Title Madness

Did we miss anything? Know of an interesting paper that just got out? Have you read any of these? Tell us in the comments.

Bi-Weekly Digest 22/02/09

Bi-Weekly Digest 31/01/09

Bi-Weekly Digest 08/01/09

Bi-Weekly Digest 27/11/08

Bi-Weekly Digest 08/11/08

Weekly Digest 12/10/08


Crystal structure of opsin in its G-protein-interacting conformation.
Scheerer P, Park JH, Hildebrand PW, Kim YJ, Krauss N, Choe HW, Hofmann KP, Ernst OP.

Assembling materials with DNA as the guide.
Aldaye FA, Palmer AL, Sleiman HF.

Proteins. 2008 Sep 24;
Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study.
Ramelot TA, Raman S, Kuzin AP, Xiao R, Ma LC, Acton TB, Hunt JF, Montelione GT, Baker D, Kennedy MA.

A double S shape provides the structural basis for the extraordinary binding specificity of Dscam isoforms.

Sawaya MR, Wojtowicz WM, Andre I, Qian B, Wu W, Baker D, Eisenberg D, Zipursky SL.

Howard Hughes Medical Institute, UCLA-DOE Institute of Genomics and Proteomics, Los Angeles, CA 90095, USA.

Drosophila Dscam encodes a vast family of immunoglobulin (Ig)-containing proteins that exhibit isoform-specific homophilic binding. This diversity is essential for cell recognition events required for wiring the brain. Each isoform binds to itself but rarely to other isoforms. Specificity is determined by “matching” of three variable Ig domains within an approximately 220 kD ectodomain. Here, we present the structure of the homophilic binding region of Dscam, comprising the eight N-terminal Ig domains (Dscam(1-8)). Dscam(1-8) forms a symmetric homodimer of S-shaped molecules. This conformation, comprising two reverse turns, allows each pair of the three variable domains to “match” in an antiparallel fashion. Structural, genetic, and biochemical studies demonstrate that, in addition to variable domain “matching,” intramolecular interactions between constant domains promote homophilic binding. These studies provide insight into how “matching” at all three pairs of variable domains in Dscam mediates isoform-specific recognition.

Experimental and Computational Analyses of the Energetic Basis for Dual Recognition of Immunity Proteins by Colicin Endonucleases.

Keeble AH, Joachimiak LA, Mate MJ, Meenan N, Kirkpatrick N, Baker D, Kleanthous C.

Crystal structure of squid rhodopsin.

Murakami M, Kouyama T.

Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins.

Joh NH, Min A, Faham S, Whitelegge JP, Yang D, Woods VL, Bowie JU.

Design of Protein-Ligand Binding Based on the Molecular-Mechanics Energy Model.

Boas FE, Harbury PB.

A Simple Model of Backbone Flexibility Improves Modeling of Side-chain Conformational Variability.

Friedland GD, Linares AJ, Smith CA, Kortemme T.

Backrub-Like Backbone Simulation Recapitulates Natural Protein Conformational Variability and Improves Mutant Side-Chain Prediction.

Smith CA, Kortemme T.

Modest membrane hydrogen bonds deliver rich results.

Grigoryan G, Degrado WF.

Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements.

Altman MD, Bardhan JP, White JK, Tidor B.

Assembly reflects evolution of protein complexes.

Levy ED, Erba EB, Robinson CV, Teichmann SA.

Crystal structure of the ligand-free G-protein-coupled receptor opsin.

Park JH, Scheerer P, Hofmann KP, Choe HW, Ernst OP.

The RosettaDock server for local protein-protein docking.

Lyskov S, Gray JJ.

Structure of a beta(1)-adrenergic G-protein-coupled receptor.

Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AG, Tate CG, Schertler GF.

The interplay of functional tuning, drug resistance, and thermodynamic stability in the evolution of the m2 proton channel from the influenza a virus.

Stouffer AL, Ma C, Cristian L, Ohigashi Y, Lamb RA, Lear JD, Pinto LH, Degrado WF.

Protein-protein interactions in the membrane: sequence, structural, and biological motifs.

Moore DT, Berger BW, Degrado WF.

Structure of the Ebola virus glycoprotein bound to an antibody from a human survivor.

Lee JE, Fusco ML, Hessell AJ, Oswald WB, Burton DR, Saphire EO.

Conformer Selection and Induced Fit in Flexible Backbone Protein-Protein Docking Using Computational and NMR Ensembles.

Chaudhury S, Gray JJ.

Protein folding and design: from simple models to complex systems.

Regan L, Woolfson DN.

Synthetic biology through biomolecular design and engineering.

Channon K, Bromley EH, Woolfson DN.

Evaluating and optimizing computational protein design force fields using fixed composition-based negative design.

Alvizo O, Mayo SL.

MagicWand: A Single, Designed Peptide That Assembles to Stable, Ordered alpha-Helical Fibers.

Gribbon C, Channon KJ, Zhang W, Banwell EF, Bromley EH, Chaudhuri JB, Oreffo RO, Woolfson DN.


Plos Computational Biology:







Click here to read

The pathogen protein EspF(U) hijacks actin polymerization using mimicry and multivalency.

Sallee NA, Rivera GM, Dueber JE, Vasilescu D, Mullins RD, Mayer BJ, Lim WA.
Graduate Program in Chemistry and Chemical Biology, University of California, San Francisco, 600 16th Street, San Francisco, California 94158, USA.

Enterohaemorrhagic Escherichia coli attaches to the intestine through actin pedestals that are formed when the bacterium injects its protein EspF(U) (also known as TccP) into host cells. EspF(U) potently activates the host WASP (Wiskott-Aldrich syndrome protein) family of actin-nucleating factors, which are normally activated by the GTPase CDC42, among other signalling molecules. Apart from its amino-terminal type III secretion signal, EspF(U) consists of five-and-a-half 47-amino-acid repeats. Here we show that a 17-residue motif within this EspF(U) repeat is sufficient for interaction with N-WASP (also known as WASL). Unlike most pathogen proteins that interface with the cytoskeletal machinery, this motif does not mimic natural upstream activators: instead of mimicking an activated state of CDC42, EspF(U) mimics an autoinhibitory element found within N-WASP. Thus, EspF(U) activates N-WASP by competitively disrupting the autoinhibited state. By mimicking an internal regulatory element and not the natural activator, EspF(U) selectively activates only a precise subset of CDC42-activated processes. Although one repeat is able to stimulate actin polymerization, we show that multiple-repeat fragments have notably increased potency. The activities of these EspF(U) fragments correlate with their ability to coordinate activation of at least two N-WASP proteins. Thus, this pathogen has used a simple autoinhibitory fragment as a component to build a highly effective actin polymerization machine.

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  • Anatoly Ruvinsky


    Replying to your question what you miss here, I think you lack some good chunk of entropy:) I would want to attract you attention to new methods that account for protein-ligand binding entropy and by means of the entropy contribution increase docking accuracy significantly.

    1. A.M. Ruvinsky and A.V. Kozincev. A new and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy. J Comp Chem 26, 1089-1095, 2005.

    A.M. Ruvinsky. Role of binding entropy in the refinement of protein-ligand docking predictions: Analysis based on the use of 11 scoring functions. J Comp Chem 28, 1364-1372, 2007.

    My overall impression is that your site is interesting, and I will be visiting it from time to time.

    Good luck!

  • http://metamodern.com Eric Drexler

    Thanks for collecting these titles. They’re a useful selection.
    (Of course, it’s usually a problem that prompts a comment: the paper on backrub-like backbone simulation has a broken link; http://www.ncbi.nlm.nih.gov/pubmed/18547585 works.)

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