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Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation.

Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R.

Proc Natl Acad Sci U S A. 2019 Aug 2. pii: 201901530. doi: 10.1073/pnas.1901530116. [Epub ahead of print]


Serum electrolytes can promote hydroxyl radical-initiated biomolecular damage from inflammation.

Komaki Y, Simpson AM, Choe JK, Pinney MM, Herschlag D, Chuang YH, Mitch WA.

Free Radic Biol Med. 2019 Jul 23;141:475-482. doi: 10.1016/j.freeradbiomed.2019.07.023. [Epub ahead of print]


Ion counting demonstrates a high electrostatic field generated by the nucleosome.

Gebala M, Johnson SL, Narlikar GJ, Herschlag D.

Elife. 2019 Jun 11;8. pii: e44993. doi: 10.7554/eLife.44993.


The roles of structural dynamics in the cellular functions of RNAs.

Ganser LR, Kelly ML, Herschlag D, Al-Hashimi HM.

Nat Rev Mol Cell Biol. 2019 Aug;20(8):474-489. doi: 10.1038/s41580-019-0136-0. Review.


Enhancement of RNA/Ligand Association Kinetics via an Electrostatic Anchor.

Sengupta RN, Herschlag D.

Biochemistry. 2019 Jun 18;58(24):2760-2768. doi: 10.1021/acs.biochem.9b00231. Epub 2019 Jun 3.


A Quantitative and Predictive Model for RNA Binding by Human Pumilio Proteins.

Jarmoskaite I, Denny SK, Vaidyanathan PP, Becker WR, Andreasson JOL, Layton CJ, Kappel K, Shivashankar V, Sreenivasan R, Das R, Greenleaf WJ, Herschlag D.

Mol Cell. 2019 Jun 6;74(5):966-981.e18. doi: 10.1016/j.molcel.2019.04.012. Epub 2019 May 8.


Blind tests of RNA-protein binding affinity prediction.

Kappel K, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D, Das R.

Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8336-8341. doi: 10.1073/pnas.1819047116. Epub 2019 Apr 8.


Demonstration of protein cooperativity mediated by RNA structure using the human protein PUM2.

Becker WR, Jarmoskaite I, Vaidyanathan PP, Greenleaf WJ, Herschlag D.

RNA. 2019 Jun;25(6):702-712. doi: 10.1261/rna.068585.118. Epub 2019 Mar 26.


The Story of RNA Folding, as Told in Epochs.

Herschlag D, Bonilla S, Bisaria N.

Cold Spring Harb Perspect Biol. 2018 Oct 1;10(10). pii: a032433. doi: 10.1101/cshperspect.a032433. Review.


Increasing the length of poly-pyrimidine bulges broadens RNA conformational ensembles with minimal impact on stacking energetics.

Merriman DK, Yuan J, Shi H, Majumdar A, Herschlag D, Al-Hashimi HM.

RNA. 2018 Oct;24(10):1363-1376. doi: 10.1261/rna.066258.118. Epub 2018 Jul 16.


Structural Coupling Throughout the Active Site Hydrogen Bond Networks of Ketosteroid Isomerase and Photoactive Yellow Protein.

Pinney MM, Natarajan A, Yabukarski F, Sanchez DM, Liu F, Liang R, Doukov T, Schwans JP, Martinez TJ, Herschlag D.

J Am Chem Soc. 2018 Aug 8;140(31):9827-9843. doi: 10.1021/jacs.8b01596. Epub 2018 Jul 27.


High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding.

Denny SK, Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ.

Cell. 2018 Jul 12;174(2):377-390.e20. doi: 10.1016/j.cell.2018.05.038. Epub 2018 Jun 28.


Recording and Analyzing Nucleic Acid Distance Distributions with X-Ray Scattering Interferometry (XSI).

Zettl T, Das R, Harbury PAB, Herschlag D, Lipfert J, Mathew RS, Shi X.

Curr Protoc Nucleic Acid Chem. 2018 Jun;73(1):e54. doi: 10.1002/cpnc.54. Epub 2018 Jun 7.


Gold nanocrystal labels provide a sequence-to-3D structure map in SAXS reconstructions.

Zettl T, Mathew RS, Shi X, Doniach S, Herschlag D, Harbury PAB, Lipfert J.

Sci Adv. 2018 May 25;4(5):eaar4418. doi: 10.1126/sciadv.aar4418. eCollection 2018 May.


Hydrogen Bonds: Simple after All?

Herschlag D, Pinney MM.

Biochemistry. 2018 Jun 19;57(24):3338-3352. doi: 10.1021/acs.biochem.8b00217. Epub 2018 May 16. Review.


Correction to Uncovering the Determinants of a Highly Perturbed Tyrosine p Ka in the Active Site of Ketosteroid Isomerase.

Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D.

Biochemistry. 2018 Apr 10;57(14):2176. doi: 10.1021/acs.biochem.8b00246. Epub 2018 Mar 27. No abstract available.


Hidden Structural Modules in a Cooperative RNA Folding Transition.

Gracia B, Al-Hashimi HM, Bisaria N, Das R, Herschlag D, Russell R.

