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Items: 1 to 50 of 104

1.

Exploring the Structure and Stability of Cholesterol Dimer Formation in Multicomponent Lipid Bilayers.

Bandara A, Panahi A, Pantelopulos GA, Straub JE.

J Comput Chem. 2019 Oct 5;40(26):2348. doi: 10.1002/jcc.26039. Epub 2019 Jul 30. No abstract available.

PMID:
31418884
2.

Exploring the impact of proteins on the line tension of a phase-separating ternary lipid mixture.

Bandara A, Panahi A, Pantelopulos GA, Nagai T, Straub JE.

J Chem Phys. 2019 May 28;150(20):204702. doi: 10.1063/1.5091450.

PMID:
31153187
3.

Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins.

Baul U, Chakraborty D, Mugnai ML, Straub JE, Thirumalai D.

J Phys Chem B. 2019 Apr 25;123(16):3462-3474. doi: 10.1021/acs.jpcb.9b02575. Epub 2019 Apr 15.

PMID:
30913885
4.

Design, synthesis, and biomedical applications of synthetic sulphated polysaccharides.

Caputo HE, Straub JE, Grinstaff MW.

Chem Soc Rev. 2019 Apr 15;48(8):2338-2365. doi: 10.1039/c7cs00593h. Review.

PMID:
30742140
5.

Aerosol-OT Surfactant Forms Stable Reverse Micelles in Apolar Solvent in the Absence of Water.

Urano R, Pantelopulos GA, Straub JE.

J Phys Chem B. 2019 Mar 21;123(11):2546-2557. doi: 10.1021/acs.jpcb.8b07847. Epub 2019 Mar 6.

PMID:
30688469
6.

Regimes of Complex Lipid Bilayer Phases Induced by Cholesterol Concentration in MD Simulation.

Pantelopulos GA, Straub JE.

Biophys J. 2018 Dec 4;115(11):2167-2178. doi: 10.1016/j.bpj.2018.10.011. Epub 2018 Oct 19.

PMID:
30414630
7.

Enhanced sampling method in molecular simulations using genetic algorithm for biomolecular systems.

Sakae Y, Straub JE, Okamoto Y.

J Comput Chem. 2019 Jan 15;40(2):475-481. doi: 10.1002/jcc.25735. Epub 2018 Nov 10.

PMID:
30414195
8.

Influence of membrane lipid composition on the structure and activity of γ-secretase.

Aguayo-Ortiz R, Straub JE, Dominguez L.

Phys Chem Chem Phys. 2018 Nov 7;20(43):27294-27304. doi: 10.1039/c8cp04138e.

PMID:
30357233
9.

Characterization of dynamics and mechanism in the self-assembly of AOT reverse micelles.

Urano R, Pantelopulos GA, Song S, Straub JE.

J Chem Phys. 2018 Oct 14;149(14):144901. doi: 10.1063/1.5042771.

PMID:
30316264
10.

Membrane-wrapped nanoparticles probe divergent roles of GM3 and phosphatidylserine in lipid-mediated viral entry pathways.

Xu F, Bandara A, Akiyama H, Eshaghi B, Stelter D, Keyes T, Straub JE, Gummuluru S, Reinhard BM.

Proc Natl Acad Sci U S A. 2018 Sep 25;115(39):E9041-E9050. doi: 10.1073/pnas.1804292115. Epub 2018 Sep 6.

11.

Molecular Insights into Human Hereditary Apolipoprotein A-I Amyloidosis Caused by the Glu34Lys Mutation.

Morgado I, Panahi A, Burwash AG, Das M, Straub JE, Gursky O.

Biochemistry. 2018 Oct 2;57(39):5738-5747. doi: 10.1021/acs.biochem.8b00817. Epub 2018 Sep 19.

PMID:
30184436
12.

Structure of APP-C991-99 and implications for role of extra-membrane domains in function and oligomerization.

Pantelopulos GA, Straub JE, Thirumalai D, Sugita Y.

Biochim Biophys Acta Biomembr. 2018 Apr 24. pii: S0005-2736(18)30112-3. doi: 10.1016/j.bbamem.2018.04.002. [Epub ahead of print]

PMID:
29702072
13.

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach.

Aguayo-Ortiz R, Chávez-García C, Straub JE, Dominguez L.

Chem Sci. 2017 Aug 1;8(8):5576-5584. doi: 10.1039/c7sc00980a. Epub 2017 Jun 5.

14.

Critical size dependence of domain formation observed in coarse-grained simulations of bilayers composed of ternary lipid mixtures.

Pantelopulos GA, Nagai T, Bandara A, Panahi A, Straub JE.

J Chem Phys. 2017 Sep 7;147(9):095101. doi: 10.1063/1.4999709.

15.

Cellular prion protein targets amyloid-β fibril ends via its C-terminal domain to prevent elongation.

Bove-Fenderson E, Urano R, Straub JE, Harris DA.

J Biol Chem. 2017 Oct 13;292(41):16858-16871. doi: 10.1074/jbc.M117.789990. Epub 2017 Aug 23.

16.

