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Items: 1 to 20 of 100

1.

Cooperative Changes in Solvent Exposure Identify Cryptic Pockets, Switches, and Allosteric Coupling.

Porter JR, Moeder KE, Sibbald CA, Zimmerman MI, Hart KM, Greenberg MJ, Bowman GR.

Biophys J. 2019 Mar 5;116(5):818-830. doi: 10.1016/j.bpj.2018.11.3144. Epub 2019 Jan 25.

PMID:
30744991
2.

Designing small molecules to target cryptic pockets yields both positive and negative allosteric modulators.

Hart KM, Moeder KE, Ho CMW, Zimmerman MI, Frederick TE, Bowman GR.

PLoS One. 2017 Jun 1;12(6):e0178678. doi: 10.1371/journal.pone.0178678. eCollection 2017.

3.

Equilibrium fluctuations of a single folded protein reveal a multitude of potential cryptic allosteric sites.

Bowman GR, Geissler PL.

Proc Natl Acad Sci U S A. 2012 Jul 17;109(29):11681-6. doi: 10.1073/pnas.1209309109. Epub 2012 Jul 2.

4.
5.

Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme.

Latallo MJ, Cortina GA, Faham S, Nakamoto RK, Kasson PM.

Chem Sci. 2017 Sep 1;8(9):6484-6492. doi: 10.1039/c7sc02676e. Epub 2017 Jul 19.

6.

Discovery of multiple hidden allosteric sites by combining Markov state models and experiments.

Bowman GR, Bolin ER, Hart KM, Maguire BC, Marqusee S.

Proc Natl Acad Sci U S A. 2015 Mar 3;112(9):2734-9. doi: 10.1073/pnas.1417811112. Epub 2015 Feb 17.

7.

CryptoSite: Expanding the Druggable Proteome by Characterization and Prediction of Cryptic Binding Sites.

Cimermancic P, Weinkam P, Rettenmaier TJ, Bichmann L, Keedy DA, Woldeyes RA, Schneidman-Duhovny D, Demerdash ON, Mitchell JC, Wells JA, Fraser JS, Sali A.

J Mol Biol. 2016 Feb 22;428(4):709-719. doi: 10.1016/j.jmb.2016.01.029. Epub 2016 Feb 5.

8.

Structural and Mechanistic Basis for Extended-Spectrum Drug-Resistance Mutations in Altering the Specificity of TEM, CTX-M, and KPC β-lactamases.

Palzkill T.

Front Mol Biosci. 2018 Feb 23;5:16. doi: 10.3389/fmolb.2018.00016. eCollection 2018. Review.

9.

Dynamic profile analysis to characterize dynamics-driven allosteric sites in enzymes.

Taguchi J, Kitao A.

Biophys Physicobiol. 2016 Jul 14;13:117-126. eCollection 2016.

10.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug;10(4):040301. Epub 2013 Aug 2.

PMID:
23912807
11.

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.

Stetz G, Verkhivker GM.

PLoS One. 2015 Nov 30;10(11):e0143752. doi: 10.1371/journal.pone.0143752. eCollection 2015.

12.

Protein Binding Pocket Dynamics.

Stank A, Kokh DB, Fuller JC, Wade RC.

Acc Chem Res. 2016 May 17;49(5):809-15. doi: 10.1021/acs.accounts.5b00516. Epub 2016 Apr 25. Review.

13.

Communication between the active site and the allosteric site in class A beta-lactamases.

Meneksedag D, Dogan A, Kanlikilicer P, Ozkirimli E.

Comput Biol Chem. 2013 Apr;43:1-10. doi: 10.1016/j.compbiolchem.2012.12.002. Epub 2012 Dec 12.

PMID:
23314151
14.

Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets.

Ashford P, Moss DS, Alex A, Yeap SK, Povia A, Nobeli I, Williams MA.

BMC Bioinformatics. 2012 Mar 14;13:39. doi: 10.1186/1471-2105-13-39.

15.

Understanding Cryptic Pocket Formation in Protein Targets by Enhanced Sampling Simulations.

Oleinikovas V, Saladino G, Cossins BP, Gervasio FL.

J Am Chem Soc. 2016 Nov 2;138(43):14257-14263. Epub 2016 Oct 20.

16.

Identification of protein functional surfaces by the concept of a split pocket.

Tseng YY, Li WH.

Proteins. 2009 Sep;76(4):959-76. doi: 10.1002/prot.22402.

PMID:
19326458
17.

Crystal structure of the IMP-1 metallo beta-lactamase from Pseudomonas aeruginosa and its complex with a mercaptocarboxylate inhibitor: binding determinants of a potent, broad-spectrum inhibitor.

Concha NO, Janson CA, Rowling P, Pearson S, Cheever CA, Clarke BP, Lewis C, Galleni M, Frère JM, Payne DJ, Bateson JH, Abdel-Meguid SS.

Biochemistry. 2000 Apr 18;39(15):4288-98.

PMID:
10757977
18.

Deciphering Cryptic Binding Sites on Proteins by Mixed-Solvent Molecular Dynamics.

Kimura SR, Hu HP, Ruvinsky AM, Sherman W, Favia AD.

J Chem Inf Model. 2017 Jun 26;57(6):1388-1401. doi: 10.1021/acs.jcim.6b00623. Epub 2017 Jun 8.

PMID:
28537745
19.

Mutations Utilize Dynamic Allostery to Confer Resistance in TEM-1 β-lactamase.

Modi T, Ozkan SB.

Int J Mol Sci. 2018 Nov 29;19(12). pii: E3808. doi: 10.3390/ijms19123808.

20.

FAST Conformational Searches by Balancing Exploration/Exploitation Trade-Offs.

Zimmerman MI, Bowman GR.

J Chem Theory Comput. 2015 Dec 8;11(12):5747-57. doi: 10.1021/acs.jctc.5b00737. Epub 2015 Nov 20.

PMID:
26588361

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