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Items: 39

1.

Beyond Stability Constraints: A Biophysical Model of Enzyme Evolution with Selection on Stability and Activity.

Echave J.

Mol Biol Evol. 2019 Mar 1;36(3):613-620. doi: 10.1093/molbev/msy244.

PMID:
30590616
2.

Impact of Clinical Simulation Training in Transplantation.

Marogna N, Bernardi R, Monti M, Costa G, Aguirre Mandau M, de Echave JL.

Transplant Proc. 2018 Mar;50(2):441-443. doi: 10.1016/j.transproceed.2017.12.041.

PMID:
29579823
3.

Biophysical Models of Protein Evolution: Understanding the Patterns of Evolutionary Sequence Divergence.

Echave J, Wilke CO.

Annu Rev Biophys. 2017 May 22;46:85-103. doi: 10.1146/annurev-biophys-070816-033819. Epub 2017 Mar 15. Review.

4.

What evolution tells us about protein physics, and protein physics tells us about evolution.

Bastolla U, Dehouck Y, Echave J.

Curr Opin Struct Biol. 2017 Feb;42:59-66. doi: 10.1016/j.sbi.2016.10.020. Epub 2016 Nov 16. Review.

PMID:
27865208
5.

Functional Sites Induce Long-Range Evolutionary Constraints in Enzymes.

Jack BR, Meyer AG, Echave J, Wilke CO.

PLoS Biol. 2016 May 3;14(5):e1002452. doi: 10.1371/journal.pbio.1002452. eCollection 2016 May.

6.

Causes of evolutionary rate variation among protein sites.

Echave J, Spielman SJ, Wilke CO.

Nat Rev Genet. 2016 Feb;17(2):109-21. doi: 10.1038/nrg.2015.18. Epub 2016 Jan 19. Review.

7.

Too packed to change: side-chain packing and site-specific substitution rates in protein evolution.

Marcos ML, Echave J.

PeerJ. 2015 Apr 23;3:e911. doi: 10.7717/peerj.911. eCollection 2015.

8.

Relationship between protein thermodynamic constraints and variation of evolutionary rates among sites.

Echave J, Jackson EL, Wilke CO.

Phys Biol. 2015 Mar 19;12(2):025002. doi: 10.1088/1478-3975/12/2/025002.

9.

Local packing density is the main structural determinant of the rate of protein sequence evolution at site level.

Yeh SW, Huang TT, Liu JW, Yu SH, Shih CH, Hwang JK, Echave J.

Biomed Res Int. 2014;2014:572409. doi: 10.1155/2014/572409. Epub 2014 Jul 9.

10.

A mechanistic stress model of protein evolution accounts for site-specific evolutionary rates and their relationship with packing density and flexibility.

Huang TT, del Valle Marcos ML, Hwang JK, Echave J.

BMC Evol Biol. 2014 Apr 9;14:78. doi: 10.1186/1471-2148-14-78.

11.

Site-specific structural constraints on protein sequence evolutionary divergence: local packing density versus solvent exposure.

Yeh SW, Liu JW, Yu SH, Shih CH, Hwang JK, Echave J.

Mol Biol Evol. 2014 Jan;31(1):135-9. doi: 10.1093/molbev/mst178. Epub 2013 Oct 8.

PMID:
24109601
12.

Earlier migration timing, decreasing phenotypic variation, and biocomplexity in multiple salmonid species.

Kovach RP, Joyce JE, Echave JD, Lindberg MS, Tallmon DA.

PLoS One. 2013;8(1):e53807. doi: 10.1371/journal.pone.0053807. Epub 2013 Jan 10.

13.
14.

Measuring and comparing structural fluctuation patterns in large protein datasets.

Fuglebakk E, Echave J, Reuter N.

Bioinformatics. 2012 Oct 1;28(19):2431-40. Epub 2012 Jul 12.

PMID:
22796957
15.

The interface of protein structure, protein biophysics, and molecular evolution.

Liberles DA, Teichmann SA, Bahar I, Bastolla U, Bloom J, Bornberg-Bauer E, Colwell LJ, de Koning AP, Dokholyan NV, Echave J, Elofsson A, Gerloff DL, Goldstein RA, Grahnen JA, Holder MT, Lakner C, Lartillot N, Lovell SC, Naylor G, Perica T, Pollock DD, Pupko T, Regan L, Roger A, Rubinstein N, Shakhnovich E, Sjölander K, Sunyaev S, Teufel AI, Thorne JL, Thornton JW, Weinreich DM, Whelan S.

Protein Sci. 2012 Jun;21(6):769-85. doi: 10.1002/pro.2071. Epub 2012 Apr 23. Review.

16.

Relaxation dynamics of tryptophan in water: A UV fluorescence up-conversion and molecular dynamics study.

Bräm O, Oskouei AA, Tortschanoff A, van Mourik F, Madrid M, Echave J, Cannizzo A, Chergui M.

J Phys Chem A. 2010 Sep 2;114(34):9034-42. doi: 10.1021/jp101778u.

PMID:
20698563
17.

A perturbative view of protein structural variation.

Echave J, Fernández FM.

Proteins. 2010 Jan;78(1):173-80. doi: 10.1002/prot.22553.

PMID:
19731380
18.

Teaching noncovalent interactions using protein molecular evolution.

