Srayanta Mukherjee, Yang Zhang Structure

Slides:

Advertisements

Similar presentations

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

Advertisements

Protein Structure Fitting and Refinement Guided by Cryo-EM Density

Volume 19, Issue 8, Pages (August 2011)

Nir London, Ora Schueler-Furman Structure

Identification of Structural Mechanisms of HIV-1 Protease Specificity Using Computational Peptide Docking: Implications for Drug Resistance Sidhartha.

Volume 13, Issue 9, Pages (September 2005)

Natalie Zeytuni, Raz Zarivach Structure

Volume 13, Issue 12, Pages (December 2005)

Volume 15, Issue 6, Pages (June 2007)

The Binding of Antibiotics in OmpF Porin

Volume 18, Issue 8, Pages (August 2010)

The 19S Cap Puzzle: A New Jigsaw Piece

The Architecture of Restriction Enzymes

Srayanta Mukherjee, Yang Zhang Structure

Chromosomal DNA Replication on a Protein “Chip”

AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking

Matthew L. Baker, Tao Ju, Wah Chiu Structure

Volume 19, Issue 7, Pages (July 2011)

Structure of the Angiopoietin-2 Receptor Binding Domain and Identification of Surfaces Involved in Tie2 Recognition William A. Barton, Dorothea Tzvetkova,

Structural Determinants of Transmembrane Helical Proteins

Volume 15, Issue 2, Pages (February 2007)

A Unique Spatial Arrangement of the snRNPs within the Native Spliceosome Emerges from In Silico Studies Ziv Frankenstein, Joseph Sperling, Ruth Sperling,

Solution and Crystal Structures of a Sugar Binding Site Mutant of Cyanovirin-N: No Evidence of Domain Swapping Elena Matei, William Furey, Angela M.

Grace W. Tang, Russ B. Altman Structure

Volume 22, Issue 4, Pages (April 2014)

Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis Marcin Nowotny, Sergei A. Gaidamakov, Robert.

Folding Membrane Proteins by Deep Transfer Learning

Volume 26, Issue 7, Pages e2 (July 2018)

A Computational Tool for Designing FRET Protein Biosensors by Rigid-Body Sampling of Their Conformational Space Elizabeth Pham, Jason Chiang, Isaac Li,

Volume 21, Issue 9, Pages (September 2013)

Monica Berrondo, Marc Ostermeier, Jeffrey J. Gray Structure

GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome Jian Zhang, Jianyi Yang, Richard.

Volume 20, Issue 6, Pages (June 2012)

Volume 20, Issue 3, Pages (March 2012)

Jason O. Moore, Wayne A. Hendrickson Structure

Fan Zheng, Jian Zhang, Gevorg Grigoryan Structure

Volume 21, Issue 6, Pages (June 2013)

Binchen Mao, Rongjin Guan, Gaetano T. Montelione Structure

Nir London, Ora Schueler-Furman Structure

Geometry-Based Sampling of Conformational Transitions in Proteins

Recognizing Protein Substructure Similarity Using Segmental Threading

Probing the “Dark Matter” of Protein Fold Space

Structural Basis of EZH2 Recognition by EED

Volume 19, Issue 8, Pages (August 2011)

Protein-Protein Docking: From Interaction to Interactome

Michael Soniat, Yuh Min Chook Structure

Jason O. Moore, Wayne A. Hendrickson Structure

Volume 13, Issue 7, Pages (July 2005)

A Critical Comparative Assessment of Predictions of Protein-Binding Sites for Biologically Relevant Organic Compounds Ke Chen, Marcin J. Mizianty, Jianzhao.

Atomic-Level Protein Structure Refinement Using Fragment-Guided Molecular Dynamics Conformation Sampling Jian Zhang, Yu Liang, Yang Zhang Structure

Volume 21, Issue 7, Pages (July 2013)

Yan Xia, Axel W. Fischer, Pedro Teixeira, Brian Weiner, Jens Meiler

Deciphering the Deformation Modes Associated with Function Retention and Specialization in Members of the Ras Superfamily Francesco Raimondi, Modesto.

