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Marchiori F, Borin G, Moroder L, Rocchi R, Scoffone E. RELATION BETWEEN STRUCTURE AND FUNCTION IN SOME PARTIALLY SYNTHETIC RIBONUCLEASES S‘. II.*. ACTA ACUST UNITED AC 2009. [DOI: 10.1111/j.1399-3011.1974.tb02393.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Benner SA, Sassi SO, Gaucher EA. Molecular paleoscience: systems biology from the past. ACTA ACUST UNITED AC 2007; 75:1-132, xi. [PMID: 17124866 DOI: 10.1002/9780471224464.ch1] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
Experimental paleomolecular biology, paleobiochemistry, and paleogenetics are closely related emerging fields that infer the sequences of ancient genes and proteins from now-extinct organisms, and then resurrect them for study in the laboratory. The goal of paleogenetics is to use information from natural history to solve the conundrum of modern genomics: How can we understand deeply the function of biomolecular structures uncovered and described by modern chemical biology? Reviewed here are the first 20 cases where biomolecular resurrections have been achieved. These show how paleogenetics can lead to an understanding of the function of biomolecules, analyze changing function, and put meaning to genomic sequences, all in ways that are not possible with traditional molecular biological studies.
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Affiliation(s)
- Steven A Benner
- Foundation for Applied Molecular Evolution, 1115 NW 4th Street, Gainesville, FL 32601, USA
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Markley JL. Correlation proton magnetic resonance studies at 250 MHz of bovine pancreatic ribonuclease. II. The pH and inhibitor-induced conformational transitions affecting histidine-48 and one tyrosine residue of ribonuclease A. Biochemistry 2002. [DOI: 10.1021/bi00687a007] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Zhao W, Kote-Jarai Z, van Santen Y, Hofsteenge J, Beintema JJ. Ribonucleases from rat and bovine liver: purification, specificity and structural characterization. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1384:55-65. [PMID: 9602056 DOI: 10.1016/s0167-4838(97)00213-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The presence of four members of the pyrimidine-specific ribonuclease superfamily was demonstrated in rat liver. Three of them (RL1, RL2 and RL3) were purified and showed ribonuclease activity at pH 7.5 with yeast RNA as substrate. RL1 is identical to rat pancreatic ribonuclease (ribonuclease 1). N-terminal sequence analysis showed the presence of the native protein and several N-terminally degraded components. RL2 and RL3 were N-terminally blocked proteins. After acidic cleavage or CNBr digestion, several parts of their sequences were determined. RL2 has high sequence similarity with neurotoxin-type ribonucleases (ribonucleases 2, 3 and 6). The amino acid sequence of rat liver-type ribonuclease (ribonuclease 4) was determined from a liver cDNA library. It differs at about 20% of the amino acid positions from other mammalian liver-type ribonucleases. The sequence of a peptide of RL3 was identical to that derived from the cDNA sequence of the liver-type ribonuclease. A contaminant of the RL3 fraction had a high sequence similarity with mouse and other mammalian angiogenins. Bovine, porcine and rat liver-type ribonucleases showed a strong preference for poly(U) over poly(C). This preference is a unique property of the liver-type enzymes of the ribonuclease superfamily.
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Affiliation(s)
- W Zhao
- Biochemisch Laboratorium, Rijksuniversiteit Groningen, Netherlands
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MCLACHLAN A. Repeating Sequences and Gene Duplication in Proteins. Mol Biol 1989. [DOI: 10.1016/b978-0-12-131200-8.50034-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Beintema JJ. Rat pancreatic ribonuclease: agreement between the corrected amino acid sequence and the sequence derived from its messenger RNA. FEBS Lett 1983; 159:191-5. [PMID: 6873294 DOI: 10.1016/0014-5793(83)80444-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A corrected amino acid sequence of rat pancreatic ribonuclease is presented which is in agreement with the messenger RNA sequence in [J. Biol. Chem. (1982) 257, 14582-14585]. The corrections do not change the general position of rat ribonuclease in trees which can be constructed for ribonuclease sequences, although they do place the rat sequence somewhat closer to the mouse sequence. The evolutionary rate of ribonuclease in the rodent family of the Muridae (rat and mouse) now has been calculated to be 140 nucleotide substitutions per 10(8) years per 100 codons, and still is one of the highest rates yet observed. The occurrence of 4 additional amino acids at the C-terminus in several mammalian ribonucleases is in agreement with the position of a second stop codon in the 3' non-coding region of the rat messenger RNA sequence.
