Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer Yu-Shan Lin, Gregory R. Bowman, Kyle A.

Slides:

Advertisements

Similar presentations

Fabio Trovato, Edward P. O’Brien Biophysical Journal

Advertisements

Volume 107, Issue 9, Pages (November 2014)

Molecular Analysis of the Interaction between Staphylococcal Virulence Factor Sbi-IV and Complement C3d Ronald D. Gorham, Wilson Rodriguez, Dimitrios.

Maryam Sayadi, Seiichiro Tanizaki, Michael Feig Biophysical Journal

(Un)Folding Mechanisms of the FBP28 WW Domain in Explicit Solvent Revealed by Multiple Rare Event Simulation Methods Jarek Juraszek, Peter G. Bolhuis

Volume 106, Issue 6, Pages (March 2014)

Young Min Rhee, Vijay S. Pande Biophysical Journal

Changing Chromatin Fiber Conformation by Nucleosome Repositioning

Volume 98, Issue 3, Pages (February 2010)

Yufeng Liu, Meng Ke, Haipeng Gong Biophysical Journal

Folding Pathways of Prion and Doppel

Olivier Fisette, Stéphane Gagné, Patrick Lagüe Biophysical Journal

Volume 107, Issue 10, Pages (November 2014)

Jing Han, Kristyna Pluhackova, Tsjerk A. Wassenaar, Rainer A. Böckmann

Relation between the Conformational Heterogeneity and Reaction Cycle of Ras: Molecular Simulation of Ras Chigusa Kobayashi, Shinji Saito Biophysical.

Volume 96, Issue 4, Pages (February 2009)

Theoretical and Computational Investigation of Flagellin Translocation and Bacterial Flagellum Growth David E. Tanner, Wen Ma, Zhongzhou Chen, Klaus.

Volume 106, Issue 6, Pages (March 2014)

Clare-Louise Towse, Jiri Vymetal, Jiri Vondrasek, Valerie Daggett

Anton Arkhipov, Wouter H. Roos, Gijs J.L. Wuite, Klaus Schulten

Influence of Protein Scaffold on Side-Chain Transfer Free Energies

Volume 74, Issue 1, Pages (January 1998)

Volume 18, Issue 9, Pages (September 2010)

Volume 98, Issue 8, Pages (April 2010)

Volume 102, Issue 1, Pages (January 2012)

Binding of the Bacteriophage P22 N-Peptide to the boxB RNA Motif Studied by Molecular Dynamics Simulations Ranjit P. Bahadur, Srinivasaraghavan Kannan,

A Molecular Dynamics Study of Ca2+-Calmodulin: Evidence of Interdomain Coupling and Structural Collapse on the Nanosecond Timescale Craig M. Shepherd,

Dynamic Motions of the HIV-1 Frameshift Site RNA

Molecular-Dynamics Simulations of the ATP/apo State of a Multidrug ATP-Binding Cassette Transporter Provide a Structural and Mechanistic Basis for the.

Sukanya Sasmal, James Lincoff, Teresa Head-Gordon Biophysical Journal

Volume 96, Issue 7, Pages (April 2009)

Functional Role of Ribosomal Signatures

Comparative Molecular Dynamics Simulation Studies of Protegrin-1 Monomer and Dimer in Two Different Lipid Bilayers Huan Rui, Jinhyuk Lee, Wonpil Im

Atomistic Ensemble Modeling and Small-Angle Neutron Scattering of Intrinsically Disordered Protein Complexes: Applied to Minichromosome Maintenance Protein

Hisashi Ishida, Hidetoshi Kono Biophysical Journal

Protein Collective Motions Coupled to Ligand Migration in Myoglobin

Firdaus Samsudin, Alister Boags, Thomas J. Piggot, Syma Khalid

Sequential Unfolding of Individual Helices of Bacterioopsin Observed in Molecular Dynamics Simulations of Extraction from the Purple Membrane Michele.

Volume 85, Issue 4, Pages (October 2003)

Histone Acetylation Regulates Chromatin Accessibility: Role of H4K16 in Inter- nucleosome Interaction Ruihan Zhang, Jochen Erler, Jörg Langowski Biophysical.

Molecular Interactions of Alzheimer's Biomarker FDDNP with Aβ Peptide

Sequence and Crowding Effects in the Aggregation of a 10-Residue Fragment Derived from Islet Amyloid Polypeptide Eva Rivera, John Straub, D. Thirumalai

Activation of the Edema Factor of Bacillus anthracis by Calmodulin: Evidence of an Interplay between the EF-Calmodulin Interaction and Calcium Binding

Yuguang Mu, Lars Nordenskiöld, James P. Tam Biophysical Journal

Cholesterol Modulates the Dimer Interface of the β2-Adrenergic Receptor via Cholesterol Occupancy Sites Xavier Prasanna, Amitabha Chattopadhyay, Durba.

