Protein Engineering Design and Selection

COMMUNICATIONS:

Igor B. Kuznetsov and S. Rackovsky

Similarity between the C-terminal domain of the prion protein and chimpanzee cytomegalovirus glycoprotein UL9
Protein Eng. 2003 16: 861-863; doi:10.1093/protein/gzg113 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Qi Zheng, Wan-Ming Yang, Wen-Hao Yu, Bin Cai, Xin-Chen Teng, Yi Xie, Hong-Zhe Sun, Ming-Jie Zhang, and Zhong-Xian Huang

The effect of the EAAEAE insert on the property of human metallothionein-3
Protein Eng. 2003 16: 865-870; doi:10.1093/protein/gzg127 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Eric Alsop, Melanie Silver, and Dennis R. Livesay

Optimized electrostatic surfaces parallel increased thermostability: a structural bioinformatic analysis
Protein Eng. 2003 16: 871-874; doi:10.1093/protein/gzg131 [Abstract] [FREE Full Text] [PDF] [Supplementary data] [Request Permissions]  

Anshuman Shukla, Manoj Raje, and Purnananda Guptasarma

A backbone-reversed all-ß polypeptide (retro-CspA) folds and assembles into amyloid nanofibres
Protein Eng. 2003 16: 875-879; doi:10.1093/protein/gzg142 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

ORIGINAL ARTICLES:

Anirban Bhaduri and R. Sowdhamini

A genome-wide survey of human tyrosine phosphatases
Protein Eng. 2003 16: 881-888; doi:10.1093/protein/gzg144 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Alan J. Stewart, Ralf Schmid, Claudia A. Blindauer, Stephen J. Paisey, and Colin Farquharson

Comparative modelling of human PHOSPHO1 reveals a new group of phosphatases within the haloacid dehalogenase superfamily
Protein Eng. 2003 16: 889-895; doi:10.1093/protein/gzg126 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Jadwiga R. Bienkowska, Hyman Hartman, and Temple F. Smith

A search method for homologs of small proteins. Ubiquitin-like proteins in prokaryotic cells?
Protein Eng. 2003 16: 897-904; doi:10.1093/protein/gzg130 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

F.L. Aachmann, D.E. Otzen, K.L. Larsen, and R. Wimmer

Structural background of cyclodextrin–protein interactions
Protein Eng. 2003 16: 905-912; doi:10.1093/protein/gzg137 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

A. Williams, D.R. Gilbert, and D.R. Westhead

Multiple structural alignment for distantly related all ß structures using TOPS pattern discovery and simulated annealing
Protein Eng. 2003 16: 913-923; doi:10.1093/protein/gzg116 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Denis Znamenskiy, Jacques Chomilier, Khan Le Tuan, and Jean-Paul Mornon

A new protein folding algorithm based on hydrophobic compactness: Rigid Unconnected Secondary Structure Iterative Assembly (RUSSIA). I: Methodology
Protein Eng. 2003 16: 925-935; doi:10.1093/protein/gzg140 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Denis Znamenskiy, Khan Le Tuan, Jean-Paul Mornon, and Jacques Chomilier

A new protein folding algorithm based on hydrophobic compactness: Rigid Unconnected Secondary Structure Iterative Assembly (RUSSIA). II: Applications
Protein Eng. 2003 16: 937-948; doi:10.1093/protein/gzg141 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Linus O. Johannissen and William R. Taylor

Protein fold comparison by the alignment of topological strings
Protein Eng. 2003 16: 949-955; doi:10.1093/protein/gzg128 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Simon Penel, R.Gwilym Morrison, Paul D. Dobson, Russell J. Mortishire-Smith, and Andrew J. Doig

Length preferences and periodicity in ß-strands. Antiparallel edge ß-sheets are more likely to finish in non-hydrogen bonded rings
Protein Eng. 2003 16: 957-961; doi:10.1093/protein/gzg147 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Reshma P. Shetty, Paul I.W. de Bakker, Mark A. DePristo, and Tom L. Blundell

Advantages of fine-grained side chain conformer libraries
Protein Eng. 2003 16: 963-969; doi:10.1093/protein/gzg143 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Xiaoran Fu, Hidetoshi Kono, and Jeffery G. Saven

Probabilistic approach to the design of symmetric protein quaternary structures
Protein Eng. 2003 16: 971-977; doi:10.1093/protein/gzg132 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

E. Michalsky, A. Goede, and R. Preissner

Loops In Proteins (LIP)—a comprehensive loop database for homology modelling
Protein Eng. 2003 16: 979-985; doi:10.1093/protein/gzg119 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Giulio Gianese, Francesco Bossa, and Stefano Pascarella

Improvement in prediction of solvent accessibility by probability profiles
Protein Eng. 2003 16: 987-992; doi:10.1093/protein/gzg139 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Andreas G. Tzakos, Athanassios S. Galanis, Georgios A. Spyroulias, Paul Cordopatis, Evy Manessi-Zoupa, and Ioannis P. Gerothanassis

Structure–function discrimination of the N- and C- catalytic domains of human angiotensin-converting enzyme: implications for Cl^– activation and peptide hydrolysis mechanisms
Protein Eng. 2003 16: 993-1003; doi:10.1093/protein/gzg122 [Abstract] [FREE Full Text] [PDF] [Supplementary data] [Request Permissions]  

C.E. Skopec, M.E. Himmel, J.F. Matthews, and J.W. Brady

Energetics for displacing a single chain from the surface of microcrystalline cellulose into the active site of Acidothermus cellulolyticus Cel5A
Protein Eng. 2003 16: 1005-1015; doi:10.1093/protein/gzg115 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Jayasundar J. James, Baddireddi S. Lakshmi, Venkateshamurthy Raviprasad, Mathuranthagam J. Ananth, Pandjassarame Kangueane, and Pennathur Gautam