Exploring the structure and stability of cholesterol dimer formation in multicomponent lipid bilayers.

Bandara A, Panahi A, Pantelopulos GA, Straub JE.

J Comput Chem. 2017 Jun 15;38(16):1479-1488. doi: 10.1002/jcc.24516. Epub 2016 Oct 20. Erratum in: J Comput Chem. 2019 Oct 5;40(26):2348.

17.

Impact of membrane lipid composition on the structure and stability of the transmembrane domain of amyloid precursor protein.

Dominguez L, Foster L, Straub JE, Thirumalai D.

Proc Natl Acad Sci U S A. 2016 Sep 6;113(36):E5281-7. doi: 10.1073/pnas.1606482113. Epub 2016 Aug 24.

18.

Specific Binding of Cholesterol to C99 Domain of Amyloid Precursor Protein Depends Critically on Charge State of Protein.

Panahi A, Bandara A, Pantelopulos GA, Dominguez L, Straub JE.

J Phys Chem Lett. 2016 Sep 15;7(18):3535-41. doi: 10.1021/acs.jpclett.6b01624. Epub 2016 Aug 26.

19.

On the use of mass scaling for stable and efficient simulated tempering with molecular dynamics.

Nagai T, Pantelopulos GA, Takahashi T, Straub JE.

J Comput Chem. 2016 Aug 5;37(21):2017-28. doi: 10.1002/jcc.24430. Epub 2016 Jun 24.

PMID:
27338239
20.

Combined Molecular Dynamics Simulations and Experimental Studies of the Structure and Dynamics of Poly-Amido-Saccharides.

Chin SL, Lu Q, Dane EL, Dominguez L, McKnight CJ, Straub JE, Grinstaff MW.

J Am Chem Soc. 2016 May 25;138(20):6532-40. doi: 10.1021/jacs.6b01837. Epub 2016 May 12.

PMID:
27119983
21.

Freezing Transitions of Nanoconfined Coarse-Grained Water Show Subtle Dependence on Confining Environment.

Lu Q, Straub JE.

J Phys Chem B. 2016 Mar 10;120(9):2517-25. doi: 10.1021/acs.jpcb.5b10481. Epub 2016 Feb 24.

PMID:
26906259
22.

Extension of a protein docking algorithm to membranes and applications to amyloid precursor protein dimerization.

Viswanath S, Dominguez L, Foster LS, Straub JE, Elber R.

Proteins. 2015 Dec;83(12):2170-85. doi: 10.1002/prot.24934. Epub 2015 Oct 14.

23.

Exploring the role of hydration and confinement in the aggregation of amyloidogenic peptides Aβ(16-22) and Sup35(7-13) in AOT reverse micelles.

Martinez AV, Małolepsza E, Rivera E, Lu Q, Straub JE.

J Chem Phys. 2014 Dec 14;141(22):22D530. doi: 10.1063/1.4902550.

24.

Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method.

Lu Q, Kim J, Farrell JD, Wales DJ, Straub JE.

J Chem Phys. 2014 Nov 14;141(18):18C525. doi: 10.1063/1.4896513.

PMID:
25399190
25.

Role of Charge and Solvation in the Structure and Dynamics of Alanine-Rich Peptide AKA2 in AOT Reverse Micelles.

Martinez AV, Małolepsza E, Domínguez L, Lu Q, Straub JE.

J Phys Chem B. 2015 Jul 23;119(29):9084-90. doi: 10.1021/jp508813n. Epub 2014 Nov 6.

26.

Structural heterogeneity in transmembrane amyloid precursor protein homodimer is a consequence of environmental selection.

Dominguez L, Foster L, Meredith SC, Straub JE, Thirumalai D.

J Am Chem Soc. 2014 Jul 9;136(27):9619-26. doi: 10.1021/ja503150x. Epub 2014 Jun 30.

27.

Propensity to form amyloid fibrils is encoded as excitations in the free energy landscape of monomeric proteins.

Zhuravlev PI, Reddy G, Straub JE, Thirumalai D.

J Mol Biol. 2014 Jul 15;426(14):2653-66. doi: 10.1016/j.jmb.2014.05.007. Epub 2014 May 17.

28.

Limit of metastability for liquid and vapor phases of water.

Cho WJ, Kim J, Lee J, Keyes T, Straub JE, Kim KS.

Phys Rev Lett. 2014 Apr 18;112(15):157802. Epub 2014 Apr 16.

PMID:
24785073
29.

Empirical maps for the calculation of amide I vibrational spectra of proteins from classical molecular dynamics simulations.

Małolepsza E, Straub JE.

J Phys Chem B. 2014 Jul 17;118(28):7848-55. doi: 10.1021/jp412827s. Epub 2014 Apr 11.

30.

Membrane-Protein Interactions Are Key to Understanding Amyloid Formation.

Straub JE, Thirumalai D.

J Phys Chem Lett. 2014 Feb 6;5(3):633-5. doi: 10.1021/jz500054d. No abstract available.

PMID:
26276620
31.

Transmembrane fragment structures of amyloid precursor protein depend on membrane surface curvature.

