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Alignment of multiple protein structures based on sequence and structure features

M.S. Madhusudhan, Benjamin M. Webb, Marc A. Marti-Renom, Narayanan Eswar and Andrej Sali.

in Protein Engineering, Design and Selection

September 2009; p ublished online July 2009 .

Journal Article. Subjects: Proteins. 3854 words.

Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming...

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An allosteric anti-hepsin antibody derived from a constrained phage display library

Rajkumar Ganesan, Yingnan Zhang, Kyle E. Landgraf, S.Jack Lin, Paul Moran and Daniel Kirchhofer.

in Protein Engineering, Design and Selection

March 2012; p ublished online January 2012 .

Journal Article. Subjects: Proteins. 4224 words.

The serine protease hepsin is highly upregulated in prostate cancer and is implicated in tumor progression. Therefore, specific inhibition of hepsin enzymatic activity by an antibody...

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Alteration of product specificity of Aeropyrum pernix farnesylgeranyl diphosphate synthase (Fgs) by directed evolution

Pyung Cheon Lee, Benjamin N. Mijts, Ralf Petri, Kevin T. Watts and Claudia Schmidt-Dannert.

in Protein Engineering, Design and Selection

November 2004; p ublished online November 2004 .

Journal Article. Subjects: Proteins. 5183 words.

Directed evolution of the C25 farnesylgeranyl diphosphate synthase of Aeropyrum pernix (Fgs) was carried out by error-prone PCR with an in vivo color complementation screen utilizing...

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Alteration of substrate selection of antibiotic acylase from β-lactam to echinocandin

Yasuhiro Isogai and Kazuki Nakayama.

in Protein Engineering, Design and Selection

February 2016; p ublished online November 2015 .

Journal Article. Subjects: Proteins. 5385 words.

The antibiotic acylases belonging to the N-terminal nucleophile hydrolase superfamily are key enzymes for the industrial production of antibiotic drugs. Cephalosporin acylase (CA) and...

Alteration of substrate specificity of alanine dehydrogenase

Puja Fernandes, Hannah Aldeborgh, Lauren Carlucci, Lauren Walsh, Jordan Wasserman, Edward Zhou, Scott T. Lefurgy and Emily C. Mundorff.

in Protein Engineering, Design and Selection

February 2015; p ublished online December 2014 .

Journal Article. Subjects: Proteins. 4440 words.

The l-alanine dehydrogenase (AlaDH) has a natural history that suggests it would not be a promising candidate for expansion of substrate specificity by protein engineering: it is the only...

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Alteration of substrate specificity of cholesterol oxidase from Streptomyces sp. by site-directed mutagenesis

Mitsutoshi Toyama, Mitsuo Yamashita, Morihide Yoneda, Andrzej Zaborowski, Masaki Nagato, Hisayo Ono, Noriaki Hirayama and Yoshikatsu Murooka.

in Protein Engineering, Design and Selection

June 2002; p ublished online June 2002 .

Journal Article. Subjects: Proteins. 4547 words.

Despite the structural similarities between cholesterol oxidase from Streptomyces and that from Brevibacterium, both enzymes exhibit different characteristics, such as catalytic activity,...

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Alteration of substrate specificity of rat neurolysin from matrix metalloproteinase-2/9-type to -3-type specificity by comprehensive mutation

Tetsuya Kadonosono, Michiko Kato-Murai and Mitsuyoshi Ueda.

in Protein Engineering, Design and Selection

August 2008; p ublished online May 2008 .

Journal Article. Subjects: Proteins. 4209 words.

The substrate specificity of rat brain neurolysin was rapidly modified by semirational mutagenesis coupled with a yeast molecular display system. Neurolysin mainly recognizes substrates...

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Alteration of the specificity of the cofactor-binding pocket of Corynebacterium 2,5-diketo-D-gluconic acid reductase A

Scott Banta, Barbara A. Swanson, Shan Wu, Alisha Jarnagin and Stephen Anderson.

in Protein Engineering, Design and Selection

February 2002; p ublished online February 2002 .

Journal Article. Subjects: Proteins. 7553 words.

The NADPH-dependent 2,5-diketo-D-gluconic acid (2,5-DKG) reductase enzyme is a required component in some novel biosynthetic vitamin C production processes. This enzyme catalyzes the...

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Altered ionization of the B13 Glu in insulin B9 and B10 mutants: a computational analysis

Richard B. Greaves, Guy G. Dodson and Chandra S. Verma.

in Protein Engineering, Design and Selection

July 2004; p ublished online August 2004 .

Journal Article. Subjects: Proteins. 5154 words.

An experimentally determined pK a change of +2.50 units has been reported for the B13 Glu residue in a dimeric B9 Ser → Asp insulin mutant relative to the native dimer....

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Altering the sequence specificity of HaeIII methyltransferase by directed evolution using in vitro compartmentalization

Helen M. Cohen, Dan S. Tawfik and Andrew D. Griffiths.

in Protein Engineering, Design and Selection

January 2004; p ublished online January 2004 .

Journal Article. Subjects: Proteins. 7595 words.

Engineering the specificity of DNA‐modifying enzymes has proven extremely challenging, as sequence recognition by these enzymes is poorly understood. Here we used directed evolution to...