Volume 17, Issue 8, Pages (August 2009)

Volume 19, Issue 7, Pages (July 2011)

A YidC-like Protein in the Archaeal Plasma Membrane

Volume 26, Issue 3, Pages e3 (March 2018)

Ying Huang, Michael P. Myers, Rui-Ming Xu Structure

Volume 23, Issue 11, Pages (November 2015)

Crystal Structures of RNase H Bound to an RNA/DNA Hybrid: Substrate Specificity and Metal-Dependent Catalysis Marcin Nowotny, Sergei A. Gaidamakov, Robert.

Volume 26, Issue 1, Pages e3 (January 2018)

Vilas Menon, Brinda K. Vallat, Joseph M. Dybas, Andras Fiser Structure

Hafumi Nishi, Kosuke Hashimoto, Anna R. Panchenko Structure

Gydo C.P. van Zundert, Adrien S.J. Melquiond, Alexandre M.J.J. Bonvin

The AXH Domain Adopts Alternative Folds

Toward a Structural Understanding of Arf Family:Effector Specificity

Chengfei Yan, Xianjin Xu, Xiaoqin Zou Structure

Crystal Structure of Escherichia coli RNase D, an Exoribonuclease Involved in Structured RNA Processing Yuhong Zuo, Yong Wang, Arun Malhotra Structure

Yang Zhang, Jeffrey Skolnick Biophysical Journal

M-TASSER: An Algorithm for Protein Quaternary Structure Prediction

Presentation transcript:

Protein-Protein Complex Structure Predictions by Multimeric Threading and Template Recombination Srayanta Mukherjee, Yang Zhang Structure Volume 19, Issue 7, Pages 955-966 (July 2011) DOI: 10.1016/j.str.2011.04.006 Copyright © 2011 Elsevier Ltd Terms and Conditions

Structure 2011 19, 955-966DOI: (10.1016/j.str.2011.04.006) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 1 Flowchart of the COTH Algorithm for Protein Complex Template Identification The sequences are first joined in both permutation and threaded against a complex structure library to identify complex templates. Both monomer chains are individually threaded by MUSTER against the tertiary structure library to obtain tertiary structures. The monomer templates are then structurally superposed to the dimer template to generate the final template models. See also Figure S1. Structure 2011 19, 955-966DOI: (10.1016/j.str.2011.04.006) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 2 Complex Threading Results by COTH on 500 Nonredundant Test Proteins (A) Rmsd versus alignment coverage for the best in Top 10 models. (B) Histogram of TM-score for the first model. Structure 2011 19, 955-966DOI: (10.1016/j.str.2011.04.006) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 3 Comparison of TM-Score of the Complex Templates as Identified by Different Threading Methods (A) C-PPA versus PSI-BLAST. (B) C-MUSTER versus C-PPA. (C) C-MUSTER versus COTH threading. (D) COTH threading versus COTH. Structure 2011 19, 955-966DOI: (10.1016/j.str.2011.04.006) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 4 Examples of Improvement over Controls Template structures produced for the human pi class glutathione transferase by four different threading methods from (A) PSI-BLAST, (B) C-PPA, (C) C-MUSTER, and (D) COTH-threading, which have been superimposed onto the experimental structure of the query protein. The experimental structure of 16gsA0-16gsB0 is shown in red for chain 1 and cyan for chain 2 whereas the models from the threading algorithms are represented in silver for chain 1 and yellow for chain 2. Structure 2011 19, 955-966DOI: (10.1016/j.str.2011.04.006) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 5 Structure Superposition Improves Template Quality Superposition of the native structure (darker shade) with the template structures generated by COTH threading (lighter shade, left) and COTH threading plus recombination (lighter shade, right). (A) GTP-Bound Rab4Q67L GTPase (PDB ID: 1z0kA0-1z0kB0). (B) 1-Aminocyclopropane-1-carboxylate deaminase (PDB ID: 1f2dA0-1f2dB0). Structure 2011 19, 955-966DOI: (10.1016/j.str.2011.04.006) Copyright © 2011 Elsevier Ltd Terms and Conditions

Figure 6 Modeling Result of ZDOCK and COTH on the Ran-Importin β Complex The native complex is represented in cyan (larger chain) and blue (smaller chain). The predicted models represented as red (larger chain) and green (smaller chain). (A) ZDOCK-exp. (B) COTH-threading. (C) COTH-exp with unbound experimental structures superimposed on the COTH-threading template. Structure 2011 19, 955-966DOI: (10.1016/j.str.2011.04.006) Copyright © 2011 Elsevier Ltd Terms and Conditions