Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design Xiaozhen Hu, Huanchen.

Slides:

Advertisements

Similar presentations

Binocular rivalry Colin W.G. Clifford Current Biology Volume 19, Issue 22, Pages R1022-R1023 (December 2009) DOI: /j.cub Copyright ©

Advertisements

Site-Directed Mutagenesis Demonstrates the Plasticity of the β Helix: Implications for the Structure of the Misfolded Prion Protein Jay H. Choi, Barnaby.

Protein Design with Backbone Optimization Brian Kuhlman University of North Carolina at Chapel Hill.

Toward a Structure Determination Method for Biomineral-Associated Protein Using Combined Solid- State NMR and Computational Structure Prediction David.

A Plug Release Mechanism for Membrane Permeation by MLKL Lijing Su, Bradley Quade, Huayi Wang, Liming Sun, Xiaodong Wang, Josep Rizo Structure Volume 22,

How surgeons can find information online? Martin Hewitt International Journal of Surgery Volume 5, Issue 6, Pages (December 2007) DOI: /j.ijsu

Recognizing Protein-Ligand Binding Sites by Global Structural Alignment and Local Geometry Refinement Ambrish Roy, Yang Zhang Structure Volume 20, Issue.

Thank God for Richard Dawkins?

Heads Up S-Layer Display: The Power of Many

Adam W. Van Wynsberghe, Qiang Cui Structure

Volume 12, Issue 12, Pages (December 2004)

Heads Up S-Layer Display: The Power of Many

Liam M. Longo, Ozan S. Kumru, C. Russell Middaugh, Michael Blaber

Foundations for Directed Alkaloid Biosynthesis

Energetic Pathway Sampling in a Protein Interaction Domain

Finding the Missing Code of RNA Recognition by PUF Proteins

Volume 23, Issue 11, Pages (November 2015)

Thomas E. Edwards, Bruce H. Robinson, Snorri Th. Sigurdsson

Volume 13, Issue 2, Pages (February 2005)

Amyloid Structures from Alzheimer’s Disease Patients

Blocking HIV-1 gp120 at the Phe43 Cavity: If the Extension Fits…

Membrane Insertases Are Present in All Three Domains of Life

Gian Gaetano Tartaglia, Andrea Cavalli, Michele Vendruscolo Structure

Volume 22, Issue 11, Pages (November 2014)

Volume 16, Issue 5, Pages (August 2016)

Volume 24, Issue 3, Pages (March 2016)

Volume 23, Issue 12, Pages (December 2015)

A Consensus on Protein Structure Accuracy in NMR?

Volume 14, Issue 2, Pages (February 2006)

Volume 13, Issue 2, Pages (February 2005)

Volume 17, Issue 7, Pages (July 2009)

May the Force Be With You: Unfolding Lipid-Protein Interactions By Single-Molecule Force Spectroscopy William Dowhan, Heidi Vitrac, Mikhail Bogdanov

Volume 24, Issue 10, Pages (October 2016)

Fernando Corrêa, Jason Key, Brian Kuhlman, Kevin H. Gardner Structure

Volume 14, Issue 9, Pages (September 2006)

Foldability of a Natural De Novo Evolved Protein

Nuclear Magnetic Resonance Structure of a Novel Globular Domain in RBM10 Containing OCRE, the Octamer Repeat Sequence Motif Bryan T. Martin, Pedro Serrano,

by T. M. Jacobs, B. Williams, T. Williams, X. Xu, A. Eletsky, J. F

Volume 23, Issue 11, Pages (November 2015)

Thank God for Richard Dawkins?

Volume 14, Issue 5, Pages (May 2006)

Animal Behavior: Timing in the Wild

Structural Diversity in Integrin/Talin Interactions

Foundations for Directed Alkaloid Biosynthesis

Volume 16, Issue 2, Pages (February 2008)

Proteins in Plant Brassinosteroid Signaling

Topological Determinants of Protein Domain Swapping

Amyloid Structures from Alzheimer’s Disease Patients

Volume 20, Issue 6, Pages (June 2012)

The Dynamic Basis for Signal Propagation in Human Pin1-WW

The Unmasking of Telomerase

Scaffolding in the Spliceosome via Single α Helices

Promiscuous Protein Binding as a Function of Protein Stability

Volume 18, Issue 9, Pages (September 2010)

Eppur Si Muove! The 2013 Nobel Prize in Chemistry

L-DOPA Ropes in tRNAPhe

Volume 109, Issue 2, Pages (July 2015)

Volume 21, Issue 9, Pages (September 2014)

Improving management of neonatal infections

Clemens C. Heikaus, Jayvardhan Pandit, Rachel E. Klevit Structure

NMR Polypeptide Backbone Conformation of the E

Volume 24, Issue 3, Pages (March 2016)

Rafael Couñago, Stephen Chen, Yousif Shamoo Molecular Cell

Volume 14, Issue 2, Pages (February 2006)

Volume 13, Issue 4, Pages (April 2005)

Toward a Structural Understanding of Arf Family:Effector Specificity

A Plug Release Mechanism for Membrane Permeation by MLKL

Volume 21, Issue 9, Pages (September 2014)

Gene Regulation in the Postgenomic Era: Technology Takes the Wheel

Foldability of a Natural De Novo Evolved Protein

Presentation transcript:

Computer-Based Redesign of a β Sandwich Protein Suggests that Extensive Negative Design Is Not Required for De Novo β Sheet Design Xiaozhen Hu, Huanchen Wang, Hengming Ke, Brian Kuhlman Structure Volume 16, Issue 12, Pages 1799-1805 (December 2008) DOI: 10.1016/j.str.2008.09.013 Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 1 Sequences of the Wild-Type and Three Redesigned Proteins TEN-WT, wild-type; TEN-D1, TEN-D2, and TEN-D3, redesigned sequences. The TEN-D1 sequence is from a previously published study (Dantas et al., 2003). Structure 2008 16, 1799-1805DOI: (10.1016/j.str.2008.09.013) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 2 One-Dimensional 1H Spectra of the Redesigned Proteins (A) TEN-D2. (B) TEN-D3. Structure 2008 16, 1799-1805DOI: (10.1016/j.str.2008.09.013) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 3 Circular Dichroism Spectra of the Wild-Type Tenascin and the Redesigned Proteins at Neutral and Acidic pH with Different Temperatures 20°C(r) represents that the temperature was cooled back to 20°C. Structure 2008 16, 1799-1805DOI: (10.1016/j.str.2008.09.013) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 4 Temperature and Chemical Denaturation as Monitored by Circular Dichroism (A) Thermal unfolding of wild-type tenascin and the redesigned proteins. (B) Chemical denaturation of wild-type tenascin, TEN-D2, and TEN-D3. Structure 2008 16, 1799-1805DOI: (10.1016/j.str.2008.09.013) Copyright © 2008 Elsevier Ltd Terms and Conditions

Figure 5 Structure Alignment between the Designed Model and the Crystal Structure of TEN-D3 Designed model, cyan; TEN-D3, green. (A) Backbone only. (B) Buried residues. (C) Selected surface residues. (D) A designed salt bridge between Asp48 and Arg74. Structure 2008 16, 1799-1805DOI: (10.1016/j.str.2008.09.013) Copyright © 2008 Elsevier Ltd Terms and Conditions