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NACCESS program, 267 Natural killer (NK) cells, 165 NBT, see Nitroblue tetrazolium Nephila clavipes, 185, 186 edulis, 186 Nephilengys cruentata, 186 P-Nerve growth factor (p-NGF), 195 Neurotensin receptor-1 (NTR1), 28 p-NGF, see p-Nerve growth factor Nitroblue tetrazolium (NBT), 146 p-Nitrophenyl acetate, 355 NK cells, see Natural killer cells NMR, see Nuclear magnetic resonance Nonantibody scaffolds, design and engineering of synthetic binding proteins using, 109-130

advances in display technologies, 119-120 advances in sequence diversity design, 120-122 affibodies, 117

alternative scaffolds, 111, 112 applications, 122-124

affinity purification, 123 antibody alternatives, 122 crystallization chaperones, 123 intracellular applications, 124 therapeutics, 122-123 aromatic amino acids, 121 complementarity determining regions, 110 design considerations for new scaffolds,

113-114 designed ankyrin repeats, 117 factors governing protein-protein interactions, 112-113 hot-spots, 113

maltose-binding protein, 118 molecular display technologies, 112 molecular scaffold concept, 110-111 motivations for development of nonantibody scaffolds, 112 mRNA display, 119 NNK codon, 121 O-ring architecture, 113 peptide aptamers, 117, 124 phage display, 119 ribosome display, 119 roles of interface topography, 118 Staphylococcus aureus protein A, 117 successful scaffolds, 114-118 a-helical scaffolds, 117 P-barrel, 116 p-sheet surface, 116 immunoglobulin-like P-sandwich, 115-116

multidomain scaffolds, 117-118 recognition interfaces at junction of two domains, 118 repeat proteins, 117 single loop, 116-117 T-cell receptors, 111 tyrosine, 121 Noncanonical amino acids, protein engineering using, 205-221 amide-to-ester backbone mutations, 217 analytical equilibrium ultracentrifugation, 210

applications, 209-217

backbone mutations, 212-213 dissecting collagen, 213-214 fluorescent amino acids, 214-215 fluorinated amino acids, 209-210 illuminating structure-function relationships, 214-215 novel folds and control of orientation, 211

photoreactive amino acids, 215-216 probing ion channel function, 216-217 seeing is believing, 214 side chain packing, 209-211 chemically acylated tRNA, 207 circular dichroism, 210 fluorinated interfaces, 210 Förster resonance energy transfer, 210, 214 future outlook, 218 HIV-1 protease, 216

ketone-bearing unnatural amino acid, 214 main chain hydrogen bonding, 210 methodologies, 206-209 ribo-X, 209 SDS-PAGE, 210 Noncovalent DNA display, 72-75

advantages and limitations in comparison to other cell-free methods, 75 using CIS display, 73

using in vitro compartmentalization, 73-75 Nonpolar solvation free energy, 267 NTPs, see Nucleoside triphosphates NTR1, see Neurotensin receptor-1 Nuclear magnetic resonance (NMR), 249, 315,

320, 329, 369 Nucleoside triphosphates (NTPs), 54

OB fold, see Oligonucleotide/oligosaccharide binding fold Oligonucleotide(s)

/oligosaccharide binding (OB) fold, 110 synthetic, 91 OmpA, see Outer membrane protein A Oprelvekin, 165

Optimization of rotamers by iterative techniques

(ORBIT), 331 ORBIT, see Optimization of rotamers by iterative techniques Outer membrane protein A (OmpA), 27

Paranitrophenol acetate (PNPA), 335 Partition function problem, 273 PB equation, see Poisson-Boltzmann equation PBP, see Periplasmic binding protein PCA, see Protein-fragment complementation assay

PCR, see Polymerase chain reaction

PCS, see Primary coordination sphere

PDA software, see Protein Design Automation software PDB, see Protein Data Bank PEG, see Polyethylene glycol Pentane, conformation of, 283 Peptide aptamers, 117, 124 -MHC (pMHC) complexes, 167 Periplasmic binding protein (PBP), 333 PERLA, see Protein engineering rotamer library algorithm