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Alternating charge clusters of side chains: new surface structural invariants observed in calf eye lens gamma-crystallins

Yuri N. Chirgadze and Olga Yu. Tabolina.

in Protein Engineering, Design and Selection

September 1996 .

Journal Article. Subjects: Proteins. 0 words.

A detailed stereochemical analysis of the oppositely charged side chains of amino acid residues on the surface of calf eye lens protein gamma-crystallin B has been carried out. The refined...

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Alternative antibody Fab′ fragment PEGylation strategies: combination of strong reducing agents, disruption of the interchain disulphide bond and disulphide engineering

David P. Humphreys, Sam P. Heywood, Alistair Henry, Layla Ait-Lhadj, Pari Antoniw, Roger Palframan, Kevin J. Greenslade, Bruce Carrington, Dominc G. Reeks, Leigh C. Bowering, Shauna West and Helen A. Brand.

in Protein Engineering, Design and Selection

May 2007; p ublished online April 2007 .

Journal Article. Subjects: Proteins. 6159 words.

Antigen-binding fragments (Fab′) of antibodies can be site specifically PEGylated at thiols using cysteine reactive PEG–maleimide conjugates. For therapeutic Fab′–PEG, conjugation with 40...

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Alternative CUG codon usage (Ser for Leu) in Pichia farinosa and the effect of a mutated killer gene in Saccharomyces cerevisiae

C. Suzuki, T. Kashiwagi and K. Hirayama.

in Protein Engineering, Design and Selection

March 2002; p ublished online March 2002 .

Journal Article. Subjects: Proteins. 3294 words.

The halotolerant yeast Pichia farinosa KK1 strain produces a killer toxin termed SMKT (salt-mediated killer toxin). Mass spectrometry and Edman sequencing of peptides from the mature SMKT...

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An alternative derivation of the equations of motion in torsion space for a branched linear chain

Christopher Bystroff.

in Protein Engineering, Design and Selection

November 2001; p ublished online November 2001 .

Journal Article. Subjects: Proteins. 2129 words.

Torsion space molecular dynamics may be more efficiently encoded if the global motions are separated from the internal motions. The equations of motion for single, non-cyclic chains are...

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Amide inequivalence in the fibrillar assembly of islet amyloid polypeptide

Bon W. Koo, James A. Hebda and Andrew D. Miranker.

in Protein Engineering, Design and Selection

March 2008; p ublished online March 2008 .

Journal Article. Subjects: Proteins. 5456 words.

Amyloid fibers are aggregated, yet highly ordered, β-sheet-rich assemblies of misfolded proteins. Order is established in such systems following profiles indicative of nucleation-dependent...

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Amino acid alphabet size in protein evolution experiments: better to search a small library thoroughly or a large library sparsely?

Enrique Muñoz and Michael W. Deem.

in Protein Engineering, Design and Selection

May 2008; p ublished online March 2008 .

Journal Article. Subjects: Proteins. 5214 words.

We compare the results obtained from searching a smaller library thoroughly versus searching a more diverse, larger library sparsely. We study protein evolution with reduced amino acid...

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Amino acid changes in the repressor of bacteriophage lambda due to temperature-sensitive mutations in its cI gene and the structure of a highly temperature-sensitive mutant repressor

Nandan Kumar Jana, Siddhartha Roy, Bhabatarak Bhattacharyya and Nitai Chandra Mandal.

in Protein Engineering, Design and Selection

March 1999; p ublished online March 1999 .

Journal Article. Subjects: Proteins. 6938 words.

The mutant cIts genes from seven different λcIts phages carrying tsU50, tsU9, tsU46, ts1, tsU51, tsI-22 and ts2 mutations were cloned in plasmid. The positions of these mutations and the...

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Amino acid composition of protein termini are biased in different manners

Igor N. Berezovsky, Gelena T. Kilosanidze, Vladimir G. Tumanyan and Lev L. Kisselev.

in Protein Engineering, Design and Selection

January 1999; p ublished online January 1999 .

Journal Article. Subjects: Proteins. 5415 words.

An exhaustive statistical analysis of the amino acid sequences at the carboxyl (C) and amino (N) termini of proteins and of coding nucleic acid sequences at the 5′ side of the stop codons...

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Amino acid neighbours and detailed conformational analysis of cysteines in proteins

Maria Teresa Neves Petersen, Per Harald Jonson and Steffen B. Petersen.

in Protein Engineering, Design and Selection

July 1999; p ublished online July 1999 .

Journal Article. Subjects: Proteins. 8250 words.

Here we present an investigation of the contacts that cysteines make with residues in their three-dimensional environment and a comprehensive analysis of the conformational features of 351...

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Amino acid quantitative structure property relationship database: a web-based platform for quantitative investigations of amino acids

Yi Lu, Blazej Bulka, Marie desJardins and Stephen J. Freeland.

in Protein Engineering, Design and Selection

July 2007; p ublished online June 2007 .

Journal Article. Subjects: Proteins. 3133 words.

Here, we present the AA-QSPR Db (Amino Acid Quantitative Structure Property Relationship Database): a novel, freely available web-resource of data pertaining to amino acids, both engineered...

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