Publications

 

Publications

*Contributed equally

*Yesselman JD, *Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R “RNA tertiary structure energetics predicted by an ensemble model of the RNA double helix” in preparation (Link | Paper | Preprint)

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RNAMake-ΔΔG accounts for changes in tertiary RNA assembly affinity in a blind prediction challenge.

Scatterplot compares the dependence of the observed changes in ΔΔG (compared to the median) on the RNAMake-ΔΔG model for 1536 chip piece variants (R = 0.84). Red dashed line indicates the best-fit line (slope = 0.54); cyan dotted line indicates the line of slope 1.

Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Shi X, Costantino D, Lucks JB, Herschlag D, Jewett MC, Kieft JS, Das R "Computational Design of Asymmetric Three-dimensional RNA Structures and Function” Nature Nanotechnology,  in revisions (Link | Paper | Preprint)

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Problems in RNA nanotechnology solved by RNAMake

(a) ‘miniTTRs’ require two strands (green, purple between tetraloop (orange) and tetraloop-receptor (blue); (b) tethered ribosomes require two strands (green, purple) to link the small subunit (orange) to the large subunit (blue). c) ‘Locking’ a small-molecule binding aptamer (cyan; ATP molecule in pink spheres) by designing four strands (green, purple, teal, magenta) to a peripheral tertiary contact(orange, blue). d) Demonstration of RNAMake design algorithm, which builds an RNA path via the successive addition of motifs and helices from a starting base pair to the ending base pair.

[14] *Denny SK, *Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ (2018) “High-throughput investigation of diverse junction elements in RNA tertiary folding” Cell 174, 1–14 (Link | Paper)

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High throughput measurements of RNA tertiary structure energetics

Characterizing the thermodynamic fingerprints of >1,000 RNA junctions reveals principles for how RNA sequence affects tertiary assembly energetics, highlighting a path toward tertiary folding prediction by integrating static structural and dynamic energetic information.

[13] *Yesselman JD, *Tian S, Lui X, Shi L, Li JB, Das R (2017) "Updates to the RNA Mapping Database (RMDB), Version 2" Nucleic Acids Research 46 (D1) : D375 - D379  (Link | Paper)

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RMDB simplifies chemical mapping data distribution

Screenshot of the new interactive user interface for viewing RMDB entries: An example of an entry.

[12] *Cheng CY, *Kladwang W, Yesselman JD, Das R (2017) “Serendipitous high-resolution RNA structural information overlooked in dimethyl sulfate mapping experiments” Proceedings of the National Academy of Sciences U.S.A 114 (37) 9876-9881 (Link | Paper)

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M2-seq recovers helices across diverse RNA folds

M2-seq recovers the secondary structure of the P4–P6 domain of Tetrahymena ribozyme. Depicts the crystallographic secondary structure and M2-seq data (square graphs) with colored labels (on both display items) marking helices and multihelix domains automatically identified by M2-net analysis (A neural network).

[11] Wang Y, Yesselman JD, Zhang, Q, Kang M, Feigon J (2016) "Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human" Proceedings of the National Academy of Sciences U.S.A 113(35): 5125–5134 (Link | Paper)

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Structural comparison between medaka and human telemerase pseudoknot

Comparison of minimal mdPK and hPK (PDB ID code 2K95) structures. Secondary structure elements are P2b (red), P3 (blue), J2a/3 (green), and J2b/3 (gold).

[10] Sengupta RN, Van Schie SNS, Giambasu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D, (2016) “An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions” RNA 22: 32–48 (Link | Paper)

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Model of active state transition in Tetrahymena ribozyme

Models for active site interactions within (E•S•G)O and (E•S•G)C.. The black arrows highlight changes in the positions of active site residues in going from (E•S•G)C to (E•S•G)O. 