Cell Rep. 2018 Mar 20;22(12):3240-3250. doi: 10.1016/j.celrep.2018.02.101.


Single-Molecule Fluorescence Reveals Commonalities and Distinctions among Natural and in Vitro-Selected RNA Tertiary Motifs in a Multistep Folding Pathway.

Bonilla S, Limouse C, Bisaria N, Gebala M, Mabuchi H, Herschlag D.

J Am Chem Soc. 2017 Dec 27;139(51):18576-18589. doi: 10.1021/jacs.7b08870. Epub 2017 Dec 15.


Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution.

Sunden F, AlSadhan I, Lyubimov A, Doukov T, Swan J, Herschlag D.

J Biol Chem. 2017 Dec 22;292(51):20960-20974. doi: 10.1074/jbc.M117.788240. Epub 2017 Oct 25.


Slow molecular recognition by RNA.

Gleitsman KR, Sengupta RN, Herschlag D.

RNA. 2017 Dec;23(12):1745-1753. doi: 10.1261/rna.062026.117. Epub 2017 Sep 28.


Quantitative tests of a reconstitution model for RNA folding thermodynamics and kinetics.

Bisaria N, Greenfeld M, Limouse C, Mabuchi H, Herschlag D.

Proc Natl Acad Sci U S A. 2017 Sep 12;114(37):E7688-E7696. doi: 10.1073/pnas.1703507114. Epub 2017 Aug 24.


An Activator-Blocker Pair Provides a Controllable On-Off Switch for a Ketosteroid Isomerase Active Site Mutant.

Lamba V, Yabukarski F, Herschlag D.

J Am Chem Soc. 2017 Aug 16;139(32):11089-11095. doi: 10.1021/jacs.7b03547. Epub 2017 Aug 2.


Determination of Ion Atmosphere Effects on the Nucleic Acid Electrostatic Potential and Ligand Association Using AH+·C Wobble Formation in Double-Stranded DNA.

Allred BE, Gebala M, Herschlag D.

J Am Chem Soc. 2017 Jun 7;139(22):7540-7548. doi: 10.1021/jacs.7b01830. Epub 2017 May 26.


Pseudouridine and N6-methyladenosine modifications weaken PUF protein/RNA interactions.

Vaidyanathan PP, AlSadhan I, Merriman DK, Al-Hashimi HM, Herschlag D.

RNA. 2017 May;23(5):611-618. doi: 10.1261/rna.060053.116. Epub 2017 Jan 30.


Lessons from Enzyme Kinetics Reveal Specificity Principles for RNA-Guided Nucleases in RNA Interference and CRISPR-Based Genome Editing.

Bisaria N, Jarmoskaite I, Herschlag D.

Cell Syst. 2017 Jan 25;4(1):21-29. doi: 10.1016/j.cels.2016.12.010. Review.


Determination of the conformational ensemble of the TAR RNA by X-ray scattering interferometry.

Shi X, Walker P, Harbury PB, Herschlag D.

Nucleic Acids Res. 2017 May 5;45(8):e64. doi: 10.1093/nar/gkw1352.


Kemp Eliminase Activity of Ketosteroid Isomerase.

Lamba V, Sanchez E, Fanning LR, Howe K, Alvarez MA, Herschlag D, Forconi M.

Biochemistry. 2017 Jan 31;56(4):582-591. doi: 10.1021/acs.biochem.6b00762. Epub 2017 Jan 20.


Mechanistic and Evolutionary Insights from Comparative Enzymology of Phosphomonoesterases and Phosphodiesterases across the Alkaline Phosphatase Superfamily.

Sunden F, AlSadhan I, Lyubimov AY, Ressl S, Wiersma-Koch H, Borland J, Brown CL Jr, Johnson TA, Singh Z, Herschlag D.

J Am Chem Soc. 2016 Nov 2;138(43):14273-14287. Epub 2016 Oct 20.


Differential Assembly of Catalytic Interactions within the Conserved Active Sites of Two Ribozymes.

van Schie SN, Sengupta RN, Herschlag D.

PLoS One. 2016 Aug 8;11(8):e0160457. doi: 10.1371/journal.pone.0160457. eCollection 2016.


Kinetic and thermodynamic framework for P4-P6 RNA reveals tertiary motif modularity and modulation of the folding preferred pathway.

Bisaria N, Greenfeld M, Limouse C, Pavlichin DS, Mabuchi H, Herschlag D.

Proc Natl Acad Sci U S A. 2016 Aug 23;113(34):E4956-65. doi: 10.1073/pnas.1525082113. Epub 2016 Aug 4.


Does Cation Size Affect Occupancy and Electrostatic Screening of the Nucleic Acid Ion Atmosphere?

Gebala M, Bonilla S, Bisaria N, Herschlag D.

J Am Chem Soc. 2016 Aug 31;138(34):10925-34. doi: 10.1021/jacs.6b04289. Epub 2016 Aug 22.


RNA Structural Modules Control the Rate and Pathway of RNA Folding and Assembly.

