Publications

2021

Dynamic, but Not Necessarily Disordered, Human-Virus Interactions Mediated through SLiMs in Viral Proteins.

Elkhaligy H, Balbin CA, Gonzalez JL, Liberatore T, Siltberg-Liberles J.  

Viruses. 2021 Nov; 13(12):2369. https://doi.org/10.3390/v13122369

 

2020

A Phylogenetic Rate Parameter Indicates Different Sequence Divergence Patterns in Orthologs and Paralogs.

Ahrens JB, Teufel AI, Siltberg-Liberles J.

J Mol Evol. 2020 Dec;88(10):720-730. doi: 10.1007/s00239-020-09969-7.

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Potential RNA-dependent RNA polymerase inhibitors as prospective therapeutics against SARS-CoV-2.

Pokhrel R, Chapagain P, Siltberg-Liberles J.

J Med Microbiol. 2020 Jun;69(6):864-873. doi: 10.1099/jmm.0.001203.

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Exploring Evolutionary Constraints in the Proteomes of Zika, Dengue, and Other Flaviviruses to Find Fitness-Critical Sites.

Nunez-Castilla J, Rahaman J, Ahrens JB, Balbin CA, Siltberg-Liberles J.

J Mol Evol. 2020 May;88(4):399-414. doi: 10.1007/s00239-020-09941-5.

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An Easy Protocol for Evolutionary Analysis of Intrinsically Disordered Proteins.

Nunez-Castilla J, Siltberg-Liberles J.

Methods Mol Biol. 2020;2141:147-177. doi: 10.1007/978-1-0716-0524-0_7.

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2018

Large-Scale Analyses of Site-Specific Evolutionary Rates across Eukaryote Proteomes Reveal Confounding Interactions between Intrinsic Disorder, Secondary Structure, and Functional Domains.

Ahrens JB, Rahaman J, Siltberg-Liberles J.

Genes (Basel). 2018 Nov 14;9(11):553. doi: 10.3390/genes9110553.

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Interaction of Peptide Aptamers with Prion Protein Central Domain Promotes α-Cleavage of PrPC.

Corda E, Du X, Shim SY, Klein AN, Siltberg-Liberles J, Gilch S.

Mol Neurobiol. 2018 Oct;55(10):7758-7774. doi: 10.1007/s12035-018-0944-9.

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2017

Evolution of intrinsic disorder in eukaryotic proteins.

Ahrens JB, Nunez-Castilla J, Siltberg-Liberles J.

Cell Mol Life Sci. 2017 Sep;74(17):3163-3174. doi: 10.1007/s00018-017-2559-0. Review.

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2016

Avoiding Regions Symptomatic of Conformational and Functional Flexibility to Identify Antiviral Targets in Current and Future Coronaviruses.

Rahaman J, Siltberg-Liberles J.

Genome Biol Evol. 2016 Dec 31;8(11):3471-3484. doi: 10.1093/gbe/evw246.

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Paralog-Specific Patterns of Structural Disorder and Phosphorylation in the Vertebrate SH3-SH2-Tyrosine Kinase Protein Family.

Dos Santos HG, Siltberg-Liberles J.

Genome Biol Evol. 2016 Sep 19;8(9):2806-25. doi: 10.1093/gbe/evw194.

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The Nuanced Interplay of Intrinsic Disorder and Other Structural Properties Driving Protein Evolution.

Ahrens J, Dos Santos HG, Siltberg-Liberles J.

Mol Biol Evol. 2016 Sep;33(9):2248-56. doi: 10.1093/molbev/msw092.

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Functional Diversification after Gene Duplication: Paralog Specific Regions of Structural Disorder and Phosphorylation in p53, p63, and p73.

Dos Santos HG, Nunez-Castilla J, Siltberg-Liberles J.

PLoS One. 2016 Mar 22;11(3):e0151961. doi: 10.1371/journal.pone.0151961. eCollection 2016.

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2014

Engineering adenylate cyclases regulated by near-infrared window light.

