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Items: 13

1.

8-Oxo-guanine DNA damage induces transcription errors by escaping two distinct fidelity control checkpoints of RNA polymerase II.

Konovalov KA, Pardo-Avila F, Tse CKM, Oh J, Wang D, Huang X.

J Biol Chem. 2019 Mar 29;294(13):4924-4933. doi: 10.1074/jbc.RA118.007333. Epub 2019 Feb 4.

PMID:
30718278
2.

De novo design of potent and selective mimics of IL-2 and IL-15.

Silva DA, Yu S, Ulge UY, Spangler JB, Jude KM, Labão-Almeida C, Ali LR, Quijano-Rubio A, Ruterbusch M, Leung I, Biary T, Crowley SJ, Marcos E, Walkey CD, Weitzner BD, Pardo-Avila F, Castellanos J, Carter L, Stewart L, Riddell SR, Pepper M, Bernardes GJL, Dougan M, Garcia KC, Baker D.

Nature. 2019 Jan;565(7738):186-191. doi: 10.1038/s41586-018-0830-7. Epub 2019 Jan 9.

3.

Structural, thermodynamic and catalytic characterization of an ancestral triosephosphate isomerase reveal early evolutionary coupling between monomer association and function.

Schulte-Sasse M, Pardo-Ávila F, Pulido-Mayoral NO, Vázquez-Lobo A, Costas M, García-Hernández E, Rodríguez-Romero A, Fernández-Velasco DA.

FEBS J. 2019 Mar;286(5):882-900. doi: 10.1111/febs.14741. Epub 2019 Jan 15.

PMID:
30589511
4.

The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding.

Kudva R, Tian P, Pardo-Avila F, Carroni M, Best RB, Bernstein HD, von Heijne G.

Elife. 2018 Nov 26;7. pii: e36326. doi: 10.7554/eLife.36326.

5.

Structure of the 30S ribosomal decoding complex at ambient temperature.

Dao EH, Poitevin F, Sierra RG, Gati C, Rao Y, Ciftci HI, Akşit F, McGurk A, Obrinski T, Mgbam P, Hayes B, De Lichtenberg C, Pardo-Avila F, Corsepius N, Zhang L, Seaberg MH, Hunter MS, Liang M, Koglin JE, Wakatsuki S, Demirci H.

RNA. 2018 Dec;24(12):1667-1676. doi: 10.1261/rna.067660.118. Epub 2018 Aug 23.

6.

Aminoglycoside ribosome interactions reveal novel conformational states at ambient temperature.

O'Sullivan ME, Poitevin F, Sierra RG, Gati C, Dao EH, Rao Y, Aksit F, Ciftci H, Corsepius N, Greenhouse R, Hayes B, Hunter MS, Liang M, McGurk A, Mbgam P, Obrinsky T, Pardo-Avila F, Seaberg MH, Cheng AG, Ricci AJ, DeMirci H.

Nucleic Acids Res. 2018 Oct 12;46(18):9793-9804. doi: 10.1093/nar/gky693.

7.

Comprehensive computational design of ordered peptide macrocycles.

Hosseinzadeh P, Bhardwaj G, Mulligan VK, Shortridge MD, Craven TW, Pardo-Avila F, Rettie SA, Kim DE, Silva DA, Ibrahim YM, Webb IK, Cort JR, Adkins JN, Varani G, Baker D.

Science. 2017 Dec 15;358(6369):1461-1466. doi: 10.1126/science.aap7577.

8.

Constructing Kinetic Network Models to Elucidate Mechanisms of Functional Conformational Changes of Enzymes and Their Recognition with Ligands.

Zhang L, Jiang H, Sheong FK, Pardo-Avila F, Cheung PP, Huang X.

Methods Enzymol. 2016;578:343-71. doi: 10.1016/bs.mie.2016.05.026. Epub 2016 Jun 24. Review.

PMID:
27497174
9.

Bridge helix bending promotes RNA polymerase II backtracking through a critical and conserved threonine residue.

Da LT, Pardo-Avila F, Xu L, Silva DA, Zhang L, Gao X, Wang D, Huang X.

Nat Commun. 2016 Apr 19;7:11244. doi: 10.1038/ncomms11244.

10.

Elucidation of the Dynamics of Transcription Elongation by RNA Polymerase II using Kinetic Network Models.

Zhang L, Pardo-Avila F, Unarta IC, Cheung PP, Wang G, Wang D, Huang X.

Acc Chem Res. 2016 Apr 19;49(4):687-94. doi: 10.1021/acs.accounts.5b00536. Epub 2016 Mar 18.

11.

Structural Model of RNA Polymerase II Elongation Complex with Complete Transcription Bubble Reveals NTP Entry Routes.

Zhang L, Silva DA, Pardo-Avila F, Wang D, Huang X.

PLoS Comput Biol. 2015 Jul 2;11(7):e1004354. doi: 10.1371/journal.pcbi.1004354. eCollection 2015 Jul.

12.

Millisecond dynamics of RNA polymerase II translocation at atomic resolution.

Silva DA, Weiss DR, Pardo Avila F, Da LT, Levitt M, Wang D, Huang X.

Proc Natl Acad Sci U S A. 2014 May 27;111(21):7665-70. doi: 10.1073/pnas.1315751111. Epub 2014 Apr 21.

13.

A two-state model for the dynamics of the pyrophosphate ion release in bacterial RNA polymerase.

Da LT, Pardo Avila F, Wang D, Huang X.

PLoS Comput Biol. 2013 Apr;9(4):e1003020. doi: 10.1371/journal.pcbi.1003020. Epub 2013 Apr 4.

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