MD simulations of cotranslational folding of I27.

Slides:

Advertisements

Similar presentations

Fabio Trovato, Edward P. O’Brien Biophysical Journal

Advertisements

Interaction between the anti-EGFR Goldbody and sEGFR at the molecular level. Interaction between the anti-EGFR Goldbody and sEGFR at the molecular level.

SPR characterization of the specific interaction between AuNP–Pep1 and HEWL. (A) Binding of AuNPs functionalized with 20 Pep1 and different numbers of.

Scheme of the design of the anti-lysozyme Goldbody.

The plant respiratory chain supercomplex.

Two functional states of human CFTR

Components of the yield trend.

Volume 23, Issue 9, Pages (September 2015)

FRET change in SCORE precedes fusion.

The repeat domain of Tau cross-links to α-tubulin.

WCI evolve as organisms become more complex.

The genetic profile of LBA Khövsgöl individuals summarized by PCA and ADMIXTURE. (A) Khövsgöl (Kvs, ARS017, and ARS026) and other ancient individuals (colored.

Cotranslational folding of the titin I27 domain by force-profile analysis. Cotranslational folding of the titin I27 domain by force-profile analysis. (A)

Cryo-EM structure of I27[L = 35] RNCs

Simulations capture the experimental force profiles for mutant I27 domains. Simulations capture the experimental force profiles for mutant I27 domains.

Cotranslational Protein Folding inside the Ribosome Exit Tunnel

Complex Energy Landscape of a Giant Repeat Protein

DNA Nanomechanics in the Nucleosome

Γ-TEMPy: Simultaneous Fitting of Components in 3D-EM Maps of Their Assembly Using a Genetic Algorithm Arun Prasad Pandurangan, Daven Vasishtan, Frank.

Structural and Thermodynamic Principles of Viral Packaging

HyeongJun Kim, Jen Hsin, Yanxin Liu, Paul R. Selvin, Klaus Schulten

Introduction to Fractions

Monika Sharma, Alexander V. Predeus, Nicholas Kovacs, Michael Feig

Volume 114, Issue 1, Pages (January 2018)

Volume 96, Issue 2, Pages (January 2009)

Mechanism of the αβ Conformational Change in F1-ATPase after ATP Hydrolysis: Free- Energy Simulations Yuko Ito, Mitsunori Ikeguchi Biophysical Journal

De Novo Design of Foldable Proteins with Smooth Folding Funnel

Evolution of the global surface temperature of the last 22 ka: the reconstructions of M13 (1) (blue) after 11.3 ka and by Shakun et al. Evolution of the.

Oligosaccharide profile of VexL reaction products.

Volume 22, Issue 4, Pages (April 2014)

Detection and tracking of individual SNAP-tagged proteins on the surface of living cells. Detection and tracking of individual SNAP-tagged proteins on.

G. Fiorin, A. Pastore, P. Carloni, M. Parrinello Biophysical Journal

(A) Communication fluxes PS(T|r′) conditional to the rank r′ for dataset D3. (A) Communication fluxes PS(T|r′) conditional to the rank r′ for dataset D3.

Volume 96, Issue 7, Pages (April 2009)

Anton Arkhipov, Peter L. Freddolino, Klaus Schulten Structure

Functional Role of Ribosomal Signatures

The Unbinding of ATP from F1-ATPase

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

Volume 16, Issue 9, Pages (September 2008)

Irina V. Dobrovolskaia, Gaurav Arya Biophysical Journal

Volume 23, Issue 9, Pages (September 2015)

Volume 26, Issue 1, Pages e4 (January 2018)

Rotational and vibrational energy distributions of surface scattered molecules. Rotational and vibrational energy distributions of surface scattered molecules.

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

RLR domains and signaling.

Dynamics of the BH3-Only Protein Binding Interface of Bcl-xL

Logan S. Ahlstrom, Osamu Miyashita Biophysical Journal

Ion-Induced Defect Permeation of Lipid Membranes

Sucrose gradient analysis of ribosomes after repressing the genes for 60S r-proteins uL4 and uL22 and 60S assembly factors Rpf2 and Rrs1. Sucrose gradient.

The Atomistic Mechanism of Conformational Transition in Adenylate Kinase: A TEE-REX Molecular Dynamics Study Marcus B. Kubitzki, Bert L. de Groot Structure

Sequence conservation across the Ub-binding sites of human USPs

Phase diagrams from experiments for (A) and (B) metronome(s) per swing and from numerical simulations with metronomes (C) with metronome frequency f vs.

Γ-TEMPy: Simultaneous Fitting of Components in 3D-EM Maps of Their Assembly Using a Genetic Algorithm Arun Prasad Pandurangan, Daven Vasishtan, Frank.

Chimeras emerge with intermediate spring rate κ in a “competition” zone between two fully synchronous modes. Chimeras emerge with intermediate spring rate.

Dynamics of the model. Dynamics of the model. (A) Snapshot of a simulation. At this time, the population has adapted to the drug concentrations in compartments.

(A–F) FRET provides evidence for compaction.

Mapping the surface interaction profile of the 30S ribosomal subunit on a multifunctional graphene grid. Mapping the surface interaction profile of the.

Volume 111, Issue 11, Pages (December 2016)

Consistency of results across images and time.

Volume 106, Issue 5, Pages (March 2014)

Peel test of mucus–PCL adhesive strength.

Effect of pH and bicarbonate (HCO3) vs

Flux distributions for different rank and distance groups.

Volume 110, Issue 1, Pages (January 2016)

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

Amir Marcovitz, Yaakov Levy Biophysical Journal

Fig. 4 Relationships between light and economic parameters.

Volume 93, Issue 8, Pages (October 2007)

Fig. 5 Potential-energy energy profiles of 1-HAQ.

Presentation transcript:

MD simulations of cotranslational folding of I27. MD simulations of cotranslational folding of I27. (A) The 50S subunit of the E. coli ribosome (PDB ID code 3OFR) with I27[L = 35] attached via an unstructured linker. (B) Coarse-grained model for I27 (red) and linker (green), with surrounding ribosomal pseudoatoms in blue. Pseudoatoms colored gray are not used in the simulations. The instantaneous force exerted on the AP is calculated from the variation in the distance x between the C-terminal Pro pseudoatom and the next pseudoatom in the linker (Inset). (C) Average forces exerted on the AP by the unfolded state (Fu, empty symbols) and folded state (Ff, filled symbols) of I27 at different linker lengths L. The average fraction folded I27 for different L,Pf, is shown in cyan on the right axis. Free energy profiles at each linker length are shown in SI Appendix, Fig. S11. (D) Experimental (red square) force profiles for cotranslational folding of I27. Force profiles calculated from simulations using the full kinetic scheme or preequilibrium model are shown by blue circles and cyan triangles, respectively. The rmsd of the fFL between experiment and simulation is 0.08. Pengfei Tian et al. PNAS 2018;115:48:E11284-E11293 ©2018 by National Academy of Sciences