Cell dynamics of folding in two-dimensional model proteins

Slides:

Advertisements

Similar presentations

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

Advertisements

Volume 106, Issue 6, Pages (March 2014)

Young Min Rhee, Vijay S. Pande Biophysical Journal

Folding Pathways of Prion and Doppel

Robert G. Smock, Lila M. Gierasch Cell

Diffusion in a Fluid Membrane with a Flexible Cortical Cytoskeleton

Mechanisms of Capsid Assembly around a Polymer

Volume 106, Issue 8, Pages (April 2014)

Comparing Folding Codes in Simple Heteropolymer Models of Protein Evolutionary Landscape: Robustness of the Superfunnel Paradigm Richard Wroe, Erich.

In This Issue Cell Volume 158, Issue 5, (August 2014)

Two-Dimensional Substructure of MT Receptive Fields

Volume 2, Issue 3, Pages (September 2002)

A Model of H-NS Mediated Compaction of Bacterial DNA

Volume 95, Issue 6, Pages (September 2008)

Volume 86, Issue 2, Pages (February 2004)

A Theoretical Model of Slow Wave Regulation Using Voltage-Dependent Synthesis of Inositol 1,4,5-Trisphosphate Mohammad S. Imtiaz, David W. Smith, Dirk.

Carlos R. Baiz, Andrei Tokmakoff Biophysical Journal

Mechanically Probing the Folding Pathway of Single RNA Molecules

Volume 111, Issue 4, Pages (August 2016)

Near-Critical Fluctuations and Cytoskeleton-Assisted Phase Separation Lead to Subdiffusion in Cell Membranes Jens Ehrig, Eugene P. Petrov, Petra Schwille

Folding of the Protein Domain hbSBD

Imaging the Neural Basis of Locomotion

Responses of Collicular Fixation Neurons to Gaze Shift Perturbations in Head- Unrestrained Monkey Reveal Gaze Feedback Control Woo Young Choi, Daniel.

Meng Qin, Jian Zhang, Wei Wang Biophysical Journal

Agustí Emperador, Oliver Carrillo, Manuel Rueda, Modesto Orozco

Volume 114, Issue 1, Pages (January 2018)

Nicolas Catz, Peter W. Dicke, Peter Thier Current Biology

Raft Formation in Lipid Bilayers Coupled to Curvature

From Computer Simulations to Human Disease

De Novo Design of Foldable Proteins with Smooth Folding Funnel

Statistical Dynamics of Spatial-Order Formation by Communicating Cells

Carlos R. Baiz, Andrei Tokmakoff Biophysical Journal

Ivan V. Polozov, Klaus Gawrisch Biophysical Journal

Michael Katzer, William Stillwell Biophysical Journal

Volume 84, Issue 6, Pages (June 2003)

Volume 78, Issue 6, Pages (June 2000)

Colocalization of Multiple DNA Loci: A Physical Mechanism

Suppression without Inhibition in Visual Cortex

Power Dissipation in the Subtectorial Space of the Mammalian Cochlea Is Modulated by Inner Hair Cell Stereocilia Srdjan Prodanovic, Sheryl Gracewski,

Volume 96, Issue 6, Pages (March 2009)

Volume 105, Issue 1, Pages (July 2013)

Protein Collective Motions Coupled to Ligand Migration in Myoglobin

Volume 110, Issue 7, Pages (April 2016)

Universality and diversity of the protein folding scenarios:a comprehensive analysis with the aid of a lattice model Leonid A Mirny, Victor Abkevich,

Ivan Coluzza, Daan Frenkel Biophysical Journal

Protein folding kinetics: timescales, pathways and energy landscapes in terms of sequence-dependent properties Thomas Veitshans, Dmitri Klimov, Devarajan.

Jason K. Cheung, Thomas M. Truskett Biophysical Journal

Volume 98, Issue 11, Pages (June 2010)

Velocity-Dependent Mechanical Unfolding of Bacteriorhodopsin Is Governed by a Dynamic Interaction Network Christian Kappel, Helmut Grubmüller Biophysical.

