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Items: 21

1.

Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation.

Shrestha UR, Juneja P, Zhang Q, Gurumoorthy V, Borreguero JM, Urban V, Cheng X, Pingali SV, Smith JC, O'Neill HM, Petridis L.

Proc Natl Acad Sci U S A. 2019 Oct 8;116(41):20446-20452. doi: 10.1073/pnas.1907251116. Epub 2019 Sep 23.

PMID:
31548393
2.

Modulating Enzyme Activity by Altering Protein Dynamics with Solvent.

Duff MR Jr, Borreguero JM, Cuneo MJ, Ramanathan A, He J, Kamath G, Chennubhotla SC, Meilleur F, Howell EE, Herwig KW, Myles DAA, Agarwal PK.

Biochemistry. 2018 Jul 24;57(29):4263-4275. doi: 10.1021/acs.biochem.8b00424. Epub 2018 Jul 6.

3.

Stabilization of Polar Nanoregions in Pb-free Ferroelectrics.

Pramanick A, Dmowski W, Egami T, Budisuharto AS, Weyland F, Novak N, Christianson AD, Borreguero JM, Abernathy DL, Jørgensen MRV.

Phys Rev Lett. 2018 May 18;120(20):207603. doi: 10.1103/PhysRevLett.120.207603.

PMID:
29864364
4.

Dynamics of Charged Species in Ionic-Neutral Block Copolymer and Surfactant Complexes.

Borreguero JM, Pincus PA, Sumpter BG, Goswami M.

J Phys Chem B. 2017 Jul 20;121(28):6958-6968. doi: 10.1021/acs.jpcb.7b05047. Epub 2017 Jul 6.

PMID:
28636369
5.

Disruption of Hydrogen-Bonding Network Eliminates Water Anomalies Normally Observed on Cooling to Its Calorimetric Glass Transition.

Borreguero JM, Mamontov E.

J Phys Chem B. 2017 Apr 27;121(16):4168-4173. doi: 10.1021/acs.jpcb.7b01226. Epub 2017 Apr 17.

PMID:
28398063
6.

Precise determination of water exchanges on a mineral surface.

Stack AG, Borreguero JM, Prisk TR, Mamontov E, Wang HW, Vlcek L, Wesolowski DJ.

Phys Chem Chem Phys. 2016 Oct 19;18(41):28819-28828.

PMID:
27722503
7.

Protein-Style Dynamical Transition in a Non-Biological Polymer and a Non-Aqueous Solvent.

Mamontov E, Sharma VK, Borreguero JM, Tyagi M.

J Phys Chem B. 2016 Mar 31;120(12):3232-9. doi: 10.1021/acs.jpcb.6b00866. Epub 2016 Mar 23.

PMID:
26977709
8.

Molecular Dynamics Force-Field Refinement against Quasi-Elastic Neutron Scattering Data.

Borreguero JM, Lynch VE.

J Chem Theory Comput. 2016 Jan 12;12(1):9-17. doi: 10.1021/acs.jctc.5b00878. Epub 2015 Dec 10.

PMID:
26616475
9.

Self-assembly and structural relaxation in a model ionomer melt.

Goswami M, Borreguero JM, Sumpter BG.

J Chem Phys. 2015 Feb 28;142(8):084903. doi: 10.1063/1.4913517.

PMID:
25725753
10.

Safety and effectiveness of two treatment regimes with tranexamic acid to minimize inflammatory response in elective cardiopulmonary bypass patients: a randomized double-blind, dose-dependent, phase IV clinical trial.

Jiménez JJ, Iribarren JL, Brouard M, Hernández D, Palmero S, Jiménez A, Lorente L, Machado P, Borreguero JM, Raya JM, Martín B, Pérez R, Martínez R, Mora ML.

J Cardiothorac Surg. 2011 Oct 14;6:138. doi: 10.1186/1749-8090-6-138.

11.

Redox-promoting protein motions in rubredoxin.

Borreguero JM, He J, Meilleur F, Weiss KL, Brown CM, Myles DA, Herwig KW, Agarwal PK.

J Phys Chem B. 2011 Jul 21;115(28):8925-36. doi: 10.1021/jp201346x. Epub 2011 May 24.

PMID:
21608980
12.

Parallel folding pathways in the SH3 domain protein.

Lam AR, Borreguero JM, Ding F, Dokholyan NV, Buldyrev SV, Stanley HE, Shakhnovich E.

J Mol Biol. 2007 Nov 9;373(5):1348-60. Epub 2007 Aug 22.

PMID:
17900612
13.

Benchmarking of TASSER in the ab initio limit.

Borreguero JM, Skolnick J.

Proteins. 2007 Jul 1;68(1):48-56.

PMID:
17444524
14.

Ab initio discrete molecular dynamics approach to protein folding and aggregation.

Urbanc B, Borreguero JM, Cruz L, Stanley HE.

Methods Enzymol. 2006;412:314-38. Review.

PMID:
17046666
15.

Solvent and mutation effects on the nucleation of amyloid beta-protein folding.

Cruz L, Urbanc B, Borreguero JM, Lazo ND, Teplow DB, Stanley HE.

Proc Natl Acad Sci U S A. 2005 Dec 20;102(51):18258-63. Epub 2005 Dec 9.

16.

Folding events in the 21-30 region of amyloid beta-protein (Abeta) studied in silico.

Borreguero JM, Urbanc B, Lazo ND, Buldyrev SV, Teplow DB, Stanley HE.

Proc Natl Acad Sci U S A. 2005 Apr 26;102(17):6015-20. Epub 2005 Apr 18.

17.

Multiple folding pathways of the SH3 domain.

Borreguero JM, Ding F, Buldyrev SV, Stanley HE, Dokholyan NV.

Biophys J. 2004 Jul;87(1):521-33.

18.

Identifying importance of amino acids for protein folding from crystal structures.

Dokholyan NV, Borreguero JM, Buldyrev SV, Ding F, Stanley HE, Shakhnovich EI.

Methods Enzymol. 2003;374:616-38. No abstract available.

PMID:
14696390
19.

Possible mechanism for cold denaturation of proteins at high pressure.

Marqués MI, Borreguero JM, Stanley HE, Dokholyan NV.

Phys Rev Lett. 2003 Sep 26;91(13):138103. Epub 2003 Sep 26.

PMID:
14525339
20.

Mechanism for the alpha-helix to beta-hairpin transition.

Ding F, Borreguero JM, Buldyrey SV, Stanley HE, Dokholyan NV.

Proteins. 2003 Nov 1;53(2):220-8.

PMID:
14517973
21.

Thermodynamics and folding kinetics analysis of the SH3 domain form discrete molecular dynamics.

Borreguero JM, Dokholyan NV, Buldyrev SV, Shakhnovich EI, Stanley HE.

J Mol Biol. 2002 May 3;318(3):863-76.

PMID:
12054829

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