Disulfide-bond reshuffling in the evolution of an ape placental ribonuclease

Molecular Biology and Evolution

Volumn 24, Issue 2, 2007, Pages 505-512

  Zhang, Jianzhi ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Disulfide bond; Primate; Ribonuclease

Indexed keywords

CYSTEINE; PLACENTA PROTEIN; RIBONUCLEASE;

AMINO ACID SUBSTITUTION; APE; ARTICLE; CONTROLLED STUDY; DISULFIDE BOND; ENZYME ACTIVITY; GENE SEQUENCE; GENETIC CONSERVATION; MATHEMATICAL COMPUTING; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PREDICTION; PROTEIN FUNCTION; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; ANIMALS; CYSTEINE; DISULFIDES; EVOLUTION, MOLECULAR; HOMINIDAE; HUMANS; MOLECULAR SEQUENCE DATA; PLACENTA; PREGNANCY PROTEINS; RECOMBINANT PROTEINS; RIBONUCLEASES; SEQUENCE ALIGNMENT;

BOVINAE; HOMINIDAE; PRIMATES;

EID: 33846827106     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/msl177     Document Type: Article

References (39)

1. Anfinsen CB. 1973. Principles that govern the folding of protein chains. Science. 181:223-230.
2. Barnard EA. 1969. Biological function of pancreatic ribonuclease. Nature. 221:340-344.
3. Beintema JJ, Kleineidam RG. 1998. The ribonuclease A superfamily: general discussion. Cell Mol Life Sci. 54:825-832.
4. Breukelman HJ, Jekel PA, Dubois JY, Mulder PP, Warmels HW, Beintema JJ. 2001. Secretory ribonucleases in the primitive ruminant chevrotain (Tragulus javanicus). Eur J Biochem. 268:3890-3897.
5. Carreras E, Boix E, Rosenberg HF, Cuchillo CM, Nogues MV. 2003. Both aromatic and cationic residues contribute to the membrane-lytic and bactericidal activity of eosinophil cationic protein. Biochemistry. 42:6636-6644.
6. Castella S, Benedetti H, de Llorens R, Dacheux JL, Dacheux F. 2004. Train A, an RNase A-like protein without RNase activity, is secreted and reabsorbed by the same epididymal cells under testicular control. Biol Reprod. 71:1677-1687.
7. Chen BJ, Tsai CH, Chan CH, Kao CY. 2006. Disulfide connectivity prediction with 70% accuracy using two-level models. Proteins. 64:246-252.
8. Cheng J, Saigo H, Baldi P. 2006. Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching. Proteins. 62:617-629.
9. Cho S, Beintema JJ, Zhang J. 2005. The ribonuclease A superfamily of mammals and birds: identifying new members and tracing evolutionary histories. Genomics. 85:208-220.
10. Cho S, Zhang J. 2006. Ancient expansion of the ribonuclease A superfamily revealed by genomic analysis of placental and marsupial mammals. Gene. 373:116-125.
11. D'Alessio G, Parente A, Guida C, Leone E. 1972. Dimeric structure of seminal ribonuclease. FEBS Lett. 27:285-288.
12. Domachowske JB, Dyer KD, Bonville CA, Rosenberg HF. 1998. Recombinant human eosinophil-derived neurotoxin/RNase 2 functions as an effective antiviral agent against respiratory syncytial virus. J Infect Dis. 177:1458-1464.
13. Ferre F, Clote P. 2005a. Disulfide connectivity prediction using secondary structure information and diresidue frequencies. Bioinformatics. 21:2336-2346.
14. Ferre F, Clote P. 2005b. DiANNA: a web server for disulfide connectivity prediction. Nucleic Acids Res. 33:W230-W232.
15. Fett JW, Strydom DJ, Lobb RR, Alderman EM, Bethune JL, Riordan JF, Vallee BL. 1985. Isolation and characterization of angiogenin, an angiogenic protein from human carcinoma cells. Biochemistry. 24:5480-5486.
16. Glazko GV, Nei M. 2003. Estimation of divergence times for major lineages of primate species. Mol Biol Evol. 20:424-434.
