Author's posts
Aug 08 2008
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 …
Jul 08 2008
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 …
Jul 08 2008
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 …
May 08 2008
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 …
Jan 08 2008
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 …
Nov 08 2007
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 …
Nov 08 2007
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 …
Jun 08 2007
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 …
Dec 08 2006
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
Aug 08 2006
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 …