Gracia B, Xue Y, Bisaria N, Herschlag D, Al-Hashimi HM, Russell R.

J Mol Biol. 2016 Oct 9;428(20):3972-3985. doi: 10.1016/j.jmb.2016.07.013. Epub 2016 Jul 22.


Evaluation of the Catalytic Contribution from a Positioned General Base in Ketosteroid Isomerase.

Lamba V, Yabukarski F, Pinney M, Herschlag D.

J Am Chem Soc. 2016 Aug 10;138(31):9902-9. doi: 10.1021/jacs.6b04796. Epub 2016 Jul 27.


Correction to "Evaluating the Catalytic Contribution from the Oxyanion Hole in Ketosteroid Isomerase".

Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D.

J Am Chem Soc. 2016 Jun 22;138(24):7801-2. doi: 10.1021/jacs.6b04665. Epub 2016 Jun 14. No abstract available.


Visualizing the formation of an RNA folding intermediate through a fast highly modular secondary structure switch.

Xue Y, Gracia B, Herschlag D, Russell R, Al-Hashimi HM.

Nat Commun. 2016 Jun 13;7:ncomms11768. doi: 10.1038/ncomms11768.


Tungstate as a Transition State Analog for Catalysis by Alkaline Phosphatase.

Peck A, Sunden F, Andrews LD, Pande VS, Herschlag D.

J Mol Biol. 2016 Jul 3;428(13):2758-68. doi: 10.1016/j.jmb.2016.05.007. Epub 2016 May 14.


The solution structural ensembles of RNA kink-turn motifs and their protein complexes.

Shi X, Huang L, Lilley DM, Harbury PB, Herschlag D.

Nat Chem Biol. 2016 Mar;12(3):146-52. doi: 10.1038/nchembio.1997. Epub 2016 Jan 4.


High-throughput analysis and protein engineering using microcapillary arrays.

Chen B, Lim S, Kannan A, Alford SC, Sunden F, Herschlag D, Dimov IK, Baer TM, Cochran JR.

Nat Chem Biol. 2016 Feb;12(2):76-81. doi: 10.1038/nchembio.1978. Epub 2015 Dec 7.


Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets.

Hogan GJ, Brown PO, Herschlag D.

PLoS Biol. 2015 Nov 20;13(11):e1002307. doi: 10.1371/journal.pbio.1002307. eCollection 2015.


An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions.

Sengupta RN, Van Schie SN, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D.

RNA. 2016 Jan;22(1):32-48. doi: 10.1261/rna.053710.115. Epub 2015 Nov 13.


Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting.

Gebala M, Giambaşu GM, Lipfert J, Bisaria N, Bonilla S, Li G, York DM, Herschlag D.

J Am Chem Soc. 2015 Nov 25;137(46):14705-15. doi: 10.1021/jacs.5b08395. Epub 2015 Nov 12.


BIOPHYSICS. Comment on "Extreme electric fields power catalysis in the active site of ketosteroid isomerase".

Natarajan A, Yabukarski F, Lamba V, Schwans JP, Sunden F, Herschlag D.

Science. 2015 Aug 28;349(6251):936. doi: 10.1126/science.aab1584. Epub 2015 Aug 27.


Quantifying Nucleic Acid Ensembles with X-ray Scattering Interferometry.

Shi X, Bonilla S, Herschlag D, Harbury P.

Methods Enzymol. 2015;558:75-97. doi: 10.1016/bs.mie.2015.02.001. Epub 2015 Apr 2.


Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site.

Sunden F, Peck A, Salzman J, Ressl S, Herschlag D.

Elife. 2015 Apr 22;4. doi: 10.7554/eLife.06181.


Determination of Hydrogen Bond Structure in Water versus Aprotic Environments To Test the Relationship Between Length and Stability.

Sigala PA, Ruben EA, Liu CW, Piccoli PM, Hohenstein EG, Martínez TJ, Schultz AJ, Herschlag D.

J Am Chem Soc. 2015 May 6;137(17):5730-40. doi: 10.1021/ja512980h. Epub 2015 Apr 28.


Learning from ribozymes.

Herschlag D.

RNA. 2015 Apr;21(4):527-8. doi: 10.1261/rna.050914.115. No abstract available.


From static to dynamic: the need for structural ensembles and a predictive model of RNA folding and function.

Herschlag D, Allred BE, Gowrishankar S.

Curr Opin Struct Biol. 2015 Feb;30:125-133. doi: 10.1016/ Epub 2015 Mar 2. Review.


Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data.

Greenfeld M, van de Meent JW, Pavlichin DS, Mabuchi H, Wiggins CH, Gonzalez RL Jr, Herschlag D.

BMC Bioinformatics. 2015 Jan 16;16:3. doi: 10.1186/s12859-014-0429-4.


Three αSNAP and 10 ATP molecules are used in SNARE complex disassembly by N-ethylmaleimide-sensitive factor (NSF).

Shah N, Colbert KN, Enos MD, Herschlag D, Weis WI.

J Biol Chem. 2015 Jan 23;290(4):2175-88. doi: 10.1074/jbc.M114.620849. Epub 2014 Dec 9.

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