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Items: 1 to 50 of 51

1.

On the origin of isoprenoid biosynthesis.

Hoshino Y, Gaucher EA.

Mol Biol Evol. 2018 Jun 14. doi: 10.1093/molbev/msy120. [Epub ahead of print]

2.

Structural and Dynamics Comparison of Thermostability in Ancient, Modern, and Consensus Elongation Factor Tus.

Okafor CD, Pathak MC, Fagan CE, Bauer NC, Cole MF, Gaucher EA, Ortlund EA.

Structure. 2018 Jan 2;26(1):118-129.e3. doi: 10.1016/j.str.2017.11.018. Epub 2017 Dec 21.

PMID:
29276038
3.

De novo active sites for resurrected Precambrian enzymes.

Risso VA, Martinez-Rodriguez S, Candel AM, Krüger DM, Pantoja-Uceda D, Ortega-Muñoz M, Santoyo-Gonzalez F, Gaucher EA, Kamerlin SCL, Bruix M, Gavira JA, Sanchez-Ruiz JM.

Nat Commun. 2017 Jul 18;8:16113. doi: 10.1038/ncomms16113.

4.

Experimental Evolution of Escherichia coli Harboring an Ancient Translation Protein.

Kacar B, Ge X, Sanyal S, Gaucher EA.

J Mol Evol. 2017 Mar;84(2-3):69-84. doi: 10.1007/s00239-017-9781-0. Epub 2017 Feb 23.

5.

Enhancing the pharmaceutical properties of protein drugs by ancestral sequence reconstruction.

Zakas PM, Brown HC, Knight K, Meeks SL, Spencer HT, Gaucher EA, Doering CB.

Nat Biotechnol. 2017 Jan;35(1):35-37. doi: 10.1038/nbt.3677. Epub 2016 Sep 26.

6.

An experimental phylogeny to benchmark ancestral sequence reconstruction.

Randall RN, Radford CE, Roof KA, Natarajan DK, Gaucher EA.

Nat Commun. 2016 Sep 15;7:12847. doi: 10.1038/ncomms12847.

7.

Coevolution of URAT1 and Uricase during Primate Evolution: Implications for Serum Urate Homeostasis and Gout.

Tan PK, Farrar JE, Gaucher EA, Miner JN.

Mol Biol Evol. 2016 Sep;33(9):2193-200. doi: 10.1093/molbev/msw116. Epub 2016 Jun 26.

8.

Selection for Protein Kinetic Stability Connects Denaturation Temperatures to Organismal Temperatures and Provides Clues to Archaean Life.

Romero-Romero ML, Risso VA, Martinez-Rodriguez S, Gaucher EA, Ibarra-Molero B, Sanchez-Ruiz JM.

PLoS One. 2016 Jun 2;11(6):e0156657. doi: 10.1371/journal.pone.0156657. eCollection 2016.

9.

Molecular Evolution Directs Protein Translation Using Unnatural Amino Acids.

Cox VE, Gaucher EA.

Curr Protoc Chem Biol. 2015 Dec 2;7(4):223-8. doi: 10.1002/9780470559277.ch150115. Review.

PMID:
26629613
10.

Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history.

Risso VA, Manssour-Triedo F, Delgado-Delgado A, Arco R, Barroso-delJesus A, Ingles-Prieto A, Godoy-Ruiz R, Gavira JA, Gaucher EA, Ibarra-Molero B, Sanchez-Ruiz JM.

Mol Biol Evol. 2015 Feb;32(2):440-55. doi: 10.1093/molbev/msu312. Epub 2014 Nov 12.

11.

Engineering proteins by reconstructing evolutionary adaptive paths.

Cox VE, Gaucher EA.

Methods Mol Biol. 2014;1179:353-63. doi: 10.1007/978-1-4939-1053-3_24.

PMID:
25055790
12.

Uric acid-dependent inhibition of AMP kinase induces hepatic glucose production in diabetes and starvation: evolutionary implications of the uricase loss in hominids.

Cicerchi C, Li N, Kratzer J, Garcia G, Roncal-Jimenez CA, Tanabe K, Hunter B, Rivard CJ, Sautin YY, Gaucher EA, Johnson RJ, Lanaspa MA.

FASEB J. 2014 Aug;28(8):3339-50. doi: 10.1096/fj.13-243634. Epub 2014 Apr 22.

13.

Phenotypic comparisons of consensus variants versus laboratory resurrections of Precambrian proteins.

Risso VA, Gavira JA, Gaucher EA, Sanchez-Ruiz JM.

Proteins. 2014 Jun;82(6):887-96. doi: 10.1002/prot.24575. Epub 2014 Apr 18.

PMID:
24710963
14.

STRAD pseudokinases regulate axogenesis and LKB1 stability.

