Computational redesign of protein-protein interaction specificity

By Tanja Kortemme, L. Joachimiak, A. Bullock, A. Schuler, Barry L. Stoddard, David Baker. Nature Structural &Molecular Biology, 2004

303 citations recorded by the source corpus.

Subfields: Cell Biology, Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/e3762a0f92204d48d1742b0e31b8b6b0d57e00c8

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Cell Biology

1. I. Samish
2. Tanja Kortemme
3. John Karanicolas

In Materials Chemistry

1. David Baker
2. Tanja Kortemme
3. I. Samish
4. Jens Meiler
5. Brian Kuhlman
6. Andrew Leaver-Fay
7. Jeffrey J. Gray
8. Po-Ssu Huang

In Molecular Biology

1. David Baker
2. I. Samish
3. Tanja Kortemme
4. Jens Meiler
5. Jeffrey J. Gray
6. Andrew Leaver-Fay
7. Brian Kuhlman
8. Martin Weigt

Citations in the corpus

• Control of protein signaling using a computationally designed GTPase/GEF orthogonal pair (2012, methodology): “We performed a computational alanine scan (18) on 19 co-complex structures of Cdc42 with its binding partners (nine GEFs, two GAPs, seven effectors, and one GDI), to estimate the contribution of each interface residue to binding each partner (Fig.”
• Practically Useful: What the Rosetta Protein Modeling Suite Can Do for You (2010, methodology): “In silico alanine scanning has been implemented in the current version of R OSETTA and is available through a Web-based interface (http://robetta.bakerlab.org) ( 69 ).”
• Alteration of enzyme specificity by computational loop remodeling and design (2009, methodology): “C protein design methodology has been used to optimize properties such as protein stability (1, 2) and to introduce functions such as binding of small molecules (3), proteins (4), and nucleic acids (5), as well as enzymatic activity (6, 7).”
• Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity (2015, methodology): “Computational methods to re-engineer protein–protein specificity have typically employed a “second-site suppressor” strategy, in which a mutation is made on one protein to destabilize its interaction with a binding partner, and a second compensating mutation is made on the binding partner to re-stab”
• Fully Flexible Docking of Medium Sized Ligand Libraries with RosettaLigand (2015, unknown): “The backbone was kept fixed, and all side-chain positions were allowed to repack [27].”
• ROSETTALIGAND: Protein–small molecule docking with full side‐chain flexibility (2006, unknown): “Full side-chain flexibility is achieved by extending the repacking methodology introduced in ROSETTADESIGN 32–35 to repack protein–ligand interfaces.”
• RosettaDesign server for protein design (2006, methodology): “A similar approach was recently used to redesign a protein–protein interface so that the redesigned proteins still bind each other, but no longer bind their other naturally occurring binding partners (21).”
• Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, unknown): “…et al. , 2008; Zanghellini et al. , 2006) FixedBBProteinDesign Redesign the amino acids on a fixed protein backbone (Dantas et al. , 2003; Kortemme et al. , 2004; Kuhlman and Baker, 2000) protein_docking Predict the docked conformation of two proteins with a known structure (Gray et al.…”