Allosteric control of ligand-binding affinity using engineered conformation-specific effector proteins

Rizk SS, Paduch M, Heithaus JH, Duguid EM, Sandstrom A, Kossiakoff AA

Nat. Struct. Mol. Biol. 2011 Apr;18(4):437-42

PMID: 21378967

Abstract

We describe a phage display methodology for engineering synthetic antigen binders (sABs) that recognize either the apo or the ligand-bound conformation of maltose-binding protein (MBP). sABs that preferentially recognize the maltose-bound form of MBP …

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A portable RNA sequence whose recognition by a synthetic antibody facilitates structural determination

Koldobskaya Y, Duguid EM, Shechner DM, Suslov NB, Ye J, Sidhu SS, Bartel DP, Koide S, Kossiakoff AA, Piccirilli JA

Nat. Struct. Mol. Biol. 2011 Jan;18(1):100-6

PMID: 21151117

Abstract

RNA crystallization and phasing represent major bottlenecks in RNA structure determination. Seeking to exploit antibody fragments as RNA crystallization chaperones, we have used an arginine-enriched synthetic …

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Characterization of engineered actin binding proteins that control filament assembly and structure

Brawley CM, Uysal S, Kossiakoff AA, Rock RS

PLoS ONE 2010 Nov;5(11):e13960

PMID: 21103060

Abstract

BACKGROUND: Eukaryotic cells strictly regulate the structure and assembly of their actin filament networks in response to various stimuli. The actin binding proteins that control filament assembly are therefore attractive targets for those who wish to reorganize actin filaments and …

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Keeping signaling in check

Kossiakoff AA, Rizk S

Structure 2010 Mar;18(3):275-6

PMID: 20223207

Abstract

Cytokine signaling is triggered by a hormone-induced receptor aggregation process. IL-13 employs an unconventional sequence of steps for assembling its signaling complex to trigger activation and for turning it off. Both these processes involve some unusual molecular recognition features, as discussed by Lupardus et al. …

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An engineered substance P variant for receptor-mediated delivery of synthetic antibodies into tumor cells

Rizk SS, Luchniak A, Uysal S, Brawley CM, Rock RS, Kossiakoff AA

Proc. Natl. Acad. Sci. U.S.A. 2009 Jul;106(27):11011-5

PMID: 19549879

Abstract

We have developed and tested a robust delivery method for the transport of proteins to the cytoplasm of mammalian cells without compromising the integrity of the cell membrane. This receptor-mediated delivery (RMD) technology …

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Role of a salt bridge in the model protein crambin explored by chemical protein synthesis: X-ray structure of a unique protein analogue, [V15A]crambin-alpha-carboxamide

Bang D, Tereshko V, Kossiakoff AA, Kent SB

Mol Biosyst 2009 Jul;5(7):750-6

PMID: 19562114

Abstract

We have used total chemical synthesis to prepare [V15A]crambin-alpha-carboxamide, a unique protein analogue that eliminates a salt bridge between the delta-guanidinium of the Arg(10) side chain and the alpha-carboxylate of Asn(46) at the C-terminus of the polypeptide chain. This salt …

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Racemic crystallography of synthetic protein enantiomers used to determine the X-ray structure of plectasin by direct methods

Mandal K, Pentelute BL, Tereshko V, Thammavongsa V, Schneewind O, Kossiakoff AA, Kent SB

Protein Sci. 2009 Jun;18(6):1146-54

PMID: 19472324

Abstract

We describe the use of racemic crystallography to determine the X-ray structure of the natural product plectasin, a potent antimicrobial protein recently isolated from fungus. The protein enantiomers L-plectasin and D-plectasin were prepared by …

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Crystal structure of full-length KcsA in its closed conformation

Uysal S, Vásquez V, Tereshko V, Esaki K, Fellouse FA, Sidhu SS, Koide S, Perozo E, Kossiakoff A

Proc. Natl. Acad. Sci. U.S.A. 2009 Apr;106(16):6644-9

PMID: 19346472

Abstract

KcsA is a proton-activated, voltage-modulated K(+) channel that has served as the archetype pore domain in the Kv channel superfamily. Here, we have used synthetic antigen-binding fragments …

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X-ray structure of native scorpion toxin BmBKTx1 by racemic protein crystallography using direct methods

Mandal K, Pentelute BL, Tereshko V, Kossiakoff AA, Kent SB

J. Am. Chem. Soc. 2009 Feb;131(4):1362-3

PMID: 19133782

Abstract

Racemic protein crystallography, enabled by total chemical synthesis, has allowed us to determine the X-ray structure of native scorpion toxin BmBKTx1; direct methods were used for phase determination. This is the first example of a protein …

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Principal determinants leading to transition state formation of a protein-protein complex, orientation trumps side-chain interactions

Horn JR, Sosnick TR, Kossiakoff AA

Proc. Natl. Acad. Sci. U.S.A. 2009 Feb;106(8):2559-64

PMID: 19196954

Abstract

The binding transition state (TS) is the rate-limiting step for transient molecular interactions. This important step in the molecular recognition process, however, is largely understood only at a qualitative level. To establish a more quantitative picture of the TS …

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