Insights from molecular dynamics simulations into pH-dependent enantioselective hydrolysis of ibuprofen esters by Candida rugosa lipase
Protein Eng. 2003 16: 1017-1024; doi:10.1093/protein/gzg135 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Manish C. Saraf and Costas D. Maranas

Using a residue clash map to functionally characterize protein recombination hybrids
Protein Eng. 2003 16: 1025-1034; doi:10.1093/protein/gzg129 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Jolan de Groot and Harmen H.J. de Jongh

The presence of heat-stable conformers of ovalbumin affects properties of thermally formed aggregates
Protein Eng. 2003 16: 1035-1040; doi:10.1093/protein/gzg123 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Yvonne Markert, Jens Köditz, Renate Ulbrich-Hofmann, and Ulrich Arnold

Proline versus charge concept for protein stabilization against proteolytic attack
Protein Eng. 2003 16: 1041-1046; doi:10.1093/protein/gzg136 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Wen-Hu Wang, Jun-Xia Lu, Ping Yao, Yi Xie, and Zhong-Xian Huang

The distinct heme coordination environments and heme-binding stabilities of His39Ser and His39Cys mutants of cytochrome b₅
Protein Eng. 2003 16: 1047-1054; doi:10.1093/protein/gzg134 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Silvia Vincenzetti, Giampiero De Sanctis, Stefano Costanzi, Gloria Cristalli, Pierluigi Mariani, Giampiero Mei, Jan Neuhard, Paolo Natalini, Valeria Polzonetti, and Alberto Vita

Functional properties of subunit interactions in human cytidine deaminase
Protein Eng. 2003 16: 1055-1061; doi:10.1093/protein/gzg117 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Luciano Piubelli, Gianluca Molla, Laura Caldinelli, Mirella S. Pilone, and Loredano Pollegioni

Dissection of the structural determinants involved in formation of the dimeric form of D-amino acid oxidase from Rhodotorula gracilis: role of the size of the ßF5–ßF6 loop
Protein Eng. 2003 16: 1063-1069; doi:10.1093/protein/gzg125 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

D.J. Lalor, T. Schnyder, V. Saridakis, D.E. Pilloff, A. Dong, H. Tang, T.S. Leyh, and E.F. Pai

Structural and functional analysis of a truncated form of Saccharomyces cerevisiae ATP sulfurylase: C-terminal domain essential for oligomer formation but not for activity
Protein Eng. 2003 16: 1071-1079; doi:10.1093/protein/gzg133 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Balaji M. Rao, Andrew T. Girvin, Thomas Ciardelli, Douglas A. Lauffenburger, and K.Dane Wittrup

Interleukin-2 mutants with enhanced -receptor subunit binding affinity
Protein Eng. 2003 16: 1081-1087; doi:10.1093/protein/gzg111 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

T.K. Nevanen, M.-L. Hellman, N. Munck, G. Wohlfahrt, A. Koivula, and H. Söderlund

Model-based mutagenesis to improve the enantioselective fractionation properties of an antibody
Protein Eng. 2003 16: 1089-1097; doi:10.1093/protein/gzg118 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Sung-Hun Nam, Ki-Hoon Oh, Geun-Joong Kim, and Hak-Sung Kim

Functional tuning of a salvaged green fluorescent protein variant with a new sequence space by directed evolution
Protein Eng. 2003 16: 1099-1105; doi:10.1093/protein/gzg146 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Miriam Bach, Peter Hölig, Eva Schlosser, Tina Völkel, Andreas Graser, Rolf Müller, and Roland E. Kontermann

Isolation from phage display libraries of lysine-deficient human epidermal growth factor variants for directional conjugation as targeting ligands
Protein Eng. 2003 16: 1107-1113; doi:10.1093/protein/gzg145 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Shinya Y. Sawata and Kazunari Taira

Modified peptide selection in vitro by introduction of a protein–RNA interaction
Protein Eng. 2003 16: 1115-1124; doi:10.1093/protein/gzg112 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

T.N. Melnik, V. Villard, V. Vasiliev, G. Corradin, A.V. Kajava, and S.A. Potekhin

Shift of fibril-forming ability of the designed -helical coiled-coil peptides into the physiological pH region
Protein Eng. 2003 16: 1125-1130; doi:10.1093/protein/gzg138 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Carlos R.J. Soares, Fernanda I.C. Gomide, Eric K.M. Ueda, and Paolo Bartolini

Periplasmic expression of human growth hormone via plasmid vectors containing the P_L promoter: use of HPLC for product quantification
Protein Eng. 2003 16: 1131-1138; doi:10.1093/protein/gzg114 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Anna Musidlowska-Persson and Uwe T. Bornscheuer

Recombinant porcine intestinal carboxylesterase: cloning from the pig liver esterase gene by site-directed mutagenesis, functional expression and characterization
Protein Eng. 2003 16: 1139-1145; doi:10.1093/protein/gzg120 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

Martin Linhult, Susanne Gülich, Torbjörn Gräslund, Per-Åke Nygren, and Sophia Hober

Evaluation of different linker regions for multimerization and coupling chemistry for immobilization of a proteinaceous affinity ligand
Protein Eng. 2003 16: 1147-1152; doi:10.1093/protein/gzg121 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

I. Roy and M.N. Gupta

pH-responsive polymer-assisted refolding of urea- and organic solvent-denatured -chymotrypsin
Protein Eng. 2003 16: 1153-1157; doi:10.1093/protein/gzg124 [Abstract] [FREE Full Text] [PDF] [Request Permissions]  

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