Dominguez L, Meredith SC, Straub JE, Thirumalai D.

J Am Chem Soc. 2014 Jan 22;136(3):854-7. doi: 10.1021/ja410958j. Epub 2014 Jan 8.

32.

Spatio-temporal hierarchy in the dynamics of a minimalist protein model.

Matsunaga Y, Baba A, Li CB, Straub JE, Toda M, Komatsuzaki T, Berry RS.

J Chem Phys. 2013 Dec 7;139(21):215101. doi: 10.1063/1.4834415.

PMID:
24320403
33.

Probing the structure and dynamics of confined water in AOT reverse micelles.

Martinez AV, Dominguez L, Małolepsza E, Moser A, Ziegler Z, Straub JE.

J Phys Chem B. 2013 Jun 20;117(24):7345-51. doi: 10.1021/jp402270e. Epub 2013 Jun 6.

34.

"Strange kinetics" in the temperature dependence of methionine ligand rebinding dynamics in cytochrome c.

Zhang P, Ahn SW, Straub JE.

J Phys Chem B. 2013 Jun 20;117(24):7190-202. doi: 10.1021/jp400481m. Epub 2013 Jun 6.

PMID:
23631395
35.

Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method.

Lu Q, Kim J, Straub JE.

J Chem Phys. 2013 Mar 14;138(10):104119. doi: 10.1063/1.4794786.

PMID:
23514477
36.

Replica exchange statistical temperature molecular dynamics algorithm.

Kim J, Straub JE, Keyes T.

J Phys Chem B. 2012 Jul 26;116(29):8646-53. doi: 10.1021/jp300366j. Epub 2012 May 15.

PMID:
22540354
37.

Exploring the solid-liquid phase change of an adapted Dzugutov model using generalized replica exchange method.

Lu Q, Kim J, Straub JE.

J Phys Chem B. 2012 Jul 26;116(29):8654-61. doi: 10.1021/jp300406c. Epub 2012 Apr 10.

PMID:
22452532
38.

Dynamics of methionine ligand rebinding in cytochrome c.

Zhang P, Małolepsza E, Straub JE.

J Phys Chem B. 2012 Jun 14;116(23):6980-90. doi: 10.1021/jp300783j. Epub 2012 Apr 6.

PMID:
22432601
39.

Entropic stabilization of proteins by TMAO.

Cho SS, Reddy G, Straub JE, Thirumalai D.

J Phys Chem B. 2011 Nov 17;115(45):13401-7. doi: 10.1021/jp207289b. Epub 2011 Oct 26.

40.

Communication: Iteration-free, weighted histogram analysis method in terms of intensive variables.

Kim J, Keyes T, Straub JE.

J Chem Phys. 2011 Aug 14;135(6):061103. doi: 10.1063/1.3626150.

41.

Role of water in protein aggregation and amyloid polymorphism.

Thirumalai D, Reddy G, Straub JE.

Acc Chem Res. 2012 Jan 17;45(1):83-92. doi: 10.1021/ar2000869. Epub 2011 Jul 15.

42.

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide.

O'Brien EP, Straub JE, Brooks BR, Thirumalai D.

J Phys Chem Lett. 2011 May 19;2(10):1171-1177.

43.

Protein folding in a reverse micelle environment: the role of confinement and dehydration.

Martinez AV, DeSensi SC, Dominguez L, Rivera E, Straub JE.

J Chem Phys. 2011 Feb 7;134(5):055107. doi: 10.1063/1.3545982. Erratum in: J Chem Phys. 2011 Apr 7;134(13):139901.

44.

Factors governing fibrillogenesis of polypeptide chains revealed by lattice models.

Li MS, Co NT, Reddy G, Hu CK, Straub JE, Thirumalai D.

Phys Rev Lett. 2010 Nov 19;105(21):218101. Epub 2010 Nov 17.

PMID:
21231356
45.

Toward a molecular theory of early and late events in monomer to amyloid fibril formation.

Straub JE, Thirumalai D.

Annu Rev Phys Chem. 2011;62:437-63. doi: 10.1146/annurev-physchem-032210-103526. Review.

PMID:
21219143
46.

Dry amyloid fibril assembly in a yeast prion peptide is mediated by long-lived structures containing water wires.

Reddy G, Straub JE, Thirumalai D.

Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21459-64. doi: 10.1073/pnas.1008616107. Epub 2010 Nov 22.

47.

Generalized simulated tempering for exploring strong phase transitions.

Kim J, Straub JE.

J Chem Phys. 2010 Oct 21;133(15):154101. doi: 10.1063/1.3503503. Erratum in: J Chem Phys. 2010 Oct 28;133(16):169901.

48.

Generalized replica exchange method.

Kim J, Keyes T, Straub JE.

J Chem Phys. 2010 Jun 14;132(22):224107. doi: 10.1063/1.3432176.

49.

Principles governing oligomer formation in amyloidogenic peptides.

Straub JE, Thirumalai D.

Curr Opin Struct Biol. 2010 Apr;20(2):187-95. doi: 10.1016/j.sbi.2009.12.017. Epub 2010 Jan 26. Review.

50.

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