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Items: 35

1.

Salmonella Membrane Structural Remodeling Increases Resistance to Antimicrobial Peptide LL-37.

Martynowycz MW, Rice A, Andreev K, Nobre TM, Kuzmenko I, Wereszczynski J, Gidalevitz D.

ACS Infect Dis. 2019 Jul 12;5(7):1214-1222. doi: 10.1021/acsinfecdis.9b00066. Epub 2019 May 24.

PMID:
31083918
2.

Empirical and Computational Comparison of Alternative Therapeutic Exon Skip Repairs for Duchenne Muscular Dystrophy.

Ma KM, Thomas ES, Wereszczynski J, Menhart N.

Biochemistry. 2019 Apr 16;58(15):2061-2076. doi: 10.1021/acs.biochem.9b00062. Epub 2019 Apr 1.

PMID:
30896926
3.

Unique Dynamics in Asymmetric macroH2A-H2A Hybrid Nucleosomes Result in Increased Complex Stability.

Bowerman S, Hickok RJ, Wereszczynski J.

J Phys Chem B. 2019 Jan 17;123(2):419-427. doi: 10.1021/acs.jpcb.8b10668. Epub 2019 Jan 8.

PMID:
30557018
4.

The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome.

Morrison EA, Bowerman S, Sylvers KL, Wereszczynski J, Musselman CA.

Elife. 2018 Apr 12;7. pii: e31481. doi: 10.7554/eLife.31481.

5.

Atomistic Scale Effects of Lipopolysaccharide Modifications on Bacterial Outer Membrane Defenses.

Rice A, Wereszczynski J.

Biophys J. 2018 Mar 27;114(6):1389-1399. doi: 10.1016/j.bpj.2018.02.006.

6.

Energetics underlying hemin extraction from human hemoglobin by Staphylococcus aureus.

Sjodt M, Macdonald R, Marshall JD, Clayton J, Olson JS, Phillips M, Gell DA, Wereszczynski J, Clubb RT.

J Biol Chem. 2018 May 4;293(18):6942-6957. doi: 10.1074/jbc.RA117.000803. Epub 2018 Mar 14.

7.

Molecular Mechanisms of the Binding and Specificity of Streptococcus Pneumoniae Sortase C Enzymes for Pilin Subunits.

Naziga EB, Wereszczynski J.

Sci Rep. 2017 Oct 13;7(1):13119. doi: 10.1038/s41598-017-13135-3.

8.

Sortase Transpeptidases: Structural Biology and Catalytic Mechanism.

Jacobitz AW, Kattke MD, Wereszczynski J, Clubb RT.

Adv Protein Chem Struct Biol. 2017;109:223-264. doi: 10.1016/bs.apcsb.2017.04.008. Epub 2017 Jun 5. Review.

9.

Probing the disparate effects of arginine and lysine residues on antimicrobial peptide/bilayer association.

Rice A, Wereszczynski J.

Biochim Biophys Acta Biomembr. 2017 Oct;1859(10):1941-1950. doi: 10.1016/j.bbamem.2017.06.002. Epub 2017 Jun 3.

10.

Determining Atomistic SAXS Models of Tri-Ubiquitin Chains from Bayesian Analysis of Accelerated Molecular Dynamics Simulations.

Bowerman S, Rana ASJB, Rice A, Pham GH, Strieter ER, Wereszczynski J.

J Chem Theory Comput. 2017 Jun 13;13(6):2418-2429. doi: 10.1021/acs.jctc.7b00059. Epub 2017 May 17.

11.

NMR structure-based optimization of Staphylococcus aureus sortase A pyridazinone inhibitors.

Chan AH, Yi SW, Weiner EM, Amer BR, Sue CK, Wereszczynski J, Dillen CA, Senese S, Torres JZ, McCammon JA, Miller LS, Jung ME, Clubb RT.

Chem Biol Drug Des. 2017 Sep;90(3):327-344. doi: 10.1111/cbdd.12962. Epub 2017 Mar 6.

12.

Investigation of the Effect of Bilayer Composition on PKCα-C2 Domain Docking Using Molecular Dynamics Simulations.

Alwarawrah M, Wereszczynski J.

J Phys Chem B. 2017 Jan 12;121(1):78-88. doi: 10.1021/acs.jpcb.6b10188. Epub 2016 Dec 20.

13.

Detecting Allosteric Networks Using Molecular Dynamics Simulation.

Bowerman S, Wereszczynski J.

Methods Enzymol. 2016;578:429-47. doi: 10.1016/bs.mie.2016.05.027. Epub 2016 Jun 20. Review.

14.

Discerning the catalytic mechanism of Staphylococcus aureus sortase A with QM/MM free energy calculations.

Shrestha P, Wereszczynski J.

J Mol Graph Model. 2016 Jun;67:33-43. doi: 10.1016/j.jmgm.2016.04.006. Epub 2016 Apr 27.

15.

The "Lid" in the Streptococcus pneumoniae SrtC1 Sortase Adopts a Rigid Structure that Regulates Substrate Access to the Active Site.

Jacobitz AW, Naziga EB, Yi SW, McConnell SA, Peterson R, Jung ME, Clubb RT, Wereszczynski J.

J Phys Chem B. 2016 Aug 25;120(33):8302-12. doi: 10.1021/acs.jpcb.6b01930. Epub 2016 May 5.

16.

Effects of MacroH2A and H2A.Z on Nucleosome Dynamics as Elucidated by Molecular Dynamics Simulations.

Bowerman S, Wereszczynski J.

Biophys J. 2016 Jan 19;110(2):327-337. doi: 10.1016/j.bpj.2015.12.015.