Fornasari MS, Parisi G, Echave J.

Biochem Mol Biol Educ. 2008 Jul;36(4):284-6. doi: 10.1002/bmb.20195.

19.

Evolutionary conservation of protein vibrational dynamics.

Maguid S, Fernandez-Alberti S, Echave J.

Gene. 2008 Oct 1;422(1-2):7-13. doi: 10.1016/j.gene.2008.06.002. Epub 2008 Jun 6.

PMID:
18577430
20.

Quaternary structure constraints on evolutionary sequence divergence.

Fornasari MS, Parisi G, Echave J.

Mol Biol Evol. 2007 Feb;24(2):349-51. Epub 2006 Nov 23.

PMID:
17124181
21.

Evolutionary conservation of protein backbone flexibility.

Maguid S, Fernández-Alberti S, Parisi G, Echave J.

J Mol Evol. 2006 Oct;63(4):448-57. Epub 2006 Oct 4.

PMID:
17021932
22.

Sulfide-binding hemoglobins: Effects of mutations on active-site flexibility.

Fernandez-Alberti S, Bacelo DE, Binning RC Jr, Echave J, Chergui M, Lopez-Garriga J.

Biophys J. 2006 Sep 1;91(5):1698-709. Epub 2006 Jun 16.

23.

Molecular dynamics study of the active site of methylamine dehydrogenase.

Pierdominici-Sottile G, Echave J, Palma J.

J Phys Chem B. 2006 Jun 15;110(23):11592-9.

PMID:
16771436
24.

[Intermediate respiratory intensive care units: definitions and characteristics].

Torres A, Ferrer M, Blanquer JB, Calle M, Casolivé V, Echave JM, Masa DM; Grupo de Trabajo de Cuidados Respiratorios Intermedios de la Sociedad Española de Neumología y Cirugía Torácica (SEPAR).

Arch Bronconeumol. 2005 Sep;41(9):505-12. Spanish. No abstract available.

25.

Assessing local structural perturbations in proteins.

Lema MA, Echave J.

BMC Bioinformatics. 2005 Sep 13;6:226.

26.

Gamma carbonic anhydrase like complex interact with plant mitochondrial complex I.

Perales M, Parisi G, Fornasari MS, Colaneri A, Villarreal F, González-Schain N, Echave J, Gómez-Casati D, Braun HP, Araya A, Zabaleta E.

Plant Mol Biol. 2004 Dec;56(6):947-57. Epub 2005 Apr 7.

PMID:
15821992
27.

Exploring the common dynamics of homologous proteins. Application to the globin family.

Maguid S, Fernandez-Alberti S, Ferrelli L, Echave J.

Biophys J. 2005 Jul;89(1):3-13. Epub 2005 Mar 4.

28.
29.

Gamma carbonic anhydrases in plant mitochondria.

Parisi G, Perales M, Fornasari MS, Colaneri A, González-Schain N, Gómez-Casati D, Zimmermann S, Brennicke A, Araya A, Ferry JG, Echave J, Zabaleta E.

Plant Mol Biol. 2004 May;55(2):193-207.

PMID:
15604675
31.

Dynactins p25 and p27 are predicted to adopt the LbetaH fold.

Parisi G, Fornasari MS, Echave J.

FEBS Lett. 2004 Mar 26;562(1-3):1-4.

32.

Sequence determinants of quaternary structure in lumazine synthase.

Fornasari MS, Laplagne DA, Frankel N, Cauerhff AA, Goldbaum FA, Echave J.

Mol Biol Evol. 2004 Jan;21(1):97-107. Epub 2003 Oct 1.

PMID:
14523158
33.

Site-specific amino acid replacement matrices from structurally constrained protein evolution simulations.

Fornasari MS, Parisi G, Echave J.

Mol Biol Evol. 2002 Mar;19(3):352-6. No abstract available.

PMID:
11861895
34.

Structural constraints and emergence of sequence patterns in protein evolution.

Parisi G, Echave J.

Mol Biol Evol. 2001 May;18(5):750-6.

PMID:
11319259
35.

Delay model of the circadian pacemaker.

Lema MA, Golombek DA, Echave J.

J Theor Biol. 2000 Jun 21;204(4):565-73.

PMID:
10833356
36.

Evolutionary analysis of gamma-carbonic anhydrase and structurally related proteins.

Parisi G, Fornasari M, Echave J.

Mol Phylogenet Evol. 2000 Mar;14(3):323-34.

PMID:
10712838
37.

Rapid automated determination of adenosine deaminase and lysozyme for differentiating tuberculous and nontuberculous pleural effusions.

Villena V, Navarro-Gonzálvez JA, García-Benayas C, Manzanos JA, Echave J, López-Encuentra A, Arenas Barbero J.

Clin Chem. 1996 Feb;42(2):218-21.

38.

Computational characterisation of potential RNA-binding sites in arenavirus nucleocapsid proteins.

Parisi G, Echave J, Ghiringhelli D, Romanowski V.

Virus Genes. 1996;13(3):247-54.

PMID:
9035369
39.

Molecular transition probabilities for time-dependent, bilinear Hamiltonians in many dimensions: A recursive procedure.

Fernandez FM, Micha DA, Echave J.

Phys Rev A Gen Phys. 1989 Jul 1;40(1):74-79. No abstract available.

PMID:
9901871

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