Specific Recognition of a Single-Stranded RNA Sequence by a Synthetic Antibody Fragment

Shao Y, Huang H, Qin D, Li NS, Koide A, Staley JP, Koide S, Kossiakoff AA, Piccirilli JA

J. Mol. Biol. 2016 10;428(20):4100-4114

PMID: 27593161

Abstract

Antibodies that bind RNA represent an unrealized source of reagents for synthetic biology and for characterizing cellular transcriptomes. However, facile access to RNA-binding antibodies requires the engineering of effective …

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A polar ring endows improved specificity to an antibody fragment

Schaefer ZP, Bailey LJ, Kossiakoff AA

Protein Sci. 2016 07;25(7):1290-8

PMID: 27334407

Abstract

Engineering monovalent Fab fragments into bivalent formats like IgGs or F(ab’)2 can lead to aggregation presumably because of nonspecific off-target interactions that induce aggregation. In an effort to further understand the molecular determinants of nonspecific interactions for engineered antibodies and natively folded …

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Conformational Chaperones for Structural Studies of Membrane Proteins Using Antibody Phage Display with Nanodiscs

Dominik PK, Borowska MT, Dalmas O, Kim SS, Perozo E, Keenan RJ, Kossiakoff AA

Structure 2016 Feb;24(2):300-9

PMID: 26749445

Abstract

A major challenge in membrane biophysics is to define the mechanistic linkages between a protein’s conformational transitions and its function. We describe a novel approach to stabilize transient functional states of membrane proteins in native-like …

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Optimizing Production of Antigens and Fabs in the Context of Generating Recombinant Antibodies to Human Proteins

Zhong N, Loppnau P, Seitova A, Ravichandran M, Fenner M, Jain H, Bhattacharya A, Hutchinson A, Paduch M, Lu V, Olszewski M, Kossiakoff AA, Dowdell E, Koide A, Koide S, Huang H, Nadeem V, Sidhu SS, Greenblatt JF, Marcon E, Arrowsmith CH, Edwards AM, Gräslund S

PLoS ONE 2015;10(10):e0139695

PMID: 26437229

Abstract

We developed and …

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Architecture of the fungal nuclear pore inner ring complex

Stuwe T, Bley CJ, Thierbach K, Petrovic S, Schilbach S, Mayo DJ, Perriches T, Rundlet EJ, Jeon YE, Collins LN, Huber FM, Lin DH, Paduch M, Koide A, Lu V, Fischer J, Hurt E, Koide S, Kossiakoff AA, Hoelz A

Science 2015 Oct;350(6256):56-64

PMID: 26316600

Abstract

The nuclear pore complex (NPC) constitutes the sole gateway …

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A High Through-put Platform for Recombinant Antibodies to Folded Proteins

Hornsby M, Paduch M, Miersch S, Sääf A, Matsuguchi T, Lee B, Wypisniak K, Doak A, King D, Usatyuk S, Perry K, Lu V, Thomas W, Luke J, Goodman J, Hoey RJ, Lai D, Griffin C, Li Z, Vizeacoumar FJ, Dong D, Campbell E, Anderson S, Zhong N, Gräslund S, Koide S, Moffat J, Sidhu …

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A New Versatile Immobilization Tag Based on the Ultra High Affinity and Reversibility of the Calmodulin-Calmodulin Binding Peptide Interaction

Mukherjee S, Ura M, Hoey RJ, Kossiakoff AA

J. Mol. Biol. 2015 Aug;427(16):2707-25

PMID: 26159704

Abstract

Reversible, high-affinity immobilization tags are critical tools for myriad biological applications. However, inherent issues are associated with a number of the current methods of immobilization. Particularly, a critical element in phage display sorting is functional immobilization of target proteins. …

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Engineering Synthetic Antibody Inhibitors Specific for LD2 or LD4 Motifs of Paxillin

Nocula-Lugowska M, Lugowski M, Salgia R, Kossiakoff AA

J. Mol. Biol. 2015 Jul;427(15):2532-2547

PMID: 26087144

Abstract

Focal adhesion protein paxillin links integrin and growth factor signaling to actin cytoskeleton. Most of paxillin signaling activity is regulated via leucine-rich LD motifs (LD1-LD5) located at the N-terminus. Here, we demonstrate a method to engineer highly selective synthetic …

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Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation

Marcon E, Jain H, Bhattacharya A, Guo H, Phanse S, Pu S, Byram G, Collins BC, Dowdell E, Fenner M, Guo X, Hutchinson A, Kennedy JJ, Krastins B, Larsen B, Lin ZY, Lopez MF, Loppnau P, Miersch S, Nguyen T, Olsen JB, Paduch M, Ravichandran M, Seitova A, Vadali G, Vogelsang MS, Whiteaker JR, Zhong …

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Nuclear pores. Architecture of the nuclear pore complex coat

Stuwe T, Correia AR, Lin DH, Paduch M, Lu VT, Kossiakoff AA, Hoelz A

Science 2015 Mar;347(6226):1148-52

PMID: 25745173

Abstract

The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. Despite half a century of structural characterization, the architecture of the NPC remains unknown. Here we present the crystal structure of a …

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