Perturbation-relaxation-evaluation (PRE)

procedure, 301 Phage display, 1-22, 160 antigen-binding site, 10 DNA encoding of antibodies, 8 dsDNA plasmid, 4 erythropoietin receptor, 9 evolution of binding agents, 7-9 future perspectives, 15 human growth hormone, 14 identifying natural protein-protein interactions, 11 immunoglobulin family protein, 11 improvement of protein stability and folding, 9-11

insulin-like growth factor 1, 9

mapping binding energetics, 14-15

monoclonal antibodies, 8

PDZ domains, 13

phage display concept, 1-2

phage structure and assembly, 2-4

polyclonal antibodies, 8

quantitative saturation scanning approach, 14

selection process, 6-7

specificity profiling of peptide-binding modules, 12-14 vectors and platforms, 4-6 Phenazine methosulfate (PMS), 146 Phosphotriesterase (PTE) mutants, 138 Pichia pastoris, 30, 186

Pinacolyl methyl phosphonic acid (PMPA), 354 Platelet-derived growth factor receptor, 36 PLGA, see Poly(lactic-co-glycolic acid) pMHC complexes, see Peptide-MHC complexes PMPA, see Pinacolyl methyl phosphonic acid PMS, see Phenazine methosulfate PNPA, see Paranitrophenol acetate Poisson-Boltzmann (PB) equation, 269 Poisson's law, 269 Polyclonal antibodies, 8 Polyethylene glycol (PEG), 158 Poly(lactic-co-glycolic acid) (PLGA), 181 Polymerase chain reaction (PCR) cDNA amplification, 62 cDNA template for, 67 DNA amplification suing, 328 DNA shuffling and, 87 error-prone, 61, 68, 86, 89, 137, 336 genotypes amplified by, 56 library construction, 86 reverse transcription followed by (RT-PCR), 57, 62

site-directed mutagenesis, 88 use of programmable DNA microchips, 382 Position-specific amino acid score matrix

(PSSM), 294 PRE procedure, see Perturbation-relaxation-

evaluation procedure Primary coordination sphere (PCS), 345 PRM complex, see Protein-ribosome-mRNA

complex Proleukin®, FDA-approved, 165 PROSE, see Protein simulated evolution Protein Data Bank (PDB), 257, 281, 329, 347 Protein design, binary code for, 245, 246-252 binary-patterned beta sheet proteins, 250-252 functional activities of binary patterned four-

helix bundles, 249-250 libraries of binary patterned four-helix bundles, 247-249 Protein Design Automation (PDA) software, 358 Protein engineering rotamer library algorithm

(PERLA), 329 Protein-fragment complementation assay (PCA), 379

Protein interactions, modulation of, see Rational and computational design, modulation of protein interactions by Protein-ribosome-mRNA (PRM) complex, 62 Protein sequence, foldability of, 271 Protein simulated evolution (PROSE), 329 Protein structure, modulating, 313-325 altering protein folds, 322-323 bacteriophage protein, 319 binary patterning, 320 configuration design, 318 core repacking problem, 314

cro repressor protein, 315

early core designs, 315-317

experimentally evaluating success, 323-324

fold of ubiquitin, 316

full repacks and surface design, 320-321

globular protein, 318

hydrogen bonding and polar residues in core, 322

NMR spectroscopy, 320 overcoming limitations circumventing of fixed backbone,

318-320 rotamer library, 317 Paracelsus Challenge, 323 predicting native protein core sequences, 314 protein stability, 313 SoftROC program, 318, 319 streptococcal G p1 domain, 317 Top7 structure, 320 x-ray crystallography, 316 zinc finger domain, 321 Proto-enzyme, 355 Protozyme development, 335 Pseudoenergy, 288 Pseudomonas syringe, 26 PSSM, see Position-specific amino acid score matrix

PTE mutants, see Phosphotriesterase mutants PURE system, 55

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