[9] Yesselman JD and Das R. (2016) “Modeling small non-canonical RNA motifs with the Rosetta FARFAR server” Methods in Molecular Biology, RNA modeling. (Link | Paper)

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FARFAR RNA 3D prediction accuracy 

A) GCAA tetraloop (1ZIH), RNA Denovo lowest energy models displays a high level of convergence. B) Pseudoknot (1L2X), less converged then tetraloop but also larger, still within 3Å heavy-atom rmsd for top model. C) 4x4 internal loop solved by NMR at PDB ID 2L8F, converges despite presenting 4 non-canonical base pairs.

[8] Yesselman JD and Das R. (2015) “RNA-Redesign: A web server for fixed- backbone 3D design of RNA” Nucleic Acids Research 43 (W1): W498 - W501. (Link | Paper)

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Accessing accurate RNA 3D Rosetta modeling  

RP domain IV RNA (PDB ID: 1LNT) contains highly conserved AC base pairs that RNA-Redesign mutates to stabilize the RNA

[7] Tian, S, Yesselman JD, Cordero, P and Das, R (2015) “Primerize: automated primer assembly for transcribing non-coding RNA domains” Nucleic Acids Research 43 (W1): W522 – W526. (Link | Paper)

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Schematic and runtime of the primerize algorithm

 Schematic of the Primerize algorithm. Tm (STEP 1) and misprime matrices (STEP 2) are pre-calculated for the dynamic programming assembly. 

[6] *Yesselman JD, *Horowitz S, Brooks CL III, Trievel RC (2015) "Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures" Proteins 83(3):403-10. (Link | Paper)

Survey of C---OH hydrogen bonds in proteins

 Depiction of angles and distances measured. B: Methyl hydrogen donor to acceptor distances in which the acceptor is oxygen (solid line) or carbon (dashed line). Dashed-dot line is the difference of the latter curves. C: Elevation angles of methyl CH···O hydrogen bonds. D: Methyl CH···X angles in which X is oxygen (solid line) or carbon (dashed line).

[5] Horowitz S, Dirk LM, Yesselman JD, Nimtz JS, Adhikari U, Mehl RA, Scheiner S, Houtz RL, Al-Hashimi HM, Trievel RC (2013) "Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases" Journal of the American Chemical Society 16;135(41):15536-48 (Link | Paper)

Six classes of adomet-dependent methyltransferases

The hydrogen-bond donor and methyl C···O interaction distances are labeled in each enzyme. 

[4] *Knight, J. L., *Yesselman, J.D, Brooks, C. L. III (2013), "Assessing the Quality of Absolute Hydration Free Energies Among CHARMM-Compatible Ligand Parameterization Schemes" Journal of Computational Chemistry 34, 983-903 (Link | Paper)

Chemical classes requiring additional refinement

Average unsigned errors of hydration free energies for specific chemical classes for (top panel) CGENFF molecules and (bottom panel) non-CGENFF compounds.

[3] Yesselman, JD, Price, DJ, Knight, JL and Brooks, CL III (2012) "MATCH: An Atom-Typing Toolset for Molecular Mechanics Force Fields" Journal of Computational Chemistry 33: 189–202. (Link | Paper)

Quality of the minimized MATCH-typed molecules

PubChem drug-like molecules that were successfully processed using the CGENFF libraries within MATCH to generate their respective topology and parameter files. RMSD was computed by comparing conformations found in the PubChem database to the ones after minimization.

[2] Arthur EJ, Yesselman, JD, Brooks CL III (2011) "Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics" Proteins: Structure, Function and Bioinformatics 79(12): 3276–3286. (Link | Paper)

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Locations of ionizable residues in Δ+PHS

Δ+PHS staphylococcal nuclease is shown here with all ionizing residues highlighted. Glutamic acid is cyan, and aspartic acid is orange. (From: Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics

[1]  Horowitz S, Yesselman JD, Al-Hashimi HM, Trievel RC (2011) "Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9" Journal of Biological Chemistry May 27;286(21):18658-63. (Link | Paper)

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Optimized active site with bound adomet

Truncated AdoMet and the protein are depicted with green and gray carbon atoms, respectively. Residues labeled in red designate CH O acceptors. H O distances from methyl protons to nearest oxygen atom for optimized and broken geometry are shown in magenta and cyan, respectively.