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Prager EM, Welling GW, Wilson AC. Comparison of various immunological methods for distinguishing among mammalian pancreatic ribonucleases of known amino acid sequence. J Mol Evol 1978; 10:293-307. [PMID: 344895 DOI: 10.1007/bf01734219] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fourteen mammalian pancreatic ribonucleases of known amino acid sequence were compared by 1 or more of 3 different immunological methods: standard quantitative micro-complement fixation, spot-plate micro-complement fixation, and inhibition of phage inactivation. It was found that, while the results obtained by the 3 techniques were correlated with one another, the standard micro-complement fixation procedure was most versatile, economical of materials, and easiest to execute. The standard MC'F technique was more sensitive than the spot-plate technique to differences in amino acid sequence. The inhibition of phage inactivation method was more sensitive than the standard method for measuring differences among closely related RNases but proved impractical for amino acid differences over 15%; the MC'F method could be extended to at least 30% sequence differences. The standard method, moreover, readily detected the single amino acid difference between dromedary and camel RNases. A linear relationship was found between immunological distance (y) in the MC'F test and percent sequence difference (x) which fit the equation y = 7x. The strength of the correlation between immunological distance and percent sequence difference is consistent with the proposal that a large fraction of the evolutionary substitutions of amino acids in ribonuclease are immunologically detectable. This could be explained either by a multideterminant hypothesis or by a pauci-determinant hypothesis which says that substitutions occurring outside determinants produce small conformational changes influencing determinant reactivity.
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Rusechen F, de Vrieze G, Gaastra W, Beintema JJ. Studies on the covalent structure of eland pancreatic ribonuclease. BIOCHIMICA ET BIOPHYSICA ACTA 1976; 427:719-26. [PMID: 1268225 DOI: 10.1016/0005-2795(76)90215-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Studies on the covalent structure of eland (Taurotragus oryx) pancreatic ribonuclease have been performed on tryptic and thermolysin digests. The first 45 residues have been determined with a Beckman sequencer. From the remaining part of the sequence only those peptides were sequenced that differed in amino acid composition with the corresponding peptide of bovine ribonuclease. Eland pancreatic ribonuclease differs in four positions from bovine pancreatic ribonuclease A, but more differences due to a different state of amidation may be present. The absence of an Asn-X-Thr/Ser sequence in the covalent structure of eland ribonuclease (asparagine 34 has been substituted by aspartic acid) explains the absence of a glycosidated component in eland ribonuclease.