Ryu MH, Kang IH, Nelson MD, Jensen TM, Lyuksyutova AI, Siltberg-Liberles J, Raizen DM, Gomelsky M.

Proc Natl Acad Sci U S A. 2014 Jul 15;111(28):10167-72. doi: 10.1073/pnas.1324301111.

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Did the prion protein become vulnerable to misfolding after an evolutionary divide and conquer event?

Richmond K, Masterson P, Ortiz JF, Siltberg-Liberles J.

J Biomol Struct Dyn. 2014;32(7):1074-84. doi: 10.1080/07391102.2013.809022.

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2013

Metazoan innovation: from aromatic amino acids to extracellular signaling.

Kutchko KM, Siltberg-Liberles J.

Amino Acids. 2013 Aug;45(2):359-67. doi: 10.1007/s00726-013-1509-x.

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Rapid evolutionary dynamics of structural disorder as a potential driving force for biological divergence in flaviviruses.

Ortiz JF, MacDonald ML, Masterson P, Uversky VN, Siltberg-Liberles J.

Genome Biol Evol. 2013;5(3):504-13. doi: 10.1093/gbe/evt026.

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2011

The evolution of protein structures and structural ensembles under functional constraint.

Siltberg-Liberles J, Grahnen JA, Liberles DA.

Genes (Basel). 2011 Oct 28;2(4):748-62. doi: 10.3390/genes2040748.

PMID: 24710290 Free PMC article.

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Evolution of structurally disordered proteins promotes neostructuralization.

Siltberg-Liberles J.

Mol Biol Evol. 2011 Jan;28(1):59-62. doi: 10.1093/molbev/msq291.

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2010

Natural and engineered photoactivated nucleotidyl cyclases for optogenetic applications.

Ryu MH, Moskvin OV, Siltberg-Liberles J, Gomelsky M.

J Biol Chem. 2010 Dec 31;285(53):41501-8. doi: 10.1074/jbc.M110.177600.

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Piriform spider silk sequences reveal unique repetitive elements.

Perry DJ, Bittencourt D, Siltberg-Liberles J, Rech EL, Lewis RV.

Biomacromolecules. 2010 Nov 8;11(11):3000-6. doi: 10.1021/bm1007585.

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Superstoichiometric binding of L-Phe to phenylalanine hydroxylase from Caenorhabditis elegans: evolutionary implications.

Flydal MI, Mohn TC, Pey AL, Siltberg-Liberles J, Teigen K, Martinez A.

Amino Acids. 2010 Nov;39(5):1463-75. doi: 10.1007/s00726-010-0611-6.

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2009

Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ.

Liberles SD, Horowitz LF, Kuang D, Contos JJ, Wilson KL, Siltberg-Liberles J, Liberles DA, Buck LB.

Proc Natl Acad Sci U S A. 2009 Jun 16;106(24):9842-7. doi: 10.1073/pnas.0904464106.

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Searching distant homologs of the regulatory ACT domain in phenylalanine hydroxylase.

Siltberg-Liberles J, Martinez A.

Amino Acids. 2009 Feb;36(2):235-49. doi: 10.1007/s00726-008-0057-2.

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2008

The phylogeny of the aromatic amino acid hydroxylases revisited by characterizing phenylalanine hydroxylase from Dictyostelium discoideum.

Siltberg-Liberles J, Steen IH, Svebak RM, Martinez A.

Gene. 2008 Dec 31;427(1-2):86-92. doi: 10.1016/j.gene.2008.09.005.

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2005

Allosteric mechanisms in ACT domain containing enzymes involved in amino acid metabolism.

Liberles JS, Thórólfsson M, Martínez A.

Amino Acids. 2005 Feb;28(1):1-12. doi: 10.1007/s00726-004-0152-y. Review.

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2002

A simple covarion-based approach to analyse nucleotide substitution rates. 

Siltberg J, Liberles DA. 

J Evol Biol. 2002; 15(4):588-594. https://doi.org/10.1046/j.1420-9101.2002.00416.x