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Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics.

Rojas A, Maisuradze N, Kachlishvili K, Scheraga HA, Maisuradze GG.

ACS Chem Neurosci. 2017 Jan 18;8(1):201-209. doi: 10.1021/acschemneuro.6b00331.


Fibril elongation by Aβ(17-42): kinetic network analysis of hybrid-resolution molecular dynamics simulations.

Han W, Schulten K.

J Am Chem Soc. 2014 Sep 3;136(35):12450-60. doi: 10.1021/ja507002p.


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.


Molecular nonlinear dynamics and protein thermal uncertainty quantification.

Xia K, Wei GW.

Chaos. 2014 Mar;24(1):013103. doi: 10.1063/1.4861202.


Tranilast binds to aβ monomers and promotes aβ fibrillation.

Connors CR, Rosenman DJ, Lopes DH, Mittal S, Bitan G, Sorci M, Belfort G, Garcia A, Wang C.

Biochemistry. 2013 Jun 11;52(23):3995-4002. doi: 10.1021/bi400426t.


Tracking the mechanism of fibril assembly by simulated two-dimensional ultraviolet spectroscopy.

Lam AR, Rodriguez JJ, Rojas A, Scheraga HA, Mukamel S.

J Phys Chem A. 2013 Jan 17;117(2):342-50. doi: 10.1021/jp3101267.


Unlocking the atomic-level details of amyloid fibril growth through advanced biomolecular simulations.

Buchete NV.

Biophys J. 2012 Oct 3;103(7):1411-3. doi: 10.1016/j.bpj.2012.08.052. No abstract available.


Elucidating the locking mechanism of peptides onto growing amyloid fibrils through transition path sampling.

Schor M, Vreede J, Bolhuis PG.

Biophys J. 2012 Sep 19;103(6):1296-304. doi: 10.1016/j.bpj.2012.07.056.


Role of β-hairpin formation in aggregation: the self-assembly of the amyloid-β(25-35) peptide.

Larini L, Shea JE.

Biophys J. 2012 Aug 8;103(3):576-86. doi: 10.1016/j.bpj.2012.06.027.


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.


Structural dynamics of the ΔE22 (Osaka) familial Alzheimer's disease-linked amyloid β-protein.

Inayathullah M, Teplow DB.

Amyloid. 2011 Sep;18(3):98-107. doi: 10.3109/13506129.2011.580399.


Zinc ions promote Alzheimer Abeta aggregation via population shift of polymorphic states.

Miller Y, Ma B, Nussinov R.

Proc Natl Acad Sci U S A. 2010 May 25;107(21):9490-5. doi: 10.1073/pnas.0913114107.


Polymorphism in Alzheimer Abeta amyloid organization reflects conformational selection in a rugged energy landscape.

Miller Y, Ma B, Nussinov R.

Chem Rev. 2010 Aug 11;110(8):4820-38. doi: 10.1021/cr900377t. Review. No abstract available.


Principles governing oligomer formation in amyloidogenic peptides.

Straub JE, Thirumalai D.

Curr Opin Struct Biol. 2010 Apr;20(2):187-95. doi: 10.1016/ Review.


Dynamics of locking of peptides onto growing amyloid fibrils.

Reddy G, Straub JE, Thirumalai D.

Proc Natl Acad Sci U S A. 2009 Jul 21;106(29):11948-53. doi: 10.1073/pnas.0902473106.


Probing the mechanisms of fibril formation using lattice models.

Li MS, Klimov DK, Straub JE, Thirumalai D.

J Chem Phys. 2008 Nov 7;129(17):175101. doi: 10.1063/1.2989981.


Amyloid beta-protein monomer folding: free-energy surfaces reveal alloform-specific differences.

Yang M, Teplow DB.

J Mol Biol. 2008 Dec 12;384(2):450-64. doi: 10.1016/j.jmb.2008.09.039.


Hydrophobic cooperativity as a mechanism for amyloid nucleation.

Hills RD Jr, Brooks CL 3rd.

J Mol Biol. 2007 May 4;368(3):894-901.

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