Publications

 

Publications

*Contributed equally

[16] *Yesselman JD, *Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R, “Blind Predictions of RNA Tertiary Assembly Energetics at Chemical Accuracy”, in preparation (Link | Paper)

[15] *Denny SK, *Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ, “High-throughput, quantitative
characterization of RNA tertiary structure elements”, in preparation (Link | Paper)

[14] *Yesselman JD, *Tian S, Lui X, Shi L, Li JB, Das R, "Updates to the RNA Mapping Database (RMDB), Version 2", in review (Link | Paper)

[13] Yesselman JD, Eiler D, Carlson ED, Ooms AN, Kladwang W, Shi X, Costantino D, Herschlag D, Jewett MC, Kieft JS, Das R "Computational Design of Asymmetric Three-dimensional RNA Structures and Machines”, in review (Link | Paper)

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

[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. (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. (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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RNA-Redesign Server Output

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. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures. Proteins. 2015 Mar;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. Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. J Am Chem Soc. 2013 Oct 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, Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics. Proteins: Structure, Function and Bioinformatics. 2011. (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. J Biol Chem. 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.