. The human mitochondrial isomerase exhibits a 74% (78%) sequence identity with the corresponding rat counterpart at amino acid (nucleotide) level(s). Many basic amino acid residues in rat isomerase have been changed to acidic or neutral residues in human enzyme, explaining the differences observed between these proteins.

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45

Eble, B. E., V. R. Lingappa, and D. Ganem. "Hepatitis B surface antigen: an unusual secreted protein initially synthesized as a transmembrane polypeptide." Molecular and Cellular Biology 6, no. 5 (May 1986): 1454–63. http://dx.doi.org/10.1128/mcb.6.5.1454-1463.1986.

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Hepatitis B surface antigen (HBsAg), the major coat protein of hepatitis B virus, is also secreted from cells as a subviral particle, without concomitant cleavage of N-terminal amino acid sequences. We examined this unusual export process in a cell-free system and showed that the initial product of HBsAg biosynthesis is an integral transmembrane protein, with most or all of its C-terminal half on the lumenal side of the endoplasmic reticulum membrane. To study the nature of its topogenic signals, we synthesized fusion proteins between HBsAg and the nonsecreted protein alpha-globin. Fusion proteins in which approximately 100 amino acids of globin preceded all HBsAg sequences were successfully translocated in vitro; the same domain as in the wild-type HBsAg was transported into the vesicle lumen. Fusions in which the entire globin domain was C terminal were able to translocate both the C-terminal region of HBsAg and its attached globin domain. Thus, uncleaved signal sequences in p24s function to direct portions of the molecule across the membrane and are able to perform this function even when positioned in an internal protein domain.

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Eble, B. E., V. R. Lingappa, and D. Ganem. "Hepatitis B surface antigen: an unusual secreted protein initially synthesized as a transmembrane polypeptide." Molecular and Cellular Biology 6, no. 5 (May 1986): 1454–63. http://dx.doi.org/10.1128/mcb.6.5.1454.

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Hepatitis B surface antigen (HBsAg), the major coat protein of hepatitis B virus, is also secreted from cells as a subviral particle, without concomitant cleavage of N-terminal amino acid sequences. We examined this unusual export process in a cell-free system and showed that the initial product of HBsAg biosynthesis is an integral transmembrane protein, with most or all of its C-terminal half on the lumenal side of the endoplasmic reticulum membrane. To study the nature of its topogenic signals, we synthesized fusion proteins between HBsAg and the nonsecreted protein alpha-globin. Fusion proteins in which approximately 100 amino acids of globin preceded all HBsAg sequences were successfully translocated in vitro; the same domain as in the wild-type HBsAg was transported into the vesicle lumen. Fusions in which the entire globin domain was C terminal were able to translocate both the C-terminal region of HBsAg and its attached globin domain. Thus, uncleaved signal sequences in p24s function to direct portions of the molecule across the membrane and are able to perform this function even when positioned in an internal protein domain.

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Okagaki, T., F. E. Weber, D. A. Fischman, K. T. Vaughan, T. Mikawa, and F. C. Reinach. "The major myosin-binding domain of skeletal muscle MyBP-C (C protein) resides in the COOH-terminal, immunoglobulin C2 motif." Journal of Cell Biology 123, no. 3 (November 1, 1993): 619–26. http://dx.doi.org/10.1083/jcb.123.3.619.

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A common feature shared by myosin-binding proteins from a wide variety of species is the presence of a variable number of related internal motifs homologous to either the Ig C2 or the fibronectin (Fn) type III repeats. Despite interest in the potential function of these motifs, no group has clearly demonstrated a function for these sequences in muscle, either intra- or extracellularly. We have completed the nucleotide sequence of the fast type isoform of MyBP-C (C protein) from chicken skeletal muscle. The deduced amino acid sequence reveals seven Ig C2 sets and three Fn type III motifs in MyBP-C. alpha-chymotryptic digestion of purified MyBP-C gives rise to four peptides. NH2-terminal sequencing of these peptides allowed us to map the position of each along the primary structure of the protein. The 28-kD peptide contains the NH2-terminal sequence of MyBP-C, including the first C2 repeat. It is followed by two internal peptides, one of 5 kD containing exclusively spacer sequences between the first and second C2 motifs, and a 95-kD fragment containing five C2 domains and three fibronectin type III motifs. The C-terminal sequence of MyBP-C is present in a 14-kD peptide which contains only the last C2 repeat. We examined the binding properties of these fragments to reconstituted (synthetic) myosin filaments. Only the COOH-terminal 14-kD peptide is capable of binding myosin with high affinity. The NH2-terminal 28-kD fragment has no myosin-binding, while the long internal 100-kD peptide shows very weak binding to myosin. We have expressed and purified the 14-kD peptide in Escherichia coli. The recombinant protein exhibits saturable binding to myosin with an affinity comparable to that of the 14-kD fragment obtained by proteolytic digestion (1/2 max binding at approximately 0.5 microM). These results indicate that the binding to myosin filaments is mainly restricted to the last 102 amino acids of MyBP-C. The remainder of the molecule (1,032 amino acids) could interact with titin, MyBP-H (H protein) or thin filament components. A comparison of the highly conserved Ig C2 domains present at the COOH-terminus of five MyBPs thus far sequenced (human slow and fast MyBP-C, human and chicken MyBP-H, and chicken MyBP-C) was used to identify residues unique to these myosin-binding Ig C2 repeats.