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Welling GW, Leijenaar-van den Berg G, van Dijk B, van den Berg A, Groen G, Gaastra W, Emmens M, Beintema JJ. Evolution of mammalian pancreatic ribonucleases. Biosystems 1975; 6:239-45. [PMID: 1137724 DOI: 10.1016/0303-2647(75)90067-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Ball WD. Isolation of salivary ribonuclease, deoxyribonuclease and amylase from the parotid gland of the rat, Rattus norvegicus albinus. BIOCHIMICA ET BIOPHYSICA ACTA 1974; 341:305-17. [PMID: 4838156 DOI: 10.1016/0005-2744(74)90223-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Moore S, Stein WH. Die chemische Structur der Pankreas-Ribonuclease und-Desoxyriboncuclease (Nobel-Vortrag). Angew Chem Int Ed Engl 1973. [DOI: 10.1002/ange.19730852403] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Stewart GR, Stevenson KJ. The isolation and partial characterization of ribonuclease A from Bison bison. Biochem J 1973; 135:427-41. [PMID: 4772270 PMCID: PMC1165845 DOI: 10.1042/bj1350427] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
1. Bison ribonuclease was isolated from pancreas glands of Bison bison by acid extraction, (NH(4))(2)SO(4) fractionation, affinity chromatography on Sepharose-5'-(4-aminophenylphosphoryl)uridine 2',3'-phosphate and ion-exchange chromatography on Bio-Rex-70. 2. The selectivity of the affinity column towards bison ribonuclease in heterogeneous protein solutions was greatly improved by employing piperazine buffers at pH5.3, which decreased non-specific interactions of other proteins. Rapid desorption from the affinity column was obtained with sodium phosphate buffer (pH3). 3. Bison ribonuclease has a total amino acid content very similar to ox ribonuclease. Inactivation of bison ribonuclease with iodoacetic acid leads to the formation of 0.62 residues of pi-carboxymethylhistidine and 0.36 residues of tau-carboxymethylhistidine. The amino acid composition of peptides isolated from diagonal peptide ;maps' and also of peptides isolated after pH1.6 and 2.4 two-dimensional high-voltage electrophoresis of a digest of bison ribonuclease labelled with pyridoxal 5-phosphate indicates that there is complete homology between ox and bison ribonucleases. 4. The Schiff-base attachment site of pyridoxal 5-phosphate was identified as lysine-41 by NaBH(4) reduction followed by peptide isolation.
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Migchelsen C, Beintema JJ. Proton nuclear magnetic resonance studies of histidine residues in rat and other rodent pancreatic ribonucleases. Effects of pH and inhibitors. J Mol Biol 1973; 79:25-38. [PMID: 4745848 DOI: 10.1016/0022-2836(73)90267-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Zwiers H, Scheffer AJ, Beintema JJ. Amino-acid sequences of red-deer and roe-deer pancreatic ribonucleases. EUROPEAN JOURNAL OF BIOCHEMISTRY 1973; 36:569-74. [PMID: 4738402 DOI: 10.1111/j.1432-1033.1973.tb02946.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Beintema JJ, Gruber M. Rat pancreatic ribonuclease. II. Amino acid sequence. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 310:161-73. [PMID: 4710592 DOI: 10.1016/0005-2795(73)90020-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Wierenga RK, Huizinga JD, Gaastra W, Welling GW, Beintema JJ. Affinity chromatography of porcine pancreatic ribonuclease reinvestigation of the N-terminal amino acid sequence. FEBS Lett 1973; 31:181-185. [PMID: 11947109 DOI: 10.1016/0014-5793(73)80098-5] [Citation(s) in RCA: 74] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- R K. Wierenga
- Biochemisch Laboratorium, Rijksuniversiteit, Zernikelaan, Groningen, The Netherlands
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Beintema JJ, Scheffer AJ, van Dijk H, Welling GW, Zwiers H. Pancreatic ribonuclease distribution and comparisons in mammals. NATURE: NEW BIOLOGY 1973; 241:76-8. [PMID: 4512404 DOI: 10.1038/newbio241076a0] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Barnard EA, Cohen MS, Gold MH, Kim JK. Evolution of ribonuclease in relation to polypeptide folding mechanisms. Nature 1972; 240:395-8. [PMID: 4564316 DOI: 10.1038/240395a0] [Citation(s) in RCA: 47] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Bartelt DC, Greene LJ. The Primary Structure of the Porcine Pancreatic Secretory Trypsin Inhibitor I. J Biol Chem 1971. [DOI: 10.1016/s0021-9258(19)77211-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Jollès P, Jollès J. Primary sequences of proteins and their evolution. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 1971. [DOI: 10.1016/0079-6107(71)90006-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Klee WA, Streaty RA. Studies on the Conformation and Proteolytic Susceptibility of Rat and Bovine Pancreatic Ribonucleases. J Biol Chem 1970. [DOI: 10.1016/s0021-9258(18)63225-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Reinhold VN, Dunne FT, Wriston JC, Schwarz M, Sarda L, Hirs CHW. The Isolation of Porcine Ribonuclease, a Glycoprotein, from Pancreatic Juice. J Biol Chem 1968. [DOI: 10.1016/s0021-9258(18)93164-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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