17. Harder J, Schroder JM. 2002. RNase 7, a novel innate immune defense antimicrobial protein of healthy human skin. J Biol Chem. 277:46779-46784.
18. Hooper LV, Stappenbeck TS, Hong CV, Gordon JI. 2003. Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat Immunol. 4:269-273.
19. Jones DT, Taylor WR, Thornton JM. 1992. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 8:275-282.
20. Klink TA, Woycechowsky KJ, Taylor KM, Raines RT. 2000. Contribution of disulfide bonds to the conformational stability and catalytic activity of ribonuclease A. Eur J Biochem. 267:566-572.
21. Kreisberg R, Buchner V, Arad D. 1995. Paired natural cysteine mutation mapping: aid to constraining models of protein tertiary structure. Protein Sci. 4:2405-2410.
22. Laity JH, Shimotakahara S, Scheraga HA. 1993. Expression of wild-type and mutant bovine pancreatic ribonuclease A in Escherichia coli. Proc Natl Acad Sci USA. 90:615-619.
23. Nitto T, Dyer KD, Czapiga M, Rosenberg HF. 2006. Evolution and function of leukocyte RNase A ribonucleases of the avian species, Gallus gallus. J Biol Chem. 281:25622-25634.
24. Rosenberg HF. 1995. Recombinant human eosinophil cationic protein. Ribonuclease activity is not essential for cytotoxicity. J Biol Chem. 270:7876-7881.
25. Rosenberg HF, Dyer KD. 1995. Eosinophil cationic protein and eosinophil-derived neurotoxin. Evolution of novel function in a primate ribonuclease gene family. J Biol Chem. 270:21539-21544.
26. Rudolph B, Podschun R, Sahly H, Schubert S, Schroder JM, Harder J. 2006. Identification of RNase 8 as a novel human antimicrobial protein. Antimicrob Agents Chemother. 50:3194-3196.
27. Ruoppolo M, Vinci F, Klink TA, Raines RT, Marino G. 2000. Contribution of individual disulfide bonds to the oxidative folding of ribonuclease A. Biochemistry. 39:12033-12042.
28. Shapiro R, Riordan JF, Vallee BL. 1986. Characteristic ribonucleolytic activity of human angiogenin. Biochemistry. 25:3527-3532.
29. Strydom DJ, Fett JW, Lobb RR, Alderman EM, Bethune JL, Riordan JF, Vallee BL. 1985. Amino acid sequence of human tumor derived angiogenin. Biochemistry. 24:5486-5494.
30. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
31. Thornton JM. 1981. Disulphide bridges in globular proteins. J Mol Biol. 151:261-287.
32. Vullo A, Frasconi P. 2004. Disulfide connectivity prediction using recursive neural networks and evolutionary information. Bioinformatics. 20:653-659.
33. Young JD, Peterson CG, Venge P, Cohn ZA. 1986. Mechanism of membrane damage mediated by human eosinophil cationic protein. Nature. 321:613-616.
34. Zhang J. 2003. Parallel functional changes in the digestive RNases of ruminants and colobines by divergent amino acid substitutions. Mol Biol Evol. 20:1310-1317.
35. Zhang J. 2006. Parallel adaptive origins of digestive RNases in Asian and African leaf monkeys. Nat Genet. 38:819-823.
36. Zhang J, Dyer KD, Rosenberg HF. 2002. RNase 8, a novel RNase A superfamily ribonuclease expressed uniquely in placenta. Nucleic Acids Res. 30:1169-1175.
37. Zhang J, Dyer KD, Rosenberg HF. 2003. Human RNase 7: a new cationic ribonuclease of the RNase A superfamily. Nucleic Acids Res. 31:602-607.
38. Zhang J, Rosenberg HF, Nei M. 1998. Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc Natl Acad Sci USA. 95:3708-3713.
39. Zhang J, Zhang YP, Rosenberg HF. 2002. Adaptive evolution of a duplicated pancreatic ribonuclease gene in a leaf-eating monkey. Nat Genet. 30:411-415.