An Effective Solvent Theory Connecting the Underlying Mechanisms of Osmolytes and Denaturants for Protein Stability Apichart Linhananta, Shirin Hadizadeh,

A Monte Carlo Study of the Self-Assembly of Bacteriorhodopsin

Multiple Folding Pathways of the SH3 Domain

Volume 114, Issue 1, Pages (January 2018)

Andrew E. Blanchard, Chen Liao, Ting Lu Biophysical Journal

Effects of Receptor Interaction in Bacterial Chemotaxis

Jing Chen, John Neu, Makoto Miyata, George Oster Biophysical Journal

Volume 111, Issue 11, Pages (December 2016)

Pawel Gniewek, Andrzej Kolinski Biophysical Journal

Modeling Endoplasmic Reticulum Network Maintenance in a Plant Cell

Actin-Myosin Viscoelastic Flow in the Keratocyte Lamellipod

Dependence of Protein Folding Stability and Dynamics on the Density and Composition of Macromolecular Crowders Jeetain Mittal, Robert B. Best Biophysical.

Kiyoshi Kawai, Toru Suzuki, Masaharu Oguni Biophysical Journal

Monte Carlo simulations of protein folding using inexact potentials: how accurate must parameters be in order to preserve the essential features of the.

Wenzhe Ma, Chao Tang, Luhua Lai Biophysical Journal

Nonvisual Motor Training Influences Biological Motion Perception

Interplay between Protein Thermal Flexibility and Kinetic Stability

Kinetic Folding Mechanism of Erythropoietin

Volume 86, Issue 2, Pages (February 2004)

Ivan Coluzza, Saskia M. van der Vies, Daan Frenkel Biophysical Journal

A Model of H-NS Mediated Compaction of Bacterial DNA

Presentation transcript:

Cell dynamics of folding in two-dimensional model proteins Marek Cieplak, Jayanth R Banavar Folding and Design Volume 2, Issue 4, Pages 235-245 (August 1997) DOI: 10.1016/S1359-0278(97)00032-1 Copyright © 1997 Terms and Conditions

Figure 1 Model native conformations for DSKS and R. The numbers indicate the relative strengths of the contacts. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 2 Native conformations for sequence DSKS′. The numbers indicate the relative strengths of the contacts. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 3 The phase diagram for sequences DSKS (solid lines) and R (broken lines) in the T–B0 plane. The more vertical lines show the transition to compactness as measured by the temperature TN. The other lines are determined by TQ and are measures of the folding temperatures. The horizontal line is for sequence DSKS and indicates TQ determined only from the conformations that are maximally compact. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 4 The smoothed out (within two sizes of the data points) plots of the median folding times for R and DSKS at two values of B0 which are indicated in the figure (−1 and −2). Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 5 The plots of Tf and Tg as a function of B0 corresponding to the sequences DSKS and R as indicated (the solid lines correspond to DSKS). The inset shows the ratio Tf : Tg as a function of B0. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 6 The plots of Tf and Tg as a function of B0 corresponding to the sequence DSKS′. The inset shows the ratio Tf : Tg as a function of B0. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 7 The specific heat and fluctuation in the parameter of structural stability (multiplied by 10) for the three sequences as indicated. The solid lines refer to χ and the dotted lines to c. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 8 The mapping of a conformation to a cell as described in the text. The numbers indicate the ranking of the interaction energies in the contacts. The larger numbers correspond to contacts that are common between the quenched and the cell states. The energies indicated are for sequence R at B0 = −1. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 9 Motion in the conformation space (the top panel) and in the coarse-grained cell space (the bottom panel) of a typical 10 000 step long Monte Carlo trajectory for sequence R at T = 0.8. The energy levels of the 69 cells are shown on the right. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 10 Occupancy of the native cell as a function of T, as explained in the text. The results for 100 000 steps and for the folding stage (F) are based on 200 starting conformations. For the case with 10 million steps, we used one starting conformation. The values of Tg and Tf are indicated by the arrows. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 11 Cell-to-cell connectivity of sequence R at three temperatures as described in the text. The cutoff value for the off-diagonal entries is 10. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 12 Cell-to-cell connectivity of sequence R at T = 0.8 with the cutoff value for the off-diagonal entries equal to 5. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions

Figure 13 Cell-to-cell connectivity of sequence DSKS′ at three temperatures as described in the text. The cutoff value for the off-diagonal entries is 10. Folding and Design 1997 2, 235-245DOI: (10.1016/S1359-0278(97)00032-1) Copyright © 1997 Terms and Conditions