17.

Free-energy landscape and characteristic forces for the initiation of DNA unzipping.

Mentes A, Florescu AM, Brunk E, Wereszczynski J, Joyeux M, Andricioaei I.

Biophys J. 2015 Apr 7;108(7):1727-1738. doi: 10.1016/j.bpj.2015.01.025.

18.

Structural and computational studies of the Staphylococcus aureus sortase B-substrate complex reveal a substrate-stabilized oxyanion hole.

Jacobitz AW, Wereszczynski J, Yi SW, Amer BR, Huang GL, Nguyen AV, Sawaya MR, Jung ME, McCammon JA, Clubb RT.

J Biol Chem. 2014 Mar 28;289(13):8891-902. doi: 10.1074/jbc.M113.509273. Epub 2014 Feb 11.

19.

Simulations of biased agonists in the β(2) adrenergic receptor with accelerated molecular dynamics.

Tikhonova IG, Selvam B, Ivetac A, Wereszczynski J, McCammon JA.

Biochemistry. 2013 Aug 20;52(33):5593-603. doi: 10.1021/bi400499n. Epub 2013 Aug 7.

20.

Discovery of Staphylococcus aureus sortase A inhibitors using virtual screening and the relaxed complex scheme.

Chan AH, Wereszczynski J, Amer BR, Yi SW, Jung ME, McCammon JA, Clubb RT.

Chem Biol Drug Des. 2013 Oct;82(4):418-28. doi: 10.1111/cbdd.12167.

21.

The binding mechanism, multiple binding modes, and allosteric regulation of Staphylococcus aureus Sortase A probed by molecular dynamics simulations.

Kappel K, Wereszczynski J, Clubb RT, McCammon JA.

Protein Sci. 2012 Dec;21(12):1858-71. doi: 10.1002/pro.2168.

22.

Nucleotide-dependent mechanism of Get3 as elucidated from free energy calculations.

Wereszczynski J, McCammon JA.

Proc Natl Acad Sci U S A. 2012 May 15;109(20):7759-64. doi: 10.1073/pnas.1117441109. Epub 2012 Apr 30.

23.

Comparison of dynamics of extracellular accesses to the β(1) and β(2) adrenoceptors binding sites uncovers the potential of kinetic basis of antagonist selectivity.

Selvam B, Wereszczynski J, Tikhonova IG.

Chem Biol Drug Des. 2012 Aug;80(2):215-26. doi: 10.1111/j.1747-0285.2012.01390.x. Epub 2012 May 2.

24.

Thermodynamic integration to predict host-guest binding affinities.

Lawrenz M, Wereszczynski J, Ortiz-Sánchez JM, Nichols SE, McCammon JA.

J Comput Aided Mol Des. 2012 May;26(5):569-76. doi: 10.1007/s10822-012-9542-5. Epub 2012 Feb 16.

25.

Simulations of the p97 complex suggest novel conformational states of hydrolysis intermediates.

Wereszczynski J, McCammon JA.

Protein Sci. 2012 Apr;21(4):475-86. doi: 10.1002/pro.2024. Epub 2012 Mar 2.

26.

Accelerated molecular dynamics in computational drug design.

Wereszczynski J, McCammon JA.

Methods Mol Biol. 2012;819:515-24. doi: 10.1007/978-1-61779-465-0_30.

PMID:
22183555
27.

Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition.

Wereszczynski J, McCammon JA.

Q Rev Biophys. 2012 Feb;45(1):1-25. doi: 10.1017/S0033583511000096. Epub 2011 Nov 15. Review.

28.

A multiscale dynamic model of DNA supercoil relaxation by topoisomerase IB.

Lillian TD, Taranova M, Wereszczynski J, Andricioaei I, Perkins NC.

Biophys J. 2011 Apr 20;100(8):2016-23. doi: 10.1016/j.bpj.2011.03.003.

29.

Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations.

Wereszczynski J, McCammon JA.

J Chem Theory Comput. 2010 Nov 9;6(11):3285-3292. Epub 2010 Oct 13.

30.

Free energy calculations reveal rotating-ratchet mechanism for DNA supercoil relaxation by topoisomerase IB and its inhibition.

Wereszczynski J, Andricioaei I.

Biophys J. 2010 Aug 4;99(3):869-78. doi: 10.1016/j.bpj.2010.04.077.

31.

Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy.

Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg A, McCammon JA.

Proteins. 2010 Aug 15;78(11):2523-32. doi: 10.1002/prot.22761.

32.

Conformational and solvent entropy contributions to the thermal response of nucleic acid-based nanothermometers.

Wereszczynski J, Andricioaei I.

J Phys Chem B. 2010 Feb 11;114(5):2076-82. doi: 10.1021/jp911681n.

PMID:
20088545
33.

Poly(amidoamine) dendrimers on lipid bilayers I: Free energy and conformation of binding.

Kelly CV, Leroueil PR, Nett EK, Wereszczynski JM, Baker JR Jr, Orr BG, Banaszak Holl MM, Andricioaei I.

J Phys Chem B. 2008 Aug 7;112(31):9337-45. doi: 10.1021/jp801377a. Epub 2008 Jul 12.

34.

Directionally negative friction: a method for enhanced sampling of rare event kinetics.

MacFadyen J, Wereszczynski J, Andricioaei I.

J Chem Phys. 2008 Mar 21;128(11):114112. doi: 10.1063/1.2841102.

PMID:
18361559
35.

On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension.

Wereszczynski J, Andricioaei I.

Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16200-5. Epub 2006 Oct 23. Erratum in: Proc Natl Acad Sci U S A. 2007 Jan 2;104(1):395.

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