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Böttcher, Sindy, Barbara G. Klupp, Harald Granzow, Walter Fuchs, Kathrin Michael, and Thomas C. Mettenleiter. "Identification of a 709-Amino-Acid Internal Nonessential Region within the Essential Conserved Tegument Protein (p)UL36 of Pseudorabies Virus." Journal of Virology 80, no. 19 (October 1, 2006): 9910–15. http://dx.doi.org/10.1128/jvi.01247-06.

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ABSTRACT Tegument proteins homologous to the essential herpes simplex virus type 1 UL36 gene product (p)UL36 are conserved throughout the Herpesviridae and constitute the largest herpesvirus-encoded proteins. So far, only limited information is available on their functions, which include complex formation with the (p)UL37 homologs via an N-terminal domain and a deubiquitinating activity in the extreme N terminus. For further analysis we constructed deletion mutants lacking 437, 784, 926, 1,046, 1,217, or 1,557 amino acids (aa) from the C terminus. While none of them supported replication of a pseudorabies virus (PrV) UL36 deletion mutant, a mutant polypeptide with an internal deletion from aa 2087 to 2795, which comprises a proline/alanine-rich region, fully complemented the lethal replication defect. Thus, our data indicate that the extreme C terminus of (p)UL36 fulfills an essential role in PrV replication, while a large internal portion of the C-terminal half of the protein is dispensable for replication in cell culture.

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Goh, Zee Hong, Nur Azmina Syakirin Mohd, Soon Guan Tan, Subha Bhassu, and Wen Siang Tan. "RNA-binding region of Macrobrachium rosenbergii nodavirus capsid protein." Journal of General Virology 95, no. 9 (September 1, 2014): 1919–28. http://dx.doi.org/10.1099/vir.0.064014-0.

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White tail disease (WTD) kills prawn larvae and causes drastic losses to the freshwater prawn (Macrobrachium rosenbergii) industry. The main causative agent of WTD is Macrobrachium rosenbergii nodavirus (MrNV). The N-terminal end of the MrNV capsid protein is very rich in positively charged amino acids and is postulated to interact with RNA molecules. N-terminal and internal deletion mutagenesis revealed that the RNA-binding region is located at positions 20–29, where 80 % of amino acids are positively charged. Substitution of all these positively charged residues with alanine abolished the RNA binding. Mutants without the RNA-binding region still assembled into virus-like particles, suggesting that this region is not a part of the capsid assembly domain. This paper is, to the best of our knowledge, the first to report the specific RNA-binding region of MrNV capsid protein.

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Riedel, H., L. Su, and H. Hansen. "Yeast phenotype classifies mammalian protein kinase C cDNA mutants." Molecular and Cellular Biology 13, no. 8 (August 1993): 4728–35. http://dx.doi.org/10.1128/mcb.13.8.4728-4735.1993.

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The phorbol ester receptor protein kinase C (PKC) gene family encodes essential mediators of eukaryotic cellular signals. Molecular dissection of their mechanisms of action has been limited in part by the lack of random mutagenesis approaches and by the complexity of signaling pathways in mammalian cells which involve multiple PKC isoforms. Here we present a rapid screen which permits the quantification of mammalian PKC activity phenotypically in the yeast Saccharomyces cerevisiae. Bovine PKC alpha cDNA is functionally expressed in S. cerevisiae. This results in a phorbol ester response: a fourfold increase in the cell doubling time and a substantial decrease in yeast colony size on agar plates. We have expressed pools of bovine PKC alpha cDNAs mutagenized by Bal 31 deletion of internal, amino-terminal, or carboxyl-terminal sequences and have identified three classes of mutants on the basis of their distinct yeast phenotypes. Representatives of each class were analyzed. An internal deletion of amino acids (aa) 172 to 225 displayed ligand-dependent but reduced catalytic activity, an amino-terminal truncation of aa 1 to 153 displayed elevated and ligand-independent activity, and a carboxyl-terminal 26-aa truncation (aa 647 to 672) lacked activity under any conditions. Additional mutations confirmed the distinct functional characteristics of these classes. Our data show that deletion of the V1 and C1 regions results in elevated basal catalytic activity which is still Ca2+ responsive. Internal deletions in the V2 and C2 regions do not abolish phorbol ester or Ca2+ regulation of PKC activity, suggesting that most of the C2 domain is not essential for phorbol ester stimulation and most of the regulatory domain is dispensable for Ca2+ regulation of PKC activity. These distinct activities od the PKC mutants correlate with a specific and proportional yeast phenotype and are quantified on agar plates by yeast colony size. This provides a phenotypic screen which is suitable to identity rare, randomly altered but active mammalian PKC mutants. It quantifies their catalytic and biological activities in response to PKC activators or inhibitors for a systematic mapping of PKC structure and function or PKC-drug interaction.

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Journal articles on the topic 'Terminal and internal amino and amidoalkynes'

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