Category: publications

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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The role of protein dynamics in increasing binding affinity for an engineered protein-protein interaction established by H/D exchange mass spectrometry

Horn JR, Kraybill B, Petro EJ, Coales SJ, Morrow JA, Hamuro Y, Kossiakoff AA

Biochemistry 2006 Jul;45(28):8488-98

PMID: 16834322

Abstract

It is generally accepted that protein and solvation dynamics play fundamental roles in the mechanisms of protein-protein binding; however, assessing their contribution meaningfully has not been straightforward. Here, hydrogen/deuterium exchange mass spectrometry (H/D-Ex) was employed …

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Crystal structure and site 1 binding energetics of human placental lactogen

Walsh ST, Kossiakoff AA

J. Mol. Biol. 2006 May;358(3):773-84

PMID: 16546209

Abstract

In primates, placental lactogen (PL) is a pituitary hormone with fundamental roles during pregnancy involving fetal growth, metabolism, and stimulating lactation in the mother. Human placental lactogen (hPL) is highly conserved with human growth hormone (hGH) and both hormones bind to the hPRLR …

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Dissecting the energetics of protein alpha-helix C-cap termination through chemical protein synthesis

Bang D, Gribenko AV, Tereshko V, Kossiakoff AA, Kent SB, Makhatadze GI

Nat. Chem. Biol. 2006 Mar;2(3):139-43

PMID: 16446709

Abstract

The alpha-helix is a fundamental protein structural motif and is frequently terminated by a glycine residue. Explanations for the predominance of glycine at the C-cap terminal portions of alpha-helices have invoked uniquely favorable energetics of …

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Structure of bistramide A-actin complex at a 1.35 angstroms resolution

Rizvi SA, Tereshko V, Kossiakoff AA, Kozmin SA

J. Am. Chem. Soc. 2006 Mar;128(12):3882-3

PMID: 16551075

Abstract

Bistramide A is a highly potent antiproliferative marine natural product from Lissoclinum bistratum. We have previously established actin as the primary cellular receptor of bistramide A. We report herein the X-ray structure of bistramide A bound to monomeric …

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The crystal structure of Aq_328 from the hyperthermophilic bacteria Aquifex aeolicus shows an ancestral histone fold

Qiu Y, Tereshko V, Kim Y, Zhang R, Collart F, Yousef M, Kossiakoff A, Joachimiak A

Proteins 2006 Jan;62(1):8-16

PMID: 16287087

Abstract

The structure of Aq_328, an uncharacterized protein from hyperthermophilic bacteria Aquifex aeolicus, has been determined to 1.9 A by using multi-wavelength anomalous diffraction (MAD) phasing. Although the amino acid sequence analysis shows that …

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Alternative views of functional protein binding epitopes obtained by combinatorial shotgun scanning mutagenesis

Pál G, Fong SY, Kossiakoff AA, Sidhu SS

Protein Sci. 2005 Sep;14(9):2405-13

PMID: 16131663

Abstract

Combinatorial shotgun scanning mutagenesis was used to analyze two large, related protein binding sites to assess the specificity and importance of individual side chain contributions to binding affinity. The strategy allowed for cost-effective generation of a plethora of functional data. …

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