Judy Luke

Author's posts

Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces

Kossiakoff AA, Koide S

Curr. Opin. Struct. Biol. 2008 Aug;18(4):499-506

PMID: 18638552

Abstract

Recent advances in methodologies and design of combinatorial library selection have enabled comprehensive characterization of sequence space for protein-protein interaction interfaces and generation of fully synthetic binding interfaces. By exhaustively introducing and quantitatively analyzing mutations in natural interfaces, new insights into their …

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Toward chaperone-assisted crystallography: protein engineering enhancement of crystal packing and X-ray phasing capabilities of a camelid single-domain antibody (VHH) scaffold

Tereshko V, Uysal S, Koide A, Margalef K, Koide S, Kossiakoff AA

Protein Sci. 2008 Jul;17(7):1175-87

PMID: 18445622

Abstract

A crystallization chaperone is an auxiliary protein that binds to a target of interest, enhances and modulates crystal packing, and provides high-quality phasing information. We critically evaluated the effectiveness of a camelid single-domain antibody (V(H)H) as …

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X-ray structure of snow flea antifreeze protein determined by racemic crystallization of synthetic protein enantiomers

Pentelute BL, Gates ZP, Tereshko V, Dashnau JL, Vanderkooi JM, Kossiakoff AA, Kent SB

J. Am. Chem. Soc. 2008 Jul;130(30):9695-701

PMID: 18598029

Abstract

Chemical protein synthesis and racemic protein crystallization were used to determine the X-ray structure of the snow flea antifreeze protein (sfAFP). Crystal formation from a racemic solution containing equal amounts of the …

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The 1.38 A crystal structure of DmsD protein from Salmonella typhimurium, a proofreading chaperone on the Tat pathway

Qiu Y, Zhang R, Binkowski TA, Tereshko V, Joachimiak A, Kossiakoff A

Proteins 2008 May;71(2):525-33

PMID: 18175314

Abstract

The DmsD protein is necessary for the biogenesis of dimethyl sulphoxide (DMSO) reductase in many prokaryotes. It performs a critical chaperone function initiated through its binding to the twin-arginine signal peptide of DmsA, the catalytic subunit of …

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Synthetic antibodies for specific recognition and crystallization of structured RNA

Ye JD, Tereshko V, Frederiksen JK, Koide A, Fellouse FA, Sidhu SS, Koide S, Kossiakoff AA, Piccirilli JA

Proc. Natl. Acad. Sci. U.S.A. 2008 Jan;105(1):82-7

PMID: 18162543

Abstract

Antibodies that bind protein antigens are indispensable in biochemical research and modern medicine. However, knowledge of RNA-binding antibodies and their application in the ever-growing RNA field is …

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High-throughput generation of synthetic antibodies from highly functional minimalist phage-displayed libraries

Fellouse FA, Esaki K, Birtalan S, Raptis D, Cancasci VJ, Koide A, Jhurani P, Vasser M, Wiesmann C, Kossiakoff AA, Koide S, Sidhu SS

J. Mol. Biol. 2007 Nov;373(4):924-40

PMID: 17825836

Abstract

We have previously established a minimalist approach to antibody engineering by using a phage-displayed framework to support complementarity determining region (CDR) diversity restricted …

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Exploring the capacity of minimalist protein interfaces: interface energetics and affinity maturation to picomolar KD of a single-domain antibody with a flat paratope

Koide A, Tereshko V, Uysal S, Margalef K, Kossiakoff AA, Koide S

J. Mol. Biol. 2007 Nov;373(4):941-53

PMID: 17888451

Abstract

A major architectural class in engineered binding proteins (“antibody mimics”) involves the presentation of recognition loops off a single-domain scaffold. This class of binding proteins, both natural and synthetic, has a strong tendency to bind …

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Exploring and designing protein function with restricted diversity

Sidhu SS, Kossiakoff AA

Curr Opin Chem Biol 2007 Jun;11(3):347-54

PMID: 17500026

Abstract

Combinatorial libraries with restricted diversity can be used to rapidly map binding energetics across protein interfaces. Shotgun scanning strategies have been used for alanine scanning and for alternative mutagenesis schemes that provide high-resolution functional views of binding interfaces. In addition, synthetic antibodies …

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Time-controlled microfluidic seeding in nL-volume droplets to separate nucleation and growth stages of protein crystallization

Gerdts CJ, Tereshko V, Yadav MK, Dementieva I, Collart F, Joachimiak A, Stevens RC, Kuhn P, Kossiakoff A, Ismagilov RF

Angew. Chem. Int. Ed. Engl. 2006 Dec;45(48):8156-60

PMID: 17099920

Abstract

Comprehensive and quantitative mapping of energy landscapes for protein-protein interactions by rapid combinatorial scanning

Pál G, Kouadio JL, Artis DR, Kossiakoff AA, Sidhu SS

J. Biol. Chem. 2006 Aug;281(31):22378-85

PMID: 16762925

Abstract

A novel, quantitative saturation (QS) scanning strategy was developed to obtain a comprehensive data base of the structural and functional effects of all possible mutations across a large protein-protein interface. The QS scan approach was applied to …

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