Peptide, Protein and Enzyme Design (Volume 580) (Methods in Enzymology, Volume 580)

__De Novo Enzyme Design__, the newest volume in the __Methods in Enzymology__ series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume includes the design of metal binding maquettes, insertion of non-natural cofactors, Cu metallopeptides, non-covalent interactions in peptide assemblies, peptide binding and bundling, heteronuclear metalloenzymes, florinated peptides, De Novo imaging agents, and protein-protein interaction. * Continues the legacy of this premier serial with quality chapters on de novo enzyme design * Represents the newest volume in the __Methods in Enzymology__ series, providing premier, quality chapters authored by leaders in the field * Ideal reference for those interested in the study of enzyme design that looks at both structure and mechanism Content: Series Page Page ii Copyright Page iv Contributors Pages xiii-xvi Preface Pages xvii-xxii V.L. Pecoraro Chapter One - Chemical Posttranslational Modification with Designed Rhodium(II) Catalysts Pages 1-19 S.C. Martin, M.B. Minus, Z.T. Ball Chapter Two - Cell-Binding Assays for Determining the Affinity of Protein–Protein Interactions: Technologies and Considerations Pages 21-44 S.A. Hunter, J.R. Cochran Chapter Three - Protein and Antibody Engineering by Phage Display Pages 45-87 J.C. Frei, J.R. Lai Chapter Four - Incorporation of Unnatural Amino Acids into Proteins Expressed in Mammalian Cells Pages 89-107 R. Serfling, I. Coin Chapter Five - Method for Enzyme Design with Genetically Encoded Unnatural Amino Acids Pages 109-133 C. Hu, J. Wang Chapter Six - Methods for Solving Highly Symmetric De Novo Designed Metalloproteins: Crystallographic Examination of a Novel Three-Stranded Coiled-Coil Structure Containing d-Amino Acids Pages 135-148 L. Ruckthong, J.A. Stuckey, V.L. Pecoraro Chapter Seven - SpyRings Declassified: A Blueprint for Using Isopeptide-Mediated Cyclization to Enhance Enzyme Thermal Resilience Pages 149-167 C. Schoene, S.P. Bennett, M. Howarth Chapter Eight - Engineering and Application of LOV2-Based Photoswitches Pages 169-190 S.P. Zimmerman, B. Kuhlman, H. Yumerefendi Chapter Nine - Minimalist Design of Allosterically Regulated Protein Catalysts Pages 191-202 O.V. Makhlynets, I.V. Korendovych Chapter Ten - Combining Design and Selection to Create Novel Protein–Peptide Interactions Pages 203-222 E.B. Speltz, N. Sawyer, L. Regan Chapter Eleven - Metal-Directed Design of Supramolecular Protein Assemblies Pages 223-250 J.B. Bailey, R.H. Subramanian, L.A. Churchfield, F.A. Tezcan Chapter Twelve - Designing Fluorinated Proteins Pages 251-278 E.N.G. Marsh Chapter Thirteen - Solid Phase Synthesis of Helically Folded Aromatic Oligoamides Pages 279-301 S.J. Dawson, X. Hu, S. Claerhout, I. Huc Chapter Fourteen - Conformational Restriction of Peptides Using Dithiol Bis-Alkylation Pages 303-332 L. Peraro, T.R. Siegert, J.A. Kritzer Chapter Fifteen - Engineering Short Preorganized Peptide Sequences for Metal Ion Coordination: Copper(II) a Case Study Pages 333-364 L.M.P. Lima, O. Iranzo Chapter Sixteen - De Novo Construction of Redox Active Proteins Pages 365-388 C.C. Moser, M.M. Sheehan, N.M. Ennist, G. Kodali, C. Bialas, M.T. Englander, B.M. Discher, P.L. Dutton Chapter Seventeen - Design Strategies for Redox Active Metalloenzymes: Applications in Hydrogen Production Pages 389-416 R. Alcala-Torano, D.J. Sommer, Z. Bahrami Dizicheh, G. Ghirlanda Chapter Eighteen - Equilibrium Studies of Designed Metalloproteins Pages 417-438 B.R. Gibney Chapter Nineteen - Reconstitution of Heme Enzymes with Artificial Metalloporphyrinoids Pages 439-454 K. Oohora, T. Hayashi Chapter Twenty - Creation of a Thermally Tolerant Peroxidase Pages 455-470 Y. Watanabe, H. Nakajima Chapter Twenty-One - Designing Covalently Linked Heterodimeric Four-Helix Bundles Pages 471-499 M. Chino, L. Leone, O. Maglio, A. Lombardi Chapter Twenty-Two - Design of Heteronuclear Metalloenzymes Pages 501-537 A. Bhagi-Damodaran, P. Hosseinzadeh, E. Mirts, J. Reed, I.D. Petrik, Y. Lu Chapter Twenty-Three - Periplasmic Screening for Artificial Metalloenzymes Pages 539-556 M. Jeschek, S. Panke, T.R. Ward Chapter Twenty-Four - De Novo Designed Imaging Agents Based on Lanthanide Peptides Complexes Pages 557-580 A.F.A. Peacock Chapter Twenty-Five - Peptide Binding for Bio-Based Nanomaterials Pages 581-598 N.M. Bedford, C.J. Munro, M.R. Knecht Author Index Pages 599-637 Subject Index Pages 639-653 Front Cover; Peptide, Protein And Enzyme Design; Copyright; Contents; Contributors; Preface; References; Chapter One: Chemical Posttranslational Modification With Designed Rhodium(ii) Catalysts; 1. Introduction; 2. Synthesis Of Rhodium(ii) Conjugates As Protein Modification Catalysts; 2.1. Discussion; 2.2. Materials And General Considerations; 2.2.1. Preparation Of Metalation Buffer; 2.3. Protocol 1: Preparation Of Rh2(oac)3(tfa)1; 2.4. Protocol 2: Preparation Of Rhodium(ii) Conjugates In Organic Solution; 2.4.1. Preparation Of A Metalated Fkbp Inhibitor (coughlin Et Al., 2014). 2.5. Protocol 3: Preparation Of Rhodium(ii) Conjugates In Aqueous Solution2.5.1. Preparation Of The Metallopeptide S2erh; 3. Modification Of An Sh3 Domain And Gel-based Visualization Thereof; 3.1. Discussion; 3.2. Materials And General Considerations; 3.2.1. Preparation Of 1x Transfer Buffer; 3.2.2. Preparation Of Protein Modification Buffer; 3.2.3. Preparation Of Maldi-ms Matrix; 3.3. Protocol 4: Rhodium(ii)-catalyzed Protein Modification; 3.3.1. Modification Of Sh3 Domain Of Yes Kinase In Mammalian Cell Lysate (vohidov, Coughlin, & Ball, 2015). 3.4. Protocol 5: Visualization Of An Alkyne-tagged Protein By Chemical Blotting3.4.1. Fluorescent ``chemical Blot ́́analysis Of A Modified Sh3 Domain; References; Chapter Two: Cell-binding Assays For Determining The Affinity Of Protein-protein Interactions: Technologies And Considera ... ; 1. Introduction; 2. General Binding Theory And Relevance Of Kd; 3. General Pitfalls In Cell-based Binding Assays; 3.1. Time To Equilibrium; 3.2. Ligand Depletion; 4. Measuring Binding On The Surface Of Yeast; 4.1. Materials; 4.1.1. Yeast Cells; 4.1.2. Solutions And Media; 4.1.3. Proteins/antibodies. 4.2. Method5. Measuring Binding On The Surface Of Mammalian Cells; 5.1. Direct Binding; 5.2. Competition Binding; 6. Other Methods Of Measuring Binding: Kinetic Exclusion Assay And Surface Plasmon Resonance; 6.1. Kinetic Exclusion Assay; 6.2. Surface Plasmon Resonance; 6.3. Comparison; 7. Summary; Acknowledgments; References; Chapter Three: Protein And Antibody Engineering By Phage Display; 1. Introduction; 2. Equipment; 3. Materials; 3.1. Cell Lines; 3.1.1. Protocol 1: Production Of Ss320 Cells (modified From Tonikian, Zhang, Boone, & Sidhu, 2007). 3.1.2. Protocol 2: Production Of Xl1-blue Cells3.2. M13ko7 Helper Phage; 3.2.1. Protocol 3: Production Of M13ko7 Helper Phage (modified From Tonikian Et Al., 2007); 3.3. Phagemid Considerations; 3.4. Reagents; 3.4.1. Media; 3.4.2. Buffers (filter Sterilize); 3.4.3. Solutions; 3.4.4. Antibiotics (filter Sterilize); 3.4.5. Other Reagents; 4. Phage Display And Library Design; 4.1. Humanization Of A Murine Sudv Antibody (chen Et Al., 2014); 4.2. Mapping Hotspot Residues Of Protein-protein Interfaces (frei Et Al., 2015; Stewart Et Al., 2013); 4.2.1. Protocol 4: Cloning Into Hp153. Edited By Vincent L. Pecoraro. Includes Bibliographical References And Indexes.

De Novo Enzyme Design, the newest volume in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. This volume includes the design of metal binding maquettes, insertion of non-natural cofactors, Cu metallopeptides, non-covalent interactions in peptide assemblies, peptide binding and bundling, heteronuclear metalloenzymes, florinated peptides, De Novo imaging agents, and protein-protein interaction.

• Continues the legacy of this premier serial with quality chapters on de novo enzyme design
• Represents the newest volume in the Methods in Enzymology series, providing premier, quality chapters authored by leaders in the field
• Ideal reference for those interested in the study of enzyme design that looks at both structure and mechanism