Veleva-Rotse BO, Smart JL, Baas AF, Edmonds B, Zhao ZM, Brown A, Klug LR, Hansen K, Reilly G, Gardner AP, Subbiah K, Gaucher EA, Clevers H, Barnes AP.

Neural Dev. 2014 Mar 4;9:5. doi: 10.1186/1749-8104-9-5.

15.

Evolutionary history and metabolic insights of ancient mammalian uricases.

Kratzer JT, Lanaspa MA, Murphy MN, Cicerchi C, Graves CL, Tipton PA, Ortlund EA, Johnson RJ, Gaucher EA.

Proc Natl Acad Sci U S A. 2014 Mar 11;111(10):3763-8. doi: 10.1073/pnas.1320393111. Epub 2014 Feb 18.

16.

Conservation of protein structure over four billion years.

Ingles-Prieto A, Ibarra-Molero B, Delgado-Delgado A, Perez-Jimenez R, Fernandez JM, Gaucher EA, Sanchez-Ruiz JM, Gavira JA.

Structure. 2013 Sep 3;21(9):1690-7. doi: 10.1016/j.str.2013.06.020. Epub 2013 Aug 8.

17.

Experimental evolution of protein-protein interaction networks.

Kaçar B, Gaucher EA.

Biochem J. 2013 Aug 1;453(3):311-9. doi: 10.1042/BJ20130205. Review.

18.

Secondary structure and domain architecture of the 23S and 5S rRNAs.

Petrov AS, Bernier CR, Hershkovits E, Xue Y, Waterbury CC, Hsiao C, Stepanov VG, Gaucher EA, Grover MA, Harvey SC, Hud NV, Wartell RM, Fox GE, Williams LD.

Nucleic Acids Res. 2013 Aug;41(15):7522-35. doi: 10.1093/nar/gkt513. Epub 2013 Jun 14.

19.

Reconstructing evolutionary adaptive paths for protein engineering.

Cole MF, Cox VE, Gratton KL, Gaucher EA.

Methods Mol Biol. 2013;978:115-25. doi: 10.1007/978-1-62703-293-3_8.

PMID:
23423892
20.

Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian β-lactamases.

Risso VA, Gavira JA, Mejia-Carmona DF, Gaucher EA, Sanchez-Ruiz JM.

J Am Chem Soc. 2013 Feb 27;135(8):2899-902. doi: 10.1021/ja311630a. Epub 2013 Feb 14. Erratum in: J Am Chem Soc. 2013 Jul 17;135(28):10580.

PMID:
23394108
21.

Interchanging functionality among homologous elongation factors using signatures of heterotachy.

Cacan E, Kratzer JT, Cole MF, Gaucher EA.

J Mol Evol. 2013 Feb;76(1-2):4-12. doi: 10.1007/s00239-013-9540-9. Epub 2013 Jan 31.

22.

Hydrophobic environment is a key factor for the stability of thermophilic proteins.

Gromiha MM, Pathak MC, Saraboji K, Ortlund EA, Gaucher EA.

Proteins. 2013 Apr;81(4):715-21. doi: 10.1002/prot.24232. Epub 2013 Jan 15.

PMID:
23319168
24.
25.

The evolutionary history of the catenin gene family during metazoan evolution.

Zhao ZM, Reynolds AB, Gaucher EA.

BMC Evol Biol. 2011 Jul 8;11:198. doi: 10.1186/1471-2148-11-198.

26.

Utilizing natural diversity to evolve protein function: applications towards thermostability.

Cole MF, Gaucher EA.

Curr Opin Chem Biol. 2011 Jun;15(3):399-406. doi: 10.1016/j.cbpa.2011.03.005. Epub 2011 Apr 4. Review.

27.

Single-molecule paleoenzymology probes the chemistry of resurrected enzymes.

Perez-Jimenez R, Inglés-Prieto A, Zhao ZM, Sanchez-Romero I, Alegre-Cebollada J, Kosuri P, Garcia-Manyes S, Kappock TJ, Tanokura M, Holmgren A, Sanchez-Ruiz JM, Gaucher EA, Fernandez JM.

Nat Struct Mol Biol. 2011 May;18(5):592-6. doi: 10.1038/nsmb.2020. Epub 2011 Apr 3.

28.

The molecular evolution of the p120-catenin subfamily and its functional associations.

Carnahan RH, Rokas A, Gaucher EA, Reynolds AB.

PLoS One. 2010 Dec 31;5(12):e15747. doi: 10.1371/journal.pone.0015747.

29.

Exploiting models of molecular evolution to efficiently direct protein engineering.

Cole MF, Gaucher EA.

J Mol Evol. 2011 Feb;72(2):193-203. doi: 10.1007/s00239-010-9415-2. Epub 2010 Dec 4.

30.

Deep phylogeny--how a tree can help characterize early life on Earth.

Gaucher EA, Kratzer JT, Randall RN.