Hydrogen Bonding in Helical Polypeptides from Molecular Dynamics Simulations and Amide Hydrogen Exchange Analysis: Alamethicin and Melittin in Methanol

Replica Exchange Molecular Dynamics Simulations Provide Insight into Substrate Recognition by Small Heat Shock Proteins Sunita Patel, Elizabeth Vierling,

Structural Flexibility of CaV1. 2 and CaV2

Volume 107, Issue 9, Pages (November 2014)

Dynamics of Active Semiflexible Polymers

Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein

Molecular Dynamics Simulation of Protein Folding by Essential Dynamics Sampling: Folding Landscape of Horse Heart Cytochrome c Isabella Daidone, Andrea.

Molecular Mechanism for Stabilizing a Short Helical Peptide Studied by Generalized- Ensemble Simulations with Explicit Solvent Yuji Sugita, Yuko Okamoto

Logan S. Ahlstrom, Osamu Miyashita Biophysical Journal

Volume 114, Issue 1, Pages (January 2018)

Ion-Induced Defect Permeation of Lipid Membranes

Flow-Induced β-Hairpin Folding of the Glycoprotein Ibα β-Switch

Coupling of S4 Helix Translocation and S6 Gating Analyzed by Molecular-Dynamics Simulations of Mutated Kv Channels Manami Nishizawa, Kazuhisa Nishizawa

Coupling of S4 Helix Translocation and S6 Gating Analyzed by Molecular-Dynamics Simulations of Mutated Kv Channels Manami Nishizawa, Kazuhisa Nishizawa

Christina Bergonzo, Thomas E. Cheatham Biophysical Journal

Volume 111, Issue 11, Pages (December 2016)

Volume 74, Issue 1, Pages (January 1998)

Mijo Simunovic, Gregory A. Voth Biophysical Journal

Volume 95, Issue 7, Pages (October 2008)

Volume 114, Issue 2, Pages (January 2018)

Yongli Zhang, Junyi Jiao, Aleksander A. Rebane Biophysical Journal

Hydrophobic Core Formation and Dehydration in Protein Folding Studied by Generalized-Ensemble Simulations Takao Yoda, Yuji Sugita, Yuko Okamoto Biophysical.

Volume 98, Issue 4, Pages (February 2010)

Seongwon Kim, Takako Takeda, Dmitri K. Klimov Biophysical Journal

Volume 114, Issue 4, Pages (February 2018)

Presentation transcript:

Investigating How Peptide Length and a Pathogenic Mutation Modify the Structural Ensemble of Amyloid Beta Monomer Yu-Shan Lin, Gregory R. Bowman, Kyle A. Beauchamp, Vijay S. Pande Biophysical Journal Volume 102, Issue 2, Pages 315-324 (January 2012) DOI: 10.1016/j.bpj.2011.12.002 Copyright © 2012 Biophysical Society Terms and Conditions

Figure 1 Top: Free energy landscape (in kT) of Aβ42 as a function of the first and the second principal components from the principal component analysis using the root mean-square deviations among conformations. Bottom: Dependence of the principal component analysis results on the number of independent trajectories during the second-stage sampling. Upper left, upper right, lower left, and lower right are the results from 10, 50, 100, and 500 independent trajectories, respectively. Biophysical Journal 2012 102, 315-324DOI: (10.1016/j.bpj.2011.12.002) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 2 Conformations of the six most populated representative conformations in the Aβ42 ensemble. Secondary structure visualizations were generated using VMD (84). The blue spheres in the figure represent the N atoms in the N-terminal amino groups. α-helices are shown in purple, 310-helices in blue, extended β in yellow, isolated β bridges in tan, turns in cyan, and loops/irregulars in white. The secondary structure assignment was generated using the STRIDE program implemented in VMD. Biophysical Journal 2012 102, 315-324DOI: (10.1016/j.bpj.2011.12.002) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 3 Ensemble-averaged %population of the secondary structures based on the DSSP analysis for Aβ42. The eight DSSP assignments are α-helix (H), 310-helix (G), π-helix (I), isolated bridge (B), extended β (E), bend (S), turn (T), or loop/irregular (∼). Inset: Zoom in on the π-helix (I), isolated bridge (B), and extended β (E) curves. The 1-σ error bars were calculated by dividing the total simulation data into 10 sets. Biophysical Journal 2012 102, 315-324DOI: (10.1016/j.bpj.2011.12.002) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 4 Ensemble-averaged contact map for Aβ42 (in log scale). Two residues are considered in contact when their Cα-Cα distance is <8 Å (88). Note the (i,i), (i,i±1), and (i,i±2) contacts are not computed and result in the purple diagonal shown in the figure. Biophysical Journal 2012 102, 315-324DOI: (10.1016/j.bpj.2011.12.002) Copyright © 2012 Biophysical Society Terms and Conditions

Figure 5 Ensemble-averaged %population of α-helix (H) (top panel) and extended β (E) (bottom panel) based on the DSSP analysis for Aβ42 (black circle), Aβ40 (red square), and Aβ42-E22K (green diamond). Biophysical Journal 2012 102, 315-324DOI: (10.1016/j.bpj.2011.12.002) Copyright © 2012 Biophysical Society Terms and Conditions