Simulation study on the disordered state of an Alzheimer's β amyloid peptide Aβ(12–36) in water consisting of random‐structural, β‐structural, and helical clusters
暂无分享,去创建一个
Junichi Higo | Narutoshi Kamiya | Jinzen Ikebe | J. Higo | Jinzen Ikebe | N. Kamiya | J. Ito | H. Shindo | Heisaburo Shindo | Jun-ichi Ito
[1] K. Beyreuther,et al. Structure of amyloid A4-(1-40)-peptide of Alzheimer's disease. , 1995, European journal of biochemistry.
[2] D. Teplow,et al. Kinetic Studies of Amyloid β-Protein Fibril Assembly , 2002, The Journal of Biological Chemistry.
[3] K. Iwata,et al. The Alzheimer's peptide a beta adopts a collapsed coil structure in water. , 2000, Journal of structural biology.
[4] J. Brahms,et al. Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism. , 1980, Journal of molecular biology.
[5] M. Shiao,et al. The Effect of Aβ Conformation on the Metal Affinity and Aggregation Mechanism Studied by Circular Dichroism Spectroscopy , 2006 .
[6] Junichi Higo,et al. AMBER-based hybrid force field for conformational sampling of polypeptides , 2005 .
[7] Haruki Nakamura,et al. Presto(protein Engineering Simulator): A Vectorized Molecular Mechanics Program for Biopolymers , 1992, Comput. Chem..
[8] Haruki Nakamura,et al. Energy landscape of a peptide consisting of α‐helix, 310‐helix, β‐turn, β‐hairpin, and other disordered conformations , 2001 .
[9] A G Murzin,et al. SCOP: a structural classification of proteins database for the investigation of sequences and structures. , 1995, Journal of molecular biology.
[10] W. Goddard,et al. Atomic level simulations on a million particles: The cell multipole method for Coulomb and London nonbond interactions , 1992 .
[11] G. Ciccotti,et al. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .
[12] Gary P. Morriss,et al. The isothermal/isobaric molecular dynamics ensemble , 1983 .
[13] R. Tycko,et al. Abeta40-Lactam(D23/K28) models a conformation highly favorable for nucleation of amyloid. , 2005, Biochemistry.
[14] A. Pohorille,et al. The development/application of a ‘minimalist’ organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data , 1997 .
[15] R. Riek,et al. 3D structure of Alzheimer's amyloid-β(1–42) fibrils , 2005 .
[16] Y. Sugita,et al. Replica-exchange molecular dynamics method for protein folding , 1999 .
[17] Joan-Emma Shea,et al. Effects of Solvent on the Structure of the Alzheimer Amyloid-β(25–35) Peptide , 2006 .
[18] W. L. Jorgensen,et al. Comparison of simple potential functions for simulating liquid water , 1983 .
[19] K. Ikeda,et al. Free‐energy landscape of a chameleon sequence in explicit water and its inherent α/β bifacial property , 2003 .
[20] R. Leapman,et al. A structural model for Alzheimer's β-amyloid fibrils based on experimental constraints from solid state NMR , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[21] Richard D. Leapman,et al. Self-Propagating, Molecular-Level Polymorphism in Alzheimer's ß-Amyloid Fibrils , 2005, Science.
[22] P. Kollman,et al. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .
[23] Haruki Nakamura,et al. β‐Hairpins, α‐helices, and the intermediates among the secondary structures in the energy landscape of a peptide from a distal β‐hairpin of SH3 domain , 2003, J. Comput. Chem..
[24] Haruki Nakamura,et al. Conformational transition states of a β‐hairpin peptide between the ordered and disordered conformations in explicit water , 2002, Protein science : a publication of the Protein Society.
[25] A. Kidera,et al. Multicanonical Ensemble Generated by Molecular Dynamics Simulation for Enhanced Conformational Sampling of Peptides , 1997 .
[26] Joan-Emma Shea,et al. The structure of the Alzheimer amyloid beta 10-35 peptide probed through replica-exchange molecular dynamics simulations in explicit solvent. , 2007, Journal of molecular biology.