Cold Spring Harb Perspect Biol. 2010 Jan;2(1):a002238. doi: 10.1101/cshperspect.a002238. Review.

31.

Reconstructed evolutionary adaptive paths give polymerases accepting reversible terminators for sequencing and SNP detection.

Chen F, Gaucher EA, Leal NA, Hutter D, Havemann SA, Govindarajan S, Ortlund EA, Benner SA.

Proc Natl Acad Sci U S A. 2010 Feb 2;107(5):1948-53. doi: 10.1073/pnas.0908463107. Epub 2010 Jan 11.

32.

Diversity of chemical mechanisms in thioredoxin catalysis revealed by single-molecule force spectroscopy.

Perez-Jimenez R, Li J, Kosuri P, Sanchez-Romero I, Wiita AP, Rodriguez-Larrea D, Chueca A, Holmgren A, Miranda-Vizuete A, Becker K, Cho SH, Beckwith J, Gelhaye E, Jacquot JP, Gaucher EA, Sanchez-Ruiz JM, Berne BJ, Fernandez JM.

Nat Struct Mol Biol. 2009 Aug;16(8):890-6. doi: 10.1038/nsmb.1627. Epub 2009 Jul 13. Erratum in: Nat Struct Mol Biol. 2009 Dec;16(12):1331. Gaucher, Eric [corrected to Gaucher, Eric A].

33.

The planetary biology of ascorbate and uric acid and their relationship with the epidemic of obesity and cardiovascular disease.

Johnson RJ, Gaucher EA, Sautin YY, Henderson GN, Angerhofer AJ, Benner SA.

Med Hypotheses. 2008;71(1):22-31. doi: 10.1016/j.mehy.2008.01.017. Epub 2008 Mar 10. Review.

34.

Palaeotemperature trend for Precambrian life inferred from resurrected proteins.

Gaucher EA, Govindarajan S, Ganesh OK.

Nature. 2008 Feb 7;451(7179):704-7. doi: 10.1038/nature06510.

PMID:
18256669
35.

Molecular paleoscience: systems biology from the past.

Benner SA, Sassi SO, Gaucher EA.

Adv Enzymol Relat Areas Mol Biol. 2007;75:1-132, xi. Review.

PMID:
17124866
36.
37.
38.

The diverse biological functions of phosphatidylinositol transfer proteins in eukaryotes.

Phillips SE, Vincent P, Rizzieri KE, Schaaf G, Bankaitis VA, Gaucher EA.

Crit Rev Biochem Mol Biol. 2006 Jan-Feb;41(1):21-49. Review.

PMID:
16455519
39.

A call for likelihood phylogenetics even when the process of sequence evolution is heterogeneous.

Gaucher EA, Miyamoto MM.

Mol Phylogenet Evol. 2005 Dec;37(3):928-31. No abstract available.

PMID:
16291095
40.

Resurrecting ancestral alcohol dehydrogenases from yeast.

Thomson JM, Gaucher EA, Burgan MF, De Kee DW, Li T, Aris JP, Benner SA.

Nat Genet. 2005 Jun;37(6):630-5. Epub 2005 May 1.

41.

The planetary biology of cytochrome P450 aromatases.

Gaucher EA, Graddy LG, Li T, Simmen RC, Simmen FA, Schreiber DR, Liberles DA, Janis CM, Benner SA.

BMC Biol. 2004 Aug 17;2:19.

42.

Cytoplasmic glycosylation of protein-hydroxyproline and its relationship to other glycosylation pathways.

West CM, Van Der Wel H, Sassi S, Gaucher EA.

Biochim Biophys Acta. 2004 Jul 6;1673(1-2):29-44. Review.

PMID:
15238247
43.

Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins.

Gaucher EA, Thomson JM, Burgan MF, Benner SA.

Nature. 2003 Sep 18;425(6955):285-8.

PMID:
13679914
44.
45.

Predicting functional divergence in protein evolution by site-specific rate shifts.

Gaucher EA, Gu X, Miyamoto MM, Benner SA.

Trends Biochem Sci. 2002 Jun;27(6):315-21. Review.

PMID:
12069792
46.

Planetary biology--paleontological, geological, and molecular histories of life.

Benner SA, Caraco MD, Thomson JM, Gaucher EA.

Science. 2002 May 3;296(5569):864-8. Review.

PMID:
11988562
47.

The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors.

Gaucher EA, Das UK, Miyamoto MM, Benner SA.

Mol Biol Evol. 2002 Apr;19(4):569-73. No abstract available.

PMID:
11919299
48.
49.

Evolution, language and analogy in functional genomics.

Benner SA, Gaucher EA.

Trends Genet. 2001 Jul;17(7):414-8.

PMID:
11418223
50.

Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors.

Gaucher EA, Miyamoto MM, Benner SA.

Proc Natl Acad Sci U S A. 2001 Jan 16;98(2):548-52.

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