issn 1741-0126 (print) ISSN 1741-0134 (online) peds protein engineering design & selection

pedsprotein engineering design & selection

Special Issue: Computational Protein Structure Assessment and Design: Part III

Methods volume GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins protein engineering design & selection

29 | 29 peds Tyler S. Harmon, Michael D. Crabtree, Sarah L. Shammas, Ammon E. Posey, Jane Clarke, and Rohit V. Pappu 339

Original Articles number Conformational dynamics of cancer-associated MyD88-TIR domain mutant L252P (L265P) allosterically tilts the landscape volume 29 | number 9 | SEPTEMBER 2016

toward homo-dimerization 2016 S E PT EMBER | 9 Chendi Zhan, Ruxi Qi, Guanghong Wei, Emine Guven-Maiorov, , and Buyong Ma 347 Efficient laboratory evolution of computationally designed enzymes with low starting activities using fluorescence-activated droplet sorting Special Issue: Computational Protein Structure Assessment and Design: Part III Richard Obexer, Moritz Pott, Cathleen Zeymer, Andrew D. Griffiths, and Donald Hilvert 355 Steric interactions determine side-chain conformations in protein cores D. Caballero, A. Virrueta, C.S. O’Hern, and L. Regan 367 www.peds.oxfordjournals.org An in silico algorithm for identifying stabilizing pockets in proteins: test case, the Y220C mutant of the p53 tumor suppressor protein Dennis Bromley, Matthias R. Bauer, Alan R. Fersht, and Valerie Daggett 377 Structural difficulty index: a reliable measure for modelability of protein tertiary structures Rahul Kaushik and B. Jayaram 391

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senior editors editorial board Jeff Kelly, USA Tobin Sosnick, USA Oxford Journals Archive Thomas Kiefhaber, Germany Neil Stahl, USA Alan Fersht, UK Mikael Akke, Sweden Kent Kirshenbaum, USA Michael Sternberg, UK Valerie Daggett, USA Niels Andersen, USA Shohei Koide, USA Robert Stroud, USA Frances Arnold, USA Brian Kuhlman, USA Joel Sussman, Israel consulting editor P. Balaram, India Andreas Kungl, Austria Lukas Tamm, USA Doug Barrick, USA Zan Luthey-Schulten, USA Dan Tawfik, Israel Greg Winter, UK Hagan Bayley, UK Jianpeng Ma, USA David Thirumalai, USA • uncover backfiles of content dating from 1849 Richard Begent, Canada George Makhatadze, USA , UK Albert Berghuis, Canada Bengt Mannervik, Sweden Bruce Tidor, USA Alan Berry, UK James Marks, USA Peter Tieleman, Canada Richard Bonneau, USA Susan Marqusee, USA Jayant Udgaonkar, India Alexandre Bonvin, USA Andreas Matouschek, USA Mathias Uhlen, Sweden • instant access to 146 years of research Andrew Bradbury, USA Brian Matthews, USA Rebecca Wade, Germany Dennis Burton, USA C. Robert Matthews, USA Sally Ward, USA Silvia Cavagnero, USA Stephen Mayo, USA Jim Wells, USA Avi Chakrabartty, Canada Liz Meiering, Canada Rik Wierenga, Finland • seamless access from Volume 1, Issue 1 Ashutosh Chilkoti, USA Andrew Miranker, USA Tony Wilkinson, UK Fabrizio Chiti, Italy Kosuke Morikawa, Japan Roger Williams, UK Daniel Christ, Australia Regina Murphy, USA Stephen Withers, Canada Jane Clarke, UK Haruki Nakamura, Japan Kambo Wong, Hong Kong Marius Clore, USA Karyn O’Neil, USA Dek Woolfson, UK • access by IP range, Athens or Shibboleth Fred Cohen, USA Dario Neri, Switzerland Anna Wu, USA Matt Cordes, USA Feng Ni, Canada Todd Yeates, USA Miroslaw Cygler, Canada Ruth Nussinov, USA Huan-Xiang Zhou, USA Michael Deem, USA Robin Offord, Switzerland • COUNTER-compliant usage statistics William DeGrado, USA Mikael Oliveberg, Sweden Bauke Dijkstra, Netherlands David Ollis, Australia Christopher Dobson, UK , UK William Eaton, USA Jane Osbourn, UK David Eisenberg, USA Hartmut Oschkinat, Germany Edward Eisenstein, USA Daniel Otzen, Denmark Jacques Fastrez, Belgium Rohit V. Pappu, USA Angelo Fontana, Italy Evamaria Petersen, Denmark cover illustration Assaf Friedler, Israel Andreas Plueckthun, Switzerland Stefano Gianni, Italy Images from the paper by D. Caballero, Ron Raines, USA A. Virrueta, C. S. O'Hern, and L. Regan, Lisa M. Gloss, USA Daniel Raleigh, USA which explores the role of steric Adrian Goldman, Finland Anthony Rees, Sweden repulsion in specifying the conformation Richard Goldstein, UK Lynne Regan, USA of amino acid side-chains, both as Angela Gronenborn, USA Heinrich Roder, USA isolated ‘dipeptide mimetics’ and in the Bernd Gutte, Switzerland Peter Roepstorff, Denmark context of a protein core. Left: Kathleen Hall, USA Frederic Rousseau, Belgium Space filling representation of the Torleif Härd, Sweden Steven Russell, USA hard-sphere dipeptide mimetic model Don Hilvert, Switzerland Andrej Sali, USA for a Leu residue. Right: Space filling Florian Hollfelder, UK Jeffery G. Saven, USA representation of the hard-sphere Phil Holliger, UK , USA model for a Leu residue in the context Hennie Hoogenboom, Netherlands Gideon Schreiber, Israel of a protein core (Leu 31 in PDB Amnon Horovitz, Israel Klaus Schulten, USA 2NWD). Surrounding residues within Arthur Horwich, USA 2.8 Å of Leu 31 are displayed in stick Joost Schymkowitz, Belgium James Huston, USA representation in purple, whereas the Jamie Scott, Canada remaining residues have been faded. Laura Itzhaki, UK Luis Serrano, Germany Each atom type in the Leu residue has Leo James, UK P C Shaw, Hong Kong a different color: Carbon (teal), Dick Janssen, Netherlands Arne Skerra, Germany Nitrogen (blue), Oxygen (red) and Laurent Jespers, UK Stephen Sligar, USA Hydrogen (white). Martin Karplus, USA